First commit - second part
Former-commit-id: 202296404e6a70f8ae96db99faffb456104c57e9 Former-commit-id: 118417735d2055683607df9809c9b721cc1b1bab
This commit is contained in:
51
README.txt
Normal file
51
README.txt
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@ -0,0 +1,51 @@
|
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#
|
||||
# ------------------------------------------
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||||
# ORG.Annot - Organelle Annotator
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||||
# version 1.0.0 - Sept 2015
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||||
# ------------------------------------------
|
||||
#
|
||||
# -------------------------
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||||
# -1- Installation
|
||||
# -------------------------
|
||||
#
|
||||
# First check if binaries have been already compiled for your port
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||||
#
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||||
# $ scripts/check_port
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||||
#
|
||||
# if it prints :
|
||||
#
|
||||
# + port <PORTNAME> is correctly installed
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||||
#
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||||
# then everything is fine
|
||||
#
|
||||
# if it prints :
|
||||
#
|
||||
# ! port <PORTNAME> not installed
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||||
# ! Please read README.txt for proper installation
|
||||
#
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||||
# then, you should first compile binaries for your port
|
||||
# please consult: src/README.txt for details
|
||||
#
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||||
#
|
||||
# -------------------------
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||||
# -2- Distribution organisation
|
||||
# -------------------------
|
||||
#
|
||||
# config : config file for (re)compiling tools
|
||||
# data : internal data files (e.g. ChloroDB)
|
||||
# detectors : features specific detector scripts
|
||||
# ports : binaries for various ports
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||||
# scripts : main scripts directory
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||||
# src : sources for (re)compiling tools
|
||||
#
|
||||
# -------------------------
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||||
# -3- Usage
|
||||
# -------------------------
|
||||
#
|
||||
# note: all scripts are located in scripts, so you may add
|
||||
# this directory in your path
|
||||
# e.g. using csh
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||||
# set path = ($path <ROOTDIR>/scripts)
|
||||
#
|
||||
# @TODO : scripts description
|
||||
#
|
||||
BIN
config/.DS_Store
vendored
Normal file
BIN
config/.DS_Store
vendored
Normal file
Binary file not shown.
51
config/README.txt
Executable file
51
config/README.txt
Executable file
@ -0,0 +1,51 @@
|
||||
|
||||
$Id: README.txt 1825 2013-02-26 09:39:47Z viari $
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||||
|
||||
This directory contains Makefile machine specific configuration files
|
||||
(and default targets to help you writing Makefile's)
|
||||
|
||||
These headers should be used with GNU make or compatible
|
||||
|
||||
#
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||||
# portname
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||||
#
|
||||
|
||||
To check your port, issue :
|
||||
|
||||
./guess_port
|
||||
|
||||
if output is 'unknown <mach>:<sys>:<rel>' then you should :
|
||||
- add a port entry in guess_port for <mach>:<sys>:<rel>
|
||||
- create a ports/<port>.conf configuration file
|
||||
(the best is to start from another port file,
|
||||
choose whatever looks closest)
|
||||
|
||||
#
|
||||
# configuration flags
|
||||
#
|
||||
|
||||
auto.conf : the main configuration file :
|
||||
- determine the machine port thru 'guess_port' shell
|
||||
- include 'default.conf' file
|
||||
- include the machine specific 'ports/<port>.conf' file
|
||||
|
||||
default.conf : default configuration (included by 'auto.conf')
|
||||
|
||||
ports/<port>.conf : machine specific configuration (included by 'auto.conf')
|
||||
|
||||
#
|
||||
# utility targets
|
||||
#
|
||||
|
||||
targets/help.targ : target for standard help
|
||||
|
||||
targets/propagate.targ : target for propagating targets to subdirectories
|
||||
|
||||
targets/package.targ : default targets for standard package with 'configure'
|
||||
|
||||
targets/empty.targ : default empty targets (defined as double colon rules)
|
||||
|
||||
targets/lxbin.targ : default make targets for standard lx binary (without libraries)
|
||||
|
||||
targets/debug.targ : target to print debug information (for dev.)
|
||||
|
||||
54
config/auto.conf
Normal file
54
config/auto.conf
Normal file
@ -0,0 +1,54 @@
|
||||
#
|
||||
# $Id: auto.conf 1825 2013-02-26 09:39:47Z viari $
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||||
#
|
||||
# auto.conf
|
||||
# auto configuration file using guess_port
|
||||
#
|
||||
# this file is included in Makefile
|
||||
#
|
||||
|
||||
#
|
||||
# default shell for gnu-make
|
||||
#
|
||||
|
||||
SHELL = /bin/sh
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||||
|
||||
#
|
||||
# CFGDIR : location of config files = this file directory location
|
||||
#
|
||||
# CFGPRT : port name (as returned by guess_port)
|
||||
#
|
||||
|
||||
# because builtin 'lastword' is missing in gnu-make 3.80
|
||||
|
||||
lastword = $(word $(words $1), $1)
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|
||||
CFGDIR := $(dir $(call lastword, $(MAKEFILE_LIST)))
|
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|
||||
CFGPRT := $(shell $(CFGDIR)guess_port)
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|
||||
# check if port is correctly defined
|
||||
|
||||
ifneq (1, $(words $(CFGPRT)))
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entry := $(call lastword, $(CFGPRT))
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$(error port is undefined - add entry for "$(entry)" in configuration file -)
|
||||
endif
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||||
|
||||
#
|
||||
# PORTNAME : port name to use : default is CFGPRT but may be futher modified
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||||
# by machine specific configuration
|
||||
|
||||
PORTNAME = $(CFGPRT)
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||||
|
||||
#
|
||||
# default configuration
|
||||
# may be overriden by machine dependant definitions below
|
||||
#
|
||||
|
||||
include $(CFGDIR)default.conf
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||||
|
||||
#
|
||||
# machine dependant definitions
|
||||
#
|
||||
|
||||
include $(CFGDIR)ports/$(CFGPRT).conf
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||||
124
config/default.conf
Normal file
124
config/default.conf
Normal file
@ -0,0 +1,124 @@
|
||||
#
|
||||
# $Id: default.conf 2007 2013-12-03 14:21:39Z viari $
|
||||
#
|
||||
# default.conf
|
||||
# default configuration flags
|
||||
# maybe further redefined by machine specific configuration
|
||||
#
|
||||
# this file is included by auto.conf
|
||||
#
|
||||
|
||||
# ------------------------------------
|
||||
# General compilation flags
|
||||
# ------------------------------------
|
||||
|
||||
#
|
||||
# MACHDEF : define machine and OS specific flags
|
||||
#
|
||||
|
||||
MACHDEF =
|
||||
|
||||
#
|
||||
# CC : (ansi C) compiler command to use
|
||||
# you may add some machine specific flags (like -arch ...)
|
||||
# in the <machine>.conf configuration file
|
||||
#
|
||||
|
||||
CC = gcc
|
||||
|
||||
#
|
||||
# default compiler optimizer flag
|
||||
#
|
||||
|
||||
OPTIM = -O
|
||||
|
||||
#
|
||||
# CC_LIBS : additionnal machine specific $(CC) libraries
|
||||
# like '-lC' on some machines
|
||||
#
|
||||
|
||||
CC_LIBS =
|
||||
|
||||
#
|
||||
# MALLOC_LIBS : machine specific malloc librairies
|
||||
# like '-lmalloc' on SGI
|
||||
#
|
||||
|
||||
MALLOC_LIBS =
|
||||
|
||||
#
|
||||
# MATH_LIBS : machine specific math librairies
|
||||
# like '-lm' on Solaris
|
||||
#
|
||||
|
||||
MATH_LIBS =
|
||||
|
||||
#
|
||||
# LINT : looks like LINT command does not exist anymore
|
||||
# here is a rough replacement
|
||||
#
|
||||
|
||||
LINT = gcc -S -Wall -Wno-format-y2k -W -Wstrict-prototypes \
|
||||
-Wmissing-prototypes -Wpointer-arith -Wreturn-type \
|
||||
-Wcast-qual -Wwrite-strings -Wswitch -Wshadow \
|
||||
-Wcast-align -Wbad-function-cast -Wchar-subscripts \
|
||||
-Winline -Wnested-externs -Wredundant-decls
|
||||
|
||||
# ------------------------------------
|
||||
# General system commands
|
||||
# ------------------------------------
|
||||
|
||||
#
|
||||
# AR : AR archive command
|
||||
# ARFLAGS : $(AR) archiving flags
|
||||
# ARXFLAGS : $(AR) extraction flags
|
||||
#
|
||||
|
||||
AR = ar
|
||||
ARFLAGS = rcv
|
||||
ARXFLAGS = xv
|
||||
|
||||
#
|
||||
# RANLIB : ranlib command
|
||||
#
|
||||
|
||||
RANLIB = ranlib
|
||||
|
||||
#
|
||||
# DIFF : diff command
|
||||
#
|
||||
|
||||
DIFF = diff
|
||||
|
||||
#
|
||||
# TAR : tar command
|
||||
#
|
||||
|
||||
TAR = tar
|
||||
|
||||
# ------------------------------------
|
||||
# Default locations
|
||||
# ------------------------------------
|
||||
#
|
||||
# PRTDIR : port dependent files location (libraries and binaries)
|
||||
# BINDIR : port binaries
|
||||
# LIBDIR : port libraries
|
||||
#
|
||||
|
||||
PRTDIR = $(CFGDIR)../ports/$(PORTNAME)
|
||||
|
||||
BINDIR = $(PRTDIR)/bin
|
||||
|
||||
LIBDIR = $(PRTDIR)/lib
|
||||
|
||||
# ------------------------------------
|
||||
# default gmake variable in implicit rules
|
||||
# ------------------------------------
|
||||
|
||||
CFLAGS = $(OPTIM) $(MACHDEF) -I$(INCDIR)
|
||||
|
||||
LDFLAGS = -L$(LIBDIR) -L.
|
||||
|
||||
LDLIBS = $(LIBS) $(MALLOC_LIBS) $(MATH_LIBS) $(CC_LIBS)
|
||||
|
||||
LINTFLAGS = $(MACHDEF) -I$(INCDIR)
|
||||
33
config/guess_port
Executable file
33
config/guess_port
Executable file
@ -0,0 +1,33 @@
|
||||
#! /bin/sh
|
||||
#
|
||||
# $Id: guess_port 1825 2013-02-26 09:39:47Z viari $
|
||||
#
|
||||
# @file: guess_port
|
||||
# @desc: attempt to guess the portname
|
||||
# @usage: guess_port
|
||||
#
|
||||
# @history:
|
||||
# @+ <Gloup> Nov. 2000 first draft adapted from GNU config.guess
|
||||
# @+ <Gloup> Feb. 2010 moved to sh
|
||||
#
|
||||
|
||||
mach=`uname -m`
|
||||
syst=`uname -s`
|
||||
rels=`uname -r`
|
||||
|
||||
case ${mach}:${syst}:${rels} in
|
||||
|
||||
alpha:OSF1:* ) echo alpha-osf1;;
|
||||
sun4*:SunOS:5.* ) echo sparc-solaris;;
|
||||
i86pc:SunOS:5.* ) echo i386-solaris;;
|
||||
sun4*:SunOS:* ) echo sparc-sunos;;
|
||||
Power*:Darwin:* ) echo ppc-darwin;;
|
||||
i*86:Linux:* ) echo i386-linux;;
|
||||
x*86*:Linux:* ) echo i386-linux;;
|
||||
i*86:Darwin:* ) echo i386-darwin;;
|
||||
IP*:IRIX*:* ) echo mips-irix;;
|
||||
i*86:MINGW32*:* ) echo x86-mingw32;;
|
||||
|
||||
*) echo unknown ${mach}:${syst}:${rels}; exit 1;;
|
||||
esac
|
||||
exit 0
|
||||
26
config/ports/i386-darwin.conf
Normal file
26
config/ports/i386-darwin.conf
Normal file
@ -0,0 +1,26 @@
|
||||
#
|
||||
# $Id: i386-darwin.conf 1825 2013-02-26 09:39:47Z viari $
|
||||
#
|
||||
# i386-darwin.conf
|
||||
# configuration file for MacOS-X/Intel-Based/Darwin 1.2 with gcc compiler
|
||||
# this file is included in Makefile
|
||||
#
|
||||
# system (uname -srp) : Darwin 8.7.1 i386
|
||||
# compiler (cc --version) : i686-apple-darwin8-gcc-4.0.1
|
||||
#
|
||||
# check tags
|
||||
# @uname:uname -srp:Darwin 8.7.1 i386
|
||||
# @cc:cc --version:i686-apple-darwin8-gcc-4.0.1
|
||||
#
|
||||
#
|
||||
|
||||
# ------------------------------------
|
||||
# General compilation flags
|
||||
# ------------------------------------
|
||||
|
||||
#
|
||||
# MACHDEF : define machine and OS specific flags
|
||||
#
|
||||
|
||||
MACHDEF = -DLX_TARGET_MACINTEL -DLITTLE_ENDIAN -DMACOSX
|
||||
|
||||
32
config/ports/i386-linux.conf
Executable file
32
config/ports/i386-linux.conf
Executable file
@ -0,0 +1,32 @@
|
||||
#
|
||||
# $Id: i386-linux.conf 1825 2013-02-26 09:39:47Z viari $
|
||||
#
|
||||
# i386-linux.conf
|
||||
# configuration file for linux ix86 with GNU gcc compiler
|
||||
# this file is included in Makefile
|
||||
#
|
||||
# system (uname -srp) : Linux 2.2.14-5.0 unknown
|
||||
# compiler (gcc --version) : egcs-2.91.66
|
||||
#
|
||||
# check tags
|
||||
# @uname:uname -srp:Linux 2.2.14-5.0 unknown
|
||||
# @cc:cc --version:egcs-2.91.66
|
||||
#
|
||||
#
|
||||
|
||||
# ------------------------------------
|
||||
# General compilation flags
|
||||
# ------------------------------------
|
||||
|
||||
#
|
||||
# MACHDEF : define machine and OS specific flags
|
||||
#
|
||||
|
||||
MACHDEF = -DLX_TARGET_LINUX -DLITTLE_ENDIAN
|
||||
|
||||
#
|
||||
# MATH_LIBS : machine specific math librairies
|
||||
#
|
||||
|
||||
MATH_LIBS = -lm
|
||||
|
||||
32
config/ports/ppc-darwin.conf
Executable file
32
config/ports/ppc-darwin.conf
Executable file
@ -0,0 +1,32 @@
|
||||
#
|
||||
# $Id: ppc-darwin.conf 1825 2013-02-26 09:39:47Z viari $
|
||||
#
|
||||
# ppc-darwin.conf
|
||||
# configuration file for MacOS-X/Darwin 1.2 with native cc compiler
|
||||
# this file is included in Makefile
|
||||
#
|
||||
# system (uname -srp) : Darwin 1.2 powerpc
|
||||
# compiler (cc --version) : 2.7.2.1
|
||||
#
|
||||
# check tags
|
||||
# @uname:uname -srp:Darwin 1.2 powerpc
|
||||
# @cc:cc --version:2.7.2.1
|
||||
#
|
||||
#
|
||||
|
||||
# ------------------------------------
|
||||
# General compilation flags
|
||||
# ------------------------------------
|
||||
|
||||
#
|
||||
# MACHDEF : define machine and OS specific flags
|
||||
#
|
||||
|
||||
MACHDEF = -DLX_TARGET_MACPPC -DBIG_ENDIAN
|
||||
|
||||
#
|
||||
# CC : name of (ansi C) compiler to use
|
||||
#
|
||||
|
||||
CC = cc -arch ppc
|
||||
|
||||
31
config/ports/sparc-solaris.conf
Executable file
31
config/ports/sparc-solaris.conf
Executable file
@ -0,0 +1,31 @@
|
||||
#
|
||||
# $Id: sparc-solaris.conf 1825 2013-02-26 09:39:47Z viari $
|
||||
#
|
||||
# sparc-solaris.conf
|
||||
# configuration file for sparc solaris with GNU gcc compiler
|
||||
# this file is included in Makefile
|
||||
#
|
||||
# system (uname -srp) : SunOS 5.8 sparc
|
||||
# compiler (gcc --version) : 2.95.2
|
||||
#
|
||||
# check tags
|
||||
# @uname:uname -srp:SunOS 5.8 sparc
|
||||
# @cc:cc --version:2.95.2
|
||||
#
|
||||
#
|
||||
|
||||
# ------------------------------------
|
||||
# General compilation flags
|
||||
# ------------------------------------
|
||||
|
||||
#
|
||||
# MACHDEF : define machine and OS specific flags
|
||||
#
|
||||
|
||||
MACHDEF = -DLX_TARGET_SOLARIS -DBIG_ENDIAN
|
||||
|
||||
#
|
||||
# MATH_LIBS : machine specific math librairies
|
||||
#
|
||||
|
||||
MATH_LIBS = -lm
|
||||
54
config/ports/x86-mingw32.conf
Normal file
54
config/ports/x86-mingw32.conf
Normal file
@ -0,0 +1,54 @@
|
||||
#
|
||||
# $Id: x86-mingw32.conf 1825 2013-02-26 09:39:47Z viari $
|
||||
#
|
||||
# x86-mingw32
|
||||
# configuration file for MinGW with GNU gcc compiler.
|
||||
#
|
||||
# this file is included in Makefile
|
||||
#
|
||||
#
|
||||
|
||||
#
|
||||
# rename PORTNAME safely since MinGW produce pure win32 executables
|
||||
# without dll's
|
||||
#
|
||||
|
||||
PORTNAME = x86-win32
|
||||
|
||||
# ------------------------------------
|
||||
# General compilation flags
|
||||
# ------------------------------------
|
||||
|
||||
#
|
||||
# CC_LIBS : additionnal machine specific $(CC) libraries
|
||||
#
|
||||
# libiberty is needed for some system extensions (like mkstemps)
|
||||
#
|
||||
|
||||
CC_LIBS = -liberty
|
||||
|
||||
#
|
||||
# MACHDEF : define machine and OS specific flags
|
||||
#
|
||||
# -DDLMALLOC : use dlmalloc instead of malloc (which does not have mallinfo)
|
||||
# -posix is a new replacement for several MinGW32 flags, including:
|
||||
# -D__USE_MINGW_ANSI_STDIO : mingw gcc flag to recognize the C99 "%zu" format
|
||||
#
|
||||
|
||||
MACHDEF = -posix -DLX_TARGET_WIN32 -DWIN_MINGW -DDLMALLOC -DLITTLE_ENDIAN
|
||||
|
||||
#
|
||||
# MATH_LIBS : machine specific math librairies
|
||||
#
|
||||
|
||||
MATH_LIBS = -lm
|
||||
|
||||
# ------------------------------------
|
||||
# General system commands
|
||||
# ------------------------------------
|
||||
|
||||
#
|
||||
# DIFF : diff command / should ignore cr on windows
|
||||
#
|
||||
|
||||
DIFF = diff --strip-trailing-cr
|
||||
25
config/targets/debug.targ
Normal file
25
config/targets/debug.targ
Normal file
@ -0,0 +1,25 @@
|
||||
#
|
||||
# $Id: help.targ 1825 2013-02-26 09:39:47Z viari $
|
||||
#
|
||||
# debug.targ
|
||||
#
|
||||
# target to print debug information (dev. only)
|
||||
#
|
||||
# it defines the following targets:
|
||||
#
|
||||
# debug :
|
||||
# print debug
|
||||
#
|
||||
# it requires auto.conf
|
||||
#
|
||||
|
||||
.PHONY: debug
|
||||
|
||||
debug::
|
||||
@echo "+ PORTNAME: $(PORTNAME)"
|
||||
@echo "+ CFGPRT: $(CFGPRT)"
|
||||
@echo "+ CFGDIR: $(CFGDIR)"
|
||||
@echo "+ PRTDIR: $(PRTDIR)"
|
||||
@echo "+ MACHDEF: $(MACHDEF)"
|
||||
|
||||
|
||||
24
config/targets/empty.targ
Normal file
24
config/targets/empty.targ
Normal file
@ -0,0 +1,24 @@
|
||||
#
|
||||
# $Id: $
|
||||
#
|
||||
# epty.targ
|
||||
#
|
||||
# default empty targets (defined as double colon rules)
|
||||
#
|
||||
#
|
||||
|
||||
#
|
||||
# Rules
|
||||
#
|
||||
|
||||
.PHONY: all test clean portclean help
|
||||
|
||||
all::
|
||||
|
||||
test::
|
||||
|
||||
clean::
|
||||
|
||||
portclean:: clean
|
||||
|
||||
test::
|
||||
23
config/targets/help.targ
Normal file
23
config/targets/help.targ
Normal file
@ -0,0 +1,23 @@
|
||||
#
|
||||
# $Id: help.targ 1825 2013-02-26 09:39:47Z viari $
|
||||
#
|
||||
# help.targ
|
||||
#
|
||||
# default target to print help
|
||||
#
|
||||
# it defines the following targets:
|
||||
#
|
||||
# help :
|
||||
# print help
|
||||
#
|
||||
|
||||
.PHONY: help
|
||||
|
||||
help::
|
||||
@ echo "basic usage: make [<action>+]"
|
||||
@ echo "valid <action> :"
|
||||
@ echo " all : compile everything for current port [default target]"
|
||||
@ echo " clean : local cleanup"
|
||||
@ echo " portclean : cleanup distribution for current port"
|
||||
@ echo " test : run tests on current port"
|
||||
@ echo " help : print this help"
|
||||
51
config/targets/lxbin.targ
Normal file
51
config/targets/lxbin.targ
Normal file
@ -0,0 +1,51 @@
|
||||
#
|
||||
# $Id: $
|
||||
#
|
||||
# lxbin.targ
|
||||
#
|
||||
# default make targets for standard lx binary
|
||||
#
|
||||
# you should define the 'PROGS' and 'OSRC' variables
|
||||
# and optionnaly 'LIBS' if binaries have to be linked with libraries
|
||||
#
|
||||
# note: if main source code for binary PROG is PROG.c, there is nothing to do,
|
||||
# else (e.g. if it involves several sources files) you should also add local
|
||||
# file dependencies. e.g under the form:
|
||||
#
|
||||
# mymain: $(OBJ) mymain_base.c mymain_help.c
|
||||
# $(CC) $(CFLAGS) -o $@ $^ $(LDFLAGS) $(LDLIBS)
|
||||
#
|
||||
#
|
||||
# 'auto.conf' should have been included
|
||||
#
|
||||
|
||||
OBJ = $(OSRC:.c=.o)
|
||||
|
||||
INCDIR = ../include
|
||||
|
||||
#
|
||||
# Rules
|
||||
#
|
||||
|
||||
.PHONY: all prelib install test clean portclean
|
||||
|
||||
all:: prelib $(PROGS) install
|
||||
@echo "+++++++++++ binaries $(PROGS) done"
|
||||
|
||||
prelib::
|
||||
test -d $(PRTDIR) || mkdir $(PRTDIR) # because some linker may complain
|
||||
test -d $(LIBDIR) || mkdir $(LIBDIR) # if -L$(LIBDIR) does not exist
|
||||
|
||||
install::
|
||||
test -d $(PRTDIR) || mkdir $(PRTDIR)
|
||||
test -d $(BINDIR) || mkdir $(BINDIR)
|
||||
-for f in $(PROGS) ; do \cp -f $$f $(BINDIR) ; done
|
||||
|
||||
test::
|
||||
|
||||
clean::
|
||||
-\rm -f *.o cvstatic* *% *.bak so_loc*
|
||||
-\rm -f $(PROGS)
|
||||
|
||||
portclean:: clean
|
||||
-(! test -d $(BINDIR)) || (cd $(BINDIR) && \rm -f $(PROGS))
|
||||
43
config/targets/lxlib.targ
Normal file
43
config/targets/lxlib.targ
Normal file
@ -0,0 +1,43 @@
|
||||
#
|
||||
# $Id: $
|
||||
#
|
||||
# lxlib.targ
|
||||
#
|
||||
# default make targets for standard lx library
|
||||
#
|
||||
# you should define the 'LOCLIB' and 'OSRC' variables
|
||||
#
|
||||
# 'auto.conf' should have been included
|
||||
#
|
||||
|
||||
OBJ = $(OSRC:.c=.o)
|
||||
|
||||
INCDIR = ../include
|
||||
|
||||
#
|
||||
# Rules
|
||||
#
|
||||
|
||||
.PHONY: all lib install test clean portclean
|
||||
|
||||
all:: lib install
|
||||
@echo "+++++++++++ library $(LOCLIB) done"
|
||||
|
||||
lib:: $(OBJ)
|
||||
$(AR) $(ARFLAGS) $(LOCLIB) $(OBJ)
|
||||
$(RANLIB) $(LOCLIB)
|
||||
|
||||
install::
|
||||
test -d $(PRTDIR) || mkdir $(PRTDIR)
|
||||
test -d $(LIBDIR) || mkdir $(LIBDIR)
|
||||
\cp -f $(LOCLIB) $(LIBDIR)
|
||||
$(RANLIB) $(LIBDIR)/$(LOCLIB)
|
||||
|
||||
test::
|
||||
|
||||
clean::
|
||||
-\rm -f *.o cvstatic* *% *.bak so_loc*
|
||||
-\rm -f $(LOCLIB)
|
||||
|
||||
portclean:: clean
|
||||
-(! test -d $(LIBDIR)) || (cd $(LIBDIR) && \rm -f $(LOCLIB))
|
||||
48
config/targets/package.targ
Normal file
48
config/targets/package.targ
Normal file
@ -0,0 +1,48 @@
|
||||
#
|
||||
# $Id: package.targ 1825 2013-02-26 09:39:47Z viari $
|
||||
#
|
||||
# package.targ
|
||||
#
|
||||
# default make targets for standard package with configure
|
||||
#
|
||||
# you should define the 'PKG' variable
|
||||
# (and optionaly 'PKGTAR', 'PKGDIR')
|
||||
#
|
||||
|
||||
PKGTAR ?= $(PKG).tgz
|
||||
|
||||
PKGDIR ?= build.$(PORTNAME)
|
||||
|
||||
PRTPATH = $(abspath $(PRTDIR))
|
||||
|
||||
#
|
||||
# Rules
|
||||
#
|
||||
|
||||
.PHONY: all clean test portclean pkg pkg.expand pkg.make pkg.install
|
||||
|
||||
all:: pkg
|
||||
|
||||
pkg.expand::
|
||||
test -d $(PKGDIR) || mkdir $(PKGDIR)
|
||||
test -f $(PKGDIR)/configure || $(TAR) zxf $(PKGTAR) -C $(PKGDIR) --strip-components 1
|
||||
|
||||
pkg.make:: pkg.expand
|
||||
test -f $(PKGDIR)/Makefile || (cd $(PKGDIR) && ./configure --prefix=$(PRTPATH))
|
||||
$(MAKE) -C $(PKGDIR)
|
||||
|
||||
pkg.install:: pkg.make
|
||||
$(MAKE) -C $(PKGDIR) install
|
||||
|
||||
pkg:: pkg.install
|
||||
@echo "+++++++++++ package $(PKG) done"
|
||||
|
||||
test::
|
||||
(! test -d $(PKGDIR)) || $(MAKE) -C $(PKGDIR) test
|
||||
|
||||
clean::
|
||||
(! test -d $(PKGDIR)) || $(MAKE) -C $(PKGDIR) clean
|
||||
|
||||
portclean::
|
||||
(! test -d $(PKGDIR)) || $(MAKE) -C $(PKGDIR) distclean
|
||||
(! test -d $(PKGDIR)) || \rm -r $(PKGDIR)
|
||||
30
config/targets/propagate.targ
Normal file
30
config/targets/propagate.targ
Normal file
@ -0,0 +1,30 @@
|
||||
#
|
||||
# $Id: propagate.targ 1825 2013-02-26 09:39:47Z viari $
|
||||
#
|
||||
# propagate.targ
|
||||
#
|
||||
# default make targets for library containers
|
||||
#
|
||||
# you should define the 'DIRS' variable
|
||||
#
|
||||
# It will propagate 'MAKE <target>' to all
|
||||
# directories listed in DIRS
|
||||
#
|
||||
|
||||
#
|
||||
# Rules
|
||||
#
|
||||
|
||||
.PHONY: all _action $(DIRS)
|
||||
|
||||
.DEFAULT:
|
||||
$(MAKE) ACTION=$@ _action
|
||||
|
||||
all::
|
||||
$(MAKE) ACTION=all _action
|
||||
|
||||
_action: $(DIRS)
|
||||
@echo "$(ACTION) done"
|
||||
|
||||
$(DIRS):
|
||||
$(MAKE) -C $@ $(ACTION)
|
||||
9453
data/rrna/16S.goodali.aln
Normal file
9453
data/rrna/16S.goodali.aln
Normal file
File diff suppressed because it is too large
Load Diff
9610
data/rrna/16S.goodali.fst
Normal file
9610
data/rrna/16S.goodali.fst
Normal file
File diff suppressed because it is too large
Load Diff
381
data/rrna/4.5S.goodali.aln
Normal file
381
data/rrna/4.5S.goodali.aln
Normal file
@ -0,0 +1,381 @@
|
||||
CLUSTAL W (1.7) multiple sequence alignment
|
||||
|
||||
|
||||
NC_000932_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_001320_LCS taaggtagcggcgagacgagccg-------------------------------------
|
||||
NC_004677_LCS taaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_008115_LCS gaaggtcacggcgagacgagctg-------------------------------------
|
||||
NC_006290_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_007942_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_026134_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_011828_LCS gaaggtcacggcgagactagccg-------------------------------------
|
||||
NC_009618_LCS taaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_002693_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_005086_LCS taaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_009259_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_024021_LCS --aggtcatggcgagacgagccg-------------------------------------
|
||||
NC_008335_LCS -aaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_026295_LCS --aggtcacggcgagacgagccg-------------------------------------
|
||||
NC_016708_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_008796_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_010442_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_021425_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_007407_LCS taaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_015891_LCS taaggtcacggcaagacgagccg-------------------------------------
|
||||
NC_016064_LCS taaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_001631_LCS taaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_005087_LCS taaggtcacggcaagacgagccg-------------------------------------
|
||||
NC_021449_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_023119_LCS -aaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_023090_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_015621_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_009271_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_003119_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_007144_LCS gaaggtcacggcgagatgagccg-------------------------------------
|
||||
NC_009766_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_025744_LCS -aaggtcacggcgagactagccg-------------------------------------
|
||||
NC_001568_LCS taaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_009765_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_017006_LCS taaggtcacggcaagacgagccg-------------------------------------
|
||||
NC_008829_LCS taaggtcacggcaagacgagccg-------------------------------------
|
||||
NC_014676_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_025236_LCS taaggtagcggcgagacgagccg-------------------------------------
|
||||
NC_023533_LCS taaggtagcggcgagacgagccg-------------------------------------
|
||||
NC_014062_LCS taaggtagcggcgagacgagccg-------------------------------------
|
||||
NC_020321_LCS taaggtcaaggcgagacgagcct-------------------------------------
|
||||
NC_012818_LCS taaggtcacggcaagacgagccg-------------------------------------
|
||||
NC_022137_LCS taaggtcacggcaagacgagccg-------------------------------------
|
||||
NC_014348_LCS taaggtcacggcaagacgagccg-------------------------------------
|
||||
NC_024158_LCS taaggtcacggcaagacgagccg-------------------------------------
|
||||
NC_014699_LCS taaggtcacggcaagacgagccg-------------------------------------
|
||||
NC_010109_LCS taaggtcacggcaagacgagccg-------------------------------------
|
||||
NC_014592_LCS taaggtcacggcaagacgagccg-------------------------------------
|
||||
NC_014675_LCS taaggtcacggcaagacgagccg-------------------------------------
|
||||
NC_024291_LCS taaggtcacggcaagacgagccg-------------------------------------
|
||||
NC_019628_LCS taaggtcacggcaagacgagccg-------------------------------------
|
||||
NC_020146_LCS taaggtcacggcaagacgagccg-------------------------------------
|
||||
NC_015402_LCS taaggtcacggcaagacgagccg-------------------------------------
|
||||
NC_004766_LCS taaggtcacggcaagacgagccg-------------------------------------
|
||||
NC_012052_LCS taaggtcacggcaagacgagccg-------------------------------------
|
||||
NC_001319_LCS taaggtcacggcaagactagccg-------------------------------------
|
||||
NC_004543_LCS taaggtcacggcaagatgagccg-------------------------------------
|
||||
NC_020259_LCS taaggtcacggcaagatgagccg-------------------------------------
|
||||
NC_025659_LCS taaggtcacggcgagacgagcca-------------------------------------
|
||||
NC_026775_LCS taaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_026773_LCS taaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_025305_LCS taaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_011954_LCS taaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_026301_LCS taaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_010654_LCS taaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_026778_LCS taaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_021936_LCS taaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_026776_LCS taaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_014056_LCS taaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_026449_LCS taaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_024945_LCS taaggtcacggcgagatgagccg-------------------------------------
|
||||
NC_026785_LCS taaggtcacggctagacgagccg-------------------------------------
|
||||
NC_023805_LCS taaggtcacggtgagactagccg-------------------------------------
|
||||
NC_024827_LCS taaggtcacggtgagactagccg-------------------------------------
|
||||
NC_020365_LCS taaggtcacgtcgagacgagccg-------------------------------------
|
||||
NC_010548_LCS taaggtcatggcgagacgagccg-------------------------------------
|
||||
NC_013086_LCS tgaggtcacggcaagatgagccg-------------------------------------
|
||||
NC_006861_LCS -aaggtcacggcaagacgagccg-------------------------------------
|
||||
NC_003386_LCS -aaggtcacggcaagacgagccg-------------------------------------
|
||||
NC_016471_LCS -aaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_010359_LCS -aaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_020372_LCS -aaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_014582_LCS -aaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_024421_LCS -aaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_018114_LCS -aaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_026847_LCS -aaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_023120_LCS -aaggtcacggtgagactagccg-------------------------------------
|
||||
NC_014874_LCS -aaggtcacggttagacgagccg-------------------------------------
|
||||
NC_011942_LCS -------------agacgagccg-------------------------------------
|
||||
NC_016065_LCS agaggtcttggcgagactagcca-------------------------------------
|
||||
NC_022136_LCS caaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_014063_LCS caaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_023121_LCS -caggtcacggcgagacgagccg-------------------------------------
|
||||
NC_021110_LCS cgaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_016063_LCS cgaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_025642_LCS gaaggtcacggcgagacgagcca-------------------------------------
|
||||
NC_026202_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_009266_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_002202_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_025554_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_021111_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_023359_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_010776_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_024635_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_025907_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_008336_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_022457_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_023259_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_025909_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_024038_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_014057_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_002694_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_010433_LCS_CMP gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_001666_LCS_CMP taaggtagcggcgagacgagccg-------------------------------------
|
||||
NC_013991_LCS_CMP taaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_024168_LCS_CMP --aggtcacggcaagacgagccg-------------------------------------
|
||||
NC_023356_LCS_CMP taaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_013707_LCS_CMP gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_021372_LCS taaggtagcggcgagacgagccg-------------------------------------
|
||||
NC_007578_LCS gaaggtcacggcgagacgagccg-------------------------------------
|
||||
NC_008454_LCS gaaggtcacggcgagacgagccg------------------tttatcatattactcaatt
|
||||
NC_014569_LCS gaaggtcacggcgagacgagccgtttgttttagagtgtcaaagtcttgagaattcaggcg
|
||||
NC_026448_LCS taaggtcgcggcgagatgatccg-------------------------------------
|
||||
|
||||
|
||||
NC_000932_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_001320_LCS ----------ttta----------aataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_004677_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_008115_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_006290_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_007942_LCS ----------tttctaatt--aatgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_026134_LCS ----------tttatcatt--aacgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_011828_LCS ----------tttttcatt--aacgataggtgtcaagtggaagtgcagtaatgtatg-ca
|
||||
NC_009618_LCS ----------tttatcatc---acgataggtgtcaagtggaagtgcagtgatgcatg-ca
|
||||
NC_002693_LCS ----------tttatcatt---atgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_005086_LCS ----------tttatcatc---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_009259_LCS ----------tttctaatt--aatgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_024021_LCS ----------ttag--------gtgataggtgtcaagtggaagtgcagtgatgcatg-ca
|
||||
NC_008335_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_026295_LCS ----------ttag--------gtgataggtgtcaagtggaagtgcagtgatgcatg-ca
|
||||
NC_016708_LCS ----------tttctcatt--aacgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_008796_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_010442_LCS ----------tttatcatt---acaataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_021425_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_007407_LCS ----------tttatcatt---acgataggtgccaagtggaagtgcagtgatgtatg-ca
|
||||
NC_015891_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_016064_LCS ----------tttatcatt---acgataggtgtcaagtggaagtacagtgatgtatg-ca
|
||||
NC_001631_LCS ----------tttataatt---atgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_005087_LCS ----------tttatcatc---acgataggtgccaagtggaagtgcagtaatgtatg-ca
|
||||
NC_021449_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_023119_LCS ----------tttttcatt---ccgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_023090_LCS ----------tttctcatt--aacgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_015621_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_009271_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_003119_LCS ----------tttttcatt--aacgataggtgtcaagtggaagtgcagtaatgtatg-ca
|
||||
NC_007144_LCS ----------tttatcatc---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_009766_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_025744_LCS -----------ttttcatt--aacgataggtgtcaagtggaagtgcagtaatgtatg-ca
|
||||
NC_001568_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_009765_LCS ----------tttatcatt---acaataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_017006_LCS ----------tttatcacc---acgataggtgccaagtggaagtgcagtaatgtatg-ca
|
||||
NC_008829_LCS ----------tttatcact---acgataggtgccaagtggaagtgcagtaatgtatg-ca
|
||||
NC_014676_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_025236_LCS ----------ttta----------aataggtgtcaagtggaagtacagtgatgtatg-ca
|
||||
NC_023533_LCS ----------ttta----------aataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_014062_LCS ----------ttta----------aataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_020321_LCS ----------tttatcaa----acgataggtatcaagtggaagtgcagtgatgtacg-ca
|
||||
NC_012818_LCS ----------tttatcacc---acgataggtgccaagtggaggtgcagtaatgtatg-ca
|
||||
NC_022137_LCS ----------tttatcacc---acgataggtgccaagtggaggtgcagtgatgcatg-ca
|
||||
NC_014348_LCS ----------tttatcact---acgataggtgctaagtggaggtgcagtaatgtatg-ca
|
||||
NC_024158_LCS ----------tttatcatc---acgataggtgccaggtggaagtgcagtaatgtatg-ca
|
||||
NC_014699_LCS ----------tttatcatt---acgataggtgccaggtggaagtgcagtaatgtatg-ca
|
||||
NC_010109_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_014592_LCS ----------tttatcgcc---acaataggtgctaagtggaggtgcagtaatgtatg-ca
|
||||
NC_014675_LCS ----------tttatcgtc---acgataggtgccaagtggaagtgcagtaatgcatg-ca
|
||||
NC_024291_LCS ----------tttatgatc---acgataggtgccaagtggaagtgcagtaatgtatg-ca
|
||||
NC_019628_LCS ----------tttatgatc---acgataggtgccaagtggaagtgcagtaatgtatg-ta
|
||||
NC_020146_LCS ----------tttatgatt---acgataggtgccaggtggaagtgcagtaatgtatg-ca
|
||||
NC_015402_LCS ----------tttattata---acgataggtgccaagtggaagtgcagtaatgtatg-ta
|
||||
NC_004766_LCS ----------tttctcact---acgataggtgctaagtggaagtgcagtaatgtatg-ca
|
||||
NC_012052_LCS ----------tttgttatt---acgataggtgccaagtggaagtgcagtaatgtatg-ca
|
||||
NC_001319_LCS ----------tttattttt---acgataggtgccaagtggaagtgcagtaatgtatg-ta
|
||||
NC_004543_LCS ----------tttatcata---acaataggtgccaagtagaagtgcagtaatgtatg-ca
|
||||
NC_020259_LCS ----------tttatcata---acaataggtgccaagtggaagtgcagtaatgtatg-ca
|
||||
NC_025659_LCS ----------tttctcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_026775_LCS ----------cttatcatt---acgataggtgccaagtggaagtgcagtgatgtatg-ca
|
||||
NC_026773_LCS ----------cttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_025305_LCS --------------ttatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_011954_LCS ----------tttatcatc---acgataggtgtcaagtggaagtgcagtgatgcatg-ca
|
||||
NC_026301_LCS ----------tttatcatc---acgataggtgtcaagtggagatgcagtaatgtatg-ca
|
||||
NC_010654_LCS ----------tttatcatc---acgataggtgtcaagtggagatgcagtgatgtatg-ca
|
||||
NC_026778_LCS ----------tttatcatt---acaataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_021936_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_026776_LCS ----------tttatcatt---atgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_014056_LCS ----------tttctcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_026449_LCS ----------tgtatcaac---attataggtgccgagtgtaagtgcggcgatgcatg-ca
|
||||
NC_024945_LCS ----------tttatcag----acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_026785_LCS ----------tttatcatt---acaataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_023805_LCS ----------tttacgact---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_024827_LCS ----------tttacgact---acgataggtgtcaagtggaagtgcagtgatgtatg-ta
|
||||
NC_020365_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgcagcgatgtatg-ca
|
||||
NC_010548_LCS ----------tttattag----acgataggtgtcaagtggaagtgcagtgatgcatg-ca
|
||||
NC_013086_LCS ----------tttatcata---acgataggtgccaggtggaagtgcagtcatgtacg-ca
|
||||
NC_006861_LCS ----------tttatcatc---acgataggtgccaagtggaaatacagtaatgtatg-ca
|
||||
NC_003386_LCS ----------tttattatc---acgataggtgccaagtggaagtgcagtaatgtacg-ca
|
||||
NC_016471_LCS ----------tttataatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_010359_LCS ----------tttatcatc---acgataggtgccaggtggaagtgcagtgatgtatg-ta
|
||||
NC_020372_LCS ----------tttatcatc---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_014582_LCS ----------tttatcatt---acaataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_024421_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgcagcgatgtatg-ca
|
||||
NC_018114_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_026847_LCS ----------tttatcatt---ccaataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_023120_LCS ----------tttacgact---acgataggtgtcaagtggaagtgcagtgatgtatg-ta
|
||||
NC_014874_LCS ----------tttattatt---atgataggtgtcaagtggaagtgcagtgatgcatg-ca
|
||||
NC_011942_LCS ----------tttatcatc---acgataggtgtcaagtggagatgcagtaatgtatg-ca
|
||||
NC_016065_LCS ----------gcgattag----acgataggtgtcaagtggaagtgcagtgatgcatg-ca
|
||||
NC_022136_LCS ----------tttctcatc---acgataggtgccaagtggaagtgcagtaatgtatg-ca
|
||||
NC_014063_LCS ----------tttttcatt--aacgataggtgtcaagtggaagtgcagtaatgtatg-ca
|
||||
NC_023121_LCS ----------ttag--------gtgataggtgtcaagtggaagtgcagtgatgcatg-ca
|
||||
NC_021110_LCS ----------tttatcag----acgataggtgttaagtgaaagtacagtgatgtatg-ca
|
||||
NC_016063_LCS ----------tttatcag----acgataggtgttaagtgaaagtgcagtgatgtatg-ca
|
||||
NC_025642_LCS ----------tttatcatt---acgataggtgtcaagtgtaagtgcagtgatgtatg-ca
|
||||
NC_026202_LCS ----------tttataatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_009266_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgcatg-ca
|
||||
NC_002202_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_025554_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgtagtgatgtatg-ca
|
||||
NC_021111_LCS ----------tttatcatt---acgataggtgtcaagtgtaagtgcagtgatgtatg-ca
|
||||
NC_023359_LCS ----------tttatcatt---acgataggtgtcaagtgtaagtgcagtgatgtatg-ca
|
||||
NC_010776_LCS ----------tttatcatt---acgataggtgtcaggtggaagtgcagtgatgtatg-ca
|
||||
NC_024635_LCS ----------tttatcatt---ataataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_025907_LCS ----------tttatcatt---ccaataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_008336_LCS ----------tttattatt---acgataggtgtcaagtggaagtgcagcgatgtatg-ca
|
||||
NC_022457_LCS ----------tttattatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_023259_LCS ----------tttattatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_025909_LCS ----------tttctaatt--aacgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_024038_LCS ----------tttctaatt--aacgataggtgtcaggtggaagtgcagtaatgtacg-ca
|
||||
NC_014057_LCS ----------tttttcatt--aacgataggtgtcaagtggaagtacagtaatgtatg-ca
|
||||
NC_002694_LCS ----------tttttcatt--aacgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_010433_LCS_CMP ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_001666_LCS_CMP ----------ttta----------aataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_013991_LCS_CMP ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_024168_LCS_CMP ----------tttt---ag---acaataggtgccaggtggaagcgcagtaatgtgtg-ca
|
||||
NC_023356_LCS_CMP ----------tttatcatt---atgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_013707_LCS_CMP ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_021372_LCS ----------ttt----------aaataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_007578_LCS ----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_008454_LCS gatcattacgtttatcatt---acgataggtgttaagtggaagtgcagtgatgtatg-ca
|
||||
NC_014569_LCS cggcccgtcctttagagcaaaacaaataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
NC_026448_LCS ----------ttgatagtgactatgataggtactaagtgtaaatgcagcgatgtatgtta
|
||||
|
||||
|
||||
NC_000932_LCS gctgaggcatcctaacagaccggtagacttgaac-
|
||||
NC_001320_LCS gctgaggcatcctaac-gaacgaacgatttgaac-
|
||||
NC_004677_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_008115_LCS gctgaggcatcctaacagaccggtagacttgaac-
|
||||
NC_006290_LCS gctgaggcatcctaacagaccgatagacttgaac-
|
||||
NC_007942_LCS gctgaggcatcctaacagaccggtagacttgaac-
|
||||
NC_026134_LCS gctgaggcatcctaacagaccggtagacttgaac-
|
||||
NC_011828_LCS gctgaggcatcctaacagaccgatagacttgaac-
|
||||
NC_009618_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_002693_LCS gctgagacatcctaacagaccgctagacttgaac-
|
||||
NC_005086_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_009259_LCS gctgaggcatcctaacagaccgttagacttgaac-
|
||||
NC_024021_LCS gccgaggcatactaaaagaccgaaagatttgaac-
|
||||
NC_008335_LCS gctgaggcatcctaacagaccga------------
|
||||
NC_026295_LCS gccgaggcatactaaaagaccgaaagatttgaac-
|
||||
NC_016708_LCS gctgaggcatcctaacagaccggtagacttgaac-
|
||||
NC_008796_LCS gctgaggcatcctaacagaccaatagacttgaac-
|
||||
NC_010442_LCS gctgaggcatcctaacagaccgatagacttgaac-
|
||||
NC_021425_LCS gctgaggcatcctaacagaccgttagacttgaac-
|
||||
NC_007407_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_015891_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_016064_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_001631_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_005087_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_021449_LCS gctgaggcatcctaacagaccggtagacttgaac-
|
||||
NC_023119_LCS gctgaggcatcctaacagaccgaaagatttgaac-
|
||||
NC_023090_LCS gcggaggcatcctaacagaccggtagacttgaac-
|
||||
NC_015621_LCS gctgaggcatcctaacagaccggtagact------
|
||||
NC_009271_LCS gctgaggcatcctaacagaccggtagacttgaa--
|
||||
NC_003119_LCS gctgaggcatcctaacagaccggtagacttgaac-
|
||||
NC_007144_LCS gctgaggcatcctaacagaccggtagacttgaac-
|
||||
NC_009766_LCS gctgaggcatcctaatagaccggtagacttgaac-
|
||||
NC_025744_LCS gctgaggcatcctaacagaccgatagacttgaac-
|
||||
NC_001568_LCS gctgaggcatcctaacagaccggtagacttgaac-
|
||||
NC_009765_LCS gctgaggcatcctaacagaccggtagacttgaac-
|
||||
NC_017006_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_008829_LCS gctgaggcatcctaacagaccgagaggtttgaac-
|
||||
NC_014676_LCS gctgaggcatcctaacagaccggcagacttgaac-
|
||||
NC_025236_LCS gctgaggcatcctaac-gaacgaacgatttgaac-
|
||||
NC_023533_LCS gctgaggcatcctaaccaa-cgaacgatttgaac-
|
||||
NC_014062_LCS gctgaggcatcctaat-gaacgaacgatttgaac-
|
||||
NC_020321_LCS gctgaggcatcctaacagaccgaaagattttaac-
|
||||
NC_012818_LCS gctgaggcatcctaacagaccgagaggtttgaac-
|
||||
NC_022137_LCS gctgaggcatcctaacagaccgagaggtttgaac-
|
||||
NC_014348_LCS gctgaggcatcctaacagaccgagaggtttgaac-
|
||||
NC_024158_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_014699_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_010109_LCS gctgagacatcctaacagaccgagagatttgaac-
|
||||
NC_014592_LCS gctgaggcatcctaacagaccgagaggtttgaac-
|
||||
NC_014675_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_024291_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_019628_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_020146_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_015402_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_004766_LCS gctgaggcatcctaacagaccgagaggtttgaac-
|
||||
NC_012052_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_001319_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_004543_LCS gctgaggcattctaacagaccgagagatttgaac-
|
||||
NC_020259_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_025659_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_026775_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_026773_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_025305_LCS gctgaggcatcctaacagaccgaaagatttgaac-
|
||||
NC_011954_LCS gctgagacatcctaacagaccgagagatttgaac-
|
||||
NC_026301_LCS gctgaggcatcctaaaagaccgagagatttgaac-
|
||||
NC_010654_LCS gctgaggcatcctaaaagaccgagagatttgaac-
|
||||
NC_026778_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_021936_LCS gctgaggcattctaacagaccgagagatttgaac-
|
||||
NC_026776_LCS gctgaggcatcctaatagaccgagagatttgaac-
|
||||
NC_014056_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_026449_LCS gctgaggcatactaaaagaccgatatattttaac-
|
||||
NC_024945_LCS gctgaggcatcctaacagactaaaagatttgaac-
|
||||
NC_026785_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_023805_LCS gctaaggcatcctaatagaccgaaagatttgaac-
|
||||
NC_024827_LCS gctaaggcatcctaacagaccgaaagatttgaac-
|
||||
NC_020365_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_010548_LCS gccgaggcatcctaagagaccggaagatttgaac-
|
||||
NC_013086_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_006861_LCS gctgaggcatcctaacagaccaagagatttgaacc
|
||||
NC_003386_LCS gctgaggcatcctaacagaccgatggctttgaacc
|
||||
NC_016471_LCS gctgaggcatcctaacagaccaagagatttgaac-
|
||||
NC_010359_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_020372_LCS gctgaggcatcctaacagaccgatagatttgaac-
|
||||
NC_014582_LCS gctgaggcatcctaacagaccagtagacttgaac-
|
||||
NC_024421_LCS gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_018114_LCS gctgaggcatcctaacagaccgagagatttgaacc
|
||||
NC_026847_LCS gctgaggcatcctaacagaccgcaagacttga---
|
||||
NC_023120_LCS gctaaggcatcctaacagaccgaaagatttgaac-
|
||||
NC_014874_LCS gctgaggcatactaacagaccgagagattttaacc
|
||||
NC_011942_LCS gctgaggcatcctaaaagaccgagagatttgaac-
|
||||
NC_016065_LCS gccgagacatcctaagagaccaaaagatttgaac-
|
||||
NC_022136_LCS gctgaggcatcctaacagaccggaagatttgaac-
|
||||
NC_014063_LCS gctgagtcatcctaacagaccgatagacttgaac-
|
||||
NC_023121_LCS gccgaggcatactaaaagaccgaaagatttgaac-
|
||||
NC_021110_LCS gccaaggcatcctaacagaccga-agatttgaacc
|
||||
NC_016063_LCS gccaaggcatcctaacagaccga-agatttgaacc
|
||||
NC_025642_LCS gctgagacatcctaacagaccggtagacttgaac-
|
||||
NC_026202_LCS gctgaggcatcctaacagaccggtagacttgaac-
|
||||
NC_009266_LCS gctgaggcatcctaacagaccggtagacttgaac-
|
||||
NC_002202_LCS gctgaggcatcctaacagacccacagacttgaac-
|
||||
NC_025554_LCS gctgaggcatcctaacagaccggtagacttgaac-
|
||||
NC_021111_LCS gctgagacatcctaacagaccggtagacttgaac-
|
||||
NC_023359_LCS gctgaggcatcctaacagaccgatagacttgaac-
|
||||
NC_010776_LCS gctgaggcatcctaacagaccgatagacttgaac-
|
||||
NC_024635_LCS gctgaggcatcctaacagaccggtagacttgaac-
|
||||
NC_025907_LCS gctgaggcatcctaacagaccacaagacttgaac-
|
||||
NC_008336_LCS gctgaggcatcctaacagaccgacagacttgaac-
|
||||
NC_022457_LCS gctgaggcatcctaacagaccgccagacttgaac-
|
||||
NC_023259_LCS gctgaggcatcctaacagaccggtagacttgaac-
|
||||
NC_025909_LCS gctgaggcatcctaacagaccggtagacttgaac-
|
||||
NC_024038_LCS gctgaggcatcctaacagaccggtagacttgaac-
|
||||
NC_014057_LCS gctgaggcatcctaacagaccgatagacttgaac-
|
||||
NC_002694_LCS gctgaggcatcctaacagaccggtagacttgaac-
|
||||
NC_010433_LCS_CMP gctgaggcatcctaacagaccggtagacttgaac-
|
||||
NC_001666_LCS_CMP gctgaggcatcctaac-gaacgaacgatttgaac-
|
||||
NC_013991_LCS_CMP gctgaggcatcctaacagaccgagagatttgaac-
|
||||
NC_024168_LCS_CMP gccgaggcatcctaacagaccgagaggtttgaac-
|
||||
NC_023356_LCS_CMP gctgaggcatcctaacagaccgatagatttgaac-
|
||||
NC_013707_LCS_CMP gctgaggcatcctaacagaccggtagacttgaa--
|
||||
NC_021372_LCS gctgaggcatcctaacgaac-gaacgatttgaac-
|
||||
NC_007578_LCS gctgaggcatcctaacagaccggtagacttgaacc
|
||||
NC_008454_LCS gctgaggcatcctaacagaccgttagacttgaac-
|
||||
NC_014569_LCS gctgaggcatcctaacagaccggtagacttgaac-
|
||||
NC_026448_LCS gcttaggtatcctaaaagaccgatttatttgaac-
|
||||
|
||||
|
||||
496
data/rrna/4.5S.goodali.fst
Normal file
496
data/rrna/4.5S.goodali.fst
Normal file
@ -0,0 +1,496 @@
|
||||
>NC_000932_LCS count=162; cluster_center=True; seq_length=103; cluster=NC_000932_LCS; cluster_score=1.0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaac-
|
||||
>NC_001320_LCS count=84; cluster_center=False; seq_length=95; cluster=NC_000932_LCS; cluster_score=0.847619; cluster_weight=559;
|
||||
taaggtagcggcgagacgagccg-------------------------------------
|
||||
----------ttta----------aataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaac-gaacgaacgatttgaac-
|
||||
>NC_004677_LCS count=72; cluster_center=False; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.961538; cluster_weight=559;
|
||||
taaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_008115_LCS count=39; cluster_center=False; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.990291; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagctg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaac-
|
||||
>NC_006290_LCS count=17; cluster_center=False; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.990291; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgatagacttgaac-
|
||||
>NC_007942_LCS count=10; cluster_center=False; seq_length=104; cluster=NC_000932_LCS; cluster_score=0.961538; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttctaatt--aatgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaac-
|
||||
>NC_026134_LCS count=6; cluster_center=False; seq_length=104; cluster=NC_000932_LCS; cluster_score=0.990385; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt--aacgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaac-
|
||||
>NC_011828_LCS count=6; cluster_center=False; seq_length=104; cluster=NC_000932_LCS; cluster_score=0.951923; cluster_weight=559;
|
||||
gaaggtcacggcgagactagccg-------------------------------------
|
||||
----------tttttcatt--aacgataggtgtcaagtggaagtgcagtaatgtatg-ca
|
||||
gctgaggcatcctaacagaccgatagacttgaac-
|
||||
>NC_009618_LCS count=5; cluster_center=False; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.942308; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatc---acgataggtgtcaagtggaagtgcagtgatgcatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_002693_LCS count=5; cluster_center=False; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.970874; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---atgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgagacatcctaacagaccgctagacttgaac-
|
||||
>NC_005086_LCS count=5; cluster_center=False; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.951923; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatc---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_009259_LCS count=4; cluster_center=False; seq_length=104; cluster=NC_000932_LCS; cluster_score=0.951923; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttctaatt--aatgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgttagacttgaac-
|
||||
>NC_024021_LCS count=4; cluster_center=False; seq_length=96; cluster=NC_000932_LCS; cluster_score=0.834951; Strand=1; cluster_weight=559;
|
||||
--aggtcatggcgagacgagccg-------------------------------------
|
||||
----------ttag--------gtgataggtgtcaagtggaagtgcagtgatgcatg-ca
|
||||
gccgaggcatactaaaagaccgaaagatttgaac-
|
||||
>NC_008335_LCS count=4; cluster_center=False; seq_length=91; cluster=NC_000932_LCS; cluster_score=0.883495; Strand=0; cluster_weight=559;
|
||||
-aaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccga------------
|
||||
>NC_026295_LCS count=4; cluster_center=False; seq_length=96; cluster=NC_000932_LCS; cluster_score=0.84466; Strand=1; cluster_weight=559;
|
||||
--aggtcacggcgagacgagccg-------------------------------------
|
||||
----------ttag--------gtgataggtgtcaagtggaagtgcagtgatgcatg-ca
|
||||
gccgaggcatactaaaagaccgaaagatttgaac-
|
||||
>NC_016708_LCS count=4; cluster_center=False; seq_length=104; cluster=NC_000932_LCS; cluster_score=0.980769; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttctcatt--aacgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaac-
|
||||
>NC_008796_LCS count=3; cluster_center=False; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.980583; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccaatagacttgaac-
|
||||
>NC_010442_LCS count=3; cluster_center=False; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.980583; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acaataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgatagacttgaac-
|
||||
>NC_021425_LCS count=3; cluster_center=False; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.990291; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgttagacttgaac-
|
||||
>NC_007407_LCS count=3; cluster_center=False; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.951923; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgccaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_015891_LCS count=3; cluster_center=False; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.951923; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcaagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_016064_LCS count=3; cluster_center=False; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.951923; cluster_weight=559;
|
||||
taaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtacagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_001631_LCS count=3; cluster_center=False; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.942308; Strand=1; cluster_weight=559;
|
||||
taaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttataatt---atgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_005087_LCS count=3; cluster_center=False; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.923077; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcaagacgagccg-------------------------------------
|
||||
----------tttatcatc---acgataggtgccaagtggaagtgcagtaatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_021449_LCS count=3; cluster_center=False; seq_length=105; cluster=NC_000932_LCS; cluster_score=0.980952; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaac-
|
||||
>NC_023119_LCS count=2; cluster_center=False; seq_length=102; cluster=NC_000932_LCS; cluster_score=0.941748; Strand=0; cluster_weight=559;
|
||||
-aaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttttcatt---ccgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgaaagatttgaac-
|
||||
>NC_023090_LCS count=2; cluster_center=False; seq_length=104; cluster=NC_000932_LCS; cluster_score=0.971154; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttctcatt--aacgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gcggaggcatcctaacagaccggtagacttgaac-
|
||||
>NC_015621_LCS count=2; cluster_center=False; seq_length=98; cluster=NC_000932_LCS; cluster_score=0.951456; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccggtagact------
|
||||
>NC_009271_LCS count=2; cluster_center=False; seq_length=102; cluster=NC_000932_LCS; cluster_score=0.990291; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaa--
|
||||
>NC_003119_LCS count=2; cluster_center=False; seq_length=104; cluster=NC_000932_LCS; cluster_score=0.971154; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttttcatt--aacgataggtgtcaagtggaagtgcagtaatgtatg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaac-
|
||||
>NC_007144_LCS count=2; cluster_center=False; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.980583; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagatgagccg-------------------------------------
|
||||
----------tttatcatc---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaac-
|
||||
>NC_009766_LCS count=2; cluster_center=False; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.990291; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaatagaccggtagacttgaac-
|
||||
>NC_025744_LCS count=2; cluster_center=False; seq_length=102; cluster=NC_000932_LCS; cluster_score=0.942308; Strand=1; cluster_weight=559;
|
||||
-aaggtcacggcgagactagccg-------------------------------------
|
||||
-----------ttttcatt--aacgataggtgtcaagtggaagtgcagtaatgtatg-ca
|
||||
gctgaggcatcctaacagaccgatagacttgaac-
|
||||
>NC_001568_LCS count=2; cluster_center=False; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.990291; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaac-
|
||||
>NC_009765_LCS count=2; cluster_center=False; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.990291; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acaataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaac-
|
||||
>NC_017006_LCS count=2; cluster_center=False; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.913462; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcaagacgagccg-------------------------------------
|
||||
----------tttatcacc---acgataggtgccaagtggaagtgcagtaatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_008829_LCS count=2; cluster_center=False; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.913462; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcaagacgagccg-------------------------------------
|
||||
----------tttatcact---acgataggtgccaagtggaagtgcagtaatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagaggtttgaac-
|
||||
>NC_014676_LCS count=2; cluster_center=False; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.990291; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccggcagacttgaac-
|
||||
>NC_025236_LCS count=1; cluster_center=False; cut=117439..117533; seq_length=95; cluster=NC_000932_LCS; cluster_score=0.838095; Strand=0; cluster_weight=559;
|
||||
taaggtagcggcgagacgagccg-------------------------------------
|
||||
----------ttta----------aataggtgtcaagtggaagtacagtgatgtatg-ca
|
||||
gctgaggcatcctaac-gaacgaacgatttgaac-
|
||||
>NC_023533_LCS count=1; cluster_center=False; cut=117008..117102; seq_length=95; cluster=NC_000932_LCS; cluster_score=0.839623; Strand=0; cluster_weight=559;
|
||||
taaggtagcggcgagacgagccg-------------------------------------
|
||||
----------ttta----------aataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaaccaa-cgaacgatttgaac-
|
||||
>NC_014062_LCS count=1; cluster_center=False; cut=121161..121255; seq_length=95; cluster=NC_000932_LCS; cluster_score=0.838095; Strand=0; cluster_weight=559;
|
||||
taaggtagcggcgagacgagccg-------------------------------------
|
||||
----------ttta----------aataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaat-gaacgaacgatttgaac-
|
||||
>NC_020321_LCS count=1; cluster_center=False; cut=101414..101515; seq_length=102; cluster=NC_000932_LCS; cluster_score=0.893204; Strand=1; cluster_weight=559;
|
||||
taaggtcaaggcgagacgagcct-------------------------------------
|
||||
----------tttatcaa----acgataggtatcaagtggaagtgcagtgatgtacg-ca
|
||||
gctgaggcatcctaacagaccgaaagattttaac-
|
||||
>NC_012818_LCS count=1; cluster_center=False; cut=152550..152652; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.894231; Strand=1; cluster_weight=559;
|
||||
taaggtcacggcaagacgagccg-------------------------------------
|
||||
----------tttatcacc---acgataggtgccaagtggaggtgcagtaatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagaggtttgaac-
|
||||
>NC_022137_LCS count=1; cluster_center=False; cut=150383..150485; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.894231; Strand=1; cluster_weight=559;
|
||||
taaggtcacggcaagacgagccg-------------------------------------
|
||||
----------tttatcacc---acgataggtgccaagtggaggtgcagtgatgcatg-ca
|
||||
gctgaggcatcctaacagaccgagaggtttgaac-
|
||||
>NC_014348_LCS count=1; cluster_center=False; cut=148751..148853; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.895238; Strand=1; cluster_weight=559;
|
||||
taaggtcacggcaagacgagccg-------------------------------------
|
||||
----------tttatcact---acgataggtgctaagtggaggtgcagtaatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagaggtttgaac-
|
||||
>NC_024158_LCS count=1; cluster_center=False; cut=138359..138461; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.913462; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcaagacgagccg-------------------------------------
|
||||
----------tttatcatc---acgataggtgccaggtggaagtgcagtaatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_014699_LCS count=1; cluster_center=False; cut=125720..125822; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.923077; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcaagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgccaggtggaagtgcagtaatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_010109_LCS count=1; cluster_center=False; cut=142992..143094; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.942308; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcaagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgagacatcctaacagaccgagagatttgaac-
|
||||
>NC_014592_LCS count=1; cluster_center=False; cut=152146..152248; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.866667; Strand=1; cluster_weight=559;
|
||||
taaggtcacggcaagacgagccg-------------------------------------
|
||||
----------tttatcgcc---acaataggtgctaagtggaggtgcagtaatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagaggtttgaac-
|
||||
>NC_014675_LCS count=1; cluster_center=False; cut=134461..134563; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.903846; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcaagacgagccg-------------------------------------
|
||||
----------tttatcgtc---acgataggtgccaagtggaagtgcagtaatgcatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_024291_LCS count=1; cluster_center=False; cut=119572..119674; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.913462; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcaagacgagccg-------------------------------------
|
||||
----------tttatgatc---acgataggtgccaagtggaagtgcagtaatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_019628_LCS count=1; cluster_center=False; cut=113128..113230; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.903846; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcaagacgagccg-------------------------------------
|
||||
----------tttatgatc---acgataggtgccaagtggaagtgcagtaatgtatg-ta
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_020146_LCS count=1; cluster_center=False; cut=124175..124277; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.913462; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcaagacgagccg-------------------------------------
|
||||
----------tttatgatt---acgataggtgccaggtggaagtgcagtaatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_015402_LCS count=1; cluster_center=False; cut=111547..111649; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.903846; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcaagacgagccg-------------------------------------
|
||||
----------tttattata---acgataggtgccaagtggaagtgcagtaatgtatg-ta
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_004766_LCS count=1; cluster_center=False; cut=146832..146934; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.895238; Strand=1; cluster_weight=559;
|
||||
taaggtcacggcaagacgagccg-------------------------------------
|
||||
----------tttctcact---acgataggtgctaagtggaagtgcagtaatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagaggtttgaac-
|
||||
>NC_012052_LCS count=1; cluster_center=False; cut=114432..114534; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.913462; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcaagacgagccg-------------------------------------
|
||||
----------tttgttatt---acgataggtgccaagtggaagtgcagtaatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_001319_LCS count=1; cluster_center=False; cut=113188..113290; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.894231; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcaagactagccg-------------------------------------
|
||||
----------tttattttt---acgataggtgccaagtggaagtgcagtaatgtatg-ta
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_004543_LCS count=1; cluster_center=False; cut=147535..147637; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.884615; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcaagatgagccg-------------------------------------
|
||||
----------tttatcata---acaataggtgccaagtagaagtgcagtaatgtatg-ca
|
||||
gctgaggcattctaacagaccgagagatttgaac-
|
||||
>NC_020259_LCS count=1; cluster_center=False; cut=144766..144868; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.903846; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcaagatgagccg-------------------------------------
|
||||
----------tttatcata---acaataggtgccaagtggaagtgcagtaatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_025659_LCS count=1; cluster_center=False; cut=124686..124788; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.942308; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcgagacgagcca-------------------------------------
|
||||
----------tttctcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_026775_LCS count=1; cluster_center=False; cut=130118..130220; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.942308; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcgagacgagccg-------------------------------------
|
||||
----------cttatcatt---acgataggtgccaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_026773_LCS count=1; cluster_center=False; cut=131757..131859; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.951923; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcgagacgagccg-------------------------------------
|
||||
----------cttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_025305_LCS count=1; cluster_center=False; cut=135472..135570; seq_length=99; cluster=NC_000932_LCS; cluster_score=0.92233; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcgagacgagccg-------------------------------------
|
||||
--------------ttatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgaaagatttgaac-
|
||||
>NC_011954_LCS count=1; cluster_center=False; cut=93045..93147; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.932692; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatc---acgataggtgtcaagtggaagtgcagtgatgcatg-ca
|
||||
gctgagacatcctaacagaccgagagatttgaac-
|
||||
>NC_026301_LCS count=1; cluster_center=False; cut=97098..97200; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.914286; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatc---acgataggtgtcaagtggagatgcagtaatgtatg-ca
|
||||
gctgaggcatcctaaaagaccgagagatttgaac-
|
||||
>NC_010654_LCS count=1; cluster_center=False; cut=101596..101698; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.92381; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatc---acgataggtgtcaagtggagatgcagtgatgtatg-ca
|
||||
gctgaggcatcctaaaagaccgagagatttgaac-
|
||||
>NC_026778_LCS count=1; cluster_center=False; cut=126845..126947; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.951923; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acaataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_021936_LCS count=1; cluster_center=False; cut=132851..132953; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.951923; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcattctaacagaccgagagatttgaac-
|
||||
>NC_026776_LCS count=1; cluster_center=False; cut=134622..134724; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.942308; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---atgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaatagaccgagagatttgaac-
|
||||
>NC_014056_LCS count=1; cluster_center=False; cut=122521..122623; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.951923; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttctcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_026449_LCS count=1; cluster_center=False; cut=19564..19668; seq_length=105; cluster=NC_000932_LCS; cluster_score=0.813084; Strand=0; cluster_weight=559;
|
||||
taaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tgtatcaac---attataggtgccgagtgtaagtgcggcgatgcatg-ca
|
||||
gctgaggcatactaaaagaccgatatattttaac-
|
||||
>NC_024945_LCS count=1; cluster_center=False; cut=109064..109165; seq_length=102; cluster=NC_000932_LCS; cluster_score=0.896226; Strand=1; cluster_weight=559;
|
||||
taaggtcacggcgagatgagccg-------------------------------------
|
||||
----------tttatcag----acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagactaaaagatttgaac-
|
||||
>NC_026785_LCS count=1; cluster_center=False; cut=132320..132422; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.942308; Strand=0; cluster_weight=559;
|
||||
taaggtcacggctagacgagccg-------------------------------------
|
||||
----------tttatcatt---acaataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_023805_LCS count=1; cluster_center=False; cut=98463..98565; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.894231; Strand=0; cluster_weight=559;
|
||||
taaggtcacggtgagactagccg-------------------------------------
|
||||
----------tttacgact---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctaaggcatcctaatagaccgaaagatttgaac-
|
||||
>NC_024827_LCS count=1; cluster_center=False; cut=111970..112072; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.894231; Strand=1; cluster_weight=559;
|
||||
taaggtcacggtgagactagccg-------------------------------------
|
||||
----------tttacgact---acgataggtgtcaagtggaagtgcagtgatgtatg-ta
|
||||
gctaaggcatcctaacagaccgaaagatttgaac-
|
||||
>NC_020365_LCS count=1; cluster_center=False; cut=133176..133278; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.942308; Strand=0; cluster_weight=559;
|
||||
taaggtcacgtcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagcgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_010548_LCS count=1; cluster_center=False; cut=100631..100732; seq_length=102; cluster=NC_000932_LCS; cluster_score=0.902913; Strand=0; cluster_weight=559;
|
||||
taaggtcatggcgagacgagccg-------------------------------------
|
||||
----------tttattag----acgataggtgtcaagtggaagtgcagtgatgcatg-ca
|
||||
gccgaggcatcctaagagaccggaagatttgaac-
|
||||
>NC_013086_LCS count=1; cluster_center=False; cut=137008..137110; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.885714; Strand=0; cluster_weight=559;
|
||||
tgaggtcacggcaagatgagccg-------------------------------------
|
||||
----------tttatcata---acgataggtgccaggtggaagtgcagtcatgtacg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_006861_LCS count=1; cluster_center=False; cut=143527..143629; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.885714; Strand=0; cluster_weight=559;
|
||||
-aaggtcacggcaagacgagccg-------------------------------------
|
||||
----------tttatcatc---acgataggtgccaagtggaaatacagtaatgtatg-ca
|
||||
gctgaggcatcctaacagaccaagagatttgaacc
|
||||
>NC_003386_LCS count=1; cluster_center=False; cut=125420..125522; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.885714; Strand=0; cluster_weight=559;
|
||||
-aaggtcacggcaagacgagccg-------------------------------------
|
||||
----------tttattatc---acgataggtgccaagtggaagtgcagtaatgtacg-ca
|
||||
gctgaggcatcctaacagaccgatggctttgaacc
|
||||
>NC_016471_LCS count=1; cluster_center=False; cut=70088..70189; seq_length=102; cluster=NC_000932_LCS; cluster_score=0.942308; Strand=0; cluster_weight=559;
|
||||
-aaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttataatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccaagagatttgaac-
|
||||
>NC_010359_LCS count=1; cluster_center=False; cut=100778..100879; seq_length=102; cluster=NC_000932_LCS; cluster_score=0.923077; Strand=0; cluster_weight=559;
|
||||
-aaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatc---acgataggtgccaggtggaagtgcagtgatgtatg-ta
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_020372_LCS count=1; cluster_center=False; cut=142338..142439; seq_length=102; cluster=NC_000932_LCS; cluster_score=0.961165; Strand=0; cluster_weight=559;
|
||||
-aaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatc---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgatagatttgaac-
|
||||
>NC_014582_LCS count=1; cluster_center=False; cut=127077..127178; seq_length=102; cluster=NC_000932_LCS; cluster_score=0.970874; Strand=0; cluster_weight=559;
|
||||
-aaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acaataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccagtagacttgaac-
|
||||
>NC_024421_LCS count=1; cluster_center=False; cut=132893..132994; seq_length=102; cluster=NC_000932_LCS; cluster_score=0.951923; Strand=0; cluster_weight=559;
|
||||
-aaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagcgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac-
|
||||
>NC_018114_LCS count=1; cluster_center=False; cut=120740..120842; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.952381; Strand=0; cluster_weight=559;
|
||||
-aaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaacc
|
||||
>NC_026847_LCS count=1; cluster_center=False; cut=142523..142622; seq_length=100; cluster=NC_000932_LCS; cluster_score=0.932039; Strand=0; cluster_weight=559;
|
||||
-aaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---ccaataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgcaagacttga---
|
||||
>NC_023120_LCS count=1; cluster_center=False; cut=107871..107972; seq_length=102; cluster=NC_000932_LCS; cluster_score=0.894231; Strand=0; cluster_weight=559;
|
||||
-aaggtcacggtgagactagccg-------------------------------------
|
||||
----------tttacgact---acgataggtgtcaagtggaagtgcagtgatgtatg-ta
|
||||
gctaaggcatcctaacagaccgaaagatttgaac-
|
||||
>NC_014874_LCS count=1; cluster_center=False; cut=41650..41752; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.885714; Strand=0; cluster_weight=559;
|
||||
-aaggtcacggttagacgagccg-------------------------------------
|
||||
----------tttattatt---atgataggtgtcaagtggaagtgcagtgatgcatg-ca
|
||||
gctgaggcatactaacagaccgagagattttaacc
|
||||
>NC_011942_LCS count=1; cluster_center=False; cut=39883..39972; seq_length=90; cluster=NC_000932_LCS; cluster_score=0.8; Strand=0; cluster_weight=559;
|
||||
-------------agacgagccg-------------------------------------
|
||||
----------tttatcatc---acgataggtgtcaagtggagatgcagtaatgtatg-ca
|
||||
gctgaggcatcctaaaagaccgagagatttgaac-
|
||||
>NC_016065_LCS count=1; cluster_center=False; cut=58742..58843; seq_length=102; cluster=NC_000932_LCS; cluster_score=0.803738; Strand=0; cluster_weight=559;
|
||||
agaggtcttggcgagactagcca-------------------------------------
|
||||
----------gcgattag----acgataggtgtcaagtggaagtgcagtgatgcatg-ca
|
||||
gccgagacatcctaagagaccaaaagatttgaac-
|
||||
>NC_022136_LCS count=1; cluster_center=False; cut=152638..152740; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.932039; Strand=1; cluster_weight=559;
|
||||
caaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttctcatc---acgataggtgccaagtggaagtgcagtaatgtatg-ca
|
||||
gctgaggcatcctaacagaccggaagatttgaac-
|
||||
>NC_014063_LCS count=1; cluster_center=False; cut=89893..89996; seq_length=104; cluster=NC_000932_LCS; cluster_score=0.942308; Strand=0; cluster_weight=559;
|
||||
caaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttttcatt--aacgataggtgtcaagtggaagtgcagtaatgtatg-ca
|
||||
gctgagtcatcctaacagaccgatagacttgaac-
|
||||
>NC_023121_LCS count=1; cluster_center=False; cut=57558..57654; seq_length=97; cluster=NC_000932_LCS; cluster_score=0.84466; Strand=0; cluster_weight=559;
|
||||
-caggtcacggcgagacgagccg-------------------------------------
|
||||
----------ttag--------gtgataggtgtcaagtggaagtgcagtgatgcatg-ca
|
||||
gccgaggcatactaaaagaccgaaagatttgaac-
|
||||
>NC_021110_LCS count=1; cluster_center=False; cut=105447..105548; seq_length=102; cluster=NC_000932_LCS; cluster_score=0.87619; Strand=0; cluster_weight=559;
|
||||
cgaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcag----acgataggtgttaagtgaaagtacagtgatgtatg-ca
|
||||
gccaaggcatcctaacagaccga-agatttgaacc
|
||||
>NC_016063_LCS count=1; cluster_center=False; cut=106726..106827; seq_length=102; cluster=NC_000932_LCS; cluster_score=0.885714; Strand=0; cluster_weight=559;
|
||||
cgaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcag----acgataggtgttaagtgaaagtgcagtgatgtatg-ca
|
||||
gccaaggcatcctaacagaccga-agatttgaacc
|
||||
>NC_025642_LCS count=1; cluster_center=False; cut=69137..69239; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.970874; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagcca-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtgtaagtgcagtgatgtatg-ca
|
||||
gctgagacatcctaacagaccggtagacttgaac-
|
||||
>NC_026202_LCS count=1; cluster_center=False; cut=129378..129480; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.990291; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttataatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaac-
|
||||
>NC_009266_LCS count=1; cluster_center=False; cut=130502..130604; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.990291; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgcatg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaac-
|
||||
>NC_002202_LCS count=1; cluster_center=False; cut=128763..128865; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.970874; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagacccacagacttgaac-
|
||||
>NC_025554_LCS count=1; cluster_center=False; cut=135213..135315; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.990291; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgtagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaac-
|
||||
>NC_021111_LCS count=1; cluster_center=False; cut=32758..32860; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.980583; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtgtaagtgcagtgatgtatg-ca
|
||||
gctgagacatcctaacagaccggtagacttgaac-
|
||||
>NC_023359_LCS count=1; cluster_center=False; cut=127655..127757; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.980583; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtgtaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgatagacttgaac-
|
||||
>NC_010776_LCS count=1; cluster_center=False; cut=136579..136681; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.980583; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaggtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgatagacttgaac-
|
||||
>NC_024635_LCS count=1; cluster_center=False; cut=108314..108416; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.980583; Strand=1; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---ataataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaac-
|
||||
>NC_025907_LCS count=1; cluster_center=False; cut=127320..127422; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.951456; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---ccaataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccacaagacttgaac-
|
||||
>NC_008336_LCS count=1; cluster_center=False; cut=133098..133200; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.961165; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttattatt---acgataggtgtcaagtggaagtgcagcgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgacagacttgaac-
|
||||
>NC_022457_LCS count=1; cluster_center=False; cut=131133..131235; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.970874; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttattatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgccagacttgaac-
|
||||
>NC_023259_LCS count=1; cluster_center=False; cut=137002..137104; seq_length=103; cluster=NC_000932_LCS; cluster_score=0.990291; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttattatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaac-
|
||||
>NC_025909_LCS count=1; cluster_center=False; cut=127251..127354; seq_length=104; cluster=NC_000932_LCS; cluster_score=0.971154; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttctaatt--aacgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaac-
|
||||
>NC_024038_LCS count=1; cluster_center=False; cut=106484..106587; seq_length=104; cluster=NC_000932_LCS; cluster_score=0.942308; Strand=1; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttctaatt--aacgataggtgtcaggtggaagtgcagtaatgtacg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaac-
|
||||
>NC_014057_LCS count=1; cluster_center=False; cut=42962..43065; seq_length=104; cluster=NC_000932_LCS; cluster_score=0.951923; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttttcatt--aacgataggtgtcaagtggaagtacagtaatgtatg-ca
|
||||
gctgaggcatcctaacagaccgatagacttgaac-
|
||||
>NC_002694_LCS count=1; cluster_center=False; cut=127517..127620; seq_length=104; cluster=NC_000932_LCS; cluster_score=0.980769; Strand=0; cluster_weight=559;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttttcatt--aacgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaac-
|
||||
>NC_010433_LCS_CMP complemented=True; count=19; cluster_center=True; seq_length=103; cluster=NC_010433_LCS; cluster_score=1.0; cluster_weight=28;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaac
|
||||
>NC_001666_LCS_CMP complemented=True; count=4; cluster_center=False; seq_length=95; cluster=NC_010433_LCS; cluster_score=0.847619; cluster_weight=28;
|
||||
taaggtagcggcgagacgagccg-------------------------------------
|
||||
----------ttta----------aataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaac-gaacgaacgatttgaac
|
||||
>NC_013991_LCS_CMP complemented=True; count=2; cluster_center=False; seq_length=103; cluster=NC_010433_LCS; cluster_score=0.961538; cluster_weight=28;
|
||||
taaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgagagatttgaac
|
||||
>NC_024168_LCS_CMP complemented=True; count=1; cluster_center=False; cut=129161..129258; seq_length=98; cluster=NC_010433_LCS; cluster_score=0.826923; Strand=1; cluster_weight=28;
|
||||
--aggtcacggcaagacgagccg-------------------------------------
|
||||
----------tttt---ag---acaataggtgccaggtggaagcgcagtaatgtgtg-ca
|
||||
gccgaggcatcctaacagaccgagaggtttgaac
|
||||
>NC_023356_LCS_CMP complemented=True; count=1; cluster_center=False; cut=79931..80033; seq_length=103; cluster=NC_010433_LCS; cluster_score=0.961165; Strand=0; cluster_weight=28;
|
||||
taaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---atgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgatagatttgaac
|
||||
>NC_013707_LCS_CMP complemented=True; count=1; cluster_center=False; cut=132910..133011; seq_length=102; cluster=NC_010433_LCS; cluster_score=0.990291; Strand=1; cluster_weight=28;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaa-
|
||||
>NC_021372_LCS count=3; cluster_center=True; seq_length=104; cluster=NC_021372_LCS; cluster_score=1.0; Strand=0; cluster_weight=3;
|
||||
taaggtagcggcgagacgagccg-------------------------------------
|
||||
----------ttt----------aaataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacgaac-gaacgatttgaac
|
||||
>NC_007578_LCS count=1; cluster_center=True; cut=129597..129859; seq_length=263; cluster=NC_007578_LCS; cluster_score=1.0; Strand=0; cluster_weight=1;
|
||||
gaaggtcacggcgagacgagccg-------------------------------------
|
||||
----------tttatcatt---acgataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaacc
|
||||
>NC_008454_LCS count=1; cluster_center=True; cut=197495..197626; seq_length=132; cluster=NC_008454_LCS; cluster_score=1.0; Strand=1; cluster_weight=1;
|
||||
gaaggtcacggcgagacgagccg------------------tttatcatattactcaatt
|
||||
gatcattacgtttatcatt---acgataggtgttaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccgttagacttgaac
|
||||
>NC_014569_LCS count=1; cluster_center=True; cut=102326..102478; seq_length=153; cluster=NC_014569_LCS; cluster_score=1.0; Strand=0; cluster_weight=1;
|
||||
gaaggtcacggcgagacgagccgtttgttttagagtgtcaaagtcttgagaattcaggcg
|
||||
cggcccgtcctttagagcaaaacaaataggtgtcaagtggaagtgcagtgatgtatg-ca
|
||||
gctgaggcatcctaacagaccggtagacttgaac
|
||||
>NC_026448_LCS count=1; cluster_center=True; cut=12936..13042; seq_length=107; cluster=NC_026448_LCS; cluster_score=1.0; Strand=0; cluster_weight=1;
|
||||
taaggtcgcggcgagatgatccg-------------------------------------
|
||||
----------ttgatagtgactatgataggtactaagtgtaaatgcagcgatgtatgtta
|
||||
gcttaggtatcctaaaagaccgatttatttgaac
|
||||
BIN
detectors/rrna/.DS_Store
vendored
Normal file
BIN
detectors/rrna/.DS_Store
vendored
Normal file
Binary file not shown.
50
detectors/rrna/tools/extract_ref16S.sh
Executable file
50
detectors/rrna/tools/extract_ref16S.sh
Executable file
@ -0,0 +1,50 @@
|
||||
#!/bin/bash
|
||||
#
|
||||
|
||||
|
||||
awk 'function printfasta(seq) { \
|
||||
seqlen=length(seq); \
|
||||
for (i=1; i <= seqlen; i+=60) \
|
||||
print substr(seq,i,60); \
|
||||
} \
|
||||
function comp(seq) { \
|
||||
"echo "seq" | tr acgtACGT tgcaTGCA " | getline res; \
|
||||
close("echo "seq" | tr acgtACGT tgcaTGCA "); \
|
||||
return res; \
|
||||
} \
|
||||
function rev(seq) { \
|
||||
"echo "seq" | rev " | getline res; \
|
||||
close("echo "seq" | rev "); \
|
||||
return res; \
|
||||
} \
|
||||
function revcomp(seq) { \
|
||||
res=rev(comp(seq)); \
|
||||
return res; \
|
||||
} \
|
||||
\
|
||||
/^LOCUS / {AC=$2; sequence=""; seqon=0; FROM="";TO=""} \
|
||||
/^ rRNA / {LOCUS=$2; STRAND=1} \
|
||||
/^ rRNA / && /complement/ {STRAND=0; \
|
||||
sub("complement\\(","",LOCUS); \
|
||||
sub("\\)","",LOCUS); \
|
||||
} \
|
||||
/16S/ {split(LOCUS,POS,"."); \
|
||||
FROM=POS[1]; \
|
||||
TO=POS[3]; \
|
||||
LENGTH=TO-FROM+1 \
|
||||
} \
|
||||
/^ORIGIN/ {seqon=1} \
|
||||
/^ *[1-9][0-9]* [a-z ]+$/ && seqon {seq=$2 $3 $4 $5 $6 $7; \
|
||||
gsub("[^acgt]","n",seq);\
|
||||
sequence=sequence seq \
|
||||
} \
|
||||
/^\/\// && FROM \
|
||||
{print ">"AC"_16S Strand="STRAND";", \
|
||||
"cut="FROM".."TO";", \
|
||||
"seq_length="LENGTH";"; \
|
||||
SS=substr(sequence,FROM,LENGTH); \
|
||||
if (! STRAND) \
|
||||
SS=revcomp(SS); \
|
||||
printfasta(SS); \
|
||||
} \
|
||||
' $*
|
||||
50
detectors/rrna/tools/extract_ref4.5S.sh
Executable file
50
detectors/rrna/tools/extract_ref4.5S.sh
Executable file
@ -0,0 +1,50 @@
|
||||
#!/bin/bash
|
||||
#
|
||||
|
||||
|
||||
awk 'function printfasta(seq) { \
|
||||
seqlen=length(seq); \
|
||||
for (i=1; i <= seqlen; i+=60) \
|
||||
print substr(seq,i,60); \
|
||||
} \
|
||||
function comp(seq) { \
|
||||
"echo "seq" | tr acgtACGT tgcaTGCA " | getline res; \
|
||||
close("echo "seq" | tr acgtACGT tgcaTGCA "); \
|
||||
return res; \
|
||||
} \
|
||||
function rev(seq) { \
|
||||
"echo "seq" | rev " | getline res; \
|
||||
close("echo "seq" | rev "); \
|
||||
return res; \
|
||||
} \
|
||||
function revcomp(seq) { \
|
||||
res=rev(comp(seq)); \
|
||||
return res; \
|
||||
} \
|
||||
\
|
||||
/^LOCUS / {AC=$2; sequence=""; seqon=0; FROM="";TO=""} \
|
||||
/^ rRNA / {LOCUS=$2; STRAND=1} \
|
||||
/^ rRNA / && /complement/ {STRAND=0; \
|
||||
sub("complement\\(","",LOCUS); \
|
||||
sub("\\)","",LOCUS); \
|
||||
} \
|
||||
/4.5S/ {split(LOCUS,POS,"."); \
|
||||
FROM=POS[1]; \
|
||||
TO=POS[3]; \
|
||||
LENGTH=TO-FROM+1 \
|
||||
} \
|
||||
/^ORIGIN/ {seqon=1} \
|
||||
/^ *[1-9][0-9]* [a-z ]+$/ && seqon {seq=$2 $3 $4 $5 $6 $7; \
|
||||
gsub("[^acgt]","n",seq);\
|
||||
sequence=sequence seq \
|
||||
} \
|
||||
/^\/\// && FROM \
|
||||
{print ">"AC"_4.5S Strand="STRAND";", \
|
||||
"cut="FROM".."TO";", \
|
||||
"seq_length="LENGTH";"; \
|
||||
SS=substr(sequence,FROM,LENGTH); \
|
||||
if (! STRAND) \
|
||||
SS=revcomp(SS); \
|
||||
printfasta(SS); \
|
||||
} \
|
||||
' $*
|
||||
BIN
ports/.DS_Store
vendored
Normal file
BIN
ports/.DS_Store
vendored
Normal file
Binary file not shown.
20
scripts/check_port
Executable file
20
scripts/check_port
Executable file
@ -0,0 +1,20 @@
|
||||
#!/bin/csh
|
||||
#
|
||||
# check if port is installed
|
||||
#
|
||||
set ORG_HOME = `dirname $0`/..
|
||||
|
||||
set PORTNAME = `$ORG_HOME/config/guess_port`
|
||||
|
||||
if (-f $ORG_HOME/ports/$PORTNAME/bin/exonerate) then
|
||||
echo "+ port $PORTNAME is correctly installed"
|
||||
exit 0
|
||||
endif
|
||||
|
||||
echo "! port $PORTNAME not installed"
|
||||
echo "! Please read README.txt for proper installation"
|
||||
|
||||
exit 1
|
||||
|
||||
|
||||
|
||||
19
scripts/sample.csh
Executable file
19
scripts/sample.csh
Executable file
@ -0,0 +1,19 @@
|
||||
#!/bin/csh
|
||||
#
|
||||
# a sample script to show how to retrieve proper path for port
|
||||
#
|
||||
|
||||
set ORG_HOME = `dirname $0`/..
|
||||
|
||||
set PORTNAME = `$ORG_HOME/config/guess_port`
|
||||
|
||||
set path = ($path $ORG_HOME/ports/$PORTNAME/bin)
|
||||
|
||||
#
|
||||
|
||||
which aragorn
|
||||
|
||||
exit 0
|
||||
|
||||
|
||||
|
||||
33
src/Makefile
Executable file
33
src/Makefile
Executable file
@ -0,0 +1,33 @@
|
||||
# ---------------------------------------------------------------
|
||||
# $Id: Makefile 1825 2013-02-26 09:39:47Z viari $
|
||||
# ---------------------------------------------------------------
|
||||
# @file: Makefile
|
||||
# @desc: makefile for src
|
||||
#
|
||||
# @history:
|
||||
# @+ <Gloup> : Mar 92 : first draft
|
||||
# @+ <Gloup> : Jul 93 : revised version
|
||||
# @+ <Gloup> : Feb 01 : Adapted to LXware
|
||||
#
|
||||
# @note: should be processed with gnu compatible make
|
||||
# @note: helixware_compatible
|
||||
#
|
||||
# @end:
|
||||
# ---------------------------------------------------------------
|
||||
#
|
||||
include ../config/auto.conf
|
||||
|
||||
DIRS = exonerate \
|
||||
kimono \
|
||||
prokov \
|
||||
sequtils \
|
||||
aragorn \
|
||||
ncbiblast
|
||||
|
||||
include ../config/targets/propagate.targ
|
||||
|
||||
include ../config/targets/help.targ
|
||||
|
||||
portclean::
|
||||
$(MAKE) ACTION=$@ _action
|
||||
(! test -d $(PRTDIR)) || \rm -r $(PRTDIR)
|
||||
70
src/README.txt
Normal file
70
src/README.txt
Normal file
@ -0,0 +1,70 @@
|
||||
#
|
||||
# ------------------------------------------
|
||||
# ORG.Annot - Organelle Annotator
|
||||
# version 1.0.0 - Sept 2015
|
||||
# ------------------------------------------
|
||||
#
|
||||
# this directory contains sources for tools used by ORG.Annot
|
||||
# this is only useful if you need to recompile binaries
|
||||
#
|
||||
# -------------------------
|
||||
# -0- Requirements
|
||||
# -------------------------
|
||||
#
|
||||
# gnu tar : version >= 1.15
|
||||
# gnu make : version >= 3.81
|
||||
# gcc and g++ : version >= 3.4.6
|
||||
#
|
||||
# note: valid versions of gnu tar and make are in _unix_tools_
|
||||
#
|
||||
#
|
||||
# -------------------------
|
||||
# -1- Checking configuration files
|
||||
# -------------------------
|
||||
#
|
||||
# issue:
|
||||
# $ config/guess_port
|
||||
#
|
||||
# if output is 'unknown <mach>:<sys>:<rel>'
|
||||
# then you should :
|
||||
# - add a port entry in guess_port for <mach>:<sys>:<rel>
|
||||
# - create a ports/<port>.conf configuration file
|
||||
# (the best is to start from another port file,
|
||||
# choose whatever looks closest)
|
||||
#
|
||||
# if output is something else (e.g. i386-darwin)
|
||||
# then the configuration files are already defined for your port
|
||||
#
|
||||
# -------------------------
|
||||
# -2- Compiling
|
||||
# -------------------------
|
||||
#
|
||||
# just run make from 'src':
|
||||
#
|
||||
# $ cd src
|
||||
# $ make
|
||||
#
|
||||
#
|
||||
# if everything runs fine, you may then issue:
|
||||
#
|
||||
# $ make clean
|
||||
#
|
||||
# to cleanup unecessary files
|
||||
#
|
||||
# at this point all binaries should be located in ports/<PORTNAME>/bin
|
||||
#
|
||||
# -------------------------
|
||||
# -3- Recompiling a port
|
||||
# -------------------------
|
||||
#
|
||||
# if you need to fully recompile a port
|
||||
#
|
||||
# $ cd src
|
||||
# $ make portclean
|
||||
# $ make
|
||||
# $ make clean
|
||||
#
|
||||
|
||||
|
||||
|
||||
|
||||
BIN
src/_unix_tools_/make-3.82.tar.gz
Normal file
BIN
src/_unix_tools_/make-3.82.tar.gz
Normal file
Binary file not shown.
BIN
src/_unix_tools_/tar-1.28.tar.gz
Normal file
BIN
src/_unix_tools_/tar-1.28.tar.gz
Normal file
Binary file not shown.
29
src/aragorn/Makefile
Executable file
29
src/aragorn/Makefile
Executable file
@ -0,0 +1,29 @@
|
||||
# ---------------------------------------------------------------
|
||||
# $Id: $
|
||||
# ---------------------------------------------------------------
|
||||
# @file: Makefile
|
||||
# @desc: makefile for aragorn
|
||||
#
|
||||
# @history:
|
||||
# @history:
|
||||
# @+ <Gloup> : Sep 12: Created
|
||||
#
|
||||
# @note: should be processed with gnu compatible make
|
||||
# @note: helixware_compatible
|
||||
#
|
||||
# @end:
|
||||
# ---------------------------------------------------------------
|
||||
#
|
||||
include ../../config/auto.conf
|
||||
|
||||
OSRC = aragorn1.2.36.c
|
||||
|
||||
PROGS = aragorn
|
||||
|
||||
include ../../config/targets/lxbin.targ
|
||||
include ../../config/targets/help.targ
|
||||
|
||||
INCDIR = .
|
||||
|
||||
aragorn: $(OBJ)
|
||||
$(CC) -o $@ $^ $(LDFLAGS) $(LDLIBS)
|
||||
390
src/aragorn/aragorn.1
Normal file
390
src/aragorn/aragorn.1
Normal file
@ -0,0 +1,390 @@
|
||||
'\" t
|
||||
.\" Title: aragorn
|
||||
.\" Author: [see the "AUTHORS" section]
|
||||
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
|
||||
.\" Date: 02/24/2013
|
||||
.\" Manual: \ \&
|
||||
.\" Source: \ \&
|
||||
.\" Language: English
|
||||
.\"
|
||||
.TH "ARAGORN" "1" "02/24/2013" "\ \&" "\ \&"
|
||||
.\" -----------------------------------------------------------------
|
||||
.\" * Define some portability stuff
|
||||
.\" -----------------------------------------------------------------
|
||||
.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
.\" http://bugs.debian.org/507673
|
||||
.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
|
||||
.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
.ie \n(.g .ds Aq \(aq
|
||||
.el .ds Aq '
|
||||
.\" -----------------------------------------------------------------
|
||||
.\" * set default formatting
|
||||
.\" -----------------------------------------------------------------
|
||||
.\" disable hyphenation
|
||||
.nh
|
||||
.\" disable justification (adjust text to left margin only)
|
||||
.ad l
|
||||
.\" -----------------------------------------------------------------
|
||||
.\" * MAIN CONTENT STARTS HERE *
|
||||
.\" -----------------------------------------------------------------
|
||||
.SH "NAME"
|
||||
aragorn \- detect tRNA genes in nucleotide sequences
|
||||
.SH "SYNOPSIS"
|
||||
.sp
|
||||
\fBaragorn\fR [\fIOPTION\fR]\&... \fIFILE\fR
|
||||
.SH "OPTIONS"
|
||||
.PP
|
||||
\fB\-m\fR
|
||||
.RS 4
|
||||
Search for tmRNA genes\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-t\fR
|
||||
.RS 4
|
||||
Search for tRNA genes\&. By default, all are detected\&. If one of
|
||||
\fB\-m\fR
|
||||
or
|
||||
\fB\-t\fR
|
||||
is specified, then the other is not detected unless specified as well\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-mt\fR
|
||||
.RS 4
|
||||
Search for Metazoan mitochondrial tRNA genes\&. tRNA genes with introns not detected\&.
|
||||
\fB\-i\fR,
|
||||
\fB\-sr\fR
|
||||
switchs ignored\&. Composite Metazoan mitochondrial genetic code used\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-mtmam\fR
|
||||
.RS 4
|
||||
Search for Mammalian mitochondrial tRNA genes\&.
|
||||
\fB\-i\fR,
|
||||
\fB\-sr\fR
|
||||
switchs ignored\&.
|
||||
\fB\-tv\fR
|
||||
switch set\&. Mammalian mitochondrial genetic code used\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-mtx\fR
|
||||
.RS 4
|
||||
Same as
|
||||
\fB\-mt\fR
|
||||
but low scoring tRNA genes are not reported\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-mtd\fR
|
||||
.RS 4
|
||||
Overlapping metazoan mitochondrial tRNA genes on opposite strands are reported\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-gc\fR[\fInum\fR]
|
||||
.RS 4
|
||||
Use the GenBank transl_table = [\fInum\fR] genetic code\&. Individual modifications can be appended using
|
||||
\fI,BBB\fR=<aa> B = A,C,G, or T\&. <aa> is the three letter code for an amino\-acid\&. More than one modification can be specified\&. eg
|
||||
\fB\-gcvert\fR,aga=Trp,agg=Trp uses the Vertebrate Mitochondrial code and the codons AGA and AGG changed to Tryptophan\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-gcstd\fR
|
||||
.RS 4
|
||||
Use standard genetic code\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-gcmet\fR
|
||||
.RS 4
|
||||
Use composite Metazoan mitochondrial genetic code\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-gcvert\fR
|
||||
.RS 4
|
||||
Use Vertebrate mitochondrial genetic code\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-gcinvert\fR
|
||||
.RS 4
|
||||
Use Invertebrate mitochondrial genetic code\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-gcyeast\fR
|
||||
.RS 4
|
||||
Use Yeast mitochondrial genetic code\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-gcprot\fR
|
||||
.RS 4
|
||||
Use Mold/Protozoan/Coelenterate mitochondrial genetic code\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-gcciliate\fR
|
||||
.RS 4
|
||||
Use Ciliate genetic code\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-gcflatworm\fR
|
||||
.RS 4
|
||||
Use Echinoderm/Flatworm mitochondrial genetic code
|
||||
.RE
|
||||
.PP
|
||||
\fB\-gceuplot\fR
|
||||
.RS 4
|
||||
Use Euplotid genetic code\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-gcbact\fR
|
||||
.RS 4
|
||||
Use Bacterial/Plant Chloroplast genetic code\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-gcaltyeast\fR
|
||||
.RS 4
|
||||
Use alternative Yeast genetic code\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-gcascid\fR
|
||||
.RS 4
|
||||
Use Ascidian Mitochondrial genetic code\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-gcaltflat\fR
|
||||
.RS 4
|
||||
Use alternative Flatworm Mitochondrial genetic code\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-gcblep\fR
|
||||
.RS 4
|
||||
Use Blepharisma genetic code\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-gcchloroph\fR
|
||||
.RS 4
|
||||
Use Chlorophycean Mitochondrial genetic code\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-gctrem\fR
|
||||
.RS 4
|
||||
Use Trematode Mitochondrial genetic code\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-gcscen\fR
|
||||
.RS 4
|
||||
Use Scenedesmus obliquus Mitochondrial genetic code\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-gcthraust\fR
|
||||
.RS 4
|
||||
Use Thraustochytrium Mitochondrial genetic code\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-tv\fR
|
||||
.RS 4
|
||||
Do not search for mitochondrial TV replacement loop tRNA genes\&. Only relevant if
|
||||
\fB\-mt\fR
|
||||
used\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-c7\fR
|
||||
.RS 4
|
||||
Search for tRNA genes with 7 base C\-loops only\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-i\fR
|
||||
.RS 4
|
||||
Search for tRNA genes with introns in anticodon loop with maximum length 3000 bases\&. Minimum intron length is 0 bases\&. Ignored if
|
||||
\fB\-m\fR
|
||||
is specified\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-i\fR[\fImax\fR]
|
||||
.RS 4
|
||||
Search for tRNA genes with introns in anticodon loop with maximum length [\fImax\fR] bases\&. Minimum intron length is 0 bases\&. Ignored if
|
||||
\fB\-m\fR
|
||||
is specified\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-i\fR[\fImin\fR],[\fImax\fR]
|
||||
.RS 4
|
||||
Search for tRNA genes with introns in anticodon loop with maximum length [\fImax\fR] bases, and minimum length [\fImin\fR] bases\&. Ignored if
|
||||
\fB\-m\fR
|
||||
is specified\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-io\fR
|
||||
.RS 4
|
||||
Same as
|
||||
\fB\-i\fR, but allow tRNA genes with long introns to overlap shorter tRNA genes\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-if\fR
|
||||
.RS 4
|
||||
Same as
|
||||
\fB\-i\fR, but fix intron between positions 37 and 38 on C\-loop (one base after anticodon)\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-ifo\fR
|
||||
.RS 4
|
||||
Same as
|
||||
\fB\-if\fR
|
||||
and
|
||||
\fB\-io\fR
|
||||
combined\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-ir\fR
|
||||
.RS 4
|
||||
Same as
|
||||
\fB\-i\fR, but report tRNA genes with minimum length [\fImin\fR] bases rather than search for tRNA genes with minimum length [\fImin\fR] bases\&. With this switch, [\fImin\fR] acts as an output filter, minimum intron length for searching is still 0 bases\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-c\fR
|
||||
.RS 4
|
||||
Assume that each sequence has a circular topology\&. Search wraps around each end\&. Default setting\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-l\fR
|
||||
.RS 4
|
||||
Assume that each sequence has a linear topology\&. Search does not wrap\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-d\fR
|
||||
.RS 4
|
||||
Double\&. Search both strands of each sequence\&. Default setting\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-s\fR or \fB\-s+\fR
|
||||
.RS 4
|
||||
Single\&. Do not search the complementary (antisense) strand of each sequence\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-sc\fR or \fB\-s\-\fR
|
||||
.RS 4
|
||||
Single complementary\&. Do not search the sense strand of each sequence\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-ps\fR
|
||||
.RS 4
|
||||
Lower scoring thresholds to 95% of default levels\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-ps\fR[\fInum\fR]
|
||||
.RS 4
|
||||
Change scoring thresholds to [\fInum\fR] percent of default levels\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-rp\fR
|
||||
.RS 4
|
||||
Flag possible pseudogenes (score < 100 or tRNA anticodon loop <> 7 bases long)\&. Note that genes with score < 100 will not be detected or flagged if scoring thresholds are not also changed to below 100% (see \-ps switch)\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-seq\fR
|
||||
.RS 4
|
||||
Print out primary sequence\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-br\fR
|
||||
.RS 4
|
||||
Show secondary structure of tRNA gene primary sequence using round brackets\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-fasta\fR
|
||||
.RS 4
|
||||
Print out primary sequence in fasta format\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-fo\fR
|
||||
.RS 4
|
||||
Print out primary sequence in fasta format only (no secondary structure)\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-fon\fR
|
||||
.RS 4
|
||||
Same as
|
||||
\fB\-fo\fR, with sequence and gene numbering in header\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-fos\fR
|
||||
.RS 4
|
||||
Same as
|
||||
\fB\-fo\fR, with no spaces in header\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-fons\fR
|
||||
.RS 4
|
||||
Same as
|
||||
\fB\-fo\fR, with sequence and gene numbering, but no spaces\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-w\fR
|
||||
.RS 4
|
||||
Print out in Batch mode\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-ss\fR
|
||||
.RS 4
|
||||
Use the stricter canonical 1\-2 bp spacer1 and 1 bp spacer2\&. Ignored if
|
||||
\fB\-mt\fR
|
||||
set\&. Default is to allow 3 bp spacer1 and 0\-2 bp spacer2, which may degrade selectivity\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-v\fR
|
||||
.RS 4
|
||||
Verbose\&. Prints out information during search to STDERR\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-a\fR
|
||||
.RS 4
|
||||
Print out tRNA domain for tmRNA genes\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-a7\fR
|
||||
.RS 4
|
||||
Restrict tRNA astem length to a maximum of 7 bases
|
||||
.RE
|
||||
.PP
|
||||
\fB\-aa\fR
|
||||
.RS 4
|
||||
Display message if predicted iso\-acceptor species does not match species in sequence name (if present)\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-j\fR
|
||||
.RS 4
|
||||
Display 4\-base sequence on 3\*(Aq end of astem regardless of predicted amino\-acyl acceptor length\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-jr\fR
|
||||
.RS 4
|
||||
Allow some divergence of 3\*(Aq amino\-acyl acceptor sequence from NCCA\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-jr4\fR
|
||||
.RS 4
|
||||
Allow some divergence of 3\*(Aq amino\-acyl acceptor sequence from NCCA, and display 4 bases\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-q\fR
|
||||
.RS 4
|
||||
Dont print configuration line (which switchs and files were used)\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-rn\fR
|
||||
.RS 4
|
||||
Repeat sequence name before summary information\&.
|
||||
.RE
|
||||
.PP
|
||||
\fB\-O\fR [\fIoutfile\fR]
|
||||
.RS 4
|
||||
Print output to
|
||||
\fI\&. If [\*(Aqoutfile\fR] already exists, it is overwritten\&. By default all output goes to stdout\&.
|
||||
.RE
|
||||
.SH "DESCRIPTION"
|
||||
.sp
|
||||
aragorn detects tRNA, mtRNA, and tmRNA genes\&. A minimum requirement is at least a 32 bit compiler architecture (variable types int and unsigned int are at least 4 bytes long)\&.
|
||||
.sp
|
||||
[\fIFILE\fR] is assumed to contain one or more sequences in FASTA format\&. Results of the search are printed to STDOUT\&. All switches are optional and case\-insensitive\&. Unless \-i is specified, tRNA genes containing introns are not detected\&.
|
||||
.SH "AUTHORS"
|
||||
.sp
|
||||
Bjorn Canback <bcanback@acgt\&.se>, Dean Laslett <gaiaquark@gmail\&.com>
|
||||
.SH "REFERENCES"
|
||||
.sp
|
||||
Laslett, D\&. and Canback, B\&. (2004) ARAGORN, a program for the detection of transfer RNA and transfer\-messenger RNA genes in nucleotide sequences Nucleic Acids Research, 32;11\-16
|
||||
.sp
|
||||
Laslett, D\&. and Canback, B\&. (2008) ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences Bioinformatics, 24(2); 172\-175\&.
|
||||
10494
src/aragorn/aragorn1.2.36.c
Normal file
10494
src/aragorn/aragorn1.2.36.c
Normal file
File diff suppressed because it is too large
Load Diff
14
src/dev_config
Executable file
14
src/dev_config
Executable file
@ -0,0 +1,14 @@
|
||||
#!/bin/csh -f
|
||||
|
||||
set cfg = `find . -type d -name config -print | grep -v ncbi`
|
||||
|
||||
foreach cf ($cfg)
|
||||
echo $cf
|
||||
\rm -r $cf
|
||||
cp -r ../config $cf
|
||||
end
|
||||
|
||||
|
||||
exit 0
|
||||
|
||||
|
||||
BIN
src/exonerate/.DS_Store
vendored
Normal file
BIN
src/exonerate/.DS_Store
vendored
Normal file
Binary file not shown.
24
src/exonerate/Makefile
Normal file
24
src/exonerate/Makefile
Normal file
@ -0,0 +1,24 @@
|
||||
# ---------------------------------------------------------------
|
||||
# $Id: $
|
||||
# ---------------------------------------------------------------
|
||||
# @file: Makefile
|
||||
# @desc: makefile for package exonerate
|
||||
#
|
||||
# @history:
|
||||
# @+ <Gloup> : Sept 15 : Adapted to ORG.Annot
|
||||
#
|
||||
# @note: should be processed with gnu compatible make
|
||||
# @note: helixware_compatible
|
||||
#
|
||||
# @end:
|
||||
# ---------------------------------------------------------------
|
||||
#
|
||||
|
||||
include ../../config/auto.conf
|
||||
|
||||
PKG = exonerate-2.2.0
|
||||
|
||||
include $(CFGDIR)targets/package.targ
|
||||
|
||||
include $(CFGDIR)targets/help.targ
|
||||
|
||||
BIN
src/exonerate/exonerate-2.2.0.tgz
Normal file
BIN
src/exonerate/exonerate-2.2.0.tgz
Normal file
Binary file not shown.
BIN
src/hmmer3/hmmer-3.1b1.tar
Normal file
BIN
src/hmmer3/hmmer-3.1b1.tar
Normal file
Binary file not shown.
33
src/kimono/Makefile
Executable file
33
src/kimono/Makefile
Executable file
@ -0,0 +1,33 @@
|
||||
# ---------------------------------------------------------------
|
||||
# $Id: $
|
||||
# ---------------------------------------------------------------
|
||||
# @file: Makefile
|
||||
# @desc: makefile for lxpack
|
||||
#
|
||||
# @history:
|
||||
# @history:
|
||||
# @+ <Gloup> : Apr 97 : Created
|
||||
# @+ <Gloup> : Mar 02 : Updated for LXxware
|
||||
#
|
||||
# @note: should be processed with gnu compatible make
|
||||
# @note: helixware_compatible
|
||||
#
|
||||
# @end:
|
||||
# ---------------------------------------------------------------
|
||||
#
|
||||
include ../../config/auto.conf
|
||||
|
||||
DIRS = lxpack
|
||||
|
||||
include ../../config/targets/propagate.targ
|
||||
|
||||
include ../../config/targets/help.targ
|
||||
|
||||
all::
|
||||
$(MAKE) ACTION=$@ _action
|
||||
test -d $(PRTDIR) || mkdir $(PRTDIR)
|
||||
test -d $(BINDIR) || mkdir $(BINDIR)
|
||||
\cp -f lxpack/ports/$(PORTNAME)/bin/* $(BINDIR)
|
||||
|
||||
clean::
|
||||
$(MAKE) -C lxpack portclean
|
||||
29
src/kimono/lxpack/Makefile
Executable file
29
src/kimono/lxpack/Makefile
Executable file
@ -0,0 +1,29 @@
|
||||
# ---------------------------------------------------------------
|
||||
# $Id: $
|
||||
# ---------------------------------------------------------------
|
||||
# @file: Makefile
|
||||
# @desc: makefile for kimono
|
||||
#
|
||||
# @history:
|
||||
# @history:
|
||||
# @+ <Gloup> : Apr 97 : Created
|
||||
# @+ <Gloup> : Mar 02 : Updated for LXxware
|
||||
#
|
||||
# @note: should be processed with gnu compatible make
|
||||
# @note: helixware_compatible
|
||||
#
|
||||
# @end:
|
||||
# ---------------------------------------------------------------
|
||||
#
|
||||
include ./config/auto.conf
|
||||
|
||||
DIRS = src \
|
||||
tests
|
||||
|
||||
include ./config/targets/propagate.targ
|
||||
|
||||
include ./config/targets/help.targ
|
||||
|
||||
portclean::
|
||||
$(MAKE) ACTION=$@ _action
|
||||
(! test -d $(PRTDIR)) || \rm -r $(PRTDIR)
|
||||
51
src/kimono/lxpack/config/README.txt
Executable file
51
src/kimono/lxpack/config/README.txt
Executable file
@ -0,0 +1,51 @@
|
||||
|
||||
$Id: README.txt 1825 2013-02-26 09:39:47Z viari $
|
||||
|
||||
This directory contains Makefile machine specific configuration files
|
||||
(and default targets to help you writing Makefile's)
|
||||
|
||||
These headers should be used with GNU make or compatible
|
||||
|
||||
#
|
||||
# portname
|
||||
#
|
||||
|
||||
To check your port, issue :
|
||||
|
||||
./guess_port
|
||||
|
||||
if output is 'unknown <mach>:<sys>:<rel>' then you should :
|
||||
- add a port entry in guess_port for <mach>:<sys>:<rel>
|
||||
- create a ports/<port>.conf configuration file
|
||||
(the best is to start from another port file,
|
||||
choose whatever looks closest)
|
||||
|
||||
#
|
||||
# configuration flags
|
||||
#
|
||||
|
||||
auto.conf : the main configuration file :
|
||||
- determine the machine port thru 'guess_port' shell
|
||||
- include 'default.conf' file
|
||||
- include the machine specific 'ports/<port>.conf' file
|
||||
|
||||
default.conf : default configuration (included by 'auto.conf')
|
||||
|
||||
ports/<port>.conf : machine specific configuration (included by 'auto.conf')
|
||||
|
||||
#
|
||||
# utility targets
|
||||
#
|
||||
|
||||
targets/help.targ : target for standard help
|
||||
|
||||
targets/propagate.targ : target for propagating targets to subdirectories
|
||||
|
||||
targets/package.targ : default targets for standard package with 'configure'
|
||||
|
||||
targets/empty.targ : default empty targets (defined as double colon rules)
|
||||
|
||||
targets/lxbin.targ : default make targets for standard lx binary (without libraries)
|
||||
|
||||
targets/debug.targ : target to print debug information (for dev.)
|
||||
|
||||
54
src/kimono/lxpack/config/auto.conf
Normal file
54
src/kimono/lxpack/config/auto.conf
Normal file
@ -0,0 +1,54 @@
|
||||
#
|
||||
# $Id: auto.conf 1825 2013-02-26 09:39:47Z viari $
|
||||
#
|
||||
# auto.conf
|
||||
# auto configuration file using guess_port
|
||||
#
|
||||
# this file is included in Makefile
|
||||
#
|
||||
|
||||
#
|
||||
# default shell for gnu-make
|
||||
#
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
#
|
||||
# CFGDIR : location of config files = this file directory location
|
||||
#
|
||||
# CFGPRT : port name (as returned by guess_port)
|
||||
#
|
||||
|
||||
# because builtin 'lastword' is missing in gnu-make 3.80
|
||||
|
||||
lastword = $(word $(words $1), $1)
|
||||
|
||||
CFGDIR := $(dir $(call lastword, $(MAKEFILE_LIST)))
|
||||
|
||||
CFGPRT := $(shell $(CFGDIR)guess_port)
|
||||
|
||||
# check if port is correctly defined
|
||||
|
||||
ifneq (1, $(words $(CFGPRT)))
|
||||
entry := $(call lastword, $(CFGPRT))
|
||||
$(error port is undefined - add entry for "$(entry)" in configuration file -)
|
||||
endif
|
||||
|
||||
#
|
||||
# PORTNAME : port name to use : default is CFGPRT but may be futher modified
|
||||
# by machine specific configuration
|
||||
|
||||
PORTNAME = $(CFGPRT)
|
||||
|
||||
#
|
||||
# default configuration
|
||||
# may be overriden by machine dependant definitions below
|
||||
#
|
||||
|
||||
include $(CFGDIR)default.conf
|
||||
|
||||
#
|
||||
# machine dependant definitions
|
||||
#
|
||||
|
||||
include $(CFGDIR)ports/$(CFGPRT).conf
|
||||
124
src/kimono/lxpack/config/default.conf
Normal file
124
src/kimono/lxpack/config/default.conf
Normal file
@ -0,0 +1,124 @@
|
||||
#
|
||||
# $Id: default.conf 2007 2013-12-03 14:21:39Z viari $
|
||||
#
|
||||
# default.conf
|
||||
# default configuration flags
|
||||
# maybe further redefined by machine specific configuration
|
||||
#
|
||||
# this file is included by auto.conf
|
||||
#
|
||||
|
||||
# ------------------------------------
|
||||
# General compilation flags
|
||||
# ------------------------------------
|
||||
|
||||
#
|
||||
# MACHDEF : define machine and OS specific flags
|
||||
#
|
||||
|
||||
MACHDEF =
|
||||
|
||||
#
|
||||
# CC : (ansi C) compiler command to use
|
||||
# you may add some machine specific flags (like -arch ...)
|
||||
# in the <machine>.conf configuration file
|
||||
#
|
||||
|
||||
CC = gcc
|
||||
|
||||
#
|
||||
# default compiler optimizer flag
|
||||
#
|
||||
|
||||
OPTIM = -O
|
||||
|
||||
#
|
||||
# CC_LIBS : additionnal machine specific $(CC) libraries
|
||||
# like '-lC' on some machines
|
||||
#
|
||||
|
||||
CC_LIBS =
|
||||
|
||||
#
|
||||
# MALLOC_LIBS : machine specific malloc librairies
|
||||
# like '-lmalloc' on SGI
|
||||
#
|
||||
|
||||
MALLOC_LIBS =
|
||||
|
||||
#
|
||||
# MATH_LIBS : machine specific math librairies
|
||||
# like '-lm' on Solaris
|
||||
#
|
||||
|
||||
MATH_LIBS =
|
||||
|
||||
#
|
||||
# LINT : looks like LINT command does not exist anymore
|
||||
# here is a rough replacement
|
||||
#
|
||||
|
||||
LINT = gcc -S -Wall -Wno-format-y2k -W -Wstrict-prototypes \
|
||||
-Wmissing-prototypes -Wpointer-arith -Wreturn-type \
|
||||
-Wcast-qual -Wwrite-strings -Wswitch -Wshadow \
|
||||
-Wcast-align -Wbad-function-cast -Wchar-subscripts \
|
||||
-Winline -Wnested-externs -Wredundant-decls
|
||||
|
||||
# ------------------------------------
|
||||
# General system commands
|
||||
# ------------------------------------
|
||||
|
||||
#
|
||||
# AR : AR archive command
|
||||
# ARFLAGS : $(AR) archiving flags
|
||||
# ARXFLAGS : $(AR) extraction flags
|
||||
#
|
||||
|
||||
AR = ar
|
||||
ARFLAGS = rcv
|
||||
ARXFLAGS = xv
|
||||
|
||||
#
|
||||
# RANLIB : ranlib command
|
||||
#
|
||||
|
||||
RANLIB = ranlib
|
||||
|
||||
#
|
||||
# DIFF : diff command
|
||||
#
|
||||
|
||||
DIFF = diff
|
||||
|
||||
#
|
||||
# TAR : tar command
|
||||
#
|
||||
|
||||
TAR = tar
|
||||
|
||||
# ------------------------------------
|
||||
# Default locations
|
||||
# ------------------------------------
|
||||
#
|
||||
# PRTDIR : port dependent files location (libraries and binaries)
|
||||
# BINDIR : port binaries
|
||||
# LIBDIR : port libraries
|
||||
#
|
||||
|
||||
PRTDIR = $(CFGDIR)../ports/$(PORTNAME)
|
||||
|
||||
BINDIR = $(PRTDIR)/bin
|
||||
|
||||
LIBDIR = $(PRTDIR)/lib
|
||||
|
||||
# ------------------------------------
|
||||
# default gmake variable in implicit rules
|
||||
# ------------------------------------
|
||||
|
||||
CFLAGS = $(OPTIM) $(MACHDEF) -I$(INCDIR)
|
||||
|
||||
LDFLAGS = -L$(LIBDIR) -L.
|
||||
|
||||
LDLIBS = $(LIBS) $(MALLOC_LIBS) $(MATH_LIBS) $(CC_LIBS)
|
||||
|
||||
LINTFLAGS = $(MACHDEF) -I$(INCDIR)
|
||||
33
src/kimono/lxpack/config/guess_port
Executable file
33
src/kimono/lxpack/config/guess_port
Executable file
@ -0,0 +1,33 @@
|
||||
#! /bin/sh
|
||||
#
|
||||
# $Id: guess_port 1825 2013-02-26 09:39:47Z viari $
|
||||
#
|
||||
# @file: guess_port
|
||||
# @desc: attempt to guess the portname
|
||||
# @usage: guess_port
|
||||
#
|
||||
# @history:
|
||||
# @+ <Gloup> Nov. 2000 first draft adapted from GNU config.guess
|
||||
# @+ <Gloup> Feb. 2010 moved to sh
|
||||
#
|
||||
|
||||
mach=`uname -m`
|
||||
syst=`uname -s`
|
||||
rels=`uname -r`
|
||||
|
||||
case ${mach}:${syst}:${rels} in
|
||||
|
||||
alpha:OSF1:* ) echo alpha-osf1;;
|
||||
sun4*:SunOS:5.* ) echo sparc-solaris;;
|
||||
i86pc:SunOS:5.* ) echo i386-solaris;;
|
||||
sun4*:SunOS:* ) echo sparc-sunos;;
|
||||
Power*:Darwin:* ) echo ppc-darwin;;
|
||||
i*86:Linux:* ) echo i386-linux;;
|
||||
x*86*:Linux:* ) echo i386-linux;;
|
||||
i*86:Darwin:* ) echo i386-darwin;;
|
||||
IP*:IRIX*:* ) echo mips-irix;;
|
||||
i*86:MINGW32*:* ) echo x86-mingw32;;
|
||||
|
||||
*) echo unknown ${mach}:${syst}:${rels}; exit 1;;
|
||||
esac
|
||||
exit 0
|
||||
26
src/kimono/lxpack/config/ports/i386-darwin.conf
Normal file
26
src/kimono/lxpack/config/ports/i386-darwin.conf
Normal file
@ -0,0 +1,26 @@
|
||||
#
|
||||
# $Id: i386-darwin.conf 1825 2013-02-26 09:39:47Z viari $
|
||||
#
|
||||
# i386-darwin.conf
|
||||
# configuration file for MacOS-X/Intel-Based/Darwin 1.2 with gcc compiler
|
||||
# this file is included in Makefile
|
||||
#
|
||||
# system (uname -srp) : Darwin 8.7.1 i386
|
||||
# compiler (cc --version) : i686-apple-darwin8-gcc-4.0.1
|
||||
#
|
||||
# check tags
|
||||
# @uname:uname -srp:Darwin 8.7.1 i386
|
||||
# @cc:cc --version:i686-apple-darwin8-gcc-4.0.1
|
||||
#
|
||||
#
|
||||
|
||||
# ------------------------------------
|
||||
# General compilation flags
|
||||
# ------------------------------------
|
||||
|
||||
#
|
||||
# MACHDEF : define machine and OS specific flags
|
||||
#
|
||||
|
||||
MACHDEF = -DLX_TARGET_MACINTEL -DLITTLE_ENDIAN -DMACOSX
|
||||
|
||||
32
src/kimono/lxpack/config/ports/i386-linux.conf
Executable file
32
src/kimono/lxpack/config/ports/i386-linux.conf
Executable file
@ -0,0 +1,32 @@
|
||||
#
|
||||
# $Id: i386-linux.conf 1825 2013-02-26 09:39:47Z viari $
|
||||
#
|
||||
# i386-linux.conf
|
||||
# configuration file for linux ix86 with GNU gcc compiler
|
||||
# this file is included in Makefile
|
||||
#
|
||||
# system (uname -srp) : Linux 2.2.14-5.0 unknown
|
||||
# compiler (gcc --version) : egcs-2.91.66
|
||||
#
|
||||
# check tags
|
||||
# @uname:uname -srp:Linux 2.2.14-5.0 unknown
|
||||
# @cc:cc --version:egcs-2.91.66
|
||||
#
|
||||
#
|
||||
|
||||
# ------------------------------------
|
||||
# General compilation flags
|
||||
# ------------------------------------
|
||||
|
||||
#
|
||||
# MACHDEF : define machine and OS specific flags
|
||||
#
|
||||
|
||||
MACHDEF = -DLX_TARGET_LINUX -DLITTLE_ENDIAN
|
||||
|
||||
#
|
||||
# MATH_LIBS : machine specific math librairies
|
||||
#
|
||||
|
||||
MATH_LIBS = -lm
|
||||
|
||||
32
src/kimono/lxpack/config/ports/ppc-darwin.conf
Executable file
32
src/kimono/lxpack/config/ports/ppc-darwin.conf
Executable file
@ -0,0 +1,32 @@
|
||||
#
|
||||
# $Id: ppc-darwin.conf 1825 2013-02-26 09:39:47Z viari $
|
||||
#
|
||||
# ppc-darwin.conf
|
||||
# configuration file for MacOS-X/Darwin 1.2 with native cc compiler
|
||||
# this file is included in Makefile
|
||||
#
|
||||
# system (uname -srp) : Darwin 1.2 powerpc
|
||||
# compiler (cc --version) : 2.7.2.1
|
||||
#
|
||||
# check tags
|
||||
# @uname:uname -srp:Darwin 1.2 powerpc
|
||||
# @cc:cc --version:2.7.2.1
|
||||
#
|
||||
#
|
||||
|
||||
# ------------------------------------
|
||||
# General compilation flags
|
||||
# ------------------------------------
|
||||
|
||||
#
|
||||
# MACHDEF : define machine and OS specific flags
|
||||
#
|
||||
|
||||
MACHDEF = -DLX_TARGET_MACPPC -DBIG_ENDIAN
|
||||
|
||||
#
|
||||
# CC : name of (ansi C) compiler to use
|
||||
#
|
||||
|
||||
CC = cc -arch ppc
|
||||
|
||||
31
src/kimono/lxpack/config/ports/sparc-solaris.conf
Executable file
31
src/kimono/lxpack/config/ports/sparc-solaris.conf
Executable file
@ -0,0 +1,31 @@
|
||||
#
|
||||
# $Id: sparc-solaris.conf 1825 2013-02-26 09:39:47Z viari $
|
||||
#
|
||||
# sparc-solaris.conf
|
||||
# configuration file for sparc solaris with GNU gcc compiler
|
||||
# this file is included in Makefile
|
||||
#
|
||||
# system (uname -srp) : SunOS 5.8 sparc
|
||||
# compiler (gcc --version) : 2.95.2
|
||||
#
|
||||
# check tags
|
||||
# @uname:uname -srp:SunOS 5.8 sparc
|
||||
# @cc:cc --version:2.95.2
|
||||
#
|
||||
#
|
||||
|
||||
# ------------------------------------
|
||||
# General compilation flags
|
||||
# ------------------------------------
|
||||
|
||||
#
|
||||
# MACHDEF : define machine and OS specific flags
|
||||
#
|
||||
|
||||
MACHDEF = -DLX_TARGET_SOLARIS -DBIG_ENDIAN
|
||||
|
||||
#
|
||||
# MATH_LIBS : machine specific math librairies
|
||||
#
|
||||
|
||||
MATH_LIBS = -lm
|
||||
54
src/kimono/lxpack/config/ports/x86-mingw32.conf
Normal file
54
src/kimono/lxpack/config/ports/x86-mingw32.conf
Normal file
@ -0,0 +1,54 @@
|
||||
#
|
||||
# $Id: x86-mingw32.conf 1825 2013-02-26 09:39:47Z viari $
|
||||
#
|
||||
# x86-mingw32
|
||||
# configuration file for MinGW with GNU gcc compiler.
|
||||
#
|
||||
# this file is included in Makefile
|
||||
#
|
||||
#
|
||||
|
||||
#
|
||||
# rename PORTNAME safely since MinGW produce pure win32 executables
|
||||
# without dll's
|
||||
#
|
||||
|
||||
PORTNAME = x86-win32
|
||||
|
||||
# ------------------------------------
|
||||
# General compilation flags
|
||||
# ------------------------------------
|
||||
|
||||
#
|
||||
# CC_LIBS : additionnal machine specific $(CC) libraries
|
||||
#
|
||||
# libiberty is needed for some system extensions (like mkstemps)
|
||||
#
|
||||
|
||||
CC_LIBS = -liberty
|
||||
|
||||
#
|
||||
# MACHDEF : define machine and OS specific flags
|
||||
#
|
||||
# -DDLMALLOC : use dlmalloc instead of malloc (which does not have mallinfo)
|
||||
# -posix is a new replacement for several MinGW32 flags, including:
|
||||
# -D__USE_MINGW_ANSI_STDIO : mingw gcc flag to recognize the C99 "%zu" format
|
||||
#
|
||||
|
||||
MACHDEF = -posix -DLX_TARGET_WIN32 -DWIN_MINGW -DDLMALLOC -DLITTLE_ENDIAN
|
||||
|
||||
#
|
||||
# MATH_LIBS : machine specific math librairies
|
||||
#
|
||||
|
||||
MATH_LIBS = -lm
|
||||
|
||||
# ------------------------------------
|
||||
# General system commands
|
||||
# ------------------------------------
|
||||
|
||||
#
|
||||
# DIFF : diff command / should ignore cr on windows
|
||||
#
|
||||
|
||||
DIFF = diff --strip-trailing-cr
|
||||
25
src/kimono/lxpack/config/targets/debug.targ
Normal file
25
src/kimono/lxpack/config/targets/debug.targ
Normal file
@ -0,0 +1,25 @@
|
||||
#
|
||||
# $Id: help.targ 1825 2013-02-26 09:39:47Z viari $
|
||||
#
|
||||
# debug.targ
|
||||
#
|
||||
# target to print debug information (dev. only)
|
||||
#
|
||||
# it defines the following targets:
|
||||
#
|
||||
# debug :
|
||||
# print debug
|
||||
#
|
||||
# it requires auto.conf
|
||||
#
|
||||
|
||||
.PHONY: debug
|
||||
|
||||
debug::
|
||||
@echo "+ PORTNAME: $(PORTNAME)"
|
||||
@echo "+ CFGPRT: $(CFGPRT)"
|
||||
@echo "+ CFGDIR: $(CFGDIR)"
|
||||
@echo "+ PRTDIR: $(PRTDIR)"
|
||||
@echo "+ MACHDEF: $(MACHDEF)"
|
||||
|
||||
|
||||
24
src/kimono/lxpack/config/targets/empty.targ
Normal file
24
src/kimono/lxpack/config/targets/empty.targ
Normal file
@ -0,0 +1,24 @@
|
||||
#
|
||||
# $Id: $
|
||||
#
|
||||
# epty.targ
|
||||
#
|
||||
# default empty targets (defined as double colon rules)
|
||||
#
|
||||
#
|
||||
|
||||
#
|
||||
# Rules
|
||||
#
|
||||
|
||||
.PHONY: all test clean portclean help
|
||||
|
||||
all::
|
||||
|
||||
test::
|
||||
|
||||
clean::
|
||||
|
||||
portclean:: clean
|
||||
|
||||
test::
|
||||
23
src/kimono/lxpack/config/targets/help.targ
Normal file
23
src/kimono/lxpack/config/targets/help.targ
Normal file
@ -0,0 +1,23 @@
|
||||
#
|
||||
# $Id: help.targ 1825 2013-02-26 09:39:47Z viari $
|
||||
#
|
||||
# help.targ
|
||||
#
|
||||
# default target to print help
|
||||
#
|
||||
# it defines the following targets:
|
||||
#
|
||||
# help :
|
||||
# print help
|
||||
#
|
||||
|
||||
.PHONY: help
|
||||
|
||||
help::
|
||||
@ echo "basic usage: make [<action>+]"
|
||||
@ echo "valid <action> :"
|
||||
@ echo " all : compile everything for current port [default target]"
|
||||
@ echo " clean : local cleanup"
|
||||
@ echo " portclean : cleanup distribution for current port"
|
||||
@ echo " test : run tests on current port"
|
||||
@ echo " help : print this help"
|
||||
51
src/kimono/lxpack/config/targets/lxbin.targ
Normal file
51
src/kimono/lxpack/config/targets/lxbin.targ
Normal file
@ -0,0 +1,51 @@
|
||||
#
|
||||
# $Id: $
|
||||
#
|
||||
# lxbin.targ
|
||||
#
|
||||
# default make targets for standard lx binary
|
||||
#
|
||||
# you should define the 'PROGS' and 'OSRC' variables
|
||||
# and optionnaly 'LIBS' if binaries have to be linked with libraries
|
||||
#
|
||||
# note: if main source code for binary PROG is PROG.c, there is nothing to do,
|
||||
# else (e.g. if it involves several sources files) you should also add local
|
||||
# file dependencies. e.g under the form:
|
||||
#
|
||||
# mymain: $(OBJ) mymain_base.c mymain_help.c
|
||||
# $(CC) $(CFLAGS) -o $@ $^ $(LDFLAGS) $(LDLIBS)
|
||||
#
|
||||
#
|
||||
# 'auto.conf' should have been included
|
||||
#
|
||||
|
||||
OBJ = $(OSRC:.c=.o)
|
||||
|
||||
INCDIR = ../include
|
||||
|
||||
#
|
||||
# Rules
|
||||
#
|
||||
|
||||
.PHONY: all prelib install test clean portclean
|
||||
|
||||
all:: prelib $(PROGS) install
|
||||
@echo "+++++++++++ binaries $(PROGS) done"
|
||||
|
||||
prelib::
|
||||
test -d $(PRTDIR) || mkdir $(PRTDIR) # because some linker may complain
|
||||
test -d $(LIBDIR) || mkdir $(LIBDIR) # if -L$(LIBDIR) does not exist
|
||||
|
||||
install::
|
||||
test -d $(PRTDIR) || mkdir $(PRTDIR)
|
||||
test -d $(BINDIR) || mkdir $(BINDIR)
|
||||
-for f in $(PROGS) ; do \cp -f $$f $(BINDIR) ; done
|
||||
|
||||
test::
|
||||
|
||||
clean::
|
||||
-\rm -f *.o cvstatic* *% *.bak so_loc*
|
||||
-\rm -f $(PROGS)
|
||||
|
||||
portclean:: clean
|
||||
-(! test -d $(BINDIR)) || (cd $(BINDIR) && \rm -f $(PROGS))
|
||||
43
src/kimono/lxpack/config/targets/lxlib.targ
Normal file
43
src/kimono/lxpack/config/targets/lxlib.targ
Normal file
@ -0,0 +1,43 @@
|
||||
#
|
||||
# $Id: $
|
||||
#
|
||||
# lxlib.targ
|
||||
#
|
||||
# default make targets for standard lx library
|
||||
#
|
||||
# you should define the 'LOCLIB' and 'OSRC' variables
|
||||
#
|
||||
# 'auto.conf' should have been included
|
||||
#
|
||||
|
||||
OBJ = $(OSRC:.c=.o)
|
||||
|
||||
INCDIR = ../include
|
||||
|
||||
#
|
||||
# Rules
|
||||
#
|
||||
|
||||
.PHONY: all lib install test clean portclean
|
||||
|
||||
all:: lib install
|
||||
@echo "+++++++++++ library $(LOCLIB) done"
|
||||
|
||||
lib:: $(OBJ)
|
||||
$(AR) $(ARFLAGS) $(LOCLIB) $(OBJ)
|
||||
$(RANLIB) $(LOCLIB)
|
||||
|
||||
install::
|
||||
test -d $(PRTDIR) || mkdir $(PRTDIR)
|
||||
test -d $(LIBDIR) || mkdir $(LIBDIR)
|
||||
\cp -f $(LOCLIB) $(LIBDIR)
|
||||
$(RANLIB) $(LIBDIR)/$(LOCLIB)
|
||||
|
||||
test::
|
||||
|
||||
clean::
|
||||
-\rm -f *.o cvstatic* *% *.bak so_loc*
|
||||
-\rm -f $(LOCLIB)
|
||||
|
||||
portclean:: clean
|
||||
-(! test -d $(LIBDIR)) || (cd $(LIBDIR) && \rm -f $(LOCLIB))
|
||||
48
src/kimono/lxpack/config/targets/package.targ
Normal file
48
src/kimono/lxpack/config/targets/package.targ
Normal file
@ -0,0 +1,48 @@
|
||||
#
|
||||
# $Id: package.targ 1825 2013-02-26 09:39:47Z viari $
|
||||
#
|
||||
# package.targ
|
||||
#
|
||||
# default make targets for standard package with configure
|
||||
#
|
||||
# you should define the 'PKG' variable
|
||||
# (and optionaly 'PKGTAR', 'PKGDIR')
|
||||
#
|
||||
|
||||
PKGTAR ?= $(PKG).tgz
|
||||
|
||||
PKGDIR ?= build.$(PORTNAME)
|
||||
|
||||
PRTPATH = $(abspath $(PRTDIR))
|
||||
|
||||
#
|
||||
# Rules
|
||||
#
|
||||
|
||||
.PHONY: all clean test portclean pkg pkg.expand pkg.make pkg.install
|
||||
|
||||
all:: pkg
|
||||
|
||||
pkg.expand::
|
||||
test -d $(PKGDIR) || mkdir $(PKGDIR)
|
||||
test -f $(PKGDIR)/configure || $(TAR) zxf $(PKGTAR) -C $(PKGDIR) --strip-components 1
|
||||
|
||||
pkg.make:: pkg.expand
|
||||
test -f $(PKGDIR)/Makefile || (cd $(PKGDIR) && ./configure --prefix=$(PRTPATH))
|
||||
$(MAKE) -C $(PKGDIR)
|
||||
|
||||
pkg.install:: pkg.make
|
||||
$(MAKE) -C $(PKGDIR) install
|
||||
|
||||
pkg:: pkg.install
|
||||
@echo "+++++++++++ package $(PKG) done"
|
||||
|
||||
test::
|
||||
(! test -d $(PKGDIR)) || $(MAKE) -C $(PKGDIR) test
|
||||
|
||||
clean::
|
||||
(! test -d $(PKGDIR)) || $(MAKE) -C $(PKGDIR) clean
|
||||
|
||||
portclean::
|
||||
(! test -d $(PKGDIR)) || $(MAKE) -C $(PKGDIR) distclean
|
||||
(! test -d $(PKGDIR)) || \rm -r $(PKGDIR)
|
||||
30
src/kimono/lxpack/config/targets/propagate.targ
Normal file
30
src/kimono/lxpack/config/targets/propagate.targ
Normal file
@ -0,0 +1,30 @@
|
||||
#
|
||||
# $Id: propagate.targ 1825 2013-02-26 09:39:47Z viari $
|
||||
#
|
||||
# propagate.targ
|
||||
#
|
||||
# default make targets for library containers
|
||||
#
|
||||
# you should define the 'DIRS' variable
|
||||
#
|
||||
# It will propagate 'MAKE <target>' to all
|
||||
# directories listed in DIRS
|
||||
#
|
||||
|
||||
#
|
||||
# Rules
|
||||
#
|
||||
|
||||
.PHONY: all _action $(DIRS)
|
||||
|
||||
.DEFAULT:
|
||||
$(MAKE) ACTION=$@ _action
|
||||
|
||||
all::
|
||||
$(MAKE) ACTION=all _action
|
||||
|
||||
_action: $(DIRS)
|
||||
@echo "$(ACTION) done"
|
||||
|
||||
$(DIRS):
|
||||
$(MAKE) -C $@ $(ACTION)
|
||||
187
src/kimono/lxpack/include/Genetic.h
Normal file
187
src/kimono/lxpack/include/Genetic.h
Normal file
@ -0,0 +1,187 @@
|
||||
/* ---------------------------------------------------------------- */
|
||||
/* Copyright (c) Atelier de BioInformatique */
|
||||
/* @file: Genetic.h */
|
||||
/* @desc: Genetic codes / include file */
|
||||
/* */
|
||||
/* @history: */
|
||||
/* @+ <Gloup> : Jan 96 : first draft for PWG from acnuc */
|
||||
/* ---------------------------------------------------------------- */
|
||||
|
||||
#ifndef _H_Genetic
|
||||
|
||||
#define _H_Genetic
|
||||
|
||||
/* ==================================================== */
|
||||
/* Constants */
|
||||
/* ==================================================== */
|
||||
|
||||
#define DNA_ALPHA "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz"
|
||||
#define C_DNA_ALPHA "TVGHEFCDIJMLKNOPQYSAABWXRZtvghefcdijmlknopqysaabwxrz"
|
||||
|
||||
#define GEN_NUC_ALPHA "AaCcGgTtUu"
|
||||
#define GEN_PRO_ALPHA "RLSTPAGVKNQHEDYCFIMW*X"
|
||||
|
||||
#define GEN_MAX_CODES 9
|
||||
|
||||
#define GEN_CODE_UNIVL 0 /* Universal */
|
||||
#define GEN_CODE_MYEAS 1 /* mito yeast */
|
||||
#define GEN_CODE_MVERT 2 /* mito vertebrate */
|
||||
#define GEN_CODE_FUNGI 3 /* filamentous fungi */
|
||||
#define GEN_CODE_MINSE 4 /* mito insects & platyhelminthes */
|
||||
#define GEN_CODE_CANDI 5 /* Candida cylindracea */
|
||||
#define GEN_CODE_CILIA 6 /* Ciliata */
|
||||
#define GEN_CODE_EUPLO 7 /* Euplotes */
|
||||
#define GEN_CODE_MECHI 8 /* mito echinoderms */
|
||||
|
||||
/* ==================================================== */
|
||||
/* Data Structures */
|
||||
/* ==================================================== */
|
||||
|
||||
typedef struct GeneticCode {
|
||||
char title[256]; /* nom du code */
|
||||
char info[256]; /* informations */
|
||||
int code[65]; /* 64 codons + Error */
|
||||
} GeneticCode;
|
||||
|
||||
/* ==================================================== */
|
||||
/* Data Instanciation */
|
||||
/* ==================================================== */
|
||||
|
||||
#ifdef GENETIC_CODE_INSTANCE
|
||||
|
||||
GeneticCode theGeneticCode[GEN_MAX_CODES] = { /* Begin of codes */
|
||||
|
||||
{ /* 0: UNIVERSAL */
|
||||
{"Universal"},
|
||||
{""},
|
||||
{ 8, 9, 8, 9, 3, 3, 3, 3,
|
||||
0, 2, 0, 2, 17, 17, 18, 17,
|
||||
10, 11, 10, 11, 4, 4, 4, 4,
|
||||
0, 0, 0, 0, 1, 1, 1, 1,
|
||||
12, 13, 12, 13, 5, 5, 5, 5,
|
||||
6, 6, 6, 6, 7, 7, 7, 7,
|
||||
20, 14, 20, 14, 2, 2, 2, 2,
|
||||
20, 15, 19, 15, 1, 16, 1, 16,
|
||||
21}
|
||||
},
|
||||
|
||||
{ /* 1: MITOCHONDRIAL YEAST */
|
||||
{"Mitochondrial Yeast"},
|
||||
{"CUN=T AUA=M UGA=W"},
|
||||
{ 8, 9, 8, 9, 3, 3, 3, 3,
|
||||
0, 2, 0, 2, 18, 17, 18, 17,
|
||||
10, 11, 10, 11, 4, 4, 4, 4,
|
||||
0, 0, 0, 0, 3, 3, 3, 3,
|
||||
12, 13, 12, 13, 5, 5, 5, 5,
|
||||
6, 6, 6, 6, 7, 7, 7, 7,
|
||||
20, 14, 20, 14, 2, 2, 2, 2,
|
||||
19, 15, 19, 15, 1, 16, 1, 16,
|
||||
21}
|
||||
},
|
||||
|
||||
{ /* 2: MITOCHONDRIAL VERTEBRATES */
|
||||
{"Mitochondrial Vertebrates"},
|
||||
{"AGR=* AUA=M UGA=W"},
|
||||
{ 8, 9, 8, 9, 3, 3, 3, 3,
|
||||
20, 2, 20, 2, 18, 17, 18, 17,
|
||||
10, 11, 10, 11, 4, 4, 4, 4,
|
||||
0, 0, 0, 0, 1, 1, 1, 1,
|
||||
12, 13, 12, 13, 5, 5, 5, 5,
|
||||
6, 6, 6, 6, 7, 7, 7, 7,
|
||||
20, 14, 20, 14, 2, 2, 2, 2,
|
||||
19, 15, 19, 15, 1, 16, 1, 16,
|
||||
21}
|
||||
},
|
||||
|
||||
{ /* 3: MITOCHONDRIAL FILAMENTOUS FUNGI */
|
||||
{"Mitochondrial Filamentous Fungi"},
|
||||
{"UGA=W"},
|
||||
{ 8, 9, 8, 9, 3, 3, 3, 3,
|
||||
0, 2, 0, 2, 17, 17, 18, 17,
|
||||
10, 11, 10, 11, 4, 4, 4, 4,
|
||||
0, 0, 0, 0, 1, 1, 1, 1,
|
||||
12, 13, 12, 13, 5, 5, 5, 5,
|
||||
6, 6, 6, 6, 7, 7, 7, 7,
|
||||
20, 14, 20, 14, 2, 2, 2, 2,
|
||||
19, 15, 19, 15, 1, 16, 1, 16,
|
||||
21}
|
||||
},
|
||||
|
||||
{ /* 4: MITOCHONDRIAL CODE OF INSECT AND PLATYHELMINTHES */
|
||||
{"Mitochondrial Insects and Platyhelminthes"},
|
||||
{"AUA=M UGA=W AGR=S"},
|
||||
{ 8, 9, 8, 9, 3, 3, 3, 3,
|
||||
2, 2, 2, 2, 18, 17, 18, 17,
|
||||
10, 11, 10, 11, 4, 4, 4, 4,
|
||||
0, 0, 0, 0, 1, 1, 1, 1,
|
||||
12, 13, 12, 13, 5, 5, 5, 5,
|
||||
6, 6, 6, 6, 7, 7, 7, 7,
|
||||
20, 14, 20, 14, 2, 2, 2, 2,
|
||||
19, 15, 19, 15, 1, 16, 1, 16,
|
||||
21}
|
||||
},
|
||||
|
||||
{ /* 5: CANDIDA CYLINDRACEA (see nature 341:164) */
|
||||
{"Candida cylindracea"},
|
||||
{"CUG=S CUA=?"},
|
||||
{ 8, 9, 8, 9, 3, 3, 3, 3,
|
||||
0, 2, 0, 2, 17, 17, 18, 17,
|
||||
10, 11, 10, 11, 4, 4, 4, 4,
|
||||
0, 0, 0, 0, 21, 1, 2, 1,
|
||||
12, 13, 12, 13, 5, 5, 5, 5,
|
||||
6, 6, 6, 6, 7, 7, 7, 7,
|
||||
20, 14, 20, 14, 2, 2, 2, 2,
|
||||
20, 15, 19, 15, 1, 16, 1, 16,
|
||||
21}
|
||||
},
|
||||
|
||||
{ /* 6: CILIATA */
|
||||
{"Ciliata"},
|
||||
{"UAR=Q"},
|
||||
{ 8, 9, 8, 9, 3, 3, 3, 3,
|
||||
0, 2, 0, 2, 17, 17, 18, 17,
|
||||
10, 11, 10, 11, 4, 4, 4, 4,
|
||||
0, 0, 0, 0, 1, 1, 1, 1,
|
||||
12, 13, 12, 13, 5, 5, 5, 5,
|
||||
6, 6, 6, 6, 7, 7, 7, 7,
|
||||
10, 14, 10, 14, 2, 2, 2, 2,
|
||||
20, 15, 19, 15, 1, 16, 1, 16,
|
||||
21}
|
||||
},
|
||||
|
||||
{ /* 7: EUPLOTES */
|
||||
{"Euplotes"},
|
||||
{"UGA=C"},
|
||||
{ 8, 9, 8, 9, 3, 3, 3, 3,
|
||||
0, 2, 0, 2, 17, 17, 18, 17,
|
||||
10, 11, 10, 11, 4, 4, 4, 4,
|
||||
0, 0, 0, 0, 1, 1, 1, 1,
|
||||
12, 13, 12, 13, 5, 5, 5, 5,
|
||||
6, 6, 6, 6, 7, 7, 7, 7,
|
||||
20, 14, 20, 14, 2, 2, 2, 2,
|
||||
15, 15, 19, 15, 1, 16, 1, 16,
|
||||
21}
|
||||
},
|
||||
|
||||
{ /* 8: MITOCHONDRIAL ECHINODERMS */
|
||||
{"Mitochondrial Echinoderms"},
|
||||
{"UGA=W AGR=S AAA=N"},
|
||||
{ 9, 9, 8, 9, 3, 3, 3, 3,
|
||||
2, 2, 2, 2, 17, 17, 18, 17,
|
||||
10, 11, 10, 11, 4, 4, 4, 4,
|
||||
0, 0, 0, 0, 1, 1, 1, 1,
|
||||
12, 13, 12, 13, 5, 5, 5, 5,
|
||||
6, 6, 6, 6, 7, 7, 7, 7,
|
||||
20, 14, 20, 14, 2, 2, 2, 2,
|
||||
19, 15, 19, 15, 1, 16, 1, 16,
|
||||
21}
|
||||
}
|
||||
|
||||
/* end of codes */ };
|
||||
|
||||
#else
|
||||
|
||||
extern GeneticCode theGeneticCode[GEN_MAX_CODES];
|
||||
|
||||
#endif
|
||||
#endif
|
||||
64
src/kimono/lxpack/include/fasta_io.h
Normal file
64
src/kimono/lxpack/include/fasta_io.h
Normal file
@ -0,0 +1,64 @@
|
||||
/* ---------------------------------------------------------------- */
|
||||
/* Copyright (c) Atelier de BioInformatique */
|
||||
/* @file: fasta_io.h */
|
||||
/* @desc: sequence IO in fasta format / include file */
|
||||
/* */
|
||||
/* @history: */
|
||||
/* @+ <Gloup> : Aug 92 : first version */
|
||||
/* @+ <Gloup> : Nov 95 : last revised version */
|
||||
/* ---------------------------------------------------------------- */
|
||||
|
||||
#ifndef _H_fasta_io
|
||||
|
||||
#define _H_fasta_io
|
||||
|
||||
/* ==================================================== */
|
||||
/* Constantes */
|
||||
/* ==================================================== */
|
||||
|
||||
#define FASTA_NAMLEN 64 /* max length of seq. name */
|
||||
#define FASTA_COMLEN 512 /* max length of seq. comment */
|
||||
|
||||
#define FASTA_CHAR_PER_LINE 50 /* # of chars per line in output */
|
||||
|
||||
/* ==================================================== */
|
||||
/* Macros standards */
|
||||
/* ==================================================== */
|
||||
|
||||
#ifndef NEW
|
||||
#define NEW(typ) (typ*)malloc(sizeof(typ))
|
||||
#define NEWN(typ, dim) (typ*)malloc((unsigned)(dim) * sizeof(typ))
|
||||
#define REALLOC(typ, ptr, dim) (typ*)realloc((void *) (ptr), (unsigned long)(dim) * sizeof(typ))
|
||||
#define FREE(ptr) free(ptr)
|
||||
#endif
|
||||
|
||||
/* ==================================================== */
|
||||
/* Structures de donnees */
|
||||
/* ==================================================== */
|
||||
|
||||
typedef struct { /* -- Sequence ---------------- */
|
||||
int ok; /* error flag */
|
||||
long length, /* longueur */
|
||||
offset, /* current offset */
|
||||
bufsize; /* size of current seq buffer */
|
||||
char name[FASTA_NAMLEN+2], /* nom */
|
||||
comment[FASTA_COMLEN+2], /* commentaire */
|
||||
*seq; /* sequence */
|
||||
} FastaSequence, *FastaSequencePtr;
|
||||
|
||||
/* ==================================================== */
|
||||
/* Prototypes (generated by mkproto) */
|
||||
/* ==================================================== */
|
||||
|
||||
/* libfasta.c */
|
||||
|
||||
FastaSequencePtr NewFastaSequence ( void );
|
||||
FastaSequencePtr FreeFastaSequence ( FastaSequencePtr seq );
|
||||
|
||||
int ReadFastaSequence ( FILE *streamin, FastaSequencePtr seq );
|
||||
int GetFastaSequence ( FILE *streamin, FastaSequencePtr seq );
|
||||
void WriteFastaSequence ( FILE *streamou, FastaSequencePtr seq , int char_per_line );
|
||||
|
||||
void RewindFastaDB ( FILE *streamin );
|
||||
|
||||
#endif
|
||||
169
src/kimono/lxpack/include/kimono.h
Normal file
169
src/kimono/lxpack/include/kimono.h
Normal file
@ -0,0 +1,169 @@
|
||||
/* ==================================================== */
|
||||
/* @File kimono.h */
|
||||
/* @history: */
|
||||
/* @+ Nov. 03 <Gloup> first draft */
|
||||
/* ==================================================== */
|
||||
|
||||
#define _H_kimono
|
||||
|
||||
#ifndef _H_fasta_io
|
||||
#include "fasta_io.h"
|
||||
#endif
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* constantes */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
#define NB_NUC 4
|
||||
#define NB_AA 21
|
||||
#define NB_CODONS 64
|
||||
|
||||
#define SHIFT_NUC 2 /* # bits for NB_NUC */
|
||||
|
||||
#define KIM_DNA "ACGT"
|
||||
#define KIM_AA "ACDEFGHIKLMNPQRSTVWY*"
|
||||
|
||||
#define MASKED_SYMBOL 'X'
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* struct de donnees */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
typedef struct {
|
||||
int from, to, strand;
|
||||
} Interval;
|
||||
|
||||
typedef struct {
|
||||
int size, capacity;
|
||||
Interval *interval;
|
||||
} SetOfIntervals;
|
||||
|
||||
typedef struct {
|
||||
char index;
|
||||
char mask;
|
||||
} SeqCell;
|
||||
|
||||
typedef struct {
|
||||
int length;
|
||||
char symbol[128];
|
||||
} Alphabet;
|
||||
|
||||
typedef struct {
|
||||
Alphabet *alphabet;
|
||||
FastaSequence *fasta;
|
||||
SeqCell *cell;
|
||||
} Sequence;
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* counting, indexing and distance functions */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
typedef void (*IndexFunction) (Sequence *seq, SetOfIntervals *zones, int phase);
|
||||
typedef void (*CountFunction) (Sequence *seq, int from, int to, int count[][2], int nbins, int increment);
|
||||
typedef void (*MixFunction) (int left[][2], int right[][2], int countLeft[], int countRight[], int nbins);
|
||||
typedef float (*DistFunction) (int bins1[], int bins2[], int nbins, int ibin);
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* masks for sequence */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
#define EXCLUDE_MASK 0x01 /* 00000001 */
|
||||
#define INCLUDE_MASK 0x7e /* 01111110 */
|
||||
#define DIRECT_MASK 0x02 /* 00000010 */
|
||||
#define REVERSE_MASK 0x04 /* 00000100 */
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* macros */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
#define IS_UPPER(c) (((c) >= 'A') && ((c) <= 'Z'))
|
||||
#define IS_LOWER(c) (((c) >= 'a') && ((c) <= 'z'))
|
||||
#define IS_ALPHA(c) (IS_UPPER(c) || IS_LOWER(c))
|
||||
|
||||
#define TO_UPPER(c) ((c) - 'a' + 'A')
|
||||
#define TO_LOWER(c) ((c) - 'A' + 'a')
|
||||
|
||||
#define UPPER(x) (IS_LOWER(x) ? TO_UPPER(x) : (x))
|
||||
#define LOWER(x) (IS_UPPER(x) ? TO_LOWER(x) : (x))
|
||||
|
||||
#define MIN2(a, b) ((a) < (b) ? (a) : (b))
|
||||
#define MAX2(a, b) ((a) > (b) ? (a) : (b))
|
||||
|
||||
#ifndef NEW
|
||||
#define NEW(type) (type *) malloc(sizeof(type))
|
||||
#define NEWN(type, n) (type *) malloc((n) * sizeof(type))
|
||||
#define REALLOC(type, ptr, n) (type *) realloc(ptr, (n) * sizeof(type))
|
||||
#define FREE(ptr) free(ptr)
|
||||
#endif
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* Prototypes */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
/* kim_util.c */
|
||||
|
||||
int Erreur (char *msg , int stat);
|
||||
int MemoryErreur (char *where, int stat);
|
||||
int AssignToStdin (char *filename);
|
||||
|
||||
/* kim_alphabet.c */
|
||||
|
||||
Alphabet *FreeAlphabet (Alphabet *alpha);
|
||||
Alphabet *NewAlphabet (char *symbols);
|
||||
Alphabet *CopyAlphabet (Alphabet *alpha);
|
||||
Alphabet *NucleicAlphabet ();
|
||||
Alphabet *AminoAlphabet ();
|
||||
|
||||
/* kim_sequence.c */
|
||||
|
||||
Sequence *FreeSequence (Sequence *seq);
|
||||
Sequence *NewSequence (Alphabet *alpha);
|
||||
int ReadSequence (FILE *streamin, Sequence *seq);
|
||||
|
||||
/* kim_genetic.c */
|
||||
|
||||
int BaseComplement (int ch);
|
||||
char *SeqComplement (char *str);
|
||||
int CodonTranslate (char *codon, int codid);
|
||||
|
||||
/* kim_zone.c */
|
||||
|
||||
SetOfIntervals *FreeZones (SetOfIntervals *set);
|
||||
SetOfIntervals *ReadZones (int seqlength);
|
||||
|
||||
/* kim_indexer.c */
|
||||
|
||||
void NoZoneIndexer (Sequence *seq, SetOfIntervals *zones, int phase);
|
||||
void ExcludeIndexer (Sequence *seq, SetOfIntervals *zones, int phase);
|
||||
void GeneIndexer (Sequence *seq, SetOfIntervals *zones, int phase);
|
||||
void PhaseIndexer (Sequence *seq, SetOfIntervals *zones, int phase);
|
||||
void CodonIndexer (Sequence *seq, SetOfIntervals *zones, int phase);
|
||||
|
||||
/* kim_counter.c */
|
||||
|
||||
void BasicCounter (Sequence *seq, int from, int to,
|
||||
int count[][2], int nbins, int increment);
|
||||
void CodonSkewCounter (Sequence *seq, int from, int to,
|
||||
int count[][2], int nbins, int increment);
|
||||
|
||||
/* kim_mixer.c */
|
||||
void BasicMixer (int left[][2], int right[][2],
|
||||
int *countLeft, int *countRight, int nbins);
|
||||
void CrossMixer (int left[][2], int right[][2],
|
||||
int *countLeft, int *countRight, int nbins);
|
||||
|
||||
/* kim_distance.c */
|
||||
|
||||
float ChisTwo(int bins1[], int bins2[], int nbins, int ibin);
|
||||
float Euclid(int bins1[], int bins2[], int nbins, int ibin);
|
||||
float HellTwo(int bins1[], int bins2[], int nbins, int ibin);
|
||||
int SignTwoBins(int bins1[], int bins2[]);
|
||||
|
||||
/* kim_codonskew.c */
|
||||
|
||||
void CodonSkew (int code, float score[NB_NUC][NB_CODONS]);
|
||||
|
||||
/* kim*_help.c */
|
||||
void PrintHelp (void);
|
||||
int ExitUsage (int stat);
|
||||
|
||||
43
src/kimono/lxpack/src/Makefile
Normal file
43
src/kimono/lxpack/src/Makefile
Normal file
@ -0,0 +1,43 @@
|
||||
# ---------------------------------------------------------------
|
||||
# $Id: $
|
||||
#
|
||||
# @file: Makefile
|
||||
# @desc: makefile for kimono/src
|
||||
#
|
||||
# @history:
|
||||
#
|
||||
# @note: should be processed with gnu compatible make
|
||||
# @note: helixware_compatible
|
||||
#
|
||||
# @end:
|
||||
# ---------------------------------------------------------------
|
||||
#
|
||||
|
||||
include ../config/auto.conf
|
||||
|
||||
PROGS = kimono kimfit
|
||||
|
||||
OSRC = fasta_io.c \
|
||||
kim_util.c \
|
||||
kim_alphabet.c \
|
||||
kim_sequence.c \
|
||||
kim_zone.c \
|
||||
kim_indexer.c \
|
||||
kim_counter.c \
|
||||
kim_mixer.c \
|
||||
kim_distance.c \
|
||||
kim_genetic.c \
|
||||
kim_codonskew.c
|
||||
|
||||
include ../config/targets/lxbin.targ
|
||||
include ../config/targets/help.targ
|
||||
|
||||
#
|
||||
# file dependencies
|
||||
#
|
||||
|
||||
kimono: $(OBJ) kimono_main.c kimono_help.c
|
||||
$(CC) $(CFLAGS) -o $@ $^ $(LDFLAGS) $(LDLIBS)
|
||||
|
||||
kimfit: $(OBJ) kimfit_main.c
|
||||
$(CC) $(CFLAGS) -o $@ $^ $(LDFLAGS) $(LDLIBS)
|
||||
6
src/kimono/lxpack/src/TODO
Normal file
6
src/kimono/lxpack/src/TODO
Normal file
@ -0,0 +1,6 @@
|
||||
|
||||
- dist PHI2
|
||||
|
||||
- inversion strand -
|
||||
|
||||
|
||||
388
src/kimono/lxpack/src/fasta_io.c
Executable file
388
src/kimono/lxpack/src/fasta_io.c
Executable file
@ -0,0 +1,388 @@
|
||||
/* ---------------------------------------------------------------- */
|
||||
/* Copyright (c) Atelier de BioInformatique */
|
||||
/* @file: fasta_io.c */
|
||||
/* @desc: sequence IO in fasta format */
|
||||
/* */
|
||||
/* @history: */
|
||||
/* @+ <Gloup> : Aug 92 : first version */
|
||||
/* @+ <Gloup> : Nov 95 : last revised version */
|
||||
/* ---------------------------------------------------------------- */
|
||||
|
||||
#include <ctype.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
|
||||
#include "fasta_io.h"
|
||||
|
||||
#define SECURE 1 /* 1 : secure copy ; 0 : quickest copy */
|
||||
|
||||
#define READ_NEXT 0 /* force to read next io buffer line */
|
||||
#define PUSH_BACK 1 /* force to push back io buffer line */
|
||||
|
||||
#define SERIAL 1 /* serial reading */
|
||||
#define INDEXED 0 /* indexed reading */
|
||||
|
||||
#ifdef MAC_OS_C
|
||||
#define LINE_FEED '\r'
|
||||
#else
|
||||
#define LINE_FEED '\n'
|
||||
#endif
|
||||
|
||||
static int sRetained = 0; /* 1 : reuse last buffer line */
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* @static: lecture bufferisee */
|
||||
/* this is the main IO function */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
static char * sNextIOBuffer(FILE *streamin, int retain, int serial)
|
||||
{
|
||||
char *buf, *end;
|
||||
int reused;
|
||||
|
||||
static char sBuffer[BUFSIZ]; /* BUFSIZ in <stdio.h> */
|
||||
|
||||
reused = (retain || sRetained) && serial;
|
||||
|
||||
sRetained = retain;
|
||||
|
||||
buf = ( reused
|
||||
? sBuffer
|
||||
: fgets(sBuffer, sizeof(sBuffer), streamin));
|
||||
|
||||
if (! buf) /* end of file */
|
||||
return NULL;
|
||||
|
||||
end = buf + strlen(buf) - 1;
|
||||
|
||||
if (*end == LINE_FEED) /* remove trailing \n */
|
||||
*end = '\000';
|
||||
|
||||
return ( *buf || reused
|
||||
? buf
|
||||
: sNextIOBuffer(streamin, retain, serial));
|
||||
}
|
||||
|
||||
#if SECURE
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* compte le nombre de caracteres alpha dans */
|
||||
/* un buffer */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
static long sCountAlpha(char *buf)
|
||||
{
|
||||
long count;
|
||||
|
||||
for (count = 0 ; *buf ; buf++)
|
||||
if (isalpha(*buf))
|
||||
count++;
|
||||
|
||||
return count;
|
||||
}
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* copy only alpha chars from s2 to s1 */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
static char *sStrcpyAlpha(char *s1, char *s2)
|
||||
{
|
||||
for( ; *s2 ; s2++)
|
||||
if (isalpha(*s2))
|
||||
*s1++ = *s2;
|
||||
|
||||
*s1 = '\000';
|
||||
|
||||
return s1;
|
||||
}
|
||||
#endif
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* skip to next space in buffer */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
static char *sNextSpace(char *buffer)
|
||||
{
|
||||
for (; *buffer ; buffer++)
|
||||
if (isspace(*buffer))
|
||||
return buffer;
|
||||
|
||||
return NULL;
|
||||
}
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* returns sequence name (FASTA) */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
static char *sGetFastaName(char *buffer)
|
||||
{
|
||||
char c[2];
|
||||
static char sName[FASTA_NAMLEN+2];
|
||||
|
||||
*c = buffer[FASTA_NAMLEN];
|
||||
buffer[FASTA_NAMLEN] = '\000';
|
||||
|
||||
if (sscanf(buffer + 1, "%s", sName) != 1)
|
||||
(void) strcpy(sName, "<no Name>");
|
||||
|
||||
buffer[FASTA_NAMLEN] = *c;
|
||||
|
||||
return sName;
|
||||
}
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* returns sequence comment (FASTA) */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
static char *sGetFastaComment(char *buffer)
|
||||
{
|
||||
char c[2], *space;
|
||||
static char sComment[FASTA_COMLEN+2];
|
||||
|
||||
*c = buffer[FASTA_COMLEN];
|
||||
buffer[FASTA_COMLEN] = '\000';
|
||||
|
||||
space = sNextSpace(buffer);
|
||||
|
||||
(void) strcpy(sComment, (space ? space + 1 : "<no comment>"));
|
||||
|
||||
buffer[FASTA_COMLEN] = *c;
|
||||
|
||||
return sComment;
|
||||
}
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* API */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* liberation d'une sequence */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
FastaSequencePtr FreeFastaSequence(FastaSequencePtr seq)
|
||||
{
|
||||
if (seq) {
|
||||
if (seq->seq)
|
||||
FREE(seq->seq);
|
||||
FREE(seq);
|
||||
}
|
||||
|
||||
return NULL;
|
||||
}
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* allocation d'une sequence */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
FastaSequencePtr NewFastaSequence()
|
||||
{
|
||||
FastaSequencePtr seq;
|
||||
|
||||
if (! (seq = NEW(FastaSequence)))
|
||||
return NULL;
|
||||
|
||||
seq->length = 0;
|
||||
seq->offset = -1;
|
||||
|
||||
if (! (seq->seq = NEWN(char, BUFSIZ)))
|
||||
return FreeFastaSequence(seq);
|
||||
|
||||
seq->bufsize = BUFSIZ;
|
||||
|
||||
*(seq->name) = '\000';
|
||||
*(seq->comment) = '\000';
|
||||
|
||||
seq->ok = 1;
|
||||
|
||||
return seq;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* lecture <Serie> d'une sequence au format Fasta */
|
||||
/* returns : 0 -> last sequence */
|
||||
/* 1 -> more to read */
|
||||
/* <but> you must check seq->ok */
|
||||
/* that may be 0 (memory error) */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
int ReadFastaSequence(FILE *streamin, FastaSequencePtr seq)
|
||||
{
|
||||
long readlen, buflen;
|
||||
char *buffer, *tbuf;
|
||||
|
||||
seq->ok = 0; /* assume error */
|
||||
|
||||
buflen = seq->length = 0;
|
||||
|
||||
seq->offset = ftell(streamin);
|
||||
|
||||
buffer = sNextIOBuffer(streamin, READ_NEXT, SERIAL);
|
||||
|
||||
if (! (buffer && (*buffer == '>'))) /* sync error */
|
||||
return 0; /* last sequence */
|
||||
|
||||
if (seq->offset)
|
||||
seq->offset -= (strlen(buffer) + 1);
|
||||
|
||||
(void) strcpy(seq->name, sGetFastaName(buffer));
|
||||
|
||||
(void) strcpy(seq->comment, sGetFastaComment(buffer));
|
||||
|
||||
while (buffer = sNextIOBuffer(streamin, READ_NEXT, SERIAL)) {
|
||||
|
||||
if (*buffer == '>') {
|
||||
(void) sNextIOBuffer(streamin, PUSH_BACK, SERIAL); /* push it back */
|
||||
break;
|
||||
}
|
||||
|
||||
#if SECURE
|
||||
readlen = sCountAlpha(buffer);
|
||||
#else
|
||||
readlen = strlen(buffer);
|
||||
#endif
|
||||
|
||||
buflen += readlen;
|
||||
|
||||
if (buflen >= seq->bufsize) {
|
||||
|
||||
if (! (tbuf = REALLOC(char, seq->seq, 2 * buflen + 1)))
|
||||
return 1; /* but seq->ok is 0 */
|
||||
|
||||
seq->seq = tbuf;
|
||||
|
||||
seq->bufsize = 2 * buflen + 1;
|
||||
|
||||
}
|
||||
|
||||
#if SECURE
|
||||
sStrcpyAlpha(seq->seq + seq->length, buffer);
|
||||
#else
|
||||
(void) memcpy(seq->seq + seq->length, buffer, readlen);
|
||||
#endif
|
||||
|
||||
seq->length = buflen;
|
||||
|
||||
}
|
||||
|
||||
seq->seq[seq->length] = '\000';
|
||||
|
||||
return (seq->ok = 1);
|
||||
}
|
||||
|
||||
/* ------------------------------------------------- */
|
||||
/* lecture <Indexee> d'une sequence au format Fasta */
|
||||
/* use the internal seq->offset variable to position */
|
||||
/* on the correct sequence. */
|
||||
/* returns : 0 -> sync or memory error */
|
||||
/* 1 -> read ok */
|
||||
/* ------------------------------------------------- */
|
||||
|
||||
int GetFastaSequence(FILE *streamin, FastaSequencePtr seq)
|
||||
{
|
||||
long readlen, buflen;
|
||||
char *buffer, *tbuf;
|
||||
|
||||
seq->ok = 0; /* assume error */
|
||||
|
||||
if (seq->offset < 0)
|
||||
return 0; /* bad offset */
|
||||
|
||||
buflen = seq->length = 0;
|
||||
|
||||
(void) fseek(streamin, seq->offset, SEEK_SET);
|
||||
|
||||
buffer = sNextIOBuffer(streamin, READ_NEXT, INDEXED);
|
||||
|
||||
if (! (buffer && (*buffer == '>'))) /* sync error */
|
||||
return 0; /* last sequence */
|
||||
|
||||
(void) strcpy(seq->name, sGetFastaName(buffer));
|
||||
|
||||
(void) strcpy(seq->comment, sGetFastaComment(buffer));
|
||||
|
||||
while (buffer = sNextIOBuffer(streamin, READ_NEXT, INDEXED)) {
|
||||
|
||||
if (*buffer == '>')
|
||||
break;
|
||||
|
||||
#if SECURE
|
||||
readlen = sCountAlpha(buffer);
|
||||
#else
|
||||
readlen = strlen(buffer);
|
||||
#endif
|
||||
|
||||
buflen += readlen;
|
||||
|
||||
if (buflen >= seq->bufsize) {
|
||||
|
||||
if (! (tbuf = REALLOC(char, seq->seq, 2 * buflen + 1)))
|
||||
return 0;
|
||||
|
||||
seq->seq = tbuf;
|
||||
|
||||
seq->bufsize = 2 * buflen + 1;
|
||||
|
||||
}
|
||||
#if SECURE
|
||||
sStrcpyAlpha(seq->seq + seq->length, buffer);
|
||||
#else
|
||||
(void) memcpy(seq->seq + seq->length, buffer, readlen);
|
||||
#endif
|
||||
|
||||
seq->length = buflen;
|
||||
|
||||
}
|
||||
|
||||
seq->seq[seq->length] = '\000';
|
||||
|
||||
return (seq->ok = 1);
|
||||
}
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* ecriture d'une sequence au format Fasta */
|
||||
/* -------------------------------------------- */
|
||||
void WriteFastaSequence(FILE *streamou, FastaSequencePtr seq,
|
||||
int char_per_line)
|
||||
{
|
||||
long i, nlines, nrest, nchar;
|
||||
char *buf, *end, tempo;
|
||||
|
||||
(void) fputc('>', streamou);
|
||||
(void) fputs((*(seq->name) ? seq->name : "<no name>"), streamou);
|
||||
(void) fputc(' ', streamou);
|
||||
(void) fputs((*(seq->comment) ? seq->comment : "<no comment>"), streamou);
|
||||
(void) fputc(LINE_FEED, streamou);
|
||||
|
||||
nlines = seq->length / char_per_line;
|
||||
nrest = seq->length % char_per_line;
|
||||
|
||||
if (nrest)
|
||||
nlines++;
|
||||
|
||||
buf = seq->seq;
|
||||
|
||||
for (i = 1 ; i <= nlines ; i++) {
|
||||
nchar = ((nrest && (i == nlines)) ? nrest : char_per_line);
|
||||
end = buf + nchar;
|
||||
tempo = *end;
|
||||
*end = '\000';
|
||||
(void) fputs(buf, streamou);
|
||||
(void) fputc(LINE_FEED , streamou);
|
||||
*end = tempo;
|
||||
buf += nchar;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* rewind db file */
|
||||
/* -------------------------------------------- */
|
||||
void RewindFastaDB(FILE *streamin)
|
||||
{
|
||||
sRetained = 0; /* forget previous buffer */
|
||||
|
||||
if (streamin)
|
||||
rewind(streamin);
|
||||
}
|
||||
|
||||
83
src/kimono/lxpack/src/kim_alphabet.c
Executable file
83
src/kimono/lxpack/src/kim_alphabet.c
Executable file
@ -0,0 +1,83 @@
|
||||
/* ==================================================== */
|
||||
/* @file: kim_alphabet.c */
|
||||
/* alphabet handling */
|
||||
/* @history: */
|
||||
/* @+ Apr. 97 <AV> first draft */
|
||||
/* ==================================================== */
|
||||
|
||||
#include <ctype.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
|
||||
#include "kimono.h"
|
||||
|
||||
/* some static alphabets */
|
||||
|
||||
static char sDNA[] = KIM_DNA;
|
||||
static char sAA[] = KIM_AA;
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* API */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* free alphabet */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
Alphabet * FreeAlphabet(Alphabet *alpha) {
|
||||
if (alpha) FREE(alpha);
|
||||
return NULL;
|
||||
}
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* new alphabet */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
Alphabet *NewAlphabet(char *symbols) {
|
||||
Alphabet *alpha;
|
||||
|
||||
if (alpha = NEW(Alphabet)) {
|
||||
(void) strcpy(alpha->symbol, symbols);
|
||||
alpha->length = strlen(alpha->symbol);
|
||||
}
|
||||
|
||||
return alpha;
|
||||
}
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* copy alphabet */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
Alphabet *CopyAlphabet(Alphabet *alpha) {
|
||||
return NewAlphabet(alpha->symbol);
|
||||
}
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* standard alphabets */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
/* DNA */
|
||||
|
||||
Alphabet *NucleicAlphabet() {
|
||||
return NewAlphabet(sDNA);
|
||||
}
|
||||
|
||||
/* AA */
|
||||
|
||||
Alphabet *AminoAlphabet() {
|
||||
return NewAlphabet(sAA);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* index of symbol in alphabet */
|
||||
/* return : index of symbol in alphabet */
|
||||
/* -1 if not found */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
int AlphaIndex(Alphabet *alpha, char symbol) {
|
||||
|
||||
char *pos = strchr(alpha->symbol, UPPER(symbol));
|
||||
|
||||
return (pos ? (int) (pos - alpha->symbol) : -1);
|
||||
}
|
||||
142
src/kimono/lxpack/src/kim_codonskew.c
Executable file
142
src/kimono/lxpack/src/kim_codonskew.c
Executable file
@ -0,0 +1,142 @@
|
||||
/* ==================================================== */
|
||||
/* @file: kim_codonskew.c */
|
||||
/* general utilities functions */
|
||||
/* @history: */
|
||||
/* @+ Apr. 97 <AV> first draft */
|
||||
/* ==================================================== */
|
||||
|
||||
#include <ctype.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
|
||||
#include "kimono.h"
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* make string buffer of all codons : */
|
||||
/* "AAA/AAC/AAT/AAG/ACA/....../GGG/" */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static void sMakeStdCodons(char *buffer, char *alphaN)
|
||||
{
|
||||
int i, j, k, n;
|
||||
|
||||
n = strlen(alphaN);
|
||||
|
||||
for (i = 0 ; i < n ; i++)
|
||||
for (j = 0 ; j < n ; j++)
|
||||
for (k = 0 ; k < n ; k++) {
|
||||
*buffer++ = alphaN[i];
|
||||
*buffer++ = alphaN[j];
|
||||
*buffer++ = alphaN[k];
|
||||
*buffer++ = '/';
|
||||
}
|
||||
*buffer = '\000';
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* make string buffer of synonymous codons coding */
|
||||
/* for aa */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static void sMakeAaCodons(char *buffer, char *alphaN, int aa, int code)
|
||||
{
|
||||
int aai;
|
||||
char *c, codons[4*NB_CODONS+1];
|
||||
|
||||
sMakeStdCodons(codons, alphaN);
|
||||
|
||||
for (c = codons ; *c ; c += 4) {
|
||||
aai = CodonTranslate(c, code);
|
||||
if (aai == aa) {
|
||||
strncpy(buffer, c, 3);
|
||||
buffer[3] = '/';
|
||||
buffer += 4;
|
||||
}
|
||||
}
|
||||
*buffer = '\000';
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* return index of aa encoded by codon */
|
||||
/* or -1 if not found */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static int sAaIndex(char *codon, char *alphaA, int code)
|
||||
{
|
||||
int aa;
|
||||
char *paa;
|
||||
|
||||
aa = CodonTranslate(codon, code);
|
||||
|
||||
if ((paa = strchr(alphaA, aa)) != 0)
|
||||
return (int) (paa - alphaA);
|
||||
|
||||
return -1;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* count # occurences of char mark in buffer */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static int sCount(char *buffer, int mark)
|
||||
{
|
||||
int count;
|
||||
|
||||
for (count = 0 ; *buffer ; buffer++) {
|
||||
if (*buffer == mark)
|
||||
count++;
|
||||
}
|
||||
|
||||
return count;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* skew score of one codon */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static float sCodonSkew(char *codon, char *alphaN, char *alphaA, int symb, int code) {
|
||||
|
||||
int iaa, nsyn, n0, nM;
|
||||
char synon[4*NB_CODONS+1], buf[4];
|
||||
|
||||
strncpy(buf, codon, 3);
|
||||
buf[3] = '\000';
|
||||
|
||||
iaa = sAaIndex(buf, alphaA, code);
|
||||
|
||||
sMakeAaCodons(synon, alphaN, alphaA[iaa], code);
|
||||
|
||||
n0 = sCount(buf, symb);
|
||||
|
||||
nsyn = strlen(synon) / 4;
|
||||
|
||||
nM = sCount(synon, symb);
|
||||
|
||||
return ((float) (n0) - ((float) (nM) / (float) nsyn));
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* API */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* skew scores of all codons */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
void CodonSkew(int code, float score[NB_NUC][NB_CODONS]) {
|
||||
|
||||
int i, j;
|
||||
char *trip;
|
||||
char alpha[NB_NUC+1], codons[4*NB_CODONS+1];
|
||||
|
||||
(void) strcpy(alpha, KIM_DNA);
|
||||
|
||||
sMakeStdCodons(codons, alpha);
|
||||
|
||||
for (i = 0 ; i < NB_NUC ; i++) {
|
||||
for (j = 0, trip = codons ; j < NB_CODONS ; j++, trip += 4) {
|
||||
score[i][j] = sCodonSkew(trip, alpha, KIM_AA, alpha[i], code);
|
||||
}
|
||||
}
|
||||
}
|
||||
140
src/kimono/lxpack/src/kim_counter.c
Executable file
140
src/kimono/lxpack/src/kim_counter.c
Executable file
@ -0,0 +1,140 @@
|
||||
/* ==================================================== */
|
||||
/* @file: kim_counter.c */
|
||||
/* counting functions */
|
||||
/* @history: */
|
||||
/* @+ Jul. 06 <AV> first draft */
|
||||
/* ==================================================== */
|
||||
|
||||
#include <ctype.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
|
||||
#include "Genetic.h"
|
||||
#include "kimono.h"
|
||||
|
||||
/* holds nucleotide enrichment for each codon */
|
||||
|
||||
static float sCodonScore[NB_NUC][NB_CODONS];
|
||||
static int sScoreInited = 0;
|
||||
|
||||
/* hold DNA amhabet
|
||||
|
||||
static char sDNA[] = KIM_DNA;
|
||||
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* API */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* basic nucleotide counting */
|
||||
/* */
|
||||
/* count : second dimension is for strand */
|
||||
/* increment : 1, -1 or 0 (0 means reset then 1) */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
void BasicCounter(Sequence *seq, int from, int to,
|
||||
int count[][2], int nbins, int increment) {
|
||||
|
||||
int i, len;
|
||||
|
||||
if (increment == 0) { /* this is a reset */
|
||||
for (i = 0 ; i <= nbins ; i++)
|
||||
count[i][0] = count[i][1] = 0;
|
||||
increment = 1;
|
||||
}
|
||||
|
||||
len = seq->fasta->length;
|
||||
|
||||
for (i = from ; i < to ; i++) {
|
||||
|
||||
int mask = seq->cell[i % len].mask;
|
||||
if (mask & EXCLUDE_MASK)
|
||||
continue;
|
||||
|
||||
int index = seq->cell[i % len].index;
|
||||
if ((index < 0) || (index > nbins)) /* other symbol */
|
||||
index = nbins;
|
||||
|
||||
if (mask & DIRECT_MASK)
|
||||
count[index][0] += increment;
|
||||
if (mask & REVERSE_MASK)
|
||||
count[index][1] += increment;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* counting skewed codon */
|
||||
/* note: don't forget to init counter before */
|
||||
/* InitCodonSkewCounter(code) */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
void InitCodonSkewCounter(int code) {
|
||||
CodonSkew(code, sCodonScore);
|
||||
sScoreInited = 1;
|
||||
}
|
||||
|
||||
void CodonSkewCounter(Sequence *seq, int from, int to,
|
||||
int count[][2], int nbins, int increment) {
|
||||
|
||||
int i, len;
|
||||
|
||||
if (! sScoreInited) {
|
||||
Erreur("CodonSkewCounter: initialized with default genetic code", 0);
|
||||
InitCodonSkewCounter(GEN_CODE_UNIVL);
|
||||
}
|
||||
|
||||
if (increment == 0) { /* this is a reset */
|
||||
for (i = 0 ; i <= nbins ; i++)
|
||||
count[i][0] = count[i][1] = 0;
|
||||
increment = 1;
|
||||
}
|
||||
|
||||
len = seq->fasta->length;
|
||||
|
||||
for (i = from ; i < to ; i++) {
|
||||
|
||||
int mask = seq->cell[i % len].mask;
|
||||
if (mask & EXCLUDE_MASK)
|
||||
continue;
|
||||
|
||||
int index = seq->cell[i % len].index; /* codon index */
|
||||
if ((index < 0) || (index > NB_CODONS)) /* invalid codon */
|
||||
continue;
|
||||
|
||||
int strand = ((mask & DIRECT_MASK) ? 0 : 1);
|
||||
|
||||
int nuc;
|
||||
for (nuc = 0 ; nuc < NB_NUC ; nuc++) {
|
||||
|
||||
float score = sCodonScore[nuc][index]; /* enrichment for symbol nuc */
|
||||
|
||||
/* ---------------------------------------------------------------- */
|
||||
/* important property : */
|
||||
/* if codon causes enrichment/depletion in X and if the gene is */
|
||||
/* located on the reverse strand then choice of this codon causes */
|
||||
/* enrichment/depletion in ~X on the direct strand. */
|
||||
/* Therefore for reverse strand codons we should increment the bin */
|
||||
/* associated to ~X */
|
||||
/* */
|
||||
|
||||
int bin = nuc;
|
||||
|
||||
if (mask & REVERSE_MASK) {
|
||||
char compl = BaseComplement(seq->alphabet->symbol[nuc]);
|
||||
bin = AlphaIndex(seq->alphabet, compl);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------- */
|
||||
/* increment bin associated to null, enrichment, depletion */
|
||||
|
||||
bin = 3 * bin + ((score == 0.) ? 0 : ((score > 0) ? 1 : 2));
|
||||
|
||||
count[bin][strand] += increment;
|
||||
}
|
||||
|
||||
count[3 * NB_NUC][strand] += increment; /* total # codons */
|
||||
}
|
||||
|
||||
}
|
||||
142
src/kimono/lxpack/src/kim_distance.c
Executable file
142
src/kimono/lxpack/src/kim_distance.c
Executable file
@ -0,0 +1,142 @@
|
||||
/* ==================================================== */
|
||||
/* @file: kim_distance.c */
|
||||
/* general utilities functions */
|
||||
/* @history: */
|
||||
/* @+ Apr. 97 <AV> first draft */
|
||||
/* ==================================================== */
|
||||
|
||||
#include <ctype.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include <math.h>
|
||||
|
||||
#include "kimono.h"
|
||||
|
||||
#define SQRTF(x) (float) sqrt((float) x)
|
||||
#define FABSF(x) (float) fabs((float) x)
|
||||
|
||||
/* ---------------------- */
|
||||
/* API */
|
||||
/* ---------------------- */
|
||||
|
||||
/*
|
||||
* for all distance functions :
|
||||
* int bins1[], int bins2[] : count distributions
|
||||
* int nbins : total number of bins
|
||||
* int ibin : if < 0 : compute distance using all bins
|
||||
* : if >= 0 : compute distance only for ibin (partial distance)
|
||||
*/
|
||||
|
||||
/* ---------------------- */
|
||||
/* chisquare distance */
|
||||
|
||||
float ChisTwo(int bins1[], int bins2[], int nbins, int ibin)
|
||||
{
|
||||
int j, jmin, jmax;
|
||||
float num, s1, s2, c1, c2, sj, dist;
|
||||
|
||||
s1 = s2 = 0.;
|
||||
for (j = 0 ; j < nbins ; j++) {
|
||||
s1 += bins1[j];
|
||||
s2 += bins2[j];
|
||||
}
|
||||
|
||||
if (s1 == 0.) s1 = 1.0;
|
||||
if (s2 == 0.) s2 = 1.0;
|
||||
|
||||
c1 = SQRTF(s2/s1);
|
||||
c2 = SQRTF(s1/s2);
|
||||
|
||||
jmin = (ibin < 0 ? 0 : ibin);
|
||||
jmax = (ibin < 0 ? nbins : ibin + 1);
|
||||
|
||||
dist = 0.0;
|
||||
|
||||
for (j = jmin ; j < jmax ; j++) {
|
||||
sj = bins1[j] + bins2[j];
|
||||
if (sj == 0.) sj = 1.;
|
||||
num = (c1 * (float) bins1[j]) - (c2 * (float) bins2[j]);
|
||||
dist += (num * num) / sj;
|
||||
}
|
||||
|
||||
return SQRTF(dist);
|
||||
}
|
||||
|
||||
/* ---------------------- */
|
||||
/* euclidian distance */
|
||||
|
||||
float Euclid(int bins1[], int bins2[], int nbins, int ibin)
|
||||
{
|
||||
int j, jmin, jmax;
|
||||
float num, s1, s2, dist;
|
||||
|
||||
s1 = s2 = 0.;
|
||||
for (j = 0 ; j < nbins ; j++) {
|
||||
s1 += bins1[j];
|
||||
s2 += bins2[j];
|
||||
}
|
||||
|
||||
if (s1 == 0.) s1 = 1.0;
|
||||
if (s2 == 0.) s2 = 1.0;
|
||||
|
||||
jmin = (ibin < 0 ? 0 : ibin);
|
||||
jmax = (ibin < 0 ? nbins : ibin + 1);
|
||||
|
||||
dist = 0.0;
|
||||
|
||||
for (j = jmin ; j < jmax ; j++) {
|
||||
num = ((float) bins1[j]/s1) - ((float) bins2[j]/s2);
|
||||
dist += num*num;
|
||||
}
|
||||
|
||||
return SQRTF(dist);
|
||||
}
|
||||
|
||||
/* ---------------------- */
|
||||
/* hellinger distance */
|
||||
|
||||
float HellTwo(int bins1[], int bins2[], int nbins, int ibin)
|
||||
{
|
||||
int j, jmin, jmax;
|
||||
float num, s1, s2, dist;
|
||||
|
||||
s1 = s2 = 0.;
|
||||
for (j = 0 ; j < nbins ; j++) {
|
||||
s1 += bins1[j];
|
||||
s2 += bins2[j];
|
||||
}
|
||||
|
||||
if (s1 == 0.) s1 = 1.0;
|
||||
if (s2 == 0.) s2 = 1.0;
|
||||
|
||||
jmin = (ibin < 0 ? 0 : ibin);
|
||||
jmax = (ibin < 0 ? nbins : ibin + 1);
|
||||
|
||||
dist = 0.0;
|
||||
|
||||
for (j = jmin ; j < jmax ; j++) {
|
||||
num = SQRTF((float) bins1[j]/s1) - SQRTF((float) bins2[j]/s2);
|
||||
dist += num*num;
|
||||
}
|
||||
|
||||
return SQRTF(dist);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* compute skew sign for two-binned data */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
int SignTwoBins(int bins1[], int bins2[]) {
|
||||
|
||||
int s1, s2;
|
||||
|
||||
s1 = bins1[0] + bins1[1];
|
||||
s2 = bins2[0] + bins2[1];
|
||||
|
||||
if (s1 == 0) s1 = 1;
|
||||
if (s2 == 0) s2 = 1;
|
||||
|
||||
return ( (((float) bins1[0] / (float) s1) >= ((float) bins2[0] / (float) s2))
|
||||
? 1 : -1);
|
||||
}
|
||||
109
src/kimono/lxpack/src/kim_genetic.c
Normal file
109
src/kimono/lxpack/src/kim_genetic.c
Normal file
@ -0,0 +1,109 @@
|
||||
/* ---------------------------------------------------------------- */
|
||||
/* Copyright (c) Atelier de BioInformatique */
|
||||
/* @file: kim_genetic.c */
|
||||
/* @desc: bio. sequences utility functions */
|
||||
/* */
|
||||
/* @history: */
|
||||
/* @+ <Gloup> : Jan 96 : quick draft */
|
||||
/* ---------------------------------------------------------------- */
|
||||
|
||||
#include <ctype.h>
|
||||
#include <stdio.h>
|
||||
#include <string.h>
|
||||
|
||||
#include "kimono.h"
|
||||
|
||||
#define GENETIC_CODE_INSTANCE
|
||||
#include "Genetic.h"
|
||||
|
||||
static char sNuc[] = DNA_ALPHA;
|
||||
static char sAnuc[] = C_DNA_ALPHA;
|
||||
static char sGenNuc[] = GEN_NUC_ALPHA;
|
||||
static char sGenPro[] = GEN_PRO_ALPHA;
|
||||
static int sNucNum[5] = {0, 1, 2, 3, 3};
|
||||
|
||||
/* ---------------------------------------------------- */
|
||||
/* @Function : int BaseComplement */
|
||||
/* Purpose : return DNA/RNA-Iupac base complement */
|
||||
/* ---------------------------------------------------- */
|
||||
int BaseComplement(int ch)
|
||||
{
|
||||
char *c;
|
||||
|
||||
if (c = strchr(sNuc, ch))
|
||||
return sAnuc[(int) (c - sNuc)];
|
||||
else
|
||||
return ch;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------- */
|
||||
/* @Function : char * SeqComplement */
|
||||
/* Purpose : return sequence complement */
|
||||
/* ---------------------------------------------------- */
|
||||
char *SeqComplement(char *str)
|
||||
{
|
||||
char *s;
|
||||
|
||||
for (s = str ; *s ; s++)
|
||||
*s = BaseComplement(*s);
|
||||
|
||||
return str;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------- */
|
||||
/* @Static : int * sTranslateCodon */
|
||||
/* Purpose : translate codon -> aa */
|
||||
/* see bio_codon_translate */
|
||||
/* ---------------------------------------------------- */
|
||||
static int sTranslateCodon(char *codon, int *code)
|
||||
{
|
||||
int i, base, hash;
|
||||
char *p;
|
||||
|
||||
for (i = hash = 0 ; i < 3 ; i++) {
|
||||
if ((p = strchr(sGenNuc, *codon++)) != NULL) {
|
||||
base = ((int) (p - sGenNuc)) / 2;
|
||||
hash = (hash * 4) + sNucNum[base];
|
||||
}
|
||||
else {
|
||||
hash = 64; /* bad letter in codon */
|
||||
break; /* or incomplete codon */
|
||||
}
|
||||
}
|
||||
return (int) sGenPro[code[hash]];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------- */
|
||||
/* @Function : int * CodonTranslate */
|
||||
/* Purpose : return amino-acid */
|
||||
/* input: codon char* 3 bases (in GEN_NUC_ALPHA) */
|
||||
/* codid int (see Genetic.h) */
|
||||
/* output: aa in one letter code (in GEN_PRO_ALPHA) */
|
||||
/* ---------------------------------------------------- */
|
||||
int CodonTranslate(char *codon, int codid)
|
||||
{
|
||||
return sTranslateCodon(codon, theGeneticCode[codid].code);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------- */
|
||||
/* @Function : int * SeqTranslate */
|
||||
/* Purpose : translate sequence to protein */
|
||||
/* ---------------------------------------------------- */
|
||||
char* SeqTranslate(char *seq, int codid)
|
||||
{
|
||||
int *code;
|
||||
char *ps, *ns;
|
||||
|
||||
if ((codid < 0) || (codid >= GEN_MAX_CODES))
|
||||
return NULL;
|
||||
|
||||
code = theGeneticCode[codid].code;
|
||||
|
||||
for (ns = ps = seq ; ns[0] && ns[1] && ns[2] ; ns += 3)
|
||||
*ps++ = sTranslateCodon(ns, code);
|
||||
|
||||
*ps = '\000';
|
||||
|
||||
return seq;
|
||||
}
|
||||
|
||||
309
src/kimono/lxpack/src/kim_indexer.c
Executable file
309
src/kimono/lxpack/src/kim_indexer.c
Executable file
@ -0,0 +1,309 @@
|
||||
/* ==================================================== */
|
||||
/* @file: kim_indexer.c */
|
||||
/* indexing functions */
|
||||
/* @history: */
|
||||
/* @+ Jul. 06 <AV> first draft */
|
||||
/* ==================================================== */
|
||||
|
||||
#include <ctype.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
|
||||
#include "kimono.h"
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* internal functions */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* codon index */
|
||||
/* codon: start of codon sequence */
|
||||
/* read left to right for direct strand */
|
||||
/* right to left for reverse strand */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static int sCodonIndex(char *codon, Alphabet *alpha, int strand)
|
||||
{
|
||||
int i, code;
|
||||
|
||||
code = 0;
|
||||
|
||||
for (i = 0 ; i < 3 ; i++) { /* loop on codon positions */
|
||||
|
||||
char symb;
|
||||
|
||||
if (strand > 0) {
|
||||
symb = codon[i]; /* move to left */
|
||||
}
|
||||
else {
|
||||
symb = codon[-i]; /* move to right */
|
||||
symb = BaseComplement(symb); /* complement */
|
||||
}
|
||||
|
||||
int k = AlphaIndex(alpha, symb);
|
||||
|
||||
if (k < 0)
|
||||
return -1; /* invalid symbol */
|
||||
|
||||
code = (code << SHIFT_NUC) | k; /* encode codon */
|
||||
}
|
||||
|
||||
return code;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* basic sequence indexing */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static void sBasicIndexer(Sequence *seq) {
|
||||
int i;
|
||||
for (i = 0 ; i < seq->fasta->length ; i++) {
|
||||
seq->cell[i].index = AlphaIndex(seq->alphabet, seq->fasta->seq[i]);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* reset mask */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static void sSetMask(Sequence *seq, int mask) {
|
||||
int i;
|
||||
for (i = 0 ; i < seq->fasta->length ; i++) {
|
||||
seq->cell[i].mask = mask;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* mask masked symbol positions */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static void sMaskMaskedSymbol(Sequence *seq) {
|
||||
int i;
|
||||
for (i = 0 ; i < seq->fasta->length ; i++) {
|
||||
if (seq->fasta->seq[i] == MASKED_SYMBOL)
|
||||
seq->cell[i].mask |= EXCLUDE_MASK;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* mask overlaps */
|
||||
/* there is an overlap when a position is both on */
|
||||
/* direct and reverse strand. */
|
||||
/* this situation makes trouble since the index is */
|
||||
/* wrong on one strand. */
|
||||
/* note [AV] : overlaps on the same strand are not */
|
||||
/* detected yet but this situation is */
|
||||
/* not such a big trouble. */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static void sMaskOverlap(Sequence *seq) {
|
||||
int i;
|
||||
for (i = 0 ; i < seq->fasta->length ; i++) {
|
||||
if (seq->cell[i].mask & (DIRECT_MASK & REVERSE_MASK))
|
||||
seq->cell[i].mask |= EXCLUDE_MASK;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* API */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* no zone indexing */
|
||||
/* (no strand, no phase) */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
void NoZoneIndexer(Sequence *seq, SetOfIntervals *zones, int phase) {
|
||||
/*ARGSUSED*/
|
||||
|
||||
/* ---------------------------------- */
|
||||
/* assume everything is direct */
|
||||
|
||||
sSetMask(seq, DIRECT_MASK);
|
||||
|
||||
/* ---------------------------------- */
|
||||
/* exclude masked symbol */
|
||||
|
||||
sMaskMaskedSymbol(seq);
|
||||
|
||||
/* ---------------------------------- */
|
||||
/* just use basic indexer */
|
||||
|
||||
sBasicIndexer(seq);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* zone exclusion indexing */
|
||||
/* (no strand, no phase) */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
void ExcludeIndexer(Sequence *seq, SetOfIntervals *zones, int phase) {
|
||||
/*ARGSUSED*/
|
||||
|
||||
int i, j;
|
||||
Interval inter;
|
||||
|
||||
/* ---------------------------------- */
|
||||
/* assume everything is direct */
|
||||
|
||||
sSetMask(seq, DIRECT_MASK);
|
||||
|
||||
/* ---------------------------------- */
|
||||
/* mask zone positions */
|
||||
|
||||
for (i = 0; i < zones->size ; i++) {
|
||||
inter = zones->interval[i];
|
||||
for (j = inter.from ; j <= inter.to ; j++)
|
||||
seq->cell[j].mask |= EXCLUDE_MASK;
|
||||
}
|
||||
|
||||
/* ---------------------------------- */
|
||||
/* exclude masked symbol */
|
||||
|
||||
sMaskMaskedSymbol(seq);
|
||||
|
||||
/* ---------------------------------- */
|
||||
/* then use basic indexer */
|
||||
|
||||
sBasicIndexer(seq);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* gene indexing */
|
||||
/* (strand, no phase) */
|
||||
/* note: alpha is unused */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
void GeneIndexer(Sequence *seq, SetOfIntervals *zones, int phase) {
|
||||
/*ARGSUSED*/
|
||||
|
||||
int i;
|
||||
|
||||
/* ---------------------------------- */
|
||||
/* first reset mask, excluding all */
|
||||
|
||||
sSetMask(seq, EXCLUDE_MASK);
|
||||
|
||||
/* ---------------------------------- */
|
||||
/* then unmask start of genes */
|
||||
|
||||
for (i = 0; i < zones->size ; i++) {
|
||||
Interval inter = zones->interval[i];
|
||||
int pos = (inter.strand > 0 ? inter.from : inter.to);
|
||||
int mask = (inter.strand > 0 ? DIRECT_MASK : REVERSE_MASK);
|
||||
seq->cell[pos].mask = (seq->cell[pos].mask & INCLUDE_MASK) | mask;
|
||||
seq->cell[pos].index = (inter.strand > 0 ? 0 : 1);
|
||||
}
|
||||
|
||||
/* ---------------------------------- */
|
||||
/* finally, exclude overlaps */
|
||||
/* when two genes start at same pos */
|
||||
|
||||
sMaskOverlap(seq);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* phased nucleotide indexing */
|
||||
/* phase: binary mask indicating valid phases */
|
||||
/* 1[01] : 1 ; 2[10] : 2 ; 4[100] : 3 */
|
||||
/* or any combination eg: 3[11] : 12 */
|
||||
/* 7[111] : 123 */
|
||||
/* ----------------------------------------------- */
|
||||
void PhaseIndexer(Sequence *seq, SetOfIntervals *zones, int phase) {
|
||||
/*ARGSUSED*/
|
||||
|
||||
int i, j;
|
||||
|
||||
/* ---------------------------------- */
|
||||
/* first reset mask, excluding all */
|
||||
|
||||
sSetMask(seq, EXCLUDE_MASK);
|
||||
|
||||
/* ---------------------------------- */
|
||||
/* then unmask valid positions */
|
||||
|
||||
for (i = 0; i < zones->size ; i++) {
|
||||
Interval inter = zones->interval[i];
|
||||
int iphase = 0;
|
||||
if (inter.strand > 0) {
|
||||
for (j = inter.from ; j <= inter.to ; j++) {
|
||||
if (((0x1 << iphase) & phase) != 0)
|
||||
seq->cell[j].mask = (seq->cell[j].mask & INCLUDE_MASK) | DIRECT_MASK;
|
||||
iphase = (iphase + 1) % 3;
|
||||
}
|
||||
}
|
||||
else {
|
||||
for (j = inter.to ; j >= inter.from ; j--) {
|
||||
if (((0x1 << iphase) & phase) != 0)
|
||||
seq->cell[j].mask = (seq->cell[j].mask & INCLUDE_MASK) | REVERSE_MASK;
|
||||
iphase = (iphase + 1) % 3;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------- */
|
||||
/* exclude masked symbol */
|
||||
|
||||
sMaskMaskedSymbol(seq);
|
||||
|
||||
/* ---------------------------------- */
|
||||
/* exclude overlaps */
|
||||
|
||||
sMaskOverlap(seq);
|
||||
|
||||
/* ------------------------------------------ */
|
||||
/* finally, use basic indexer */
|
||||
|
||||
sBasicIndexer(seq);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* codon indexing */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
void CodonIndexer(Sequence *seq, SetOfIntervals *zones, int phase) {
|
||||
int i, j;
|
||||
|
||||
/* ---------------------------------- */
|
||||
/* reset mask, excluding all */
|
||||
|
||||
sSetMask(seq, EXCLUDE_MASK);
|
||||
|
||||
/* ------------------------------------------ */
|
||||
/* now unmask phase 1 and compute codon index */
|
||||
|
||||
for (i = 0; i < zones->size ; i++) {
|
||||
Interval inter = zones->interval[i];
|
||||
int iphase = 0;
|
||||
if (inter.strand > 0) {
|
||||
for (j = inter.from ; j <= inter.to - 2 ; j++) { // ZZ to - 2
|
||||
if (iphase == 0) {
|
||||
int k = sCodonIndex(seq->fasta->seq + j, seq->alphabet, 1);
|
||||
seq->cell[j].mask = (seq->cell[j].mask & INCLUDE_MASK) | DIRECT_MASK;
|
||||
seq->cell[j].index = k;
|
||||
}
|
||||
iphase = (iphase + 1) % 3;
|
||||
}
|
||||
}
|
||||
else {
|
||||
for (j = inter.to ; j >= inter.from + 2 ; j--) { // ZZ from + 2
|
||||
if (iphase == 0) {
|
||||
int k = sCodonIndex(seq->fasta->seq + j, seq->alphabet, -1);
|
||||
seq->cell[j].mask = (seq->cell[j].mask & INCLUDE_MASK) | REVERSE_MASK;
|
||||
seq->cell[j].index = k;
|
||||
}
|
||||
iphase = (iphase + 1) % 3;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------- */
|
||||
/* exclude overlaps */
|
||||
|
||||
sMaskOverlap(seq);
|
||||
|
||||
}
|
||||
|
||||
|
||||
56
src/kimono/lxpack/src/kim_mixer.c
Executable file
56
src/kimono/lxpack/src/kim_mixer.c
Executable file
@ -0,0 +1,56 @@
|
||||
/* ==================================================== */
|
||||
/* @file: kim_mixer.c */
|
||||
/* count mixing functions */
|
||||
/* @history: */
|
||||
/* @+ Apr. 97 <AV> first draft */
|
||||
/* ==================================================== */
|
||||
|
||||
#include <ctype.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
|
||||
#include "kimono.h"
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* basic mixer */
|
||||
/* */
|
||||
/* this mixer just pool the two strands on both */
|
||||
/* sides */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
void BasicMixer(int left[][2], int right[][2],
|
||||
int *countLeft, int *countRight,
|
||||
int nbins) {
|
||||
int i;
|
||||
|
||||
for (i = 0 ; i <= nbins ; i++)
|
||||
countLeft[i] = countRight[i] = 0;
|
||||
|
||||
for (i = 0 ; i <= nbins ; i++) {
|
||||
countLeft[i] += left[i][0] + left[i][1]; /* leftDirect + leftReverse */
|
||||
countRight[i] += right[i][0] + right[i][1]; /* rightDirect + rightReverse */
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* cross mixer */
|
||||
/* */
|
||||
/* this mixer cross the two strands on both */
|
||||
/* sides */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
void CrossMixer(int left[][2], int right[][2],
|
||||
int *countLeft, int *countRight,
|
||||
int nbins) {
|
||||
int i;
|
||||
|
||||
for (i = 0 ; i <= nbins ; i++)
|
||||
countLeft[i] = countRight[i] = 0;
|
||||
|
||||
for (i = 0 ; i <= nbins ; i++) {
|
||||
countLeft[i] += left[i][0] + right[i][1]; /* leftDirect + rightReverse */
|
||||
countRight[i] += right[i][0] + left[i][1]; /* rightDirect + leftReverse */
|
||||
}
|
||||
}
|
||||
|
||||
87
src/kimono/lxpack/src/kim_sequence.c
Executable file
87
src/kimono/lxpack/src/kim_sequence.c
Executable file
@ -0,0 +1,87 @@
|
||||
/* ==================================================== */
|
||||
/* @file: kim_sequence.c */
|
||||
/* sequence handling */
|
||||
/* @history: */
|
||||
/* @+ Jul. 06 <AV> first draft */
|
||||
/* ==================================================== */
|
||||
|
||||
#include <ctype.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
|
||||
#include "kimono.h"
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* internal functions */
|
||||
/* -------------------------------------------- */
|
||||
static int sReallocCells(Sequence *seq) {
|
||||
SeqCell *buf;
|
||||
|
||||
buf = ( seq->cell
|
||||
? REALLOC(SeqCell, seq->cell, seq->fasta->length)
|
||||
: NEWN(SeqCell, seq->fasta->length));
|
||||
|
||||
if (! buf) {
|
||||
MemoryErreur("NewSequence", 2);
|
||||
return 0;
|
||||
}
|
||||
|
||||
seq->cell = buf;
|
||||
return 1;
|
||||
}
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* API */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* Sequence deallocation */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
Sequence *FreeSequence(Sequence *seq) {
|
||||
if (seq) {
|
||||
if (seq->alphabet) FreeAlphabet(seq->alphabet);
|
||||
if (seq->fasta) FreeFastaSequence(seq->fasta);
|
||||
if (seq->cell) FREE(seq->cell);
|
||||
FREE(seq);
|
||||
}
|
||||
return NULL;
|
||||
}
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* Sequence allocation */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
Sequence *NewSequence(Alphabet *alpha) {
|
||||
Sequence *seq;
|
||||
|
||||
if (! (seq = NEW(Sequence)))
|
||||
MemoryErreur("NewSequence", 2);
|
||||
|
||||
seq->alphabet = NULL;
|
||||
seq->fasta = NULL;
|
||||
seq->cell = NULL;
|
||||
|
||||
if (! (seq->alphabet = CopyAlphabet(alpha)))
|
||||
MemoryErreur("NewSequence", 2);
|
||||
|
||||
if (! (seq->fasta = NewFastaSequence()))
|
||||
MemoryErreur("NewSequence", 2);
|
||||
|
||||
return seq;
|
||||
}
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* read sequence */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
int ReadSequence(FILE *streamin, Sequence *seq) {
|
||||
int ok;
|
||||
|
||||
ok = ReadFastaSequence(streamin, seq->fasta)
|
||||
&& seq->fasta->ok
|
||||
&& sReallocCells(seq);
|
||||
|
||||
return ok;
|
||||
}
|
||||
82
src/kimono/lxpack/src/kim_util.c
Executable file
82
src/kimono/lxpack/src/kim_util.c
Executable file
@ -0,0 +1,82 @@
|
||||
/* ==================================================== */
|
||||
/* @file: kim_util.c */
|
||||
/* general utilities functions */
|
||||
/* @history: */
|
||||
/* @+ Apr. 97 <AV> first draft */
|
||||
/* ==================================================== */
|
||||
|
||||
#include <ctype.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
|
||||
#include "kimono.h"
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* error reporting */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
int Erreur(char *msg, int stat)
|
||||
{
|
||||
|
||||
fprintf(stderr, "*%s* [%d] %s\n", (stat > 0 ? "Error" : "Warning"),
|
||||
stat, msg);
|
||||
|
||||
if (stat > 0)
|
||||
exit(stat);
|
||||
|
||||
fflush(stderr);
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* memory error */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
int MemoryErreur(char *where, int stat)
|
||||
{
|
||||
char buffer[BUFSIZ];
|
||||
|
||||
sprintf(buffer, "Not enough memory in %s", where);
|
||||
|
||||
return Erreur(buffer, stat);
|
||||
}
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* open a file and assign it to stdin */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
int AssignToStdin(char *filename)
|
||||
{
|
||||
char buffer[256];
|
||||
|
||||
if (! freopen(filename, "r", stdin)) {
|
||||
sprintf(buffer, "cant open file %s to read", filename);
|
||||
return Erreur(buffer, -1);
|
||||
}
|
||||
|
||||
return 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------- */
|
||||
/* Trim leading spaces from string 'str' */
|
||||
/* ---------------------------------------------------- */
|
||||
char *StrTrimLeading(char *str)
|
||||
{
|
||||
char *sb, *sn;
|
||||
|
||||
if (! (str && isspace(*str)))
|
||||
return str;
|
||||
|
||||
for (sb = sn = str ; isspace(*sn) ; sn++)
|
||||
/* nop */ ;
|
||||
|
||||
while (*sn)
|
||||
*sb++ = *sn++;
|
||||
|
||||
*sb = '\000';
|
||||
|
||||
return str;
|
||||
}
|
||||
|
||||
98
src/kimono/lxpack/src/kim_zone.c
Executable file
98
src/kimono/lxpack/src/kim_zone.c
Executable file
@ -0,0 +1,98 @@
|
||||
/* ==================================================== */
|
||||
/* @file: kim_zone.c */
|
||||
/* zones handling */
|
||||
/* @history: */
|
||||
/* @+ Jul. 06 <AV> first draft */
|
||||
/* ==================================================== */
|
||||
|
||||
#include <ctype.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
|
||||
#include "kimono.h"
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* internal functions */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* API */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* free zones */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
SetOfIntervals *FreeZones(SetOfIntervals *set) {
|
||||
|
||||
if (set) {
|
||||
if (set->interval)
|
||||
FREE(set->interval);
|
||||
FREE(set);
|
||||
}
|
||||
|
||||
return NULL;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* read zones */
|
||||
/* note: zones are read as 1-based intervals */
|
||||
/* but stored as 0-based intervals */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
SetOfIntervals *ReadZones(int seqlength) {
|
||||
|
||||
int from, to;
|
||||
SetOfIntervals *set;
|
||||
Interval *tbuf;
|
||||
char buffer[BUFSIZ], err[BUFSIZ];
|
||||
char strand[2];
|
||||
|
||||
set = NEW(SetOfIntervals);
|
||||
set->capacity = 256; /* just to start with */
|
||||
set->size = 0;
|
||||
set->interval = NEWN(Interval, set->capacity);
|
||||
|
||||
while (fgets(buffer, sizeof(buffer), stdin)) {
|
||||
|
||||
StrTrimLeading(buffer);
|
||||
|
||||
if ( (*buffer == '#')
|
||||
|| (*buffer == '/')
|
||||
|| (strlen(buffer) == 0))
|
||||
continue;
|
||||
|
||||
if (sscanf(buffer, "%d%d%1s", &from, &to, strand) != 3) {
|
||||
(void) sprintf(err, "include buffer: invalid format : %s", buffer);
|
||||
Erreur(err, -1);
|
||||
// return FreeZones(set);
|
||||
continue;
|
||||
}
|
||||
|
||||
if ((from > to) || (from <= 0) || (to <= 0) || (to > seqlength)) {
|
||||
(void) sprintf(err, "include buffer: invalid from/to values : %s", buffer);
|
||||
Erreur(err, -1);
|
||||
// return FreeZones(set);
|
||||
continue;
|
||||
}
|
||||
|
||||
set->size++;
|
||||
|
||||
if (set->size >= set->capacity) {
|
||||
set->capacity *= 2;
|
||||
if (! (tbuf = REALLOC(Interval, set->interval, set->capacity))) {
|
||||
MemoryErreur("ReadZones", 2);
|
||||
return FreeZones(set);
|
||||
}
|
||||
set->interval = tbuf;
|
||||
}
|
||||
|
||||
tbuf = set->interval + set->size - 1;
|
||||
tbuf->from = from - 1;
|
||||
tbuf->to = to - 1;
|
||||
tbuf->strand = (strcmp(strand, "D") && strcmp(strand, "+") ? -1 : +1);
|
||||
}
|
||||
|
||||
return set;
|
||||
}
|
||||
205
src/kimono/lxpack/src/kimfit_main.c
Executable file
205
src/kimono/lxpack/src/kimfit_main.c
Executable file
@ -0,0 +1,205 @@
|
||||
/* ==================================================== */
|
||||
/* @file: kimfit_main.c */
|
||||
/* triangle fit program */
|
||||
/* @history: */
|
||||
/* @+ Apr. 97 <AV> first draft */
|
||||
/* ==================================================== */
|
||||
|
||||
#include <ctype.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include <math.h>
|
||||
|
||||
#include "kimono.h"
|
||||
|
||||
#ifndef BUFSIZ
|
||||
#define BUFSIZ 1024
|
||||
#endif
|
||||
|
||||
#define NBEST 2
|
||||
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* look for best window on signal */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static float sLookBest(float *x, int n, int iwidth) {
|
||||
int i;
|
||||
float sum, best;
|
||||
|
||||
if (iwidth > n) iwidth = n;
|
||||
|
||||
sum = 0.;
|
||||
|
||||
for (i = 0 ; i < iwidth ; i++) {
|
||||
sum += x[i];
|
||||
}
|
||||
|
||||
best = sum;
|
||||
|
||||
for (i = 1 ; i < n ; i++) {
|
||||
|
||||
sum -= x[i-1];
|
||||
sum += x[(i+iwidth-1) % n];
|
||||
|
||||
if (sum > best)
|
||||
best = sum;
|
||||
|
||||
}
|
||||
|
||||
return best;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* fit triangle on signal */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static int sFitTriangle(float *x, int n, int iwidth, float height) {
|
||||
int i, j, fitpos;
|
||||
|
||||
if (iwidth <= 1) iwidth = 2;
|
||||
|
||||
/* -------------------------- */
|
||||
/* fit sliding triangle */
|
||||
|
||||
for (i = 0 ; i < n ; i++) {
|
||||
|
||||
int j;
|
||||
float sum, fitval;
|
||||
|
||||
sum = 0.;
|
||||
|
||||
for (j = 0 ; j < iwidth ; j++) {
|
||||
int k = (j < iwidth/2 ? j : iwidth - j);
|
||||
float val = x[(i+j) % n] - (2. * (float) k / (float) iwidth * height);
|
||||
sum += val * val;
|
||||
}
|
||||
|
||||
if ((i == 0) || (sum < fitval)) {
|
||||
fitval = sum;
|
||||
fitpos = i;
|
||||
}
|
||||
}
|
||||
|
||||
fitpos = (fitpos + (iwidth /2)) % n;
|
||||
|
||||
return fitpos;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* zero signal */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static void sZero(float *x, int from, int to, int n) {
|
||||
int i;
|
||||
|
||||
for (i = from ; i < to ; i++) {
|
||||
x[(i+n) % n] = 0.;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* integrate signal */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static float sIntegrate(float *x, int from, int to, int n) {
|
||||
int i;
|
||||
float sum;
|
||||
|
||||
sum = 0.;
|
||||
for (i = from ; i < to ; i++) {
|
||||
sum += x[(i+n) % n];
|
||||
}
|
||||
|
||||
return sum;
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* main */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
main() {
|
||||
|
||||
int i, npt, nread, seqlength, window, iwidth;
|
||||
float sum, tsum, best;
|
||||
float *x, *xx;
|
||||
char buffer[BUFSIZ];
|
||||
|
||||
/* --------------------------------------------- */
|
||||
/* first line : npt, seqlength, window */
|
||||
|
||||
fgets(buffer, sizeof(buffer), stdin);
|
||||
|
||||
if ( (sscanf(buffer, "%d%d%d", &npt, &seqlength, &window) != 3)
|
||||
|| ((npt <= 0) || (seqlength <= 0) || (window <= 0))) {
|
||||
fprintf(stderr, "bad header (npt seqlength window) %s\n", buffer);
|
||||
exit(1);
|
||||
}
|
||||
|
||||
/* --------------------------------------------- */
|
||||
/* allocate buffer */
|
||||
|
||||
if (! (x = NEWN(float, npt))) {
|
||||
MemoryErreur("main", 2);
|
||||
}
|
||||
|
||||
if (! (xx = NEWN(float, npt))) {
|
||||
MemoryErreur("main", 2);
|
||||
}
|
||||
|
||||
/* --------------------------------------------- */
|
||||
/* other lines : data */
|
||||
|
||||
nread = 0;
|
||||
while (fscanf(stdin, "%f", x + nread) == 1) {
|
||||
if (nread > npt) {
|
||||
(void) sprintf(buffer, "too many points (declared=%d)", npt);
|
||||
Erreur(buffer, 3);
|
||||
}
|
||||
nread++;
|
||||
}
|
||||
|
||||
if (nread != npt) {
|
||||
(void) sprintf(buffer, "number of points does not match : declared=%d actual=%d", npt, nread);
|
||||
Erreur(buffer, 0);
|
||||
}
|
||||
|
||||
/* --------------------------------------------- */
|
||||
/* print header */
|
||||
|
||||
printf("seqlength : %d\n", seqlength);
|
||||
printf("window : %d\n", window);
|
||||
|
||||
/* --------------------------------------------- */
|
||||
/* fit */
|
||||
|
||||
iwidth = (int) ((float) window * (float) npt / (float) seqlength);
|
||||
|
||||
sum = sIntegrate(x, 0, npt, npt);
|
||||
|
||||
for (i = 1 ; i < npt ; i++)
|
||||
xx[i] = x[i];
|
||||
|
||||
|
||||
for (i = 0 ; i < NBEST ; i++) {
|
||||
|
||||
tsum = sLookBest(xx, npt, iwidth);
|
||||
|
||||
best = sFitTriangle(xx, npt, iwidth, tsum / (iwidth /2));
|
||||
|
||||
tsum = sIntegrate(x, best - iwidth/2, best + iwidth/2, npt);
|
||||
|
||||
best = sFitTriangle(xx, npt, iwidth, tsum / (iwidth /2));
|
||||
|
||||
tsum = sIntegrate(x, best - iwidth/2, best + iwidth/2, npt);
|
||||
|
||||
sZero(xx, best - iwidth/2, best + iwidth/2, npt);
|
||||
|
||||
printf("best[%d] : %.0f %.0f %.2f\n", i, best, 1 + best * (float) seqlength / (float) npt,
|
||||
tsum * 100. / sum);
|
||||
}
|
||||
|
||||
exit(0);
|
||||
}
|
||||
132
src/kimono/lxpack/src/kimono_help.c
Executable file
132
src/kimono/lxpack/src/kimono_help.c
Executable file
@ -0,0 +1,132 @@
|
||||
/* ==================================================== */
|
||||
/* @file: kim_help.c */
|
||||
/* Help & usage */
|
||||
/* @history: */
|
||||
/* @+ Apr. 97 <AV> first draft */
|
||||
/* ==================================================== */
|
||||
|
||||
#include <ctype.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
|
||||
#include "kimono.h"
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* printout help */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
#define PP fprintf(stdout,
|
||||
|
||||
void PrintHelp()
|
||||
{
|
||||
PP "------------------------------------------ \n");
|
||||
PP " Kimono Version 0.2 Nov. 05 \n");
|
||||
PP "------------------------------------------ \n");
|
||||
PP "synopsis : \n");
|
||||
PP " \n");
|
||||
PP "usage: kimono [options] [fastafile] \n");
|
||||
PP "------------------------------------------ \n");
|
||||
PP "options: \n");
|
||||
PP "----- General options ------------------ \n");
|
||||
PP "-a string : use symbols from string as [A]lphabet\n");
|
||||
PP " default = acgt \n");
|
||||
PP " \n");
|
||||
PP "-b string : exclude symbols from string \n");
|
||||
PP " in practice replace symbols from \n");
|
||||
PP " string by X's \n");
|
||||
PP " default = <none> \n");
|
||||
PP " \n");
|
||||
PP "-c selector : use selector as [C]ount selector \n");
|
||||
PP " selector: \n");
|
||||
PP " count : counts symbols \n");
|
||||
PP " cumul : cumulative plot \n");
|
||||
PP " codon : count codons \n");
|
||||
PP " genes : count genes \n");
|
||||
PP " default = count \n");
|
||||
PP " \n");
|
||||
PP "-e code : g[E]netic code \n");
|
||||
PP " code: \n");
|
||||
PP " 0 : Universal \n");
|
||||
PP " 1 : mito yeast \n");
|
||||
PP " 2 : mito vertebrate \n");
|
||||
PP " 3 : filamentous fungi \n");
|
||||
PP " 4 : mito insects & platyhelminthes\n");
|
||||
PP " 5 : Candida cylindracea \n");
|
||||
PP " 6 : Ciliata \n");
|
||||
PP " 7 : Euplotes \n");
|
||||
PP " 8 : mito echinoderms \n");
|
||||
PP " default = 0 \n");
|
||||
PP " \n");
|
||||
PP "-d selector : use selector as [D]istance \n");
|
||||
PP " selector: \n");
|
||||
PP " chi : chi square distance \n");
|
||||
PP " hell : hellinger distance \n");
|
||||
PP " euclid : euclidian distance \n");
|
||||
PP " default = chi \n");
|
||||
PP " \n");
|
||||
PP "-h : [H]elp - print <this> help \n");
|
||||
PP " \n");
|
||||
PP "-i filename : genes [I]nclude file \n");
|
||||
PP " default = <none> \n");
|
||||
PP " \n");
|
||||
PP "-m selector : use selector as [M]ixer \n");
|
||||
PP " selector: \n");
|
||||
PP " basic : basic mixer \n");
|
||||
PP " cross : cross strands mixer \n");
|
||||
PP " default = basic \n");
|
||||
PP " \n");
|
||||
PP "-p [1[2[3]]] : [P]hase(s) for counts \n");
|
||||
PP " default = <nophase> \n");
|
||||
PP " \n");
|
||||
PP "-P [1[2[3]]] : [P]hase(s) for counts \n");
|
||||
PP " same as -p + base complement on \n");
|
||||
PP " reverse strand \n");
|
||||
PP " default = <nophase> <nocomplement>\n");
|
||||
PP " \n");
|
||||
PP "-s step : window [S]tep in bp \n");
|
||||
PP " default = 1000 \n");
|
||||
PP " \n");
|
||||
PP "-w width : window [W]idth in bp \n");
|
||||
PP " default = <see -W> \n");
|
||||
PP " \n");
|
||||
PP "-W %%width : window [W]idth in %% of chromosome length\n");
|
||||
PP " default = 25%% \n");
|
||||
PP " \n");
|
||||
PP "-x filename : genes e[X]clude file \n");
|
||||
PP " default = <none> \n");
|
||||
PP " \n");
|
||||
PP "------------------------------------------ \n");
|
||||
PP "file formats \n");
|
||||
PP " \n");
|
||||
PP "fastafile: fasta format \n");
|
||||
PP "include/exclude files: one gene per line : \n");
|
||||
PP " from to strand [comments] \n");
|
||||
PP " from, to : integers (from <= to) \n");
|
||||
PP " strand : C|D|+|- \n");
|
||||
PP "-------------------------------- \n");
|
||||
PP " see documentation for more information \n");
|
||||
PP "-------------------------------- \n");
|
||||
PP " \n");
|
||||
}
|
||||
|
||||
#undef PP
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* printout usage and exit */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
#define PP fprintf(stderr,
|
||||
|
||||
int ExitUsage(int stat)
|
||||
{
|
||||
PP "usage: \n");
|
||||
PP "type \"kimono -h\" for help \n");
|
||||
|
||||
if (stat)
|
||||
exit(stat);
|
||||
|
||||
return stat;
|
||||
}
|
||||
|
||||
#undef PP
|
||||
800
src/kimono/lxpack/src/kimono_main.c
Executable file
800
src/kimono/lxpack/src/kimono_main.c
Executable file
@ -0,0 +1,800 @@
|
||||
/* ==================================================== */
|
||||
/* @File kimono_main.c */
|
||||
/* @history: */
|
||||
/* @+ Apr. 97 <Gloup> first draft */
|
||||
/* ==================================================== */
|
||||
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
|
||||
#include "Genetic.h"
|
||||
#include "fasta_io.h"
|
||||
#include "kimono.h"
|
||||
|
||||
#ifdef HAS_UNISTD_H
|
||||
#include HAS_UNISTD_H
|
||||
#endif
|
||||
|
||||
#ifdef HAS_GETOPT_H
|
||||
#include HAS_GETOPT_H
|
||||
#endif
|
||||
|
||||
#ifndef FILENAME_MAX
|
||||
#define FILENAME_MAX 1024 /* max # of characters in a path name */
|
||||
#endif
|
||||
|
||||
#ifndef BUFSIZ
|
||||
#define BUFSIZ 1024
|
||||
#endif
|
||||
|
||||
#define SELECTOR_NONE 0
|
||||
#define SELECTOR_COUNT 1
|
||||
#define SELECTOR_CUMUL 2
|
||||
#define SELECTOR_CODON 3
|
||||
#define SELECTOR_GENE 4
|
||||
|
||||
#define DISTANCE_NONE 0
|
||||
#define DISTANCE_CHI 1
|
||||
#define DISTANCE_EUCLID 2
|
||||
#define DISTANCE_HELL 3
|
||||
|
||||
#define MIXER_NONE 0
|
||||
#define MIXER_BASIC 1
|
||||
#define MIXER_CROSS 2
|
||||
|
||||
#define DFT_WINDOW -25 /* aka 25% */
|
||||
#define DFT_STEP 1000
|
||||
|
||||
#define CUMUL_NORM 1.0e6
|
||||
|
||||
#define DEBUG 0
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* macros */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* globals */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
static char sDNA[] = KIM_DNA;
|
||||
|
||||
static float sCodonScore[NB_NUC][NB_CODONS];
|
||||
|
||||
/* -------------------------------------------- */
|
||||
/* getopt globals */
|
||||
/* -------------------------------------------- */
|
||||
|
||||
extern char *optarg;
|
||||
extern int optind;
|
||||
|
||||
/* =============================================== */
|
||||
/* Utilities Functions */
|
||||
/* =============================================== */
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* make a count selector */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static int sSetSelector(char *buf) {
|
||||
|
||||
if (! strcmp(buf, "count"))
|
||||
return SELECTOR_COUNT;
|
||||
|
||||
if (! strcmp(buf, "cumul"))
|
||||
return SELECTOR_CUMUL;
|
||||
|
||||
if (! strcmp(buf, "codon"))
|
||||
return SELECTOR_CODON;
|
||||
|
||||
if (! strcmp(buf, "genes"))
|
||||
return SELECTOR_GENE;
|
||||
|
||||
return SELECTOR_NONE;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* get the count selector */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static char *sGetSelector(int selector) {
|
||||
|
||||
switch (selector) {
|
||||
|
||||
case SELECTOR_COUNT : return "count";
|
||||
case SELECTOR_CUMUL : return "cumul";
|
||||
case SELECTOR_CODON : return "codon";
|
||||
case SELECTOR_GENE : return "genes";
|
||||
|
||||
}
|
||||
|
||||
return "<unknown>";
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* make a distance selector */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static int sSetDistance(char *buf) {
|
||||
|
||||
if (! strcmp(buf, "chi"))
|
||||
return DISTANCE_CHI;
|
||||
|
||||
if (! strcmp(buf, "euclid"))
|
||||
return DISTANCE_EUCLID;
|
||||
|
||||
if (! strcmp(buf, "hell"))
|
||||
return DISTANCE_HELL;
|
||||
|
||||
return DISTANCE_NONE;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* get the count selector */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static char *sGetDistance(int selector) {
|
||||
|
||||
switch (selector) {
|
||||
|
||||
case DISTANCE_CHI : return "chi";
|
||||
case DISTANCE_EUCLID : return "euclid";
|
||||
case DISTANCE_HELL : return "hell";
|
||||
}
|
||||
|
||||
return "<unknown>";
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* make a mixer selector */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static int sSetMixer(char *buf) {
|
||||
|
||||
if (! strcmp(buf, "basic"))
|
||||
return MIXER_BASIC;
|
||||
|
||||
if (! strcmp(buf, "cross"))
|
||||
return MIXER_CROSS;
|
||||
|
||||
return MIXER_NONE;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* get the mixer selector */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static char *sGetMixer(int selector) {
|
||||
|
||||
switch (selector) {
|
||||
|
||||
case MIXER_BASIC : return "basic";
|
||||
case MIXER_CROSS : return "cross";
|
||||
}
|
||||
|
||||
return "<unknown>";
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* make a phase mask */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static int sGetPhaseMask(char *buf) {
|
||||
|
||||
int mask = 0x0;
|
||||
|
||||
if (strchr(buf, '1'))
|
||||
mask |= 0x1;
|
||||
|
||||
if (strchr(buf, '2'))
|
||||
mask |= 0x2;
|
||||
|
||||
if (strchr(buf, '3'))
|
||||
mask |= 0x4;
|
||||
|
||||
return mask;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* uppercase string */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static char *sUpper(char *buf) {
|
||||
|
||||
char *c;
|
||||
|
||||
for (c = buf ; *c ; c++) {
|
||||
*c = UPPER(*c);
|
||||
}
|
||||
|
||||
return buf;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* replace symbols in alphaOut by MASKED_SYMBOL */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static char *sExcludeFromSeq(char *buf, char *alphaOut, char maskSymbol) {
|
||||
|
||||
char *c;
|
||||
|
||||
if (! *alphaOut)
|
||||
return buf;
|
||||
|
||||
for (c = buf ; *c ; c++) {
|
||||
if (strchr(alphaOut, *c))
|
||||
*c = maskSymbol;
|
||||
}
|
||||
|
||||
return buf;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* check alphabet */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
static int sCheckAlphabet(char *alpha) {
|
||||
|
||||
char *c;
|
||||
for (c = alpha ; *c ; c++) {
|
||||
if (! strchr(sDNA, *c)) /* invalid symbol */
|
||||
return 0;
|
||||
if (strchr(c+1, *c)) /* duplicate symbol */
|
||||
return 0;
|
||||
}
|
||||
|
||||
return strlen(alpha);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------- */
|
||||
/* main */
|
||||
/* ----------------------------------------------- */
|
||||
|
||||
main(int argn, char *argv[])
|
||||
{
|
||||
int i, j, carg, errflag;
|
||||
int gflag, iflag, xflag, dflag, code;
|
||||
int selector, mixer, phase;
|
||||
int pos, len, step, window, nopen, nvalid, nbins, sign;
|
||||
int allLeft[3 * NB_NUC + 1][2], allRight[3 * NB_NUC + 1][2],
|
||||
countLeft[3 * NB_NUC + 1], countRight[3 * NB_NUC + 1],
|
||||
tmpLeft[2], tmpRight[2];
|
||||
float skew, sum;
|
||||
|
||||
Alphabet *alpha;
|
||||
Sequence *seq;
|
||||
SetOfIntervals *zones;
|
||||
char alphaOut[128];
|
||||
char inputfile[FILENAME_MAX], includefile[FILENAME_MAX];
|
||||
|
||||
|
||||
IndexFunction indexingFunction;
|
||||
CountFunction countingFunction;
|
||||
DistFunction distanceFunction;
|
||||
MixFunction mixingFunction;
|
||||
|
||||
|
||||
/* ---------------------------- */
|
||||
/* defaut options */
|
||||
|
||||
errflag = 0;
|
||||
selector = SELECTOR_COUNT; /* mono countings */
|
||||
mixer = MIXER_BASIC; /* basic mixer */
|
||||
dflag = DISTANCE_CHI; /* chi-square distance */
|
||||
iflag = 0; /* no inclusion */
|
||||
phase = 0x7; /* all phases */
|
||||
xflag = 0; /* no exclusion */
|
||||
code = 0; /* universal code */
|
||||
step = DFT_STEP;
|
||||
window = DFT_WINDOW;
|
||||
|
||||
alpha = NucleicAlphabet();
|
||||
|
||||
alphaOut[0] = '\000';
|
||||
|
||||
(void) strcpy(inputfile, "<stdin>");
|
||||
(void) strcpy(includefile, "<none>");
|
||||
|
||||
/* ---------------------------- */
|
||||
/* parse cmdline arguments */
|
||||
|
||||
while ((carg = getopt(argn, argv, "a:b:c:d:e:g:hi:m:p:s:w:W:x:")) != -1) {
|
||||
|
||||
switch(carg) {
|
||||
|
||||
case 'a' : /* [a]lphabet */
|
||||
(void) FreeAlphabet(alpha);
|
||||
alpha = NewAlphabet(sUpper(optarg));
|
||||
if (! sCheckAlphabet(alpha->symbol)) {
|
||||
Erreur("bad alphabet", -1);
|
||||
errflag++;
|
||||
}
|
||||
break;
|
||||
|
||||
case 'b' : /* excluded symbols */
|
||||
(void) strcpy(alphaOut, sUpper(optarg));
|
||||
break;
|
||||
|
||||
|
||||
case 'c' : /* [c]ount selector */
|
||||
selector = sSetSelector(optarg);
|
||||
if (selector == SELECTOR_NONE) {
|
||||
Erreur("bad count selector", -1);
|
||||
errflag++;
|
||||
}
|
||||
break;
|
||||
|
||||
case 'e': /* g[e]netic code */
|
||||
if ( (sscanf(optarg, "%d", &code) != 1)
|
||||
|| (code < 0) || (code > GEN_MAX_CODES)) {
|
||||
Erreur("bad code value: -e (0-8)", -1);
|
||||
errflag++;
|
||||
}
|
||||
else {
|
||||
InitCodonSkewCounter(code);
|
||||
}
|
||||
break;
|
||||
|
||||
case 'd' : /* [d]istance selector */
|
||||
dflag = sSetDistance(optarg);
|
||||
if (dflag == DISTANCE_NONE) {
|
||||
Erreur("bad distance selector", -1);
|
||||
errflag++;
|
||||
}
|
||||
break;
|
||||
|
||||
case 'h' : /* help */
|
||||
PrintHelp();
|
||||
exit(0);
|
||||
|
||||
case 'i' : /* [i]nclude file */
|
||||
if (xflag) {
|
||||
Erreur("-x and -i options are incompatibles", -1);
|
||||
errflag++;
|
||||
}
|
||||
iflag = 1;
|
||||
(void) strcpy(includefile, optarg);
|
||||
break;
|
||||
|
||||
case 'm' : /* [m]ixer selector */
|
||||
mixer = sSetMixer(optarg);
|
||||
if (mixer == MIXER_NONE) {
|
||||
Erreur("bad mixer selector", -1);
|
||||
errflag++;
|
||||
}
|
||||
break;
|
||||
|
||||
case 'p' : /* [p]hase mask */
|
||||
phase = sGetPhaseMask(optarg);
|
||||
if (phase == 0) {
|
||||
Erreur("bad phase value", -1);
|
||||
errflag++;
|
||||
}
|
||||
break;
|
||||
|
||||
case 's': /* [s]tep */
|
||||
if ( (sscanf(optarg, "%d", &step) != 1)
|
||||
|| (step <= 0) ) {
|
||||
Erreur("bad step value", 0);
|
||||
errflag++;
|
||||
}
|
||||
break;
|
||||
|
||||
case 'w': /* [w]indow */
|
||||
if ( (sscanf(optarg, "%d", &window) != 1)
|
||||
|| (window <= 0) ) {
|
||||
Erreur("bad window value", -1);
|
||||
errflag++;
|
||||
}
|
||||
break;
|
||||
|
||||
case 'W': /* [W]indow */
|
||||
if ( (sscanf(optarg, "%d", &window) != 1)
|
||||
|| (window <= 0)
|
||||
|| (window > 100)) {
|
||||
Erreur("bad bad window percent value", -1);
|
||||
errflag++;
|
||||
}
|
||||
window = -window;
|
||||
break;
|
||||
|
||||
case 'x' : /* e[X]lude file */
|
||||
if (iflag) {
|
||||
Erreur("-x and -i options are incompatibles", -1);
|
||||
errflag++;
|
||||
}
|
||||
xflag = 1;
|
||||
(void) strcpy(includefile, optarg);
|
||||
break;
|
||||
|
||||
case '?' : /* misusage */
|
||||
errflag++;
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
/* -------------------------------- */
|
||||
/* check some options compatibility */
|
||||
|
||||
if ((phase != 0x7) && (! iflag)) {
|
||||
Erreur("-p flag requires -i flag", -1);
|
||||
errflag++;
|
||||
}
|
||||
|
||||
if (selector == SELECTOR_CUMUL) {
|
||||
if (alpha->length != 2) {
|
||||
Erreur("need a two-letters alphabet for -c cumul", -1);
|
||||
errflag++;
|
||||
}
|
||||
}
|
||||
|
||||
if (selector == SELECTOR_GENE) {
|
||||
if (! iflag) {
|
||||
Erreur("-c gene requires -i flag", -1);
|
||||
errflag++;
|
||||
}
|
||||
if (phase != 0x7) {
|
||||
Erreur("-c gene needs -p 123", -1);
|
||||
errflag++;
|
||||
}
|
||||
if (strcmp(alpha->symbol, sDNA)) {
|
||||
Erreur("-a ignored for -c gene", 0);
|
||||
(void) FreeAlphabet(alpha);
|
||||
alpha = NucleicAlphabet();
|
||||
}
|
||||
}
|
||||
|
||||
if (selector == SELECTOR_CODON) {
|
||||
if (! iflag) {
|
||||
Erreur("-c codon requires -i flag", -1);
|
||||
errflag++;
|
||||
}
|
||||
if (phase != 0x7) {
|
||||
Erreur("-c codon is incompatible with -p flag", -1);
|
||||
errflag++;
|
||||
}
|
||||
if (strcmp(alpha->symbol, sDNA)) {
|
||||
Erreur("-a ignored for -c codon", 0);
|
||||
(void) FreeAlphabet(alpha);
|
||||
alpha = NucleicAlphabet();
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------- */
|
||||
/* may remain 1 argument */
|
||||
|
||||
argn -= optind;
|
||||
|
||||
if (argn > 1)
|
||||
errflag++;
|
||||
|
||||
if (errflag)
|
||||
ExitUsage(1);
|
||||
|
||||
/* ---------------------------- */
|
||||
/* allocate sequences */
|
||||
|
||||
seq = NewSequence(alpha);
|
||||
|
||||
/* ---------------------------- */
|
||||
/* read genome */
|
||||
|
||||
if (argn == 1) {
|
||||
(void) strcpy(inputfile, argv[optind]);
|
||||
if (! AssignToStdin(inputfile))
|
||||
Erreur("cannot open sequence file", 3);
|
||||
}
|
||||
|
||||
if (! ReadSequence(stdin, seq))
|
||||
Erreur("cannot read sequence file", 4);
|
||||
|
||||
(void) sUpper(seq->fasta->seq); /* upper case sequence */
|
||||
|
||||
(void) sExcludeFromSeq(seq->fasta->seq, alphaOut, MASKED_SYMBOL);
|
||||
|
||||
/* ---------------------------- */
|
||||
/* read include file */
|
||||
|
||||
if (iflag || xflag) {
|
||||
if (! (AssignToStdin(includefile)))
|
||||
Erreur("cannot open include file", 4);
|
||||
if (! (zones = ReadZones(seq->fasta->length)))
|
||||
Erreur("cannot read include zones", 5);
|
||||
}
|
||||
else {
|
||||
zones = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------- */
|
||||
/* adjust parameters */
|
||||
|
||||
/* -------------------- */
|
||||
len = seq->fasta->length; /* sequence length */
|
||||
|
||||
/* -------------------- */
|
||||
if (window < 0) /* window */
|
||||
window = len * (-window) / 100;
|
||||
|
||||
window /= 2; /* actual wondow for each half */
|
||||
|
||||
/* -------------------- */
|
||||
if (selector == SELECTOR_GENE) { /* alphabet */
|
||||
(void) strcpy(alpha->symbol, "DR");
|
||||
alpha->length = 2;
|
||||
}
|
||||
/* -------------------- */
|
||||
nbins = alpha->length; /* # bins (for chi2) */
|
||||
/* -------------------- */
|
||||
if (xflag) { /* indexing function */
|
||||
indexingFunction = ExcludeIndexer;
|
||||
}
|
||||
else if (iflag) {
|
||||
indexingFunction = PhaseIndexer;
|
||||
}
|
||||
else {
|
||||
indexingFunction = NoZoneIndexer;
|
||||
}
|
||||
|
||||
if (selector == SELECTOR_GENE) {
|
||||
indexingFunction = GeneIndexer;
|
||||
}
|
||||
if (selector == SELECTOR_CODON) {
|
||||
indexingFunction = CodonIndexer;
|
||||
}
|
||||
|
||||
/* -------------------- */
|
||||
if (selector == SELECTOR_CODON) { /* counting function */
|
||||
|
||||
/* precompute score for each possible codon */
|
||||
/* to speedup computation */
|
||||
|
||||
CodonSkew(code, sCodonScore);
|
||||
|
||||
countingFunction = CodonSkewCounter;
|
||||
|
||||
nbins = 3 * NB_NUC;
|
||||
}
|
||||
else {
|
||||
countingFunction = BasicCounter;
|
||||
}
|
||||
|
||||
/* -------------------- */
|
||||
if (dflag == DISTANCE_EUCLID) { /* distance function */
|
||||
distanceFunction = Euclid;
|
||||
}
|
||||
else if (dflag == DISTANCE_HELL) {
|
||||
distanceFunction = HellTwo;
|
||||
}
|
||||
else {
|
||||
distanceFunction = ChisTwo;
|
||||
}
|
||||
|
||||
|
||||
/* -------------------- */
|
||||
if (mixer == MIXER_CROSS) { /* mixing function */
|
||||
mixingFunction = CrossMixer;
|
||||
}
|
||||
else {
|
||||
mixingFunction = BasicMixer;
|
||||
}
|
||||
|
||||
/* ---------------------------- */
|
||||
/* index sequence */
|
||||
|
||||
indexingFunction(seq, zones, phase);
|
||||
|
||||
/* ---------------------------- */
|
||||
/* # included positions */
|
||||
|
||||
for (i = nopen = nvalid = 0 ; i < len ; i++) {
|
||||
if ((seq->cell[i].mask & EXCLUDE_MASK) == 0) {
|
||||
nopen++;
|
||||
if (seq->cell[i].index >= 0)
|
||||
nvalid++;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* ---------------------------- */
|
||||
/* printout header */
|
||||
|
||||
printf("# input : %s\n", inputfile);
|
||||
printf("# %s : %s\n", (xflag ? "exclude" : "include"), includefile);
|
||||
printf("# selector : %s\n", sGetSelector(selector));
|
||||
printf("# mixer : %s\n", sGetMixer(mixer));
|
||||
printf("# distance : %s\n", sGetDistance(dflag));
|
||||
printf("# phase : %d\n", phase);
|
||||
printf("# alphabet : %s\n", alpha->symbol);
|
||||
printf("# excluded : X%s\n", alphaOut);
|
||||
printf("# seqname : %s\n", seq->fasta->name);
|
||||
printf("# seqlength : %d\n", len);
|
||||
printf("# unmasked : %d\n", nopen);
|
||||
printf("# valid : %d\n", nvalid);
|
||||
printf("# window : %d\n", 2 * window);
|
||||
printf("# step : %d\n", step);
|
||||
printf("#\n");
|
||||
|
||||
printf("# pos");
|
||||
|
||||
if (selector == SELECTOR_COUNT) {
|
||||
for (i = 0 ; i < alpha->length ; i++) {
|
||||
printf(" Left%c Right%c", alpha->symbol[i], alpha->symbol[i]);
|
||||
}
|
||||
printf(" LeftOther RightOther");
|
||||
printf(" %s%s", sGetDistance(dflag), alpha->symbol);
|
||||
printf(" %s[%s]Other", sGetDistance(dflag), alpha->symbol);
|
||||
for (i = 0 ; i < alpha->length ; i++) {
|
||||
printf(" %s%c", sGetDistance(dflag), alpha->symbol[i]);
|
||||
}
|
||||
}
|
||||
|
||||
if (selector == SELECTOR_CUMUL) {
|
||||
printf(" %c-%c/%c+%c", alpha->symbol[0], alpha->symbol[1], alpha->symbol[0], alpha->symbol[1]);
|
||||
}
|
||||
|
||||
if (selector == SELECTOR_GENE) {
|
||||
printf(" LeftDirect RightDirect LeftReverse RightReverse");
|
||||
printf(" %s_Direct", sGetDistance(dflag));
|
||||
}
|
||||
|
||||
if (selector == SELECTOR_CODON) {
|
||||
printf(" LeftTotalCodon RightTotalCodon");
|
||||
for (i = 0 ; i < alpha->length ; i++) {
|
||||
printf(" Left%c0 Left%cP Left%cM", alpha->symbol[i], alpha->symbol[i], alpha->symbol[i]);
|
||||
printf(" Right%c0 Right%cP Right%cM", alpha->symbol[i], alpha->symbol[i], alpha->symbol[i]);
|
||||
}
|
||||
for (i = 0 ; i < alpha->length ; i++) {
|
||||
printf(" Total%s%c", sGetDistance(dflag), alpha->symbol[i]);
|
||||
}
|
||||
}
|
||||
|
||||
printf("\n");
|
||||
|
||||
/* ---------------------------- */
|
||||
/* now go ahead ! */
|
||||
|
||||
skew = 0.; /* just for SELECTOR_CUMUL */
|
||||
|
||||
for (pos = 0 ; pos < len ; pos += step) {
|
||||
|
||||
/* compute skew */
|
||||
|
||||
if ((pos == 0) || (window < step)) {
|
||||
countingFunction(seq, pos, pos + window, allRight, nbins, 0);
|
||||
countingFunction(seq, pos + len - window, pos + len, allLeft, nbins, 0);
|
||||
}
|
||||
else {
|
||||
countingFunction(seq, pos - step, pos, allRight, nbins, -1);
|
||||
countingFunction(seq, pos - step + window, pos + window, allRight, nbins, 1);
|
||||
countingFunction(seq, pos - step + len - window, pos + len - window, allLeft, nbins, -1);
|
||||
countingFunction(seq, pos - step, pos, allLeft, nbins, 1);
|
||||
}
|
||||
|
||||
mixingFunction(allLeft, allRight, countLeft, countRight, nbins);
|
||||
|
||||
|
||||
/* printout result */
|
||||
|
||||
printf("%d", pos+1);
|
||||
|
||||
/* printout skew */
|
||||
|
||||
if (selector == SELECTOR_COUNT) {
|
||||
|
||||
/* -- printout counts -- */
|
||||
|
||||
for (i = 0 ; i <= alpha->length ; i++) {
|
||||
printf(" %d %d", countLeft[i], countRight[i]);
|
||||
}
|
||||
|
||||
/* -- printout total alphabet chisquare -- */
|
||||
|
||||
skew = distanceFunction(countLeft, countRight, nbins, -1);
|
||||
sign = ((nbins == 2) ? SignTwoBins(countRight, countLeft) : 1);
|
||||
printf(" %g", skew * sign);
|
||||
|
||||
/* -- printout anti alphabet chisquare -- */
|
||||
|
||||
tmpLeft[1] = countLeft[alpha->length];
|
||||
tmpRight[1] = countRight[alpha->length];
|
||||
tmpLeft[0] = tmpRight[0] = 0;
|
||||
for (i = 0 ; i < alpha->length ; i++) {
|
||||
tmpLeft[0] += countLeft[i];
|
||||
tmpRight[0] += countRight[i];
|
||||
}
|
||||
skew = distanceFunction(tmpLeft, tmpRight, 2, -1);
|
||||
sign = SignTwoBins(tmpRight, tmpLeft);
|
||||
printf(" %g", skew * sign);
|
||||
|
||||
/* -- printout partial chisquares -- */
|
||||
|
||||
tmpLeft[0] = tmpRight[0] = 0;
|
||||
tmpLeft[1] = tmpRight[1] = 0;
|
||||
for (j = 0 ; j < alpha->length ; j++) {
|
||||
tmpLeft[1] += countLeft[j];
|
||||
tmpRight[1] += countRight[j];
|
||||
}
|
||||
|
||||
for (i = 0 ; i < alpha->length ; i++) {
|
||||
skew = distanceFunction(countLeft, countRight, nbins, i);
|
||||
tmpLeft[0] = countLeft[i];
|
||||
tmpRight[0] = countRight[i];
|
||||
tmpLeft[1] -= countLeft[i];
|
||||
tmpRight[1] -= countRight[i];
|
||||
sign = SignTwoBins(tmpRight, tmpLeft);
|
||||
tmpLeft[1] += countLeft[i];
|
||||
tmpRight[1] += countRight[i];
|
||||
printf(" %g", skew * sign);
|
||||
}
|
||||
}
|
||||
|
||||
if (selector == SELECTOR_CUMUL) {
|
||||
|
||||
/* -- printout XY cumulatives -- */
|
||||
|
||||
sum = (float) ((countRight[0] + countLeft[0]) + (countRight[1] + countLeft[1]));
|
||||
if (sum != 0.) {
|
||||
skew += (float) ((countRight[0] + countLeft[0]) - (countRight[1] + countLeft[1]))
|
||||
/ (sum * (float) len) * CUMUL_NORM;
|
||||
}
|
||||
printf(" %g", skew);
|
||||
}
|
||||
|
||||
if (selector == SELECTOR_GENE) {
|
||||
|
||||
/* -- printout direct -- */
|
||||
|
||||
printf(" %d %d", countLeft[0], countRight[0]);
|
||||
|
||||
/* -- printout reverse -- */
|
||||
|
||||
printf(" %d %d", countLeft[1], countRight[1]);
|
||||
|
||||
/* -- printout chi direct -- */
|
||||
|
||||
skew = distanceFunction(countLeft, countRight, nbins, -1);
|
||||
sign = SignTwoBins(countRight, countLeft);
|
||||
printf(" %g", skew * sign);
|
||||
}
|
||||
|
||||
if (selector == SELECTOR_CODON) {
|
||||
|
||||
/* -- printout total codons -- */
|
||||
|
||||
printf(" %d %d", countLeft[3* NB_NUC], countRight[3 * NB_NUC]);
|
||||
|
||||
/* -- printout nuc-enrichment -- */
|
||||
|
||||
for (i = 0 ; i < NB_NUC ; i++) {
|
||||
for (j = 0 ; j < 3 ; j++) {
|
||||
printf(" %d", countLeft[3*i + j]);
|
||||
}
|
||||
for (j = 0 ; j < 3 ; j++) {
|
||||
printf(" %d", countRight[3*i + j]);
|
||||
}
|
||||
}
|
||||
|
||||
/* -- printout total chi nuc-enrichment -- */
|
||||
|
||||
for (i = 0 ; i < NB_NUC ; i++) {
|
||||
skew = distanceFunction(countLeft + 3*i, countRight + 3*i, 3, -1);
|
||||
printf(" %g", skew);
|
||||
}
|
||||
}
|
||||
|
||||
printf("\n");
|
||||
}
|
||||
|
||||
FreeAlphabet(alpha);
|
||||
FreeSequence(seq);
|
||||
FreeZones(zones);
|
||||
|
||||
exit(0);
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
25
src/kimono/lxpack/tests/Makefile
Executable file
25
src/kimono/lxpack/tests/Makefile
Executable file
@ -0,0 +1,25 @@
|
||||
# ---------------------------------------------------------------
|
||||
# $Id: $
|
||||
# ---------------------------------------------------------------
|
||||
# @file: Makefile
|
||||
# @desc: makefile for kimono/test
|
||||
#
|
||||
# @history:
|
||||
# @history:
|
||||
# @+ <Gloup> : Apr 97 : Created
|
||||
# @+ <Gloup> : Mar 02 : Updated for LXxware
|
||||
#
|
||||
# @note: should be processed with gnu compatible make
|
||||
# @note: helixware_compatible
|
||||
#
|
||||
# @end:
|
||||
# ---------------------------------------------------------------
|
||||
#
|
||||
|
||||
include ../config/targets/empty.targ
|
||||
|
||||
clean::
|
||||
-\rm -f *.tst
|
||||
|
||||
test::
|
||||
./test.csh
|
||||
15180
src/kimono/lxpack/tests/borbu1.fst
Normal file
15180
src/kimono/lxpack/tests/borbu1.fst
Normal file
File diff suppressed because it is too large
Load Diff
850
src/kimono/lxpack/tests/borbu1.lst
Normal file
850
src/kimono/lxpack/tests/borbu1.lst
Normal file
@ -0,0 +1,850 @@
|
||||
105 677 D
|
||||
768 1796 C
|
||||
1784 3148 C
|
||||
3395 5188 D
|
||||
5251 6312 C
|
||||
6309 7433 C
|
||||
7458 8315 C
|
||||
8412 9197 D
|
||||
9202 10206 D
|
||||
10203 10577 D
|
||||
10581 11420 D
|
||||
11421 12161 D
|
||||
12154 12753 D
|
||||
12746 14728 D
|
||||
14725 15348 C
|
||||
15345 15722 C
|
||||
15845 16804 D
|
||||
16807 17817 C
|
||||
17792 18304 C
|
||||
18312 19979 C
|
||||
20445 21092 C
|
||||
21058 22101 C
|
||||
22146 22739 C
|
||||
22819 23958 D
|
||||
23965 24696 C
|
||||
24697 25623 C
|
||||
25753 26391 D
|
||||
26399 27448 D
|
||||
27434 27865 C
|
||||
27855 28490 C
|
||||
28492 29472 C
|
||||
29543 31015 D
|
||||
31027 31479 D
|
||||
31550 32089 C
|
||||
32157 34037 C
|
||||
34037 35836 C
|
||||
35857 36609 C
|
||||
36606 38123 C
|
||||
38136 39638 C
|
||||
39826 40677 D
|
||||
40677 40769 D
|
||||
40761 41432 C
|
||||
41443 42483 C
|
||||
42480 42881 C
|
||||
42907 45366 C
|
||||
45446 45991 D
|
||||
46011 46394 C
|
||||
46601 46771 C
|
||||
46921 47040 C
|
||||
47167 47841 D
|
||||
47905 48606 D
|
||||
48603 49259 C
|
||||
49341 50012 D
|
||||
50112 50489 C
|
||||
50490 51251 C
|
||||
51253 52434 C
|
||||
52454 53461 C
|
||||
53534 55504 C
|
||||
55501 56280 C
|
||||
56281 56748 C
|
||||
56832 57185 C
|
||||
57259 57975 D
|
||||
58029 59036 C
|
||||
59101 60039 C
|
||||
60036 60554 C
|
||||
60568 61257 C
|
||||
61254 63032 C
|
||||
63147 64028 D
|
||||
64038 65276 D
|
||||
65291 65752 D
|
||||
65768 67240 D
|
||||
67248 69569 D
|
||||
69566 70126 D
|
||||
70173 71219 D
|
||||
71201 72610 D
|
||||
72647 73492 D
|
||||
73489 74517 D
|
||||
74518 75039 D
|
||||
75110 75772 D
|
||||
75732 76454 D
|
||||
76451 77701 D
|
||||
77711 79009 C
|
||||
79002 79376 C
|
||||
79505 80773 D
|
||||
80983 81408 D
|
||||
81405 82940 D
|
||||
82970 83920 C
|
||||
84041 85720 C
|
||||
85880 86854 C
|
||||
86926 87360 C
|
||||
87377 89203 C
|
||||
89200 89814 C
|
||||
89811 91115 C
|
||||
91137 92792 C
|
||||
92878 93423 C
|
||||
93433 94035 C
|
||||
94219 94605 C
|
||||
94611 96953 C
|
||||
96943 97866 C
|
||||
97863 98648 C
|
||||
98805 100205 D
|
||||
100228 100749 D
|
||||
100746 101339 C
|
||||
101525 102976 C
|
||||
103016 103771 C
|
||||
103764 105473 C
|
||||
105418 105855 C
|
||||
105884 106894 C
|
||||
106974 108170 C
|
||||
108307 109671 D
|
||||
109675 111042 C
|
||||
111046 111567 C
|
||||
111585 111875 C
|
||||
111889 112338 C
|
||||
112350 112769 C
|
||||
112909 114633 C
|
||||
114807 115508 D
|
||||
115505 116818 C
|
||||
117678 118370 C
|
||||
118375 118929 C
|
||||
118964 119803 C
|
||||
119807 120589 C
|
||||
120804 121082 C
|
||||
121101 121823 C
|
||||
121880 122491 C
|
||||
122491 124152 C
|
||||
124149 124814 C
|
||||
124798 125547 C
|
||||
125534 126301 C
|
||||
126316 127413 C
|
||||
127427 130132 C
|
||||
130170 131114 C
|
||||
131277 132425 D
|
||||
132472 133845 C
|
||||
133975 135864 D
|
||||
135874 137766 C
|
||||
137880 138089 C
|
||||
138434 138823 C
|
||||
138850 141960 C
|
||||
141979 142935 C
|
||||
142944 144266 C
|
||||
144307 144597 D
|
||||
144586 145458 C
|
||||
145471 146370 C
|
||||
146377 147495 C
|
||||
147649 148659 C
|
||||
148710 148805 D
|
||||
148786 150783 C
|
||||
150805 150897 C
|
||||
150974 152179 D
|
||||
152206 153012 D
|
||||
153075 153719 C
|
||||
153701 156400 C
|
||||
156462 157598 D
|
||||
157627 158061 D
|
||||
158058 158474 D
|
||||
158628 159344 D
|
||||
159368 160042 D
|
||||
160090 161208 D
|
||||
161200 162864 C
|
||||
162878 163045 D
|
||||
163072 164820 C
|
||||
164901 165914 C
|
||||
165915 167759 C
|
||||
167879 169399 C
|
||||
169539 170708 D
|
||||
170720 171097 C
|
||||
171212 171484 D
|
||||
171532 173580 C
|
||||
173529 174116 C
|
||||
174098 175138 C
|
||||
175081 176106 C
|
||||
176069 176974 C
|
||||
176978 177853 C
|
||||
177868 178881 C
|
||||
178917 179543 C
|
||||
179540 181423 C
|
||||
181408 182802 C
|
||||
182886 183380 D
|
||||
183392 185275 D
|
||||
185278 186552 D
|
||||
186554 186946 D
|
||||
186949 187194 D
|
||||
187178 187831 C
|
||||
187824 188237 C
|
||||
188234 188494 C
|
||||
188708 189055 C
|
||||
189076 189276 C
|
||||
189299 189859 C
|
||||
189949 190044 D
|
||||
190064 190717 D
|
||||
190719 191459 D
|
||||
191518 192327 C
|
||||
192324 193463 C
|
||||
193800 194873 D
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194876 195736 D
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195693 197696 D
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197686 199950 D
|
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|
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201052 202578 C
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202850 204088 D
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204137 205072 D
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205073 206044 D
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206529 208106 D
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211301 212068 D
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212061 215420 D
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215427 217259 D
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217278 218312 D
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219797 220639 D
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220729 221637 D
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222192 223178 D
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223179 223961 D
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223964 224785 C
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224826 226610 C
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226610 227836 C
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227814 228521 C
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228542 228895 C
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228864 229148 C
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229217 230224 D
|
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230214 231491 C
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231621 232322 D
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232338 235253 D
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235289 235534 C
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235595 237142 C
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237222 237629 C
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237630 237956 C
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237969 238292 C
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238301 239128 C
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239144 240250 C
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240283 242289 C
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242438 244003 D
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243943 244731 C
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244777 245394 C
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|
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246597 248102 D
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248156 248434 D
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248506 250089 D
|
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250176 250670 C
|
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251212 252237 C
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255646 256260 D
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256463 258985 D
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267313 269676 C
|
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269673 270473 C
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270488 272701 C
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272634 273647 C
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273854 275236 D
|
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276558 277064 D
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277090 278565 C
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278537 279058 C
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279078 279386 C
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279407 281311 C
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300780 302489 C
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312729 314123 C
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314146 314427 C
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314424 315314 C
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315307 316143 C
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317247 318026 C
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318119 318256 C
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318277 319158 C
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319106 319636 C
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319680 320258 C
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322040 322846 C
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322847 323779 C
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325236 326288 C
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326325 326432 C
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326469 326666 C
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326699 327757 C
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329262 329621 D
|
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|
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|
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|
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341274 342323 D
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342335 343207 D
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343208 344179 D
|
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|
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346431 346841 C
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346861 347301 C
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347351 348160 C
|
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348153 349610 C
|
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349600 351090 C
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351056 351331 C
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351341 353440 C
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353440 354636 C
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354648 355298 C
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|
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|
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|
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359217 359495 C
|
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359513 361081 C
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362318 364117 C
|
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364130 365170 C
|
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365115 365603 C
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365643 366137 C
|
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366144 366236 C
|
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366229 366960 C
|
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366964 368391 C
|
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|
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370027 371013 D
|
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371034 373046 D
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|
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377039 379330 C
|
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379341 380558 C
|
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380555 381892 C
|
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381910 383382 C
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383395 384162 C
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|
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|
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|
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|
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387818 388480 C
|
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|
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388977 390341 C
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390392 391819 C
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391932 392957 C
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393044 394063 C
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395481 396563 C
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397544 401677 C
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401693 405160 C
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405243 405617 C
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|
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407922 408092 C
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408201 408380 C
|
||||
408554 409402 C
|
||||
409416 410447 C
|
||||
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|
||||
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|
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|
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|
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|
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417724 418335 D
|
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|
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|
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|
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|
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422471 423058 D
|
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423055 423834 D
|
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|
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|
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|
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426736 427950 D
|
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427987 428622 D
|
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|
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|
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|
||||
441713 442552 C
|
||||
442688 443248 C
|
||||
443763 444053 C
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|
||||
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|
||||
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|
||||
446969 447760 C
|
||||
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|
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|
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|
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|
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452040 454472 C
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|
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|
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|
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|
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469961 471220 C
|
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471223 471756 C
|
||||
471771 472475 C
|
||||
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|
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|
||||
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|
||||
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
||||
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|
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|
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|
||||
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|
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|
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|
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|
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|
||||
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|
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|
||||
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|
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|
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|
||||
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|
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|
||||
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|
||||
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|
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|
||||
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|
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|
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|
||||
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|
||||
548920 549618 C
|
||||
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|
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|
||||
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|
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|
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|
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|
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|
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|
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|
||||
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|
||||
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|
||||
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|
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|
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|
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|
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|
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|
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|
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575981 576526 C
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|
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|
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|
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595943 596521 D
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|
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|
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|
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|
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|
||||
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|
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|
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|
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
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|
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|
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|
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|
||||
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|
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|
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|
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|
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|
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|
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|
||||
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|
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|
||||
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
||||
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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764371 765342 D
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769547 771145 C
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771162 771563 C
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771570 774368 C
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774632 775462 D
|
||||
775666 776679 C
|
||||
776746 777573 D
|
||||
777625 777768 D
|
||||
777747 778754 D
|
||||
778758 781385 D
|
||||
781486 782073 C
|
||||
782152 782829 C
|
||||
782976 783257 C
|
||||
783324 785021 D
|
||||
785057 786754 D
|
||||
786860 788962 D
|
||||
789270 789938 D
|
||||
789947 790807 C
|
||||
790807 791787 C
|
||||
791794 792252 C
|
||||
792333 793625 D
|
||||
793693 793836 D
|
||||
793842 794915 C
|
||||
794875 796383 C
|
||||
796388 797122 C
|
||||
797119 798048 C
|
||||
798057 799016 C
|
||||
799208 800275 C
|
||||
800452 801072 D
|
||||
800996 801778 D
|
||||
801941 802798 C
|
||||
802838 803212 C
|
||||
803278 804165 D
|
||||
804240 804353 C
|
||||
804417 805778 C
|
||||
805775 806923 C
|
||||
806920 807966 C
|
||||
807976 808464 C
|
||||
808461 809552 C
|
||||
809701 810495 C
|
||||
810470 811510 C
|
||||
811507 812388 C
|
||||
812439 813239 C
|
||||
813690 814697 C
|
||||
814868 815302 C
|
||||
815502 816299 C
|
||||
816312 817214 C
|
||||
817393 817956 D
|
||||
818018 818548 D
|
||||
818605 818916 D
|
||||
818922 819242 D
|
||||
819242 819487 D
|
||||
819542 820528 D
|
||||
820568 821188 D
|
||||
821185 822369 D
|
||||
822335 822694 D
|
||||
822810 823103 D
|
||||
823167 823811 D
|
||||
823816 824382 D
|
||||
824382 825704 D
|
||||
825701 827620 D
|
||||
827625 829112 D
|
||||
829218 830321 D
|
||||
830318 830941 C
|
||||
830955 831728 C
|
||||
831646 836043 D
|
||||
836061 838526 D
|
||||
838523 839080 D
|
||||
839244 841832 D
|
||||
841834 842451 D
|
||||
842501 842989 D
|
||||
843003 844451 D
|
||||
844454 847102 D
|
||||
847105 847488 D
|
||||
847491 848339 D
|
||||
848538 848804 D
|
||||
848819 850987 D
|
||||
850994 852514 D
|
||||
852489 853778 D
|
||||
853775 854842 D
|
||||
854869 855996 D
|
||||
855971 857509 D
|
||||
857506 858915 D
|
||||
858939 860111 C
|
||||
860186 860362 D
|
||||
860440 861774 D
|
||||
861784 862677 D
|
||||
862696 863646 D
|
||||
863636 865042 D
|
||||
865053 865919 D
|
||||
865916 866458 D
|
||||
866494 866694 D
|
||||
866681 867601 D
|
||||
867605 867700 D
|
||||
867743 868114 C
|
||||
868189 868740 D
|
||||
868733 869515 C
|
||||
869508 870023 C
|
||||
870112 872583 C
|
||||
872586 875132 C
|
||||
875207 876448 D
|
||||
876429 879281 D
|
||||
879303 880250 D
|
||||
880267 881091 C
|
||||
881085 884213 C
|
||||
884228 886447 C
|
||||
886470 888182 C
|
||||
888297 890318 D
|
||||
890322 893174 D
|
||||
893129 896569 D
|
||||
897096 897740 C
|
||||
897704 899320 C
|
||||
899499 900731 D
|
||||
900796 901782 D
|
||||
901810 903258 D
|
||||
903929 904900 C
|
||||
905120 905227 D
|
||||
905752 905865 C
|
||||
905839 905946 D
|
||||
905928 906032 D
|
||||
906162 906263 D
|
||||
907935 908081 D
|
||||
908407 909591 D
|
||||
927
src/kimono/lxpack/tests/ref/borbu1.0.ref
Normal file
927
src/kimono/lxpack/tests/ref/borbu1.0.ref
Normal file
@ -0,0 +1,927 @@
|
||||
# input : borbu1.fst
|
||||
# include : <none>
|
||||
# selector : count
|
||||
# mixer : basic
|
||||
# distance : chi
|
||||
# phase : 7
|
||||
# alphabet : ACGT
|
||||
# excluded : X
|
||||
# seqname : borbu1
|
||||
# seqlength : 910724
|
||||
# unmasked : 910724
|
||||
# valid : 910681
|
||||
# window : 227680
|
||||
# step : 1000
|
||||
#
|
||||
# pos LeftA RightA LeftC
|
||||
1 36566 44476 13342 18949
|
||||
1001 36655 44524 13339 18989
|
||||
2001 36782 44547 13364 18962
|
||||
3001 36858 44580 13415 18951
|
||||
4001 37042 44544 13413 19003
|
||||
5001 37142 44434 13449 19062
|
||||
6001 37169 44406 13498 19085
|
||||
7001 37270 44326 13557 19097
|
||||
8001 37350 44361 13624 19095
|
||||
9001 37490 44294 13596 19130
|
||||
10001 37685 44156 13595 19223
|
||||
11001 37856 44039 13616 19296
|
||||
12001 37999 43953 13627 19316
|
||||
13001 38183 43804 13615 19393
|
||||
14001 38354 43662 13612 19477
|
||||
15001 38499 43597 13580 19499
|
||||
16001 38618 43545 13630 19522
|
||||
17001 38733 43519 13644 19561
|
||||
18001 38821 43555 13691 19562
|
||||
19001 38914 43623 13756 19502
|
||||
20001 38997 43648 13772 19512
|
||||
21001 39060 43694 13800 19517
|
||||
22001 39024 43853 13901 19448
|
||||
23001 39089 43809 13992 19469
|
||||
24001 39182 43772 14043 19474
|
||||
25001 39136 43869 14174 19413
|
||||
26001 39122 43859 14280 19413
|
||||
27001 39222 43861 14291 19445
|
||||
28001 39293 43803 14333 19478
|
||||
29001 39315 43737 14433 19504
|
||||
30001 39438 43681 14438 19496
|
||||
31001 39538 43610 14449 19529
|
||||
32001 39613 43536 14519 19577
|
||||
33001 39628 43599 14582 19577
|
||||
34001 39659 43600 14655 19583
|
||||
35001 39668 43582 14731 19583
|
||||
36001 39687 43550 14826 19595
|
||||
37001 39731 43486 14903 19605
|
||||
38001 39764 43521 14956 19608
|
||||
39001 39817 43536 15005 19611
|
||||
40001 39896 43487 15067 19651
|
||||
41001 39988 43397 15092 19711
|
||||
42001 40046 43362 15156 19736
|
||||
43001 40058 43363 15239 19739
|
||||
44001 40030 43469 15307 19699
|
||||
45001 40047 43557 15341 19666
|
||||
46001 40116 43543 15419 19639
|
||||
47001 40081 43661 15506 19579
|
||||
48001 40077 43708 15542 19583
|
||||
49001 40072 43692 15558 19582
|
||||
50001 40160 43643 15578 19604
|
||||
51001 40169 43648 15668 19572
|
||||
52001 40125 43775 15810 19510
|
||||
53001 40112 43869 15910 19467
|
||||
54001 40149 43910 15984 19425
|
||||
55001 40164 43887 16083 19445
|
||||
56001 40209 43936 16151 19406
|
||||
57001 40231 44014 16226 19381
|
||||
58001 40357 43954 16265 19391
|
||||
59001 40386 43993 16310 19369
|
||||
60001 40458 44005 16377 19346
|
||||
61001 40528 44049 16477 19328
|
||||
62001 40558 44072 16546 19329
|
||||
63001 40627 44134 16617 19291
|
||||
64001 40798 44057 16647 19336
|
||||
65001 40948 43949 16669 19414
|
||||
66001 40975 43930 16708 19421
|
||||
67001 41028 43833 16772 19456
|
||||
68001 41181 43686 16801 19536
|
||||
69001 41251 43635 16850 19589
|
||||
70001 41263 43701 16901 19574
|
||||
71001 41310 43708 16933 19572
|
||||
72001 41535 43641 16926 19603
|
||||
73001 41741 43566 16932 19642
|
||||
74001 41932 43511 16947 19656
|
||||
75001 42172 43400 16929 19704
|
||||
76001 42364 43215 16881 19800
|
||||
77001 42578 43156 16880 19806
|
||||
78001 42757 43212 16867 19809
|
||||
79001 42790 43225 16929 19817
|
||||
80001 42882 43187 16948 19844
|
||||
81001 42915 43228 16981 19867
|
||||
82001 42942 43251 17022 19860
|
||||
83001 43037 43266 17074 19844
|
||||
84001 43090 43353 17169 19805
|
||||
85001 43194 43474 17233 19713
|
||||
86001 43268 43588 17264 19670
|
||||
87001 43417 43555 17241 19703
|
||||
88001 43542 43558 17317 19668
|
||||
89001 43680 43559 17333 19678
|
||||
90001 43752 43652 17386 19651
|
||||
91001 43831 43757 17452 19569
|
||||
92001 43833 43865 17543 19497
|
||||
93001 43844 43958 17634 19420
|
||||
94001 43799 44055 17722 19357
|
||||
95001 43852 44114 17775 19322
|
||||
96001 43846 44246 17828 19278
|
||||
97001 43841 44335 17852 19262
|
||||
98001 43902 44417 17918 19210
|
||||
99001 43941 44475 17946 19205
|
||||
100001 44030 44507 17980 19270
|
||||
101001 44182 44513 17993 19321
|
||||
102001 44291 44604 18064 19272
|
||||
103001 44308 44739 18198 19199
|
||||
104001 44308 44889 18291 19106
|
||||
105001 44372 44984 18308 19109
|
||||
106001 44477 44969 18363 19115
|
||||
107001 44485 45057 18438 19066
|
||||
108001 44549 45087 18470 19009
|
||||
109001 44604 45113 18503 19027
|
||||
110001 44660 45136 18585 19035
|
||||
111001 44599 45193 18656 19067
|
||||
112001 44502 45187 18741 19074
|
||||
113001 44415 45197 18858 19075
|
||||
114001 44485 45094 18977 19045
|
||||
115001 44516 45064 18984 19031
|
||||
116001 44561 45065 18953 19020
|
||||
117001 44572 45038 18966 19011
|
||||
118001 44528 44986 19009 19010
|
||||
119001 44414 45104 19077 18956
|
||||
120001 44401 45231 19089 18880
|
||||
121001 44337 45312 19096 18821
|
||||
122001 44354 45295 19091 18814
|
||||
123001 44279 45303 19152 18807
|
||||
124001 44139 45330 19228 18805
|
||||
125001 44019 45370 19298 18749
|
||||
126001 43930 45405 19316 18757
|
||||
127001 43787 45422 19408 18728
|
||||
128001 43630 45481 19490 18699
|
||||
129001 43581 45506 19507 18689
|
||||
130001 43556 45543 19533 18665
|
||||
131001 43521 45571 19566 18653
|
||||
132001 43578 45578 19558 18643
|
||||
133001 43623 45511 19509 18635
|
||||
134001 43646 45500 19509 18618
|
||||
135001 43718 45494 19513 18595
|
||||
136001 43852 45463 19440 18609
|
||||
137001 43806 45500 19471 18563
|
||||
138001 43800 45451 19465 18616
|
||||
139001 43876 45530 19401 18580
|
||||
140001 43862 45625 19423 18523
|
||||
141001 43859 45622 19446 18510
|
||||
142001 43805 45662 19479 18464
|
||||
143001 43751 45712 19499 18413
|
||||
144001 43671 45774 19511 18391
|
||||
145001 43593 45806 19550 18376
|
||||
146001 43530 45880 19580 18312
|
||||
147001 43592 45911 19598 18292
|
||||
148001 43589 45909 19579 18312
|
||||
149001 43564 45960 19587 18323
|
||||
150001 43552 45945 19602 18296
|
||||
151001 43517 46025 19598 18269
|
||||
152001 43515 46101 19610 18240
|
||||
153001 43540 46148 19614 18223
|
||||
154001 43462 46185 19655 18215
|
||||
155001 43380 46225 19719 18197
|
||||
156001 43375 46347 19733 18125
|
||||
157001 43364 46358 19735 18115
|
||||
158001 43490 46270 19694 18175
|
||||
159001 43566 46243 19661 18197
|
||||
160001 43580 46185 19615 18250
|
||||
161001 43660 46190 19565 18252
|
||||
162001 43694 46190 19582 18266
|
||||
163001 43712 46199 19571 18241
|
||||
164001 43636 46245 19614 18200
|
||||
165001 43689 46178 19562 18241
|
||||
166001 43800 46088 19500 18251
|
||||
167001 43870 46059 19463 18311
|
||||
168001 43911 46001 19423 18355
|
||||
169001 43885 45982 19445 18357
|
||||
170001 43959 45893 19397 18406
|
||||
171001 44006 45818 19377 18450
|
||||
172001 43971 45796 19385 18496
|
||||
173001 44007 45787 19358 18545
|
||||
174001 44011 45883 19348 18515
|
||||
175001 44063 45905 19328 18497
|
||||
176001 44083 45878 19326 18474
|
||||
177001 44130 45781 19291 18529
|
||||
178001 44037 45755 19359 18521
|
||||
179001 43960 45761 19411 18517
|
||||
180001 43911 45752 19423 18572
|
||||
181001 43818 45755 19476 18583
|
||||
182001 43667 45746 19549 18567
|
||||
183001 43657 45696 19582 18555
|
||||
184001 43692 45610 19579 18561
|
||||
185001 43694 45546 19579 18638
|
||||
186001 43627 45399 19607 18708
|
||||
187001 43583 45286 19638 18767
|
||||
188001 43480 45180 19680 18827
|
||||
189001 43361 45166 19725 18853
|
||||
190001 43213 45187 19800 18851
|
||||
191001 43168 45074 19811 18932
|
||||
192001 43207 44949 19813 19001
|
||||
193001 43238 44930 19811 19010
|
||||
194001 43210 44874 19834 19036
|
||||
195001 43232 44713 19864 19138
|
||||
196001 43244 44593 19853 19237
|
||||
197001 43273 44579 19837 19238
|
||||
198001 43389 44536 19784 19257
|
||||
199001 43486 44516 19708 19330
|
||||
200001 43604 44398 19660 19378
|
||||
201001 43573 44364 19676 19382
|
||||
202001 43555 44376 19676 19355
|
||||
203001 43568 44407 19673 19339
|
||||
204001 43678 44396 19643 19341
|
||||
205001 43784 44380 19559 19364
|
||||
206001 43896 44289 19474 19403
|
||||
207001 43965 44265 19412 19420
|
||||
208001 44063 44282 19351 19423
|
||||
209001 44155 44314 19305 19425
|
||||
210001 44264 44314 19282 19442
|
||||
211001 44344 44236 19264 19492
|
||||
212001 44429 44155 19202 19564
|
||||
213001 44475 44100 19205 19559
|
||||
214001 44513 44071 19284 19488
|
||||
215001 44530 44074 19310 19429
|
||||
216001 44625 44024 19266 19444
|
||||
217001 44752 43935 19187 19467
|
||||
218001 44927 43766 19096 19536
|
||||
219001 44988 43679 19094 19570
|
||||
220001 44986 43672 19102 19571
|
||||
221001 45062 43648 19054 19605
|
||||
222001 45096 43715 19004 19586
|
||||
223001 45097 43727 19034 19567
|
||||
224001 45143 43712 19033 19568
|
||||
225001 45193 43749 19068 19492
|
||||
226001 45191 43843 19070 19467
|
||||
227001 45192 43910 19069 19409
|
||||
228001 45079 43995 19046 19368
|
||||
229001 45061 44004 19025 19362
|
||||
230001 45070 44013 19011 19389
|
||||
231001 45033 44022 19010 19363
|
||||
232001 45001 44011 19000 19372
|
||||
233001 45123 43969 18944 19398
|
||||
234001 45250 43870 18869 19449
|
||||
235001 45292 43797 18820 19496
|
||||
236001 45290 43774 18824 19512
|
||||
237001 45317 43817 18802 19505
|
||||
238001 45336 43835 18789 19486
|
||||
239001 45399 43816 18749 19497
|
||||
240001 45407 43815 18756 19465
|
||||
241001 45428 43859 18709 19457
|
||||
242001 45485 43921 18698 19402
|
||||
243001 45509 44016 18682 19368
|
||||
244001 45553 44033 18665 19355
|
||||
245001 45564 44111 18647 19311
|
||||
246001 45554 44040 18646 19355
|
||||
247001 45526 44054 18627 19362
|
||||
248001 45487 44138 18620 19321
|
||||
249001 45498 44160 18602 19322
|
||||
250001 45480 44121 18610 19307
|
||||
251001 45491 44241 18574 19257
|
||||
252001 45446 44308 18615 19224
|
||||
253001 45545 44203 18559 19260
|
||||
254001 45639 44082 18520 19304
|
||||
255001 45626 44029 18505 19331
|
||||
256001 45670 44066 18445 19329
|
||||
257001 45715 44041 18410 19336
|
||||
258001 45781 44109 18395 19323
|
||||
259001 45851 44109 18351 19333
|
||||
260001 45866 44107 18318 19325
|
||||
261001 45909 44083 18286 19331
|
||||
262001 45915 44156 18302 19277
|
||||
263001 45937 44198 18319 19246
|
||||
264001 45964 44197 18291 19280
|
||||
265001 46039 44082 18270 19327
|
||||
266001 46119 43994 18235 19365
|
||||
267001 46137 43900 18229 19405
|
||||
268001 46187 43859 18213 19454
|
||||
269001 46231 43872 18191 19430
|
||||
270001 46369 43759 18115 19490
|
||||
271001 46336 43831 18132 19437
|
||||
272001 46270 43887 18182 19414
|
||||
273001 46237 43932 18209 19423
|
||||
274001 46167 43951 18246 19417
|
||||
275001 46187 43883 18256 19451
|
||||
276001 46183 43912 18267 19458
|
||||
277001 46233 43828 18225 19501
|
||||
278001 46235 43823 18207 19517
|
||||
279001 46151 43843 18243 19529
|
||||
280001 46086 43811 18252 19550
|
||||
281001 46056 43840 18315 19516
|
||||
282001 45993 43882 18356 19491
|
||||
283001 45981 43887 18359 19521
|
||||
284001 45872 43849 18413 19530
|
||||
285001 45815 43831 18449 19552
|
||||
286001 45808 43738 18505 19583
|
||||
287001 45787 43697 18542 19592
|
||||
288001 45880 43551 18510 19661
|
||||
289001 45885 43425 18498 19719
|
||||
290001 45857 43397 18486 19758
|
||||
291001 45780 43408 18526 19760
|
||||
292001 45743 43399 18522 19785
|
||||
293001 45766 43372 18522 19774
|
||||
294001 45755 43327 18572 19780
|
||||
295001 45758 43342 18589 19761
|
||||
296001 45749 43348 18561 19761
|
||||
297001 45690 43412 18558 19750
|
||||
298001 45602 43498 18579 19724
|
||||
299001 45526 43488 18648 19679
|
||||
300001 45378 43599 18709 19609
|
||||
301001 45241 43665 18801 19554
|
||||
302001 45163 43685 18833 19565
|
||||
303001 45170 43749 18855 19504
|
||||
304001 45170 43800 18865 19456
|
||||
305001 45042 43856 18943 19402
|
||||
306001 44949 43885 19006 19371
|
||||
307001 44955 43860 19004 19445
|
||||
308001 44844 43893 19054 19417
|
||||
309001 44685 44004 19148 19327
|
||||
310001 44589 44051 19241 19234
|
||||
311001 44551 44093 19250 19198
|
||||
312001 44527 44087 19280 19163
|
||||
313001 44499 44109 19340 19123
|
||||
314001 44400 44171 19387 19089
|
||||
315001 44376 44230 19377 19036
|
||||
316001 44390 44215 19352 19027
|
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||||
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||||
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|
||||
745001 36154 36871 13419 13365
|
||||
746001 36124 36853 13432 13384
|
||||
747001 36125 36797 13438 13364
|
||||
748001 36091 36723 13425 13389
|
||||
749001 36117 36717 13402 13421
|
||||
750001 36161 36688 13430 13393
|
||||
751001 36241 36628 13401 13387
|
||||
752001 36208 36624 13410 13386
|
||||
753001 36216 36652 13406 13364
|
||||
754001 36201 36707 13416 13353
|
||||
755001 36146 36663 13417 13373
|
||||
756001 36167 36594 13407 13371
|
||||
757001 36188 36579 13363 13382
|
||||
758001 36170 36560 13345 13421
|
||||
759001 36168 36484 13358 13437
|
||||
760001 36192 36412 13332 13477
|
||||
761001 36249 36283 13330 13523
|
||||
762001 36285 36293 13304 13532
|
||||
763001 36249 36312 13286 13545
|
||||
764001 36271 36391 13254 13511
|
||||
765001 36343 36486 13220 13489
|
||||
766001 36404 36476 13160 13505
|
||||
767001 36440 36473 13174 13465
|
||||
768001 36402 36479 13228 13442
|
||||
769001 36315 36478 13275 13429
|
||||
770001 36256 36454 13297 13454
|
||||
771001 36196 36435 13339 13435
|
||||
772001 36177 36425 13318 13452
|
||||
773001 36128 36439 13381 13398
|
||||
774001 36046 36434 13377 13383
|
||||
775001 36111 36440 13332 13393
|
||||
776001 36073 36467 13299 13412
|
||||
777001 36027 36594 13307 13368
|
||||
778001 36098 36590 13309 13380
|
||||
779001 36154 36602 13302 13390
|
||||
780001 36216 36632 13304 13383
|
||||
781001 36278 36605 13304 13388
|
||||
782001 36348 36652 13288 13403
|
||||
783001 36383 36666 13303 13398
|
||||
784001 36427 36637 13319 13409
|
||||
785001 36494 36557 13300 13417
|
||||
786001 36536 36562 13311 13397
|
||||
787001 36617 36544 13238 13422
|
||||
788001 36673 36482 13250 13435
|
||||
789001 36743 36359 13248 13450
|
||||
790001 36809 36354 13231 13433
|
||||
791001 36889 36279 13245 13487
|
||||
792001 36951 36281 13237 13487
|
||||
793001 36991 36278 13202 13460
|
||||
794001 36987 36332 13178 13456
|
||||
795001 36977 36461 13145 13422
|
||||
796001 36975 36590 13152 13358
|
||||
797001 37017 36576 13154 13331
|
||||
798001 37042 36669 13171 13334
|
||||
799001 37007 36783 13203 13361
|
||||
800001 37023 36875 13175 13427
|
||||
801001 37035 37050 13199 13418
|
||||
802001 37059 37164 13182 13445
|
||||
803001 37043 37182 13203 13500
|
||||
804001 37024 37282 13190 13562
|
||||
805001 36947 37372 13228 13627
|
||||
806001 36917 37506 13279 13592
|
||||
807001 36869 37698 13301 13604
|
||||
808001 36784 37880 13310 13626
|
||||
809001 36787 38024 13327 13626
|
||||
810001 36775 38201 13342 13608
|
||||
811001 36753 38381 13365 13605
|
||||
812001 36703 38522 13411 13592
|
||||
813001 36674 38618 13392 13634
|
||||
814001 36682 38743 13361 13654
|
||||
815001 36679 38839 13351 13698
|
||||
816001 36655 38924 13385 13761
|
||||
817001 36625 39023 13444 13759
|
||||
818001 36620 39050 13459 13804
|
||||
819001 36604 39027 13465 13914
|
||||
820001 36589 39107 13454 13997
|
||||
821001 36566 39179 13453 14051
|
||||
822001 36536 39136 13451 14190
|
||||
823001 36563 39123 13419 14279
|
||||
824001 36521 39225 13440 14299
|
||||
825001 36540 39296 13440 14347
|
||||
826001 36573 39330 13421 14434
|
||||
827001 36547 39436 13465 14445
|
||||
828001 36585 39545 13480 14448
|
||||
829001 36616 39621 13437 14535
|
||||
830001 36580 39631 13433 14576
|
||||
831001 36596 39654 13433 14675
|
||||
832001 36613 39663 13404 14754
|
||||
833001 36684 39685 13380 14838
|
||||
834001 36705 39735 13361 14909
|
||||
835001 36705 39779 13344 14963
|
||||
836001 36701 39836 13329 15010
|
||||
837001 36697 39910 13277 15076
|
||||
838001 36728 40008 13250 15095
|
||||
839001 36747 40027 13223 15183
|
||||
840001 36760 40057 13223 15247
|
||||
841001 36818 40030 13222 15308
|
||||
842001 36802 40055 13226 15348
|
||||
843001 36856 40109 13202 15439
|
||||
844001 36885 40098 13195 15514
|
||||
845001 36986 40064 13166 15541
|
||||
846001 37007 40067 13196 15562
|
||||
847001 36977 40170 13224 15578
|
||||
848001 37014 40164 13237 15684
|
||||
849001 37032 40134 13216 15820
|
||||
850001 37030 40117 13235 15908
|
||||
851001 36986 40139 13252 15992
|
||||
852001 37010 40179 13232 16087
|
||||
853001 36984 40203 13260 16163
|
||||
854001 36946 40243 13277 16233
|
||||
855001 36921 40367 13284 16269
|
||||
856001 36944 40379 13310 16321
|
||||
857001 36897 40471 13337 16387
|
||||
858001 36849 40531 13350 16482
|
||||
859001 36898 40561 13354 16555
|
||||
860001 36844 40647 13378 16620
|
||||
861001 36782 40816 13374 16640
|
||||
862001 36723 40938 13394 16680
|
||||
863001 36695 40986 13420 16719
|
||||
864001 36665 41055 13400 16769
|
||||
865001 36638 41193 13373 16807
|
||||
866001 36621 41250 13382 16852
|
||||
867001 36687 41267 13351 16904
|
||||
868001 36693 41337 13362 16931
|
||||
869001 36655 41559 13391 16918
|
||||
870001 36590 41740 13367 16942
|
||||
871001 36585 41968 13392 16942
|
||||
872001 36531 42204 13427 16922
|
||||
873001 36477 42391 13445 16879
|
||||
874001 36414 42603 13474 16873
|
||||
875001 36270 42774 13522 16873
|
||||
876001 36298 42787 13538 16934
|
||||
877001 36326 42891 13539 16953
|
||||
878001 36410 42932 13513 16980
|
||||
879001 36491 42940 13492 17035
|
||||
880001 36486 43037 13498 17089
|
||||
881001 36493 43088 13456 17181
|
||||
882001 36493 43190 13429 17244
|
||||
883001 36473 43283 13428 17259
|
||||
884001 36445 43430 13459 17254
|
||||
885001 36433 43559 13434 17322
|
||||
886001 36424 43694 13459 17331
|
||||
887001 36454 43751 13396 17385
|
||||
888001 36420 43833 13368 17465
|
||||
889001 36430 43830 13386 17566
|
||||
890001 36483 43847 13405 17641
|
||||
891001 36604 43805 13366 17731
|
||||
892001 36580 43843 13390 17782
|
||||
893001 36585 43848 13395 17832
|
||||
894001 36640 43862 13386 17854
|
||||
895001 36631 43887 13394 17925
|
||||
896001 36647 43958 13406 17947
|
||||
897001 36678 44034 13383 17989
|
||||
898001 36627 44188 13420 17998
|
||||
899001 36559 44298 13420 18077
|
||||
900001 36551 44333 13404 18203
|
||||
901001 36552 44302 13423 18294
|
||||
902001 36454 44375 13436 18320
|
||||
903001 36354 44481 13430 18368
|
||||
904001 36361 44481 13434 18448
|
||||
905001 36283 44559 13494 18480
|
||||
906001 36286 44632 13483 18514
|
||||
907001 36280 44652 13465 18586
|
||||
908001 36335 44596 13458 18663
|
||||
909001 36476 44490 13410 18761
|
||||
910001 36580 44431 13351 18869
|
||||
924
src/kimono/lxpack/tests/ref/borbu1.00.ref
Normal file
924
src/kimono/lxpack/tests/ref/borbu1.00.ref
Normal file
@ -0,0 +1,924 @@
|
||||
# input : borbu1.fst
|
||||
# include : <none>
|
||||
# selector : count
|
||||
# distance : chi
|
||||
# phase : 7
|
||||
# alphabet : ACGT
|
||||
# seqname : borbu1
|
||||
# seqlength : 910724
|
||||
# unmasked : 910681
|
||||
# window : 227680
|
||||
# step : 1000
|
||||
#
|
||||
# pos LeftA RightA LeftC RightC LeftG RightG LeftT RightX chiACGT/not*s chiA chiC chiG chiT
|
||||
1 36566 44476 13342 18949 18446 13078 45482 37333 58.8352 27.7857 31.2025 -30.2337 -28.3172
|
||||
1001 36655 44524 13339 18989 18400 13116 45442 37207 58.7935 27.6183 31.4238 -29.7644 -28.6447
|
||||
2001 36782 44547 13364 18962 18360 13151 45330 37176 58.1183 27.2282 31.1356 -29.3443 -28.3876
|
||||
3001 36858 44580 13415 18951 18332 13135 45231 37170 57.6715 27.0593 30.7717 -29.2971 -28.0817
|
||||
4001 37042 44544 13413 19003 18275 13135 45106 37154 57.1282 26.2645 31.0479 -29.0021 -27.7257
|
||||
5001 37142 44434 13449 19062 18276 13084 44969 37256 56.6039 25.5309 31.1301 -29.3188 -26.8981
|
||||
6001 37169 44406 13498 19085 18259 13071 44910 37274 56.2905 25.3384 30.9516 -29.3103 -26.6362
|
||||
7001 37270 44326 13557 19097 18246 13048 44763 37365 55.4966 24.7015 30.6578 -29.3836 -25.8148
|
||||
8001 37350 44361 13624 19095 18202 13048 44662 37332 54.9699 24.5292 30.2475 -29.1539 -25.5959
|
||||
9001 37490 44294 13596 19130 18174 13026 44578 37386 54.6109 23.7945 30.5925 -29.1433 -25.1186
|
||||
10001 37685 44156 13595 19223 18183 12999 44375 37458 54.0676 22.6222 31.0685 -29.3555 -24.1773
|
||||
11001 37856 44039 13616 19296 18200 12945 44166 37556 53.5572 21.6083 31.3107 -29.7753 -23.1198
|
||||
12001 37999 43953 13627 19316 18196 12894 44016 37673 53.0257 20.8009 31.3456 -30.0682 -22.1903
|
||||
13001 38183 43804 13615 19393 18164 12882 43876 37757 52.4797 19.6334 31.8046 -29.976 -21.414
|
||||
14001 38354 43662 13612 19477 18140 12883 43732 37814 51.9943 18.537 32.2439 -29.8451 -20.7215
|
||||
15001 38499 43597 13580 19499 18134 12835 43625 37905 51.8044 17.7951 32.5457 -30.1098 -20.0301
|
||||
16001 38618 43545 13630 19522 18109 12831 43481 37938 51.1894 17.1913 32.3615 -30.0045 -19.4234
|
||||
17001 38733 43519 13644 19561 18110 12798 43351 37958 51.0247 16.6903 32.4729 -30.2135 -18.9105
|
||||
18001 38821 43555 13691 19562 18098 12785 43228 37934 50.675 16.4966 32.1972 -30.2314 -18.5801
|
||||
19001 38914 43623 13756 19502 18058 12789 43109 37923 49.933 16.391 31.5078 -30 -18.2181
|
||||
20001 38997 43648 13772 19512 18018 12770 43050 37907 49.7284 16.1785 31.4626 -29.9091 -18.0755
|
||||
21001 39060 43694 13800 19517 17962 12774 43015 37852 49.4553 16.1087 31.321 -29.5921 -18.1558
|
||||
22001 39024 43853 13901 19448 17900 12771 43012 37765 49.0158 16.7741 30.375 -29.2866 -18.4615
|
||||
23001 39089 43809 13992 19469 17761 12792 42995 37767 48.0812 16.3934 29.9415 -28.4277 -18.3964
|
||||
24001 39182 43772 14043 19474 17702 12783 42910 37808 47.4363 15.9365 29.6652 -28.173 -17.9579
|
||||
25001 39136 43869 14174 19413 17665 12748 42862 37807 46.8913 16.428 28.5866 -28.1949 -17.7979
|
||||
26001 39122 43859 14280 19413 17601 12771 42834 37794 46.2121 16.4442 27.9641 -27.7147 -17.7496
|
||||
27001 39222 43861 14291 19445 17526 12743 42798 37788 45.9748 16.0942 28.0606 -27.4917 -17.6485
|
||||
28001 39293 43803 14333 19478 17461 12767 42750 37788 45.4127 15.6467 27.9814 -26.9977 -17.4834
|
||||
29001 39315 43737 14433 19504 17377 12800 42712 37795 44.5834 15.3454 27.5277 -26.3469 -17.3281
|
||||
30001 39438 43681 14438 19496 17266 12799 42695 37860 43.8681 14.7184 27.4583 -25.7616 -17.0341
|
||||
31001 39538 43610 14449 19529 17167 12794 42683 37903 43.3672 14.1228 27.5599 -25.2632 -16.837
|
||||
32001 39613 43536 14519 19577 17161 12763 42544 37960 42.9281 13.606 27.393 -25.4233 -16.1548
|
||||
33001 39628 43599 14582 19577 17077 12780 42550 37880 42.5377 13.766 27.0269 -24.8673 -16.4655
|
||||
34001 39659 43600 14655 19583 17064 12754 42459 37899 42.1615 13.6594 26.6336 -24.9589 -16.0848
|
||||
35001 39668 43582 14731 19583 17048 12801 42390 37870 41.5803 13.5666 26.1938 -24.5813 -15.9535
|
||||
36001 39687 43550 14826 19595 16976 12801 42348 37890 40.9033 13.3908 25.7057 -24.1937 -15.7368
|
||||
37001 39731 43486 14903 19605 16946 12829 42257 37916 40.1799 13.0181 25.3126 -23.8584 -15.3299
|
||||
38001 39764 43521 14956 19608 16881 12888 42237 37819 39.6863 13.0209 25.024 -23.1414 -15.6121
|
||||
39001 39817 43536 15005 19611 16793 12941 42223 37748 39.0927 12.884 24.7579 -22.3373 -15.8219
|
||||
40001 39896 43487 15067 19651 16711 12952 42164 37746 38.4774 12.4384 24.6035 -21.824 -15.6263
|
||||
41001 39988 43397 15092 19711 16631 12967 42127 37761 38.0076 11.808 24.761 -21.2958 -15.4445
|
||||
42001 40046 43362 15156 19736 16557 12996 42079 37742 37.3864 11.4843 24.5206 -20.7128 -15.3483
|
||||
43001 40058 43363 15239 19739 16485 13033 42056 37701 36.761 11.4454 24.0627 -20.0907 -15.4182
|
||||
44001 40030 43469 15307 19699 16431 13059 42070 37609 36.4418 11.9037 23.4759 -19.6344 -15.8013
|
||||
45001 40047 43557 15341 19666 16335 13097 42115 37516 36.1046 12.1418 23.1174 -18.8726 -16.2951
|
||||
46001 40116 43543 15419 19639 16282 13124 42021 37530 35.2283 11.8509 22.5398 -18.4144 -15.9204
|
||||
47001 40081 43661 15506 19579 16205 13111 42046 37485 34.8423 12.3737 21.7464 -18.0689 -16.1706
|
||||
48001 40077 43708 15542 19583 16098 13084 42121 37461 34.7336 12.5467 21.5632 -17.642 -16.5163
|
||||
49001 40072 43692 15558 19582 16001 13086 42207 37476 34.5003 12.5103 21.4679 -17.0904 -16.7574
|
||||
50001 40160 43643 15578 19604 15893 13078 42207 37511 33.9944 12.0341 21.4658 -16.537 -16.6297
|
||||
51001 40169 43648 15668 19572 15811 13065 42190 37551 33.2853 12.0193 20.7982 -16.1582 -16.4255
|
||||
52001 40125 43775 15810 19510 15767 13031 42136 37520 32.7692 12.6037 19.6892 -16.1211 -16.3528
|
||||
53001 40112 43869 15910 19467 15688 13005 42128 37495 32.3446 12.9669 18.913 -15.8377 -16.4164
|
||||
54001 40149 43910 15984 19425 15554 12996 42151 37505 31.6676 12.9747 18.288 -15.1375 -16.4591
|
||||
55001 40164 43887 16083 19445 15473 13000 42118 37504 31.068 12.8442 17.8383 -14.6543 -16.3492
|
||||
56001 40209 43936 16151 19406 15438 12993 42040 37501 30.5341 12.8508 17.2635 -14.499 -16.0916
|
||||
57001 40231 44014 16226 19381 15402 13023 41979 37418 30.1752 13.0361 16.7215 -14.1091 -16.1842
|
||||
58001 40357 43954 16265 19391 15346 13025 41870 37466 29.3576 12.3905 16.5564 -13.7782 -15.633
|
||||
59001 40386 43993 16310 19369 15271 13006 41871 37468 29.0213 12.4199 16.1964 -13.468 -15.6292
|
||||
60001 40458 44005 16377 19346 15223 13011 41780 37474 28.3366 12.2073 15.7102 -13.1629 -15.293
|
||||
61001 40528 44049 16477 19328 15162 13005 41671 37454 27.6319 12.1096 15.0686 -12.8508 -14.9891
|
||||
62001 40558 44072 16546 19329 15094 12990 41640 37444 27.2407 12.0831 14.6957 -12.5528 -14.9171
|
||||
63001 40627 44134 16617 19291 15057 12991 41536 37420 26.6642 12.0471 14.1121 -12.3354 -14.6469
|
||||
64001 40798 44057 16647 19336 15048 12960 41344 37483 25.9016 11.1891 14.1765 -12.4757 -13.7506
|
||||
65001 40948 43949 16669 19414 15080 12933 41140 37540 25.3806 10.3009 14.4516 -12.8271 -12.833
|
||||
66001 40975 43930 16708 19421 15082 12862 41072 37623 25.1813 10.1425 14.2741 -13.2796 -12.2935
|
||||
67001 41028 43833 16772 19456 14983 12924 41054 37623 24.3537 9.63023 14.1022 -12.3246 -12.2307
|
||||
68001 41181 43686 16801 19536 14900 12947 40955 37667 23.543 8.60009 14.3486 -11.7027 -11.725
|
||||
69001 41251 43635 16850 19589 14830 12946 40906 37666 23.1134 8.18383 14.3494 -11.3036 -11.5575
|
||||
70001 41263 43701 16901 19574 14756 12997 40917 37564 22.8163 8.36533 13.9968 -10.558 -11.9676
|
||||
71001 41310 43708 16933 19572 14758 13002 40836 37554 22.5145 8.22549 13.8131 -10.5386 -11.7209
|
||||
72001 41535 43641 16926 19603 14711 13054 40665 37538 21.7296 7.21734 14.0073 -9.94355 -11.1807
|
||||
73001 41741 43566 16932 19642 14721 13076 40443 37552 21.0797 6.24971 14.1713 -9.86586 -10.3505
|
||||
74001 41932 43511 16947 19656 14716 13066 40242 37603 20.4238 5.40315 14.1604 -9.89852 -9.45731
|
||||
75001 42172 43400 16929 19704 14682 13049 40054 37683 19.9076 4.1992 14.4995 -9.80553 -8.50266
|
||||
76001 42364 43215 16881 19800 14661 13045 39931 37775 19.8702 2.91158 15.2427 -9.7071 -7.73187
|
||||
77001 42578 43156 16880 19806 14619 13017 39760 37856 19.4124 1.97658 15.2782 -9.63517 -6.83181
|
||||
78001 42757 43212 16867 19809 14580 13004 39633 37810 19.2707 1.55439 15.3638 -9.4877 -6.54837
|
||||
79001 42790 43225 16929 19817 14541 12992 39577 37801 18.8968 1.48578 15.0675 -9.33377 -6.38217
|
||||
80001 42882 43187 16948 19844 14460 12987 39547 37817 18.6218 1.0422 15.0998 -8.88964 -6.21737
|
||||
81001 42915 43228 16981 19867 14425 13019 39516 37721 18.4641 1.06901 15.0362 -8.48569 -6.45637
|
||||
82001 42942 43251 17022 19860 14431 13014 39442 37709 18.2092 1.05636 14.7802 -8.55121 -6.23553
|
||||
83001 43037 43266 17074 19844 14373 13014 39353 37710 17.6326 0.783371 14.4191 -8.20979 -5.91489
|
||||
84001 43090 43353 17169 19805 14316 13043 39261 37634 16.8044 0.895823 13.7096 -7.6955 -5.86608
|
||||
85001 43194 43474 17233 19713 14309 13005 39100 37643 16.0403 0.952407 12.9032 -7.88941 -5.25823
|
||||
86001 43268 43588 17264 19670 14259 12972 39045 37604 15.679 1.08839 12.5211 -7.79769 -5.20246
|
||||
87001 43417 43555 17241 19703 14226 12974 38952 37602 15.6756 0.470522 12.8107 -7.58992 -4.87679
|
||||
88001 43542 43558 17317 19668 14221 12960 38756 37648 14.9672 0.0567954 12.2264 -7.64717 -4.00607
|
||||
89001 43680 43559 17333 19678 14184 12980 38638 37618 14.6886 -0.409666 12.1893 -7.30516 -3.69371
|
||||
90001 43752 43652 17386 19651 14180 13011 38517 37521 14.2104 -0.338247 11.7693 -7.08928 -3.61197
|
||||
91001 43831 43757 17452 19569 14179 13013 38373 37496 13.4632 -0.25004 11.0026 -7.07095 -3.18396
|
||||
92001 43833 43865 17543 19497 14164 13037 38295 37436 12.6305 0.108058 10.1529 -6.83332 -3.12145
|
||||
93001 43844 43958 17634 19420 14070 13066 38288 37391 11.5763 0.38604 9.27905 -6.09409 -3.25944
|
||||
94001 43799 44055 17722 19357 13984 13098 38331 37325 10.7333 0.864994 8.49175 -5.38313 -3.65622
|
||||
95001 43852 44114 17775 19322 13890 13118 38319 37281 10.0802 0.884687 8.0328 -4.69682 -3.77396
|
||||
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||||
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||||
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||||
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||||
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||||
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||||
201001 43573 44364 19676 19382 12975 13719 37610 36372 7.12607 2.66352 -1.49022 4.55157 -4.5551
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||||
202001 43555 44376 19676 19355 12960 13709 37643 36397 7.23255 2.76478 -1.6274 4.58432 -4.58272
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||||
203001 43568 44407 19673 19339 12985 13655 37609 36436 6.80396 2.82607 -1.69275 4.10352 -4.31311
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||||
204001 43678 44396 19643 19341 13012 13610 37502 36490 5.9554 2.41676 -1.53128 3.66363 -3.72278
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||||
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||||
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||||
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||||
209001 44155 44314 19305 19425 13125 13447 37250 36649 3.07365 0.534566 0.609758 1.97535 -2.21083
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211001 44344 44236 19264 19492 13140 13407 37086 36701 2.48338 -0.365485 1.15642 1.63729 -1.41971
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214001 44513 44071 19284 19488 13140 13297 36897 36980 2.07469 -1.48767 1.0343 0.964168 0.302989
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215001 44530 44074 19310 19429 13172 13327 36822 37006 2.01929 -1.53453 0.602882 0.950751 0.674805
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216001 44625 44024 19266 19444 13213 13321 36730 37047 2.58739 -2.02114 0.902982 0.661585 1.16469
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217001 44752 43935 19187 19467 13202 13307 36693 37127 3.53865 -2.74603 1.42245 0.643472 1.59498
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218001 44927 43766 19096 19536 13196 13310 36615 37224 5.07169 -3.90102 2.23689 0.698788 2.23878
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||||
219001 44988 43679 19094 19570 13207 13317 36545 37270 5.72381 -4.39862 2.41905 0.67399 2.66612
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||||
220001 44986 43672 19102 19571 13211 13315 36535 37278 5.74885 -4.41563 2.38317 0.637125 2.7324
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||||
221001 45062 43648 19054 19605 13227 13281 36491 37302 6.27813 -4.75008 2.80065 0.330242 2.9831
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||||
222001 45096 43715 19004 19586 13245 13288 36489 37247 6.17363 -4.63665 2.96096 0.262556 2.78907
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||||
223001 45097 43727 19034 19567 13262 13322 36441 37220 6.07156 -4.5994 2.71114 0.366567 2.86787
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||||
224001 45143 43712 19033 19568 13290 13327 36368 37229 6.37065 -4.80325 2.72132 0.225362 3.17138
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||||
225001 45193 43749 19068 19492 13308 13354 36265 37241 6.4144 -4.84449 2.1575 0.280283 3.5975
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||||
226001 45191 43843 19070 19467 13331 13379 36242 37147 5.97873 -4.52026 2.02061 0.292267 3.33829
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||||
227001 45192 43910 19069 19409 13350 13389 36223 37128 5.71598 -4.29743 1.73158 0.237069 3.33915
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||||
228001 45079 43995 19046 19368 13333 13453 36376 37020 4.69885 -3.63468 1.64118 0.731773 2.37474
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||||
229001 45061 44004 19025 19362 13311 13526 36437 36944 4.55281 -3.54439 1.71832 1.31098 1.86924
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||||
230001 45070 44013 19011 19389 13323 13535 36430 36899 4.57554 -3.54403 1.92725 1.29216 1.72958
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||||
231001 45033 44022 19010 19363 13340 13531 36451 36920 4.36809 -3.39044 1.80031 1.16374 1.72908
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||||
232001 45001 44011 19000 19372 13353 13605 36480 36848 4.33817 -3.32087 1.89733 1.53338 1.35661
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||||
233001 45123 43969 18944 19398 13371 13635 36396 36834 5.05212 -3.86884 2.31685 1.60504 1.61619
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||||
234001 45250 43870 18869 19449 13392 13628 36323 36889 6.04856 -4.62527 2.96125 1.43428 2.08945
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||||
235001 45292 43797 18820 19496 13444 13599 36278 36944 6.63024 -5.01136 3.45176 0.941108 2.45886
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||||
236001 45290 43774 18824 19512 13454 13620 36266 36930 6.72258 -5.08243 3.51215 1.00742 2.45191
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||||
237001 45317 43817 18802 19505 13491 13624 36224 36890 6.69799 -5.02685 3.59012 0.806252 2.46068
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||||
238001 45336 43835 18789 19486 13488 13627 36221 36887 6.68867 -5.02785 3.56181 0.843404 2.46196
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||||
239001 45399 43816 18749 19497 13480 13643 36206 36879 7.06358 -5.30114 3.82394 0.989007 2.48824
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||||
240001 45407 43815 18756 19465 13491 13661 36180 36894 7.04266 -5.33107 3.6257 1.03096 2.6401
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||||
241001 45428 43859 18709 19457 13499 13612 36198 36907 7.04118 -5.25215 3.82795 0.68556 2.62105
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||||
242001 45485 43921 18698 19402 13502 13603 36149 36909 6.97496 -5.23194 3.60584 0.612748 2.81057
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||||
243001 45509 44016 18682 19368 13524 13611 36119 36840 6.68359 -4.99117 3.51593 0.52742 2.6681
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||||
244001 45553 44033 18665 19355 13569 13627 36047 36820 6.82905 -5.07967 3.53784 0.350977 2.86242
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||||
245001 45564 44111 18647 19311 13569 13673 36054 36740 6.48228 -4.85342 3.40727 0.62938 2.5414
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||||
246001 45554 44040 18646 19355 13563 13655 36071 36785 6.79121 -5.0594 3.63619 0.556921 2.64405
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||||
247001 45526 44054 18627 19362 13649 13578 36032 36841 6.89746 -4.91947 3.77016 -0.431017 2.99566
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||||
248001 45487 44138 18620 19321 13763 13454 35964 36922 7.02539 -4.50738 3.59799 -1.87373 3.54729
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||||
249001 45498 44160 18602 19322 13758 13429 35976 36924 7.06725 -4.46981 3.69636 -1.99606 3.50991
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||||
250001 45480 44121 18610 19307 13801 13358 35943 37049 7.57688 -4.54139 3.57859 -2.68883 4.09252
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||||
251001 45491 44241 18574 19257 13777 13341 35992 36996 7.11087 -4.1742 3.51067 -2.64836 3.71508
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||||
252001 45446 44308 18615 19224 13810 13288 35963 37015 7.03212 -3.79985 3.12989 -3.17176 3.89302
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||||
253001 45545 44203 18559 19260 13808 13290 35922 37082 7.83544 -4.48093 3.60379 -3.14747 4.29204
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||||
254001 45639 44082 18520 19304 13796 13288 35879 37160 8.67557 -5.19806 4.03118 -3.08679 4.73993
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||||
255001 45626 44029 18505 19331 13817 13236 35886 37238 9.16267 -5.33357 4.24646 -3.53239 4.99973
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||||
256001 45670 44066 18445 19329 13810 13246 35910 37193 9.14511 -5.3532 4.54923 -3.42812 4.74645
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||||
257001 45715 44041 18410 19336 13880 13228 35830 37229 9.81882 -5.58625 4.7671 -3.95931 5.17703
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||||
258001 45781 44109 18395 19323 13936 13145 35723 37257 10.4537 -5.57542 4.77916 -4.80594 5.67955
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||||
259001 45851 44109 18351 19333 13984 13111 35649 37281 11.1342 -5.80663 5.05948 -5.30286 6.04439
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||||
260001 45866 44107 18318 19325 13979 13138 35672 37264 11.0526 -5.86289 5.19109 -5.10638 5.89603
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||||
261001 45909 44083 18286 19331 14029 13134 35610 37287 11.5823 -6.08826 5.38711 -5.43115 6.21005
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||||
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265001 46039 44082 18270 19327 13995 13143 35530 37283 11.8813 -6.52028 5.45043 -5.17263 6.49528
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266001 46119 43994 18235 19365 13938 13129 35542 37347 12.3673 -7.08021 5.82668 -4.91805 6.6845
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||||
267001 46137 43900 18229 19405 13939 13103 35529 37427 12.9441 -7.45646 6.06116 -5.08451 7.02574
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268001 46187 43859 18213 19454 13964 13092 35469 37431 13.4901 -7.76196 6.39173 -5.30349 7.26312
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269001 46231 43872 18191 19430 13946 13097 35465 37437 13.5116 -7.86278 6.38532 -5.1649 7.30006
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271001 46336 43831 18132 19437 13897 13128 35468 37440 13.7893 -8.34622 6.73025 -4.67998 7.29976
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||||
272001 46270 43887 18182 19414 13872 13170 35509 37365 12.9943 -7.94036 6.35135 -4.27108 6.87176
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274001 46167 43951 18246 19417 13799 13301 35621 37167 11.5277 -7.38577 6.03136 -3.0273 5.72678
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||||
275001 46187 43883 18256 19451 13789 13293 35601 37209 11.8914 -7.68096 6.15144 -3.01615 5.95568
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||||
276001 46183 43912 18267 19458 13835 13280 35548 37186 11.9622 -7.56995 6.12937 -3.37262 6.07005
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||||
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||||
278001 46235 43823 18207 19517 13852 13282 35539 37211 12.6685 -8.03741 6.7447 -3.46033 6.19897
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279001 46151 43843 18243 19529 13887 13277 35552 37184 12.3811 -7.69359 6.61692 -3.70112 6.05126
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||||
282001 45993 43882 18356 19491 13840 13305 35644 37155 11.2039 -7.04156 5.83418 -3.2472 5.60018
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||||
283001 45981 43887 18359 19521 13855 13302 35638 37123 11.2252 -6.98512 5.97037 -3.35571 5.50525
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||||
284001 45872 43849 18413 19530 13833 13332 35715 37122 10.7199 -6.75381 5.73439 -3.03972 5.21336
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||||
285001 45815 43831 18449 19552 13847 13302 35722 37148 10.7131 -6.62638 5.6582 -3.30765 5.28257
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||||
286001 45808 43738 18505 19583 13860 13273 35660 37239 11.1921 -6.91747 5.52363 -3.5636 5.84819
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||||
287001 45787 43697 18542 19592 13860 13309 35644 37235 11.119 -6.98672 5.37691 -3.34283 5.89344
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||||
288001 45880 43551 18510 19661 13870 13322 35573 37299 12.1361 -7.78799 5.89126 -3.32323 6.39382
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289001 45885 43425 18498 19719 13916 13331 35534 37358 12.8441 -8.23162 6.24579 -3.54402 6.75593
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||||
290001 45857 43397 18486 19758 13917 13369 35574 37309 12.7443 -8.23288 6.50524 -3.31677 6.42786
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291001 45780 43408 18526 19760 13959 13344 35569 37321 12.6025 -7.94126 6.30746 -3.72122 6.49052
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292001 45743 43399 18522 19785 13944 13355 35625 37294 12.4172 -7.84952 6.4539 -3.56413 6.18186
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||||
293001 45766 43372 18522 19774 13957 13324 35589 37363 12.7693 -8.01717 6.39862 -3.8317 6.56922
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294001 45755 43327 18572 19780 13964 13322 35543 37404 12.9154 -8.13361 6.16927 -3.88583 6.89156
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295001 45758 43342 18589 19761 13944 13302 35543 37428 12.851 -8.09258 5.9856 -3.88868 6.97927
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296001 45749 43348 18561 19761 13934 13325 35590 37399 12.6775 -8.04247 6.13082 -3.68788 6.6971
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297001 45690 43412 18558 19750 13912 13308 35674 37363 12.1569 -7.63018 6.09106 -3.66021 6.25087
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||||
298001 45602 43498 18579 19724 13845 13308 35808 37303 11.1849 -7.04736 5.85131 -3.25813 5.53023
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299001 45526 43488 18648 19679 13782 13328 35878 37338 10.5409 -6.82954 5.26717 -2.75662 5.39693
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301001 45241 43665 18801 19554 13708 13297 36084 37317 8.34791 -5.28424 3.84575 -2.50031 4.55225
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||||
302001 45163 43685 18833 19565 13725 13299 36113 37284 7.9962 -4.95719 3.73644 -2.59068 4.32353
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||||
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304001 45170 43800 18865 19456 13762 13315 36038 37262 7.61765 -4.59041 3.02075 -2.71504 4.52331
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305001 45042 43856 18943 19402 13771 13357 36079 37218 6.73308 -3.97514 2.34572 -2.51213 4.20944
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306001 44949 43885 19006 19371 13790 13367 36090 37210 6.31802 -3.56725 1.86491 -2.5654 4.13919
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307001 44955 43860 19004 19445 13792 13392 36084 37136 6.28958 -3.67165 2.25075 -2.42462 3.89014
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||||
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309001 44685 44004 19148 19327 13792 13375 36211 37127 4.88912 -2.2828 0.915141 -2.5278 3.386
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311001 44551 44093 19250 19198 13704 13356 36331 37186 4.10557 -1.53439 -0.262617 -2.11335 3.15692
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312001 44527 44087 19280 19163 13707 13349 36322 37234 4.31108 -1.47418 -0.594153 -2.1743 3.36624
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313001 44499 44109 19340 19123 13738 13389 36260 37212 4.44591 -1.30495 -1.10302 -2.11608 3.51693
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314001 44400 44171 19387 19089 13749 13429 36301 37144 4.04273 -0.764241 -1.51577 -1.93817 3.11537
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||||
315001 44376 44230 19377 19036 13729 13482 36355 37085 3.57295 -0.485252 -1.73643 -1.49446 2.69851
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316001 44390 44215 19352 19027 13694 13545 36401 37046 3.09468 -0.58268 -1.65553 -0.899899 2.38474
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317001 44418 44128 19327 19064 13656 13580 36436 37061 2.87721 -0.969347 -1.33883 -0.457615 2.31015
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318001 44381 44081 19345 19083 13604 13584 36507 37085 2.71256 -1.00343 -1.33309 -0.1184 2.13541
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319001 44381 44012 19373 19118 13564 13579 36518 37125 2.87074 -1.23853 -1.29803 0.0924926 2.23915
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320001 44280 44049 19410 19096 13518 13560 36628 37129 2.57543 -0.774645 -1.59844 0.256677 1.84713
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321001 44253 44042 19427 19091 13483 13541 36673 37160 2.60229 -0.707487 -1.71029 0.354262 1.79465
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322001 44280 43879 19425 19192 13455 13599 36676 37164 2.68727 -1.34795 -1.18395 0.876925 1.79825
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323001 44336 43643 19413 19323 13429 13671 36657 37198 3.43391 -2.33638 -0.457283 1.47005 1.99071
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324001 44291 43426 19454 19439 13412 13734 36678 37236 4.07035 -2.92061 -0.0760599 1.95435 2.05244
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325001 44226 43338 19504 19498 13402 13775 36704 37224 4.21702 -2.99958 -0.0295108 2.26333 1.91368
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326001 44157 43221 19569 19587 13356 13869 36754 37158 4.68075 -3.16516 0.0918357 3.10982 1.48722
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327001 44088 43037 19566 19724 13324 13939 36858 37135 5.31261 -3.55936 0.797978 3.7254 1.01953
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||||
328001 44077 42921 19460 19805 13293 13973 37006 37136 5.96478 -3.91795 1.74194 4.11884 0.478636
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329001 44057 42855 19432 19822 13338 13895 37009 37263 5.72359 -4.07592 1.96932 3.37599 0.933216
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330001 44011 42824 19452 19822 13319 13894 37054 37295 5.71334 -4.02682 1.8679 3.48634 0.885057
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331001 43931 42763 19472 19876 13297 13953 37136 37243 5.98583 -3.96557 2.03754 3.97466 0.39354
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332001 43733 42643 19536 20001 13313 14029 37254 37162 6.1715 -3.70748 2.33945 4.33083 -0.33605
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||||
333001 43683 42604 19566 20022 13313 14026 37274 37183 6.11976 -3.67194 2.29271 4.31292 -0.332292
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334001 43655 42632 19581 20030 13306 14018 37294 37155 6.00255 -3.4813 2.25687 4.30806 -0.508229
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335001 43677 42592 19596 20030 13265 14021 37298 37192 6.28461 -3.69276 2.18109 4.57742 -0.387178
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||||
336001 43699 42611 19585 20012 13298 13983 37254 37229 5.96052 -3.70209 2.14671 4.14798 -0.0904005
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||||
337001 43724 42662 19564 19998 13334 13931 37214 37244 5.55887 -3.612 2.18285 3.61625 0.111146
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||||
338001 43712 42611 19566 19971 13332 13870 37226 37383 5.4002 -3.74606 2.0377 3.26271 0.575987
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||||
339001 43752 42564 19491 20029 13372 13800 37221 37442 5.57411 -4.04233 2.70716 2.59719 0.810002
|
||||
340001 43845 42466 19449 20068 13382 13763 37160 37538 6.24411 -4.69257 3.11473 2.31322 1.38425
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||||
341001 43930 42387 19403 20126 13402 13758 37101 37564 6.95298 -5.25061 3.63735 2.16089 1.69563
|
||||
342001 43988 42313 19366 20193 13455 13700 37027 37629 7.54078 -5.70043 4.15886 1.48749 2.20446
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||||
343001 44000 42336 19367 20231 13527 13639 36942 37629 7.59697 -5.66184 4.34275 0.680251 2.51698
|
||||
344001 43993 42381 19396 20222 13536 13626 36911 37606 7.35435 -5.48366 4.15074 0.546813 2.5472
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||||
345001 44046 42443 19352 20168 13523 13650 36915 37574 7.27891 -5.44941 4.10558 0.77116 2.41578
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||||
346001 44007 42436 19369 20103 13624 13609 36836 37687 7.20599 -5.34202 3.69534 -0.0901651 3.11855
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||||
347001 43936 42430 19412 20015 13641 13637 36847 37753 6.81812 -5.12322 3.03771 -0.0234881 3.31831
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||||
348001 43865 42379 19451 19953 13629 13707 36891 37794 6.5681 -5.05618 2.53152 0.47394 3.30782
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||||
349001 43769 42415 19498 19853 13597 13792 36972 37773 5.86914 -4.60831 1.79219 1.18045 2.93342
|
||||
350001 43786 42402 19501 19765 13618 13864 36931 37802 6.0293 -4.71039 1.33489 1.4861 3.18972
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||||
351001 43831 42363 19492 19692 13624 13929 36889 37849 6.45988 -4.99634 1.01296 1.83963 3.51515
|
||||
352001 43862 42323 19484 19617 13624 14003 36865 37891 6.87132 -5.24101 0.673473 2.28093 3.75374
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||||
353001 43779 42233 19494 19604 13650 14059 36912 37938 6.94252 -5.27016 0.55718 2.45778 3.75139
|
||||
354001 43826 42127 19458 19603 13641 14073 36910 38031 7.59106 -5.79384 0.734535 2.59572 4.09614
|
||||
355001 43862 42062 19450 19562 13618 14137 36905 38073 8.11968 -6.13936 0.567919 3.11602 4.26677
|
||||
356001 43937 41894 19398 19573 13605 14191 36895 38176 9.1448 -6.97213 0.887349 3.51558 4.67655
|
||||
357001 44030 41675 19355 19585 13605 14191 36845 38383 10.4817 -8.043 1.16642 3.51558 5.60868
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||||
358001 44039 41579 19361 19532 13637 14147 36798 38576 11.0786 -8.40593 0.867955 3.0604 6.47743
|
||||
359001 44113 41466 19296 19514 13667 14170 36759 38684 11.8872 -9.04708 1.10746 3.01553 7.00966
|
||||
360001 44046 41387 19357 19441 13642 14229 36790 38777 12.147 -9.09586 0.427328 3.51684 7.22945
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||||
361001 44051 41292 19358 19414 13563 14262 36863 38866 12.6417 -9.44296 0.285271 4.19117 7.27985
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||||
362001 44132 41204 19320 19371 13447 14312 36936 38947 13.4454 -10.0219 0.260149 5.19249 7.3015
|
||||
363001 44157 41057 19315 19342 13418 14353 36945 39082 14.2948 -10.6183 0.138196 5.61142 7.75156
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||||
364001 44125 40916 19316 19344 13357 14396 37037 39178 14.8375 -11.0028 0.143277 6.23751 7.75648
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||||
365001 44270 40743 19236 19321 13346 14467 36983 39302 16.1924 -12.094 0.434601 6.7232 8.39859
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||||
366001 44289 40683 19227 19267 13281 14574 37038 39309 16.7524 -12.368 0.205595 7.7487 8.22147
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||||
367001 44189 40649 19279 19209 13289 14615 37078 39360 16.7026 -12.1511 -0.35509 7.93945 8.25636
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||||
368001 44065 40636 19323 19134 13285 14668 37161 39396 16.5354 -11.7821 -0.963772 8.27195 8.07765
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||||
369001 44027 40575 19332 19111 13243 14750 37232 39398 16.8664 -11.8681 -1.12715 9.00717 7.82454
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||||
370001 44097 40473 19321 19090 13246 14787 37170 39484 17.6423 -12.4618 -1.17865 9.20381 8.35788
|
||||
371001 44040 40496 19347 19002 13212 14806 37235 39530 17.6345 -12.1891 -1.76174 9.52291 8.28326
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||||
372001 44131 40322 19314 18971 13133 14892 37256 39649 18.9666 -13.107 -1.75299 10.5073 8.6291
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||||
373001 44128 40266 19324 18925 13111 14958 37271 39685 19.4462 -13.294 -2.04015 11.0244 8.70194
|
||||
374001 44088 40247 19330 18877 13139 15011 37278 39699 19.5177 -13.2251 -2.31667 11.1582 8.7272
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||||
375001 44102 40149 19328 18842 13149 15038 37256 39805 20.0641 -13.6175 -2.4867 11.2522 9.18355
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||||
376001 44168 40050 19267 18769 13208 15035 37192 39980 20.6588 -14.1888 -2.55261 10.8721 10.0373
|
||||
377001 44202 40007 19250 18678 13192 15119 37191 40030 21.2872 -14.4549 -2.93623 11.4533 10.2176
|
||||
378001 44198 39940 19276 18632 13142 15277 37219 39985 22.0435 -14.6782 -3.30679 12.6654 9.95602
|
||||
379001 44065 39926 19330 18505 13140 15322 37300 40081 22.1175 -14.2804 -4.24052 12.9344 9.99855
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||||
380001 43970 39847 19385 18427 13125 15389 37355 40171 22.5639 -14.2399 -4.92578 13.4082 10.1149
|
||||
381001 43884 39785 19426 18328 13106 15392 37419 40329 22.9137 -14.1696 -5.65008 13.5423 10.4376
|
||||
382001 43861 39798 19450 18229 13085 15478 37440 40329 23.3388 -14.0447 -6.28852 14.1607 10.3621
|
||||
383001 43866 39782 19439 18179 13099 15574 37432 40299 23.6851 -14.1182 -6.4947 14.6178 10.2857
|
||||
384001 43751 39747 19485 18113 13122 15702 37478 40272 23.9459 -13.854 -7.07404 15.198 10.0226
|
||||
385001 43844 39639 19435 18098 13135 15794 37422 40303 24.7107 -14.551 -6.8995 15.6348 10.3363
|
||||
386001 43890 39552 19413 18091 13181 15871 37352 40320 25.1915 -15.015 -6.82471 15.7836 10.652
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||||
387001 43936 39496 19423 18038 13256 15925 37221 40375 25.6867 -15.369 -7.15413 15.6257 11.3249
|
||||
388001 43930 39439 19411 17985 13304 16020 37191 40390 26.0724 -15.5514 -7.37237 15.862 11.4876
|
||||
389001 43892 39414 19458 17914 13277 16140 37209 40366 26.6761 -15.5123 -7.98513 16.694 11.3372
|
||||
390001 43889 39393 19471 17824 13280 16233 37196 40384 27.2383 -15.5769 -8.52672 17.1907 11.4482
|
||||
391001 43830 39415 19521 17750 13293 16342 37189 40330 27.5549 -15.3072 -9.17684 17.7085 11.2765
|
||||
392001 43836 39397 19501 17694 13267 16424 37229 40322 27.9923 -15.3915 -9.37287 18.3185 11.1018
|
||||
393001 43831 39352 19538 17612 13282 16487 37182 40386 28.6081 -15.5348 -9.99594 18.5727 11.4992
|
||||
394001 43818 39419 19536 17511 13318 16578 37161 40329 28.778 -15.2525 -10.5242 18.8513 11.3756
|
||||
395001 43851 39387 19512 17418 13321 16680 37149 40352 29.438 -15.4777 -10.8999 19.3898 11.5005
|
||||
396001 43878 39410 19497 17323 13318 16781 37140 40323 29.9545 -15.4869 -11.333 19.9577 11.4315
|
||||
397001 43882 39394 19520 17228 13299 16926 37132 40289 30.8026 -15.5573 -11.9597 20.8594 11.3412
|
||||
398001 43843 39486 19546 17132 13321 16971 37123 40247 30.8648 -15.0973 -12.6073 20.9692 11.2275
|
||||
399001 43811 39484 19557 17020 13295 17015 37170 40317 31.3866 -14.9964 -13.2678 21.365 11.3016
|
||||
400001 43745 39489 19583 16893 13277 17085 37228 40369 31.9491 -14.7558 -14.0872 21.8518 11.2721
|
||||
401001 43688 39529 19600 16775 13317 17095 37228 40437 32.0808 -14.4211 -14.8146 21.6617 11.5112
|
||||
402001 43521 39537 19689 16661 13320 17158 37303 40480 32.5024 -13.8276 -15.8844 21.982 11.3877
|
||||
403001 43429 39594 19727 16549 13328 17187 37349 40506 32.7352 -13.3134 -16.6882 22.0888 11.3107
|
||||
404001 43398 39661 19762 16403 13372 17239 37301 40533 33.2089 -12.9705 -17.6656 22.0999 11.5811
|
||||
405001 43414 39736 19768 16303 13344 17297 37307 40500 33.7128 -12.7588 -18.2467 22.5804 11.4433
|
||||
406001 43409 39832 19787 16173 13346 17355 37291 40476 34.2179 -12.4018 -19.0605 22.8779 11.4175
|
||||
407001 43337 39946 19783 16048 13317 17433 37396 40409 34.5691 -11.7541 -19.734 23.4698 10.7981
|
||||
408001 43343 40026 19775 15923 13320 17485 37395 40402 35.0283 -11.4918 -20.39 23.7281 10.7772
|
||||
409001 43353 40133 19754 15802 13301 17537 37425 40364 35.4452 -11.148 -20.961 24.1197 10.5339
|
||||
410001 43347 40149 19764 15711 13326 17629 37396 40347 35.9959 -11.0712 -21.5211 24.4548 10.5801
|
||||
411001 43439 40014 19743 15709 13311 17750 37340 40363 36.7639 -11.8598 -21.4272 25.1847 10.8411
|
||||
412001 43497 39949 19720 15654 13306 17832 37310 40401 37.4036 -12.2861 -21.621 25.6466 11.0845
|
||||
413001 43498 39939 19678 15590 13326 17902 37331 40405 37.6532 -12.3249 -21.7706 25.8926 11.0217
|
||||
414001 43620 39834 19588 15564 13328 17976 37297 40462 38.0967 -13.1094 -21.4651 26.268 11.3464
|
||||
415001 43657 39719 19560 15527 13303 18009 37313 40581 38.6517 -13.6419 -21.533 26.5925 11.7056
|
||||
416001 43688 39619 19556 15513 13287 18033 37302 40671 39.11 -14.1015 -21.5919 26.8151 12.0614
|
||||
417001 43775 39434 19495 15566 13254 18117 37309 40719 39.6185 -15.0527 -20.9856 27.4538 12.2039
|
||||
418001 43808 39317 19448 15595 13323 18052 37254 40872 39.3269 -15.5806 -20.585 26.6956 12.9404
|
||||
419001 43874 39260 19404 15514 13349 18100 37206 40962 39.8453 -16.0063 -20.8198 26.7882 13.4305
|
||||
420001 43887 39225 19386 15420 13374 18135 37186 41056 40.3016 -16.1749 -21.2606 26.819 13.8317
|
||||
421001 43852 39229 19458 15269 13396 18165 37127 41173 41.1368 -16.0426 -22.4814 26.842 14.4555
|
||||
422001 43908 39143 19409 15194 13378 18210 37138 41289 41.7812 -16.5383 -22.6614 27.1849 14.8188
|
||||
423001 44018 39080 19305 15174 13375 18237 37135 41345 41.9763 -17.1337 -22.2498 27.3434 15.0244
|
||||
424001 44080 39020 19226 15132 13361 18286 37166 41398 42.3124 -17.5567 -22.0893 27.6824 15.0948
|
||||
425001 44081 38888 19190 15121 13345 18342 37217 41485 42.744 -18.0323 -21.9694 28.0694 15.2099
|
||||
426001 44100 38738 19151 15129 13347 18339 37235 41630 43.0158 -18.6337 -21.7255 28.0417 15.6464
|
||||
427001 44126 38579 19119 15132 13396 18322 37192 41799 43.2421 -19.287 -21.5424 27.6601 16.3931
|
||||
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|
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|
||||
758001 36170 36560 13345 13421 19127 18825 45195 45027 2.24121 1.45087 0.467409 -1.54679 -0.554044
|
||||
759001 36168 36484 13358 13437 19200 18758 45110 45155 2.60319 1.17473 0.484051 -2.26696 0.152414
|
||||
760001 36192 36412 13332 13477 19225 18736 45087 45209 2.81333 0.818839 0.887012 -2.5081 0.408635
|
||||
761001 36249 36283 13330 13523 19174 18743 45083 45285 2.59879 0.128607 1.1792 -2.21169 0.674597
|
||||
762001 36285 36293 13304 13532 19173 18754 45074 45255 2.6324 0.0320566 1.39323 -2.14978 0.60487
|
||||
763001 36249 36312 13286 13545 19155 18784 45145 45194 2.49186 0.233878 1.58118 -1.90472 0.163027
|
||||
764001 36271 36391 13254 13511 19191 18759 45119 45174 2.7599 0.445172 1.5709 -2.21757 0.183036
|
||||
765001 36343 36486 13220 13489 19255 18719 45017 45141 3.27508 0.529888 1.64598 -2.75056 0.412971
|
||||
766001 36404 36476 13160 13505 19328 18713 44943 45141 3.86168 0.266703 2.11275 -3.15318 0.659692
|
||||
767001 36440 36473 13174 13465 19393 18697 44828 45200 4.17715 0.122211 1.78293 -3.56618 1.23981
|
||||
768001 36402 36479 13228 13442 19402 18686 44803 45228 4.15506 0.285222 1.3104 -3.66876 1.41642
|
||||
769001 36315 36478 13275 13429 19435 18660 44810 45268 4.39867 0.604147 0.942394 -3.97071 1.52601
|
||||
770001 36256 36454 13297 13454 19396 18666 44886 45261 4.1257 0.734291 0.959908 -3.74177 1.24898
|
||||
771001 36196 36435 13339 13435 19344 18654 44956 45311 3.88026 0.886823 0.586698 -3.53972 1.18158
|
||||
772001 36177 36425 13318 13452 19314 18693 45026 45265 3.50672 0.920402 0.818994 -3.18537 0.795382
|
||||
773001 36128 36439 13381 13398 19330 18626 44998 45372 3.99364 1.15686 0.105319 -3.61183 1.24675
|
||||
774001 36046 36434 13377 13383 19325 18621 45089 45397 4.02341 1.44355 0.0381125 -3.61231 1.02654
|
||||
775001 36111 36440 13332 13393 19335 18594 45059 45408 4.17781 1.22381 0.374569 -3.8031 1.16297
|
||||
776001 36073 36467 13299 13412 19360 18624 45105 45331 4.17659 1.46642 0.693552 -3.77383 0.755466
|
||||
777001 36027 36594 13307 13368 19332 18660 45171 45212 4.05848 2.10756 0.375632 -3.44509 0.140324
|
||||
778001 36098 36590 13309 13380 19367 18679 45063 45185 4.01563 1.82842 0.436752 -3.52466 0.410056
|
||||
779001 36154 36602 13302 13390 19427 18690 44954 45152 4.21115 1.66445 0.540777 -3.77236 0.663562
|
||||
780001 36216 36632 13304 13383 19534 18662 44783 45157 4.90632 1.54484 0.485734 -4.4592 1.25102
|
||||
781001 36278 36605 13304 13388 19574 18663 44681 45178 5.11712 1.2148 0.516293 -4.65626 1.66191
|
||||
782001 36348 36652 13288 13403 19612 18637 44588 45143 5.48159 1.12635 0.704628 -4.98448 1.85409
|
||||
783001 36383 36666 13303 13398 19591 18658 44559 45113 5.25505 1.04827 0.5821 -4.76972 1.85136
|
||||
784001 36427 36637 13319 13409 19648 18591 44442 45198 6.04153 0.778095 0.551223 -5.40447 2.52637
|
||||
785001 36494 36557 13300 13417 19716 18561 44326 45300 6.78258 0.234281 0.716521 -5.90268 3.25475
|
||||
786001 36536 36562 13311 13397 19771 18517 44218 45359 7.476 0.0973546 0.526953 -6.40778 3.81362
|
||||
787001 36617 36544 13238 13422 19812 18544 44169 45325 7.62845 -0.2687 1.12763 -6.47358 3.86553
|
||||
788001 36673 36482 13250 13435 19851 18561 44062 45357 7.99114 -0.704986 1.13322 -6.58111 4.33199
|
||||
789001 36743 36359 13248 13450 19851 18598 43994 45428 8.20824 -1.41907 1.23699 -6.38925 4.79675
|
||||
790001 36809 36354 13231 13433 19838 18595 43958 45453 8.34016 -1.68095 1.23778 -6.33957 5.00104
|
||||
791001 36889 36279 13245 13487 19806 18560 43896 45509 8.76603 -2.25392 1.48085 -6.36042 5.39585
|
||||
792001 36951 36281 13237 13487 19802 18503 43846 45564 9.24832 -2.47465 1.53001 -6.63628 5.74686
|
||||
793001 36991 36278 13202 13460 19837 18464 43806 45633 9.79665 -2.63289 1.58078 -7.01475 6.11038
|
||||
794001 36987 36332 13178 13456 19849 18436 43822 45611 9.83311 -2.41779 1.70416 -7.22064 5.98352
|
||||
795001 36977 36461 13145 13422 19816 18460 43898 45492 9.10916 -1.9029 1.70017 -6.93014 5.33276
|
||||
796001 36975 36590 13152 13358 19834 18476 43875 45411 8.84181 -1.41827 1.26592 -6.93728 5.14176
|
||||
797001 37017 36576 13154 13331 19839 18432 43825 45497 9.31937 -1.62682 1.08689 -7.19302 5.59313
|
||||
798001 37042 36669 13171 13334 19759 18393 43863 45440 8.92449 -1.37506 1.00049 -6.99432 5.27582
|
||||
799001 37007 36783 13203 13361 19692 18346 43933 45346 8.46239 -0.825813 0.968695 -6.90224 4.72766
|
||||
800001 37023 36875 13175 13427 19660 18323 43977 45211 8.17431 -0.545636 1.54433 -6.86106 4.13069
|
||||
801001 37035 37050 13199 13418 19702 18266 43899 45102 8.50746 0.0539063 1.34162 -7.37048 4.03112
|
||||
802001 37059 37164 13182 13445 19721 18279 43873 44948 8.39506 0.384204 1.61102 -7.39817 3.60572
|
||||
803001 37043 37182 13203 13500 19667 18258 43922 44896 8.16041 0.508995 1.81679 -7.23602 3.26688
|
||||
804001 37024 37282 13190 13562 19572 18236 44049 44756 7.67507 0.945267 2.27367 -6.87177 2.37115
|
||||
805001 36947 37372 13228 13627 19516 18195 44142 44644 7.58095 1.55299 2.43118 -6.80677 1.67819
|
||||
806001 36917 37506 13279 13592 19416 18186 44222 44554 7.05574 2.15425 1.90655 -6.34647 1.10904
|
||||
807001 36869 37698 13301 13604 19372 18182 44292 44354 7.09792 3.03107 1.84437 -6.14412 0.203009
|
||||
808001 36784 37880 13310 13626 19357 18196 44383 44136 7.50856 4.00622 1.92252 -5.99455 -0.835413
|
||||
809001 36787 38024 13327 13626 19362 18185 44358 44003 7.8799 4.51779 1.81836 -6.0776 -1.19948
|
||||
810001 36775 38201 13342 13608 19360 18165 44357 43864 8.39985 5.20304 1.61745 -6.1723 -1.66503
|
||||
811001 36753 38381 13365 13605 19335 18136 44381 43716 8.98868 5.9345 1.45852 -6.1974 -2.24569
|
||||
812001 36703 38522 13411 13592 19291 18135 44429 43589 9.42977 6.62729 1.09858 -5.97885 -2.83655
|
||||
813001 36674 38618 13392 13634 19300 18110 44468 43476 10.0699 7.07988 1.46917 -6.15591 -3.35029
|
||||
814001 36682 38743 13361 13654 19264 18113 44527 43328 10.55 7.49965 1.77976 -5.9569 -4.05037
|
||||
815001 36679 38839 13351 13698 19249 18097 44555 43204 11.0709 7.85528 2.10697 -5.96455 -4.56567
|
||||
816001 36655 38924 13385 13761 19224 18049 44570 43103 11.6153 8.24981 2.27993 -6.08866 -4.95837
|
||||
817001 36625 39023 13444 13759 19246 18005 44519 43050 12.0685 8.71506 1.90769 -6.43241 -4.96805
|
||||
818001 36620 39050 13459 13804 19242 17959 44513 43024 12.3279 8.83012 2.08728 -6.65449 -5.03656
|
||||
819001 36604 39027 13465 13914 19280 17886 44485 43010 12.7334 8.80694 2.71137 -7.23339 -4.99044
|
||||
820001 36589 39107 13454 13997 19326 17742 44465 42991 13.676 9.14845 3.27515 -8.2298 -4.98817
|
||||
821001 36566 39179 13453 14051 19322 17697 44493 42910 14.2529 9.49067 3.60363 -8.44834 -5.35837
|
||||
822001 36536 39136 13451 14190 19314 17661 44533 42850 14.6766 9.44799 4.44277 -8.59897 -5.69726
|
||||
823001 36563 39123 13419 14279 19296 17588 44556 42847 15.0267 9.30172 5.16524 -8.89595 -5.78457
|
||||
824001 36521 39225 13440 14299 19335 17527 44538 42786 15.7149 9.82125 5.15542 -9.41945 -5.9327
|
||||
825001 36540 39296 13440 14347 19312 17449 44542 42745 16.1608 10.0042 5.43891 -9.71923 -6.08627
|
||||
826001 36573 39330 13421 14434 19331 17373 44509 42700 16.702 10.0035 6.06738 -10.2226 -6.12961
|
||||
827001 36547 39436 13465 14445 19424 17248 44398 42708 17.4974 10.477 5.86386 -11.3655 -5.73003
|
||||
828001 36585 39545 13480 14448 19473 17172 44296 42672 17.9847 10.7242 5.79016 -12.0227 -5.51077
|
||||
829001 36616 39621 13437 14535 19489 17153 44292 42528 18.6095 10.8797 6.56289 -12.206 -5.99059
|
||||
830001 36580 39631 13433 14576 19462 17074 44359 42556 19.0334 11.0482 6.82744 -12.4957 -6.11961
|
||||
831001 36596 39654 13433 14675 19425 17057 44380 42451 19.3411 11.0707 7.40589 -12.4002 -6.55016
|
||||
832001 36613 39663 13404 14754 19385 17044 44432 42376 19.6422 11.0398 8.04292 -12.2678 -6.98207
|
||||
833001 36684 39685 13380 14838 19361 16975 44409 42339 19.9833 10.8558 8.67728 -12.5196 -7.03201
|
||||
834001 36705 39735 13361 14909 19299 16943 44469 42250 20.3669 10.9557 9.20458 -12.3782 -7.53916
|
||||
835001 36705 39779 13344 14963 19248 16873 44536 42223 20.8319 11.1092 9.61907 -12.5005 -7.85916
|
||||
836001 36701 39836 13329 15010 19266 16788 44537 42204 21.4753 11.3258 9.98193 -13.0546 -7.92788
|
||||
837001 36697 39910 13277 15076 19239 16700 44620 42152 22.3265 11.6024 10.6802 -13.3972 -8.38476
|
||||
838001 36728 40008 13250 15095 19297 16622 44558 42113 22.9887 11.8345 10.955 -14.1185 -8.31151
|
||||
839001 36747 40027 13223 15183 19276 16559 44587 42069 23.5486 11.8316 11.6255 -14.3569 -8.56021
|
||||
840001 36760 40057 13223 15247 19232 16488 44618 42046 23.9275 11.8896 11.9918 -14.5229 -8.74326
|
||||
841001 36818 40030 13222 15308 19187 16419 44606 42081 23.9896 11.5806 12.3462 -14.6733 -8.58245
|
||||
842001 36802 40055 13226 15348 19179 16328 44626 42107 24.4407 11.7278 12.5496 -15.1342 -8.55982
|
||||
843001 36856 40109 13202 15439 19151 16265 44624 42025 25.0069 11.7196 13.2145 -15.3396 -8.83573
|
||||
844001 36885 40098 13195 15514 19166 16187 44587 42039 25.4438 11.574 13.6828 -15.8479 -8.66362
|
||||
845001 36986 40064 13166 15541 19233 16085 44448 42148 25.7124 11.0826 14.0137 -16.755 -7.82237
|
||||
846001 37007 40067 13196 15562 19220 15993 44410 42216 25.8349 11.0161 13.9482 -17.2009 -7.46086
|
||||
847001 36977 40170 13224 15578 19275 15875 44357 42215 26.5786 11.4897 13.8669 -18.1391 -7.28645
|
||||
848001 37014 40164 13237 15684 19260 15810 44322 42180 26.9822 11.3326 14.3852 -18.4267 -7.2894
|
||||
849001 37032 40134 13216 15820 19264 15744 44321 42140 27.6979 11.1607 15.278 -18.8171 -7.42375
|
||||
850001 37030 40117 13235 15908 19272 15682 44296 42131 28.1361 11.1081 15.6541 -19.2061 -7.37079
|
||||
851001 36986 40139 13252 15992 19292 15543 44303 42164 29.0174 11.3473 16.0188 -20.0908 -7.28067
|
||||
852001 37010 40179 13232 16087 19261 15464 44330 42108 29.6718 11.4002 16.6699 -20.3801 -7.56419
|
||||
853001 36984 40203 13260 16163 19207 15433 44382 42039 29.9226 11.5803 16.9203 -20.2815 -7.97653
|
||||
854001 36946 40243 13277 16233 19171 15399 44439 41963 30.3225 11.8609 17.2038 -20.2913 -8.42989
|
||||
855001 36921 40367 13284 16269 19136 15329 44492 41873 30.9045 12.3893 17.36 -20.5107 -8.91828
|
||||
856001 36944 40379 13310 16321 19191 15263 44388 41875 31.2984 12.3469 17.4881 -21.1658 -8.56263
|
||||
857001 36897 40471 13337 16387 19192 15216 44407 41764 31.9151 12.843 17.687 -21.4387 -9.01005
|
||||
858001 36849 40531 13350 16482 19192 15150 44442 41675 32.6905 13.2303 18.1297 -21.8155 -9.43543
|
||||
859001 36898 40561 13354 16555 19199 15094 44382 41628 33.0964 13.1553 18.5053 -22.1712 -9.39695
|
||||
860001 36844 40647 13378 16620 19179 15044 44432 41526 33.6878 13.6567 18.7153 -22.3553 -9.91694
|
||||
861001 36782 40816 13374 16640 19155 15045 44522 41336 34.3111 14.4765 18.8488 -22.2276 -10.8783
|
||||
862001 36723 40938 13394 16680 19110 15082 44606 41137 34.6796 15.1201 18.9453 -21.7867 -11.852
|
||||
863001 36695 40986 13420 16719 19060 15068 44658 41064 34.8679 15.3909 18.9998 -21.6123 -12.2804
|
||||
864001 36665 41055 13400 16769 19032 14967 44736 41046 35.6222 15.7421 19.3933 -22.0491 -12.6039
|
||||
865001 36638 41193 13373 16807 18985 14904 44837 40933 36.4205 16.3223 19.7639 -22.1718 -13.3355
|
||||
866001 36621 41250 13382 16852 19017 14814 44813 40921 37.0441 16.5833 19.9533 -22.8541 -13.2973
|
||||
867001 36687 41267 13351 16904 18949 14742 44846 40924 37.2962 16.399 20.4236 -22.9233 -13.397
|
||||
868001 36693 41337 13362 16931 18944 14761 44834 40808 37.487 16.6201 20.5027 -22.7878 -13.7623
|
||||
869001 36655 41559 13391 16918 18960 14709 44827 40651 38.1923 17.5302 20.256 -23.1705 -14.2886
|
||||
870001 36590 41740 13367 16942 18876 14734 45000 40421 38.9382 18.3962 20.5317 -22.5963 -15.6722
|
||||
871001 36585 41968 13392 16942 18830 14716 45026 40211 39.5078 19.2013 20.3797 -22.465 -16.4975
|
||||
872001 36531 42204 13427 16922 18809 14683 45066 40028 40.222 20.2126 20.059 -22.5487 -17.2758
|
||||
873001 36477 42391 13445 16879 18754 14644 45158 39923 40.746 21.055 19.7177 -22.492 -17.9512
|
||||
874001 36414 42603 13474 16873 18739 14622 45207 39739 41.5392 22.0134 19.5093 -22.5428 -18.7649
|
||||
875001 36270 42774 13522 16873 18736 14570 45306 39620 42.5017 23.1301 19.2186 -22.8299 -19.5151
|
||||
876001 36298 42787 13538 16934 18763 14536 45236 39580 42.716 23.0719 19.4528 -23.1658 -19.4235
|
||||
877001 36326 42891 13539 16953 18780 14457 45190 39536 43.196 23.3227 19.5495 -23.7139 -19.4269
|
||||
878001 36410 42932 13513 16980 18750 14419 45162 39506 43.2857 23.1517 19.8527 -23.7822 -19.4405
|
||||
879001 36491 42940 13492 17035 18718 14429 45134 39433 43.2908 22.8797 20.2767 -23.5593 -19.6068
|
||||
880001 36486 43037 13498 17089 18711 14361 45140 39350 43.934 23.2282 20.5312 -23.9215 -19.9219
|
||||
881001 36493 43088 13456 17181 18696 14310 45190 39257 44.7114 23.3769 21.2808 -24.1427 -20.4178
|
||||
882001 36493 43190 13429 17244 18682 14302 45231 39100 45.4391 23.7233 21.7822 -24.1178 -21.1137
|
||||
883001 36473 43283 13428 17259 18649 14261 45285 39033 45.9171 24.1125 21.8685 -24.189 -21.532
|
||||
884001 36445 43430 13459 17254 18664 14230 45267 38922 46.4289 24.7138 21.6539 -24.4485 -21.869
|
||||
885001 36433 43559 13434 17322 18657 14221 45311 38734 47.3235 25.1942 22.169 -24.4654 -22.688
|
||||
886001 36424 43694 13459 17331 18690 14179 45262 38631 47.8522 25.6844 22.0663 -24.8817 -22.8937
|
||||
887001 36454 43751 13396 17385 18619 14178 45366 38521 48.3809 25.7658 22.7365 -24.5224 -23.6334
|
||||
888001 36420 43833 13368 17465 18625 14177 45422 38360 49.2702 26.1676 23.3323 -24.5592 -24.3979
|
||||
889001 36430 43830 13386 17566 18602 14154 45417 38285 49.5831 26.1205 23.7592 -24.5765 -24.6515
|
||||
890001 36483 43847 13405 17641 18636 14060 45310 38288 49.8328 25.9797 24.0395 -25.3085 -24.2889
|
||||
891001 36604 43805 13366 17731 18650 13971 45214 38329 49.9613 25.3921 24.7513 -25.9078 -23.8229
|
||||
892001 36580 43843 13390 17782 18672 13882 45192 38329 50.4329 25.6085 24.8744 -26.5497 -23.7499
|
||||
893001 36585 43848 13395 17832 18696 13788 45158 38368 50.7918 25.6069 25.1072 -27.233 -23.4966
|
||||
894001 36640 43862 13386 17854 18656 13701 45152 38419 50.874 25.4514 25.2773 -27.5476 -23.2931
|
||||
895001 36631 43887 13394 17925 18654 13642 45155 38382 51.3454 25.5687 25.6014 -27.8908 -23.4363
|
||||
896001 36647 43958 13406 17947 18642 13632 45140 38299 51.5695 25.7499 25.6448 -27.8884 -23.6842
|
||||
897001 36678 44034 13383 17989 18664 13656 45110 38157 51.9928 25.8912 26.004 -27.8574 -24.0968
|
||||
898001 36627 44188 13420 17998 18587 13626 45201 38024 52.5111 26.5958 25.827 -27.6418 -24.8793
|
||||
899001 36559 44298 13420 18077 18550 13578 45306 37883 53.4891 27.2149 26.2397 -27.7397 -25.7376
|
||||
900001 36551 44333 13404 18203 18510 13540 45370 37760 54.2652 27.3615 26.9927 -27.7623 -26.3953
|
||||
901001 36552 44302 13423 18294 18542 13457 45318 37783 54.6096 27.254 27.3501 -28.4272 -26.1397
|
||||
902001 36454 44375 13436 18320 18560 13319 45385 37822 55.4657 27.8597 27.4063 -29.3544 -26.2202
|
||||
903001 36354 44481 13430 18368 18596 13215 45455 37772 56.5984 28.5832 27.691 -30.1707 -26.633
|
||||
904001 36361 44481 13434 18448 18584 13191 45456 37716 56.9188 28.5574 28.0801 -30.2551 -26.8394
|
||||
905001 36283 44559 13494 18480 18541 13206 45517 37591 57.2467 29.106 27.8831 -29.9429 -27.4949
|
||||
906001 36286 44632 13483 18514 18512 13198 45554 37492 57.6631 29.3385 28.1247 -29.8425 -27.9771
|
||||
907001 36280 44652 13465 18586 18452 13196 45638 37402 58.0863 29.4273 28.6037 -29.5457 -28.582
|
||||
908001 36335 44596 13458 18663 18442 13181 45600 37396 58.0765 29.0373 29.0412 -29.5855 -28.4784
|
||||
909001 36476 44490 13410 18761 18463 13128 45486 37457 57.9779 28.163 29.8326 -30.0168 -27.8799
|
||||
910001 36580 44431 13351 18869 18471 13072 45433 37464 58.2757 27.5825 30.7403 -30.4 -27.6792
|
||||
927
src/kimono/lxpack/tests/ref/borbu1.1.ref
Normal file
927
src/kimono/lxpack/tests/ref/borbu1.1.ref
Normal file
@ -0,0 +1,927 @@
|
||||
# input : borbu1.fst
|
||||
# include : borbu1.lst
|
||||
# selector : count
|
||||
# mixer : basic
|
||||
# distance : chi
|
||||
# phase : 1
|
||||
# alphabet : ACGT
|
||||
# excluded : X
|
||||
# seqname : borbu1
|
||||
# seqlength : 910724
|
||||
# unmasked : 284128
|
||||
# valid : 284117
|
||||
# window : 227680
|
||||
# step : 1000
|
||||
#
|
||||
# pos LeftA RightA LeftC
|
||||
1 10620 11521 5303 8176
|
||||
1001 10649 11516 5252 8212
|
||||
2001 10687 11570 5253 8172
|
||||
3001 10714 11567 5286 8173
|
||||
4001 10772 11466 5269 8151
|
||||
5001 10793 11397 5270 8210
|
||||
6001 10792 11385 5292 8237
|
||||
7001 10795 11327 5319 8235
|
||||
8001 10824 11333 5349 8244
|
||||
9001 10903 11285 5292 8291
|
||||
10001 11016 11179 5241 8375
|
||||
11001 11095 11098 5211 8447
|
||||
12001 11171 11042 5179 8484
|
||||
13001 11283 10941 5148 8540
|
||||
14001 11361 10853 5112 8618
|
||||
15001 11430 10812 5058 8659
|
||||
16001 11456 10799 5070 8687
|
||||
17001 11555 10741 5077 8726
|
||||
18001 11604 10757 5096 8698
|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
357001 10840 9850 8736 7496
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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|
||||
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||||
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||||
392001 10838 9714 8891 6474
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||||
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|
||||
394001 10834 9852 8925 6309
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||||
395001 10839 9896 8901 6232
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||||
396001 10814 9960 8883 6183
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||||
397001 10837 10006 8883 6117
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||||
398001 10827 10110 8872 6055
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||||
399001 10808 10164 8886 5977
|
||||
400001 10786 10204 8905 5890
|
||||
401001 10740 10287 8916 5819
|
||||
402001 10677 10350 8963 5748
|
||||
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||||
404001 10616 10483 9035 5567
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||||
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||||
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||||
407001 10603 10708 9065 5322
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||||
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||||
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||||
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||||
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||||
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|
||||
413001 10637 10990 8895 5080
|
||||
414001 10720 10929 8789 5096
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||||
415001 10754 10878 8754 5093
|
||||
416001 10775 10856 8735 5127
|
||||
417001 10828 10774 8693 5201
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
426001 11135 10584 8305 5001
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||||
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|
||||
428001 11225 10410 8210 5026
|
||||
429001 11271 10376 8171 5016
|
||||
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|
||||
431001 11237 10441 8160 4929
|
||||
432001 11238 10480 8189 4863
|
||||
433001 11216 10510 8194 4796
|
||||
434001 11231 10501 8175 4731
|
||||
435001 11187 10477 8215 4732
|
||||
436001 11043 10548 8182 4807
|
||||
437001 10911 10603 8105 4921
|
||||
438001 10789 10649 8041 5022
|
||||
439001 10703 10723 7948 5036
|
||||
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|
||||
441001 10504 10928 7797 5091
|
||||
442001 10450 11028 7766 5091
|
||||
443001 10373 11074 7798 5063
|
||||
444001 10320 11090 7772 5076
|
||||
445001 10254 11121 7703 5154
|
||||
446001 10169 11188 7613 5236
|
||||
447001 10137 11194 7573 5256
|
||||
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|
||||
875001 10893 11401 5652 6787
|
||||
876001 10888 11384 5657 6828
|
||||
877001 10890 11391 5663 6844
|
||||
878001 10890 11382 5665 6843
|
||||
879001 10900 11390 5664 6848
|
||||
880001 10903 11401 5654 6877
|
||||
881001 10893 11365 5629 6930
|
||||
882001 10910 11383 5608 6962
|
||||
883001 10922 11379 5593 6968
|
||||
884001 10935 11408 5618 6960
|
||||
885001 10939 11445 5603 6964
|
||||
886001 10945 11486 5612 6961
|
||||
887001 10945 11495 5588 6958
|
||||
888001 10936 11495 5575 7000
|
||||
889001 10933 11477 5589 7071
|
||||
890001 10976 11439 5594 7117
|
||||
891001 11042 11373 5569 7178
|
||||
892001 11032 11328 5589 7216
|
||||
893001 11036 11281 5577 7269
|
||||
894001 11057 11257 5575 7300
|
||||
895001 11048 11232 5582 7356
|
||||
896001 11088 11210 5571 7387
|
||||
897001 11095 11268 5513 7419
|
||||
898001 11070 11338 5538 7408
|
||||
899001 11029 11326 5566 7432
|
||||
900001 10988 11316 5572 7510
|
||||
901001 10993 11266 5570 7588
|
||||
902001 10977 11254 5563 7637
|
||||
903001 10979 11234 5567 7697
|
||||
904001 10915 11260 5551 7768
|
||||
905001 10880 11284 5578 7797
|
||||
906001 10828 11354 5546 7812
|
||||
907001 10740 11440 5511 7871
|
||||
908001 10654 11503 5465 7968
|
||||
909001 10655 11487 5416 8027
|
||||
910001 10682 11456 5339 8100
|
||||
924
src/kimono/lxpack/tests/ref/borbu1.11.ref
Normal file
924
src/kimono/lxpack/tests/ref/borbu1.11.ref
Normal file
@ -0,0 +1,924 @@
|
||||
# input : borbu1.fst
|
||||
# include : borbu1.lst
|
||||
# selector : count
|
||||
# distance : chi
|
||||
# phase : 1
|
||||
# alphabet : ACGT
|
||||
# seqname : borbu1
|
||||
# seqlength : 910724
|
||||
# unmasked : 284117
|
||||
# window : 227680
|
||||
# step : 1000
|
||||
#
|
||||
# pos LeftA RightA LeftC RightC LeftG RightG LeftT RightX chiACGT/not*s chiA chiC chiG chiT
|
||||
1 10619 11521 5303 8176 7756 5291 11375 11287 33.0842 3.51336 22.7604 -23.5408 -3.16408
|
||||
1001 10648 11516 5252 8212 7742 5294 11344 11262 33.4884 3.11949 23.4003 -23.524 -3.28422
|
||||
2001 10686 11570 5253 8172 7731 5310 11323 11228 33.1173 3.2322 23.1044 -23.2661 -3.34483
|
||||
3001 10713 11567 5286 8173 7734 5306 11324 11227 32.9256 3.17724 22.9108 -23.2124 -3.20642
|
||||
4001 10771 11466 5269 8151 7715 5263 11278 11195 33.0028 2.47574 23.1831 -23.1955 -2.75071
|
||||
5001 10792 11397 5270 8210 7725 5207 11257 11259 33.6652 1.90639 23.6448 -23.7902 -2.15803
|
||||
6001 10791 11385 5292 8237 7738 5197 11234 11263 33.7875 1.83912 23.6426 -23.9864 -1.97226
|
||||
7001 10794 11327 5319 8235 7722 5185 11241 11263 33.5679 1.6296 23.5193 -23.8258 -1.82453
|
||||
8001 10823 11333 5349 8244 7697 5187 11246 11242 33.2612 1.56164 23.372 -23.5369 -1.90552
|
||||
9001 10902 11285 5292 8291 7699 5165 11190 11283 34.0008 0.600148 24.1921 -23.8449 -1.3636
|
||||
10001 11015 11179 5241 8375 7737 5126 11088 11346 35.2589 -0.879103 25.3095 -24.531 -0.268041
|
||||
11001 11094 11098 5211 8447 7781 5083 10994 11405 36.4359 -1.9697 26.1257 -25.31 0.740571
|
||||
12001 11170 11042 5179 8484 7805 5037 10928 11474 37.3839 -2.86039 26.7075 -25.9499 1.63827
|
||||
13001 11282 10941 5148 8540 7837 4999 10869 11548 38.5083 -4.15634 27.5282 -26.4716 2.65855
|
||||
14001 11360 10853 5112 8618 7857 4981 10799 11571 39.5823 -5.27694 28.4494 -26.8102 3.28049
|
||||
15001 11429 10812 5058 8659 7886 4942 10754 11609 40.7405 -6.01368 29.2754 -27.42 3.83661
|
||||
16001 11455 10799 5070 8687 7876 4947 10704 11628 40.805 -6.40198 29.2651 -27.3894 4.17603
|
||||
17001 11554 10741 5077 8726 7922 4921 10700 11662 41.5721 -7.1143 29.7476 -27.7494 4.76189
|
||||
18001 11603 10757 5096 8698 7935 4927 10685 11606 41.3279 -7.06085 29.5683 -27.5883 4.76818
|
||||
19001 11648 10798 5118 8653 7944 4951 10672 11574 40.8173 -6.92086 29.1477 -27.3032 4.80617
|
||||
20001 11665 10808 5121 8654 7929 4955 10664 11565 40.7044 -6.98375 29.1115 -27.161 4.7835
|
||||
21001 11638 10889 5120 8642 7880 4998 10652 11559 39.9943 -6.66875 28.7129 -26.6666 4.41997
|
||||
22001 11592 10982 5195 8571 7841 5029 10712 11494 38.4569 -5.6087 27.5662 -25.9576 3.7122
|
||||
23001 11568 10959 5246 8597 7766 5035 10739 11522 37.8045 -5.72624 27.1751 -25.3971 3.58973
|
||||
24001 11578 10902 5255 8635 7751 4993 10746 11561 38.2299 -6.10658 27.4249 -25.6353 3.86561
|
||||
25001 11505 10911 5343 8559 7702 4979 10778 11509 36.918 -5.29078 26.2348 -25.177 3.57735
|
||||
26001 11460 10893 5404 8578 7642 4983 10807 11543 36.2315 -5.22672 25.7094 -24.7437 3.48929
|
||||
27001 11489 10863 5397 8625 7616 4933 10831 11578 36.7842 -5.58325 26.1557 -24.9976 3.59261
|
||||
28001 11487 10821 5415 8666 7581 4916 10857 11589 36.8349 -5.8245 26.3133 -24.8622 3.5166
|
||||
29001 11452 10788 5481 8683 7527 4924 10878 11591 36.1208 -5.80761 25.8245 -24.3425 3.39489
|
||||
30001 11476 10759 5492 8695 7456 4915 10892 11637 35.8645 -6.25129 25.7402 -23.9227 3.51152
|
||||
31001 11509 10719 5487 8735 7403 4887 10918 11656 36.0927 -6.72072 26.0996 -23.7534 3.47944
|
||||
32001 11491 10698 5530 8765 7380 4862 10889 11695 36.0524 -6.84884 25.8346 -23.8917 3.82512
|
||||
33001 11456 10718 5589 8771 7318 4876 10939 11675 35.1447 -6.49678 25.3153 -23.2578 3.33885
|
||||
34001 11428 10707 5639 8756 7293 4866 10941 11661 34.6302 -6.28431 24.8211 -23.0768 3.33634
|
||||
35001 11405 10701 5669 8769 7286 4877 10918 11626 34.3616 -6.18553 24.6284 -22.9201 3.25098
|
||||
36001 11369 10679 5741 8781 7221 4885 10941 11634 33.5128 -6.12058 24.0321 -22.324 3.1216
|
||||
37001 11331 10672 5790 8794 7179 4890 10972 11616 32.9275 -5.9004 23.6895 -21.9163 2.80841
|
||||
38001 11297 10698 5857 8755 7125 4949 10995 11544 31.4699 -5.43851 22.8346 -20.8408 2.24037
|
||||
39001 11257 10743 5911 8714 7061 5001 11041 11484 30.0582 -4.86528 22.0377 -19.794 1.53549
|
||||
40001 11234 10733 5947 8734 6992 5022 11041 11499 29.4029 -4.99172 21.6858 -19.1657 1.41869
|
||||
41001 11257 10666 5962 8780 6954 5019 11044 11521 29.4823 -5.59095 21.8993 -18.8668 1.55316
|
||||
42001 11241 10638 6011 8805 6909 5023 11051 11523 29.0363 -5.69116 21.6271 -18.4589 1.50199
|
||||
43001 11210 10651 6076 8791 6857 5053 11116 11482 27.9665 -5.27127 21.0389 -17.6312 0.919579
|
||||
44001 11162 10723 6132 8737 6807 5082 11158 11426 26.6772 -4.44029 20.1504 -16.9066 0.287457
|
||||
45001 11127 10770 6169 8698 6750 5094 11214 11355 25.7378 -3.77861 19.6167 -16.2216 -0.448155
|
||||
46001 11113 10783 6199 8675 6742 5124 11193 11357 25.1454 -3.66876 19.1172 -15.9131 -0.367673
|
||||
47001 11044 10865 6218 8662 6656 5164 11211 11355 24.0918 -3.11659 18.4654 -15.1253 -0.976879
|
||||
48001 11018 10887 6211 8706 6597 5150 11241 11367 24.1222 -3.05422 18.6405 -14.9405 -1.36546
|
||||
49001 11004 10849 6224 8732 6531 5138 11309 11391 23.9401 -3.21296 18.7195 -14.4783 -1.66157
|
||||
50001 11008 10838 6240 8748 6460 5120 11333 11417 23.6653 -3.39782 18.6267 -14.0901 -1.73656
|
||||
51001 10956 10857 6308 8741 6385 5116 11360 11436 22.7136 -3.03888 17.8683 -13.5543 -1.91782
|
||||
52001 10917 10895 6412 8689 6353 5115 11398 11431 21.4865 -2.3269 16.7192 -13.141 -2.00968
|
||||
53001 10865 10941 6485 8665 6280 5107 11443 11423 20.4702 -1.6899 15.8757 -12.5868 -2.38985
|
||||
54001 10805 10973 6557 8625 6185 5106 11502 11430 19.2321 -1.11109 14.9073 -11.7754 -2.78398
|
||||
55001 10783 10960 6625 8625 6116 5108 11528 11427 18.4053 -1.01245 14.344 -11.1055 -2.9405
|
||||
56001 10741 10985 6692 8574 6075 5101 11536 11414 17.4767 -0.47942 13.444 -10.7455 -2.9997
|
||||
57001 10681 11052 6747 8533 6044 5138 11543 11374 16.5331 0.273553 12.569 -10.1779 -3.42013
|
||||
58001 10680 11002 6762 8558 6022 5128 11527 11388 16.4728 -0.0613001 12.6221 -10.0797 -3.22973
|
||||
59001 10625 11032 6809 8553 5977 5114 11571 11386 16.0382 0.481639 12.1487 -9.83027 -3.57303
|
||||
60001 10576 11044 6867 8559 5946 5111 11563 11410 15.5091 0.758414 11.5766 -9.67607 -3.50919
|
||||
61001 10545 11075 6927 8549 5904 5097 11571 11412 14.952 1.1513 10.9641 -9.44547 -3.57884
|
||||
62001 10510 11088 6998 8547 5843 5092 11598 11423 14.2302 1.4507 10.3192 -8.94943 -3.71688
|
||||
63001 10529 11117 7023 8524 5843 5087 11562 11435 13.9099 1.50194 9.92515 -9.00534 -3.40949
|
||||
64001 10571 11081 7027 8571 5879 5032 11492 11515 14.4716 0.922939 10.2057 -9.9155 -2.47024
|
||||
65001 10588 11010 7030 8651 5910 4989 11441 11548 15.2638 0.333589 10.7839 -10.6264 -1.91297
|
||||
66001 10582 10962 7032 8694 5929 4934 11423 11607 15.9292 0.0499121 11.0856 -11.3512 -1.41287
|
||||
67001 10611 10866 7047 8742 5878 4946 11426 11643 15.6819 -0.803555 11.3103 -10.7655 -1.2075
|
||||
68001 10645 10772 7049 8817 5845 4927 11420 11689 16.0435 -1.6948 11.8326 -10.6638 -0.892232
|
||||
69001 10674 10689 7056 8890 5815 4895 11418 11718 16.5142 -2.42225 12.3443 -10.6789 -0.65497
|
||||
70001 10687 10670 7066 8894 5770 4928 11447 11681 16.0548 -2.58787 12.3352 -9.89108 -1.03306
|
||||
71001 10687 10682 7061 8896 5802 4940 11420 11670 16.1903 -2.53674 12.3661 -10.0925 -0.95588
|
||||
72001 10781 10652 7044 8896 5817 4969 11359 11664 16.3455 -3.30851 12.5777 -9.88818 -0.505281
|
||||
73001 10875 10637 7006 8914 5869 4976 11236 11666 17.1034 -4.1104 12.9842 -10.3425 0.275218
|
||||
74001 10971 10597 6982 8948 5912 4945 11152 11703 18.1439 -4.97264 13.4942 -11.0028 1.14821
|
||||
75001 11073 10501 6936 8986 5946 4889 11061 11748 19.6406 -6.18272 14.2828 -11.7772 2.19691
|
||||
76001 11192 10389 6871 9045 5972 4862 10973 11823 21.3309 -7.76172 15.2635 -12.2915 3.27181
|
||||
77001 11308 10348 6825 9051 5983 4842 10893 11841 22.3245 -8.74565 15.7667 -12.5384 4.01211
|
||||
78001 11400 10345 6780 9063 5980 4848 10845 11810 22.8887 -9.35685 16.2607 -12.4334 4.16474
|
||||
79001 11389 10347 6824 9073 5942 4858 10875 11789 22.3331 -9.21907 16.0001 -11.9479 3.87585
|
||||
80001 11384 10293 6843 9078 5891 4844 10866 11780 22.2118 -9.50819 15.9174 -11.5822 3.93058
|
||||
81001 11375 10323 6845 9101 5878 4868 10815 11773 22.0719 -9.53379 15.818 -11.4271 3.93542
|
||||
82001 11391 10330 6841 9114 5895 4865 10788 11769 22.3156 -9.61472 15.9279 -11.6304 4.07188
|
||||
83001 11405 10326 6867 9124 5864 4876 10776 11762 22.0638 -9.76252 15.7558 -11.2516 4.08174
|
||||
84001 11374 10436 6929 9064 5837 4918 10750 11701 20.5675 -8.90884 14.6958 -10.6581 3.75415
|
||||
85001 11386 10544 6956 8986 5846 4924 10687 11678 19.7872 -8.30863 13.8448 -10.7231 3.97981
|
||||
86001 11376 10663 6964 8937 5834 4942 10647 11643 18.9776 -7.65598 13.2265 -10.5889 3.80394
|
||||
87001 11407 10634 6951 8956 5825 4951 10615 11662 19.2943 -8.14614 13.404 -10.4757 4.06212
|
||||
88001 11442 10619 6968 8960 5829 4944 10558 11680 19.5307 -8.48395 13.2871 -10.5841 4.57175
|
||||
89001 11482 10591 6964 8944 5827 4942 10524 11639 19.6681 -8.76213 13.3548 -10.4602 4.72138
|
||||
90001 11498 10672 6963 8905 5836 4975 10510 11559 19.0532 -8.28672 13.1026 -10.1943 4.33045
|
||||
91001 11501 10755 6990 8825 5845 5016 10471 11499 18.0556 -7.71186 12.3091 -9.84943 4.2436
|
||||
92001 11485 10845 7054 8754 5816 5063 10483 11439 16.5097 -6.94448 11.2843 -9.07784 3.82133
|
||||
93001 11445 10859 7109 8669 5744 5072 10512 11368 15.033 -6.36809 10.3656 -8.16418 3.3673
|
||||
94001 11388 10920 7181 8612 5679 5115 10560 11325 13.289 -5.59041 9.32152 -7.13814 2.73867
|
||||
95001 11338 10980 7212 8595 5609 5138 10587 11304 12.1692 -5.08049 8.74332 -6.40641 2.18889
|
||||
96001 11285 11069 7263 8538 5537 5189 10660 11226 10.3869 -4.14335 7.876 -5.22989 1.1565
|
||||
97001 11251 11129 7296 8500 5467 5210 10720 11180 9.21816 -3.53308 7.29831 -4.36456 0.42076
|
||||
98001 11244 11178 7351 8451 5416 5239 10724 11140 8.04587 -3.13579 6.48959 -3.57278 0.152628
|
||||
99001 11205 11243 7386 8421 5384 5277 10709 11121 7.06124 -2.66522 5.78439 -3.04803 -0.0894082
|
||||
100001 11257 11246 7409 8455 5429 5259 10694 11103 7.51416 -2.77112 6.04094 -3.50388 0.115609
|
||||
101001 11338 11242 7407 8461 5448 5295 10648 11071 7.71926 -3.24162 6.18664 -3.27159 0.318126
|
||||
102001 11323 11332 7427 8408 5429 5358 10600 11031 6.64429 -2.80636 5.40098 -2.66147 0.130379
|
||||
103001 11315 11419 7502 8342 5408 5394 10605 10982 5.24885 -2.08748 4.35593 -2.04918 -0.140022
|
||||
104001 11270 11507 7581 8268 5350 5425 10648 10933 3.64813 -1.15985 3.18026 -1.15536 -0.717459
|
||||
105001 11256 11545 7629 8236 5270 5439 10703 10875 3.05973 -0.718748 2.62359 -0.171085 -1.39027
|
||||
106001 11240 11526 7688 8235 5190 5425 10749 10854 2.94864 -0.600632 2.24769 0.576598 -1.7173
|
||||
107001 11260 11599 7763 8176 5199 5464 10828 10798 2.94177 0.142983 1.51854 1.13267 -2.24603
|
||||
108001 11276 11628 7782 8092 5195 5492 10812 10757 2.89042 0.3999 0.857127 1.55746 -2.24371
|
||||
109001 11344 11619 7812 8075 5231 5496 10871 10707 3.11488 0.453926 0.954698 1.62858 -2.43571
|
||||
110001 11433 11644 7863 8068 5274 5525 10930 10662 3.3909 0.540046 0.91884 1.83466 -2.64505
|
||||
111001 11502 11660 7957 8076 5315 5531 11060 10617 3.90912 0.932068 0.851534 2.00144 -3.11152
|
||||
112001 11491 11662 8017 8094 5293 5537 11146 10602 4.54952 1.23395 0.698512 2.41996 -3.5821
|
||||
113001 11447 11680 8087 8110 5251 5554 11210 10602 5.27175 1.63572 0.267409 2.98575 -4.01617
|
||||
114001 11537 11646 8190 8095 5294 5547 11289 10665 4.78998 1.46811 -0.113996 2.94431 -3.47946
|
||||
115001 11524 11648 8204 8109 5299 5544 11256 10702 4.43235 1.40423 -0.249074 2.7562 -3.16468
|
||||
116001 11576 11643 8171 8103 5308 5550 11225 10695 4.18694 1.04904 -0.0229131 2.73913 -2.98775
|
||||
117001 11547 11669 8161 8101 5302 5587 11213 10695 4.49056 1.16118 -0.168798 2.97807 -3.1495
|
||||
118001 11453 11713 8162 8152 5258 5615 11201 10756 4.82719 1.36726 -0.364441 3.19009 -3.33511
|
||||
119001 11381 11780 8219 8106 5198 5664 11264 10693 6.48416 2.2408 -1.20426 4.21038 -4.2244
|
||||
120001 11382 11863 8244 8027 5191 5713 11265 10641 7.43295 2.81338 -1.9869 4.76506 -4.54754
|
||||
121001 11331 11952 8234 7994 5184 5755 11260 10615 8.22401 3.42213 -2.42474 5.01552 -4.98884
|
||||
122001 11321 11961 8241 7961 5189 5775 11242 10611 8.40245 3.52965 -2.75434 5.14031 -4.91259
|
||||
123001 11270 11942 8311 7951 5155 5795 11289 10619 9.17729 3.81681 -3.32022 5.70816 -5.10371
|
||||
124001 11162 11962 8387 7933 5119 5776 11358 10610 10.2224 4.72463 -4.00437 5.92629 -5.56943
|
||||
125001 11090 11988 8449 7897 5069 5769 11424 10614 11.3047 5.41537 -4.73486 6.38415 -5.94092
|
||||
126001 11024 11998 8493 7906 5026 5768 11491 10586 12.2324 5.94918 -4.98066 6.81999 -6.55129
|
||||
127001 10929 12003 8551 7902 4997 5769 11550 10578 13.1627 6.62087 -5.45899 7.11733 -6.99734
|
||||
128001 10840 12017 8627 7892 4973 5753 11583 10594 13.9065 7.29783 -6.13302 7.19758 -7.12127
|
||||
129001 10815 12017 8656 7858 4938 5773 11613 10560 14.7128 7.56577 -6.54073 7.80162 -7.45505
|
||||
130001 10792 12075 8693 7788 4946 5817 11630 10527 15.7093 8.17894 -7.30884 8.18602 -7.71076
|
||||
131001 10742 12093 8727 7791 4916 5814 11665 10526 16.3146 8.57658 -7.59222 8.41979 -8.00468
|
||||
132001 10775 12028 8685 7801 4935 5784 11593 10533 15.2949 7.96691 -7.16611 7.97356 -7.45197
|
||||
133001 10799 12024 8653 7781 4950 5839 11573 10505 15.3791 7.74423 -7.11142 8.3082 -7.54622
|
||||
134001 10816 12071 8656 7733 4955 5915 11566 10472 16.1043 7.88069 -7.56102 8.92187 -7.77661
|
||||
135001 10892 12032 8633 7744 4999 5918 11552 10456 15.3889 7.37427 -7.07791 8.68852 -7.53988
|
||||
136001 10985 12034 8571 7738 5032 5928 11499 10453 14.6076 6.77544 -6.63944 8.46296 -7.1952
|
||||
137001 10945 12060 8606 7700 5031 5940 11531 10429 15.3295 7.31771 -7.12331 8.65523 -7.46926
|
||||
138001 10913 12038 8617 7739 4989 5949 11559 10440 15.5995 7.24142 -7.02103 9.05176 -7.72514
|
||||
139001 10914 12088 8551 7732 4980 5963 11510 10442 15.5038 7.17352 -6.89563 9.00567 -7.7626
|
||||
140001 10883 12153 8589 7661 4977 5990 11548 10382 16.6758 7.97021 -7.61363 9.39893 -8.26148
|
||||
141001 10851 12179 8636 7621 4924 6045 11589 10340 18.0327 8.36197 -8.2874 10.435 -8.81392
|
||||
142001 10822 12242 8657 7560 4917 6078 11589 10308 18.9367 8.92307 -8.97255 10.7773 -9.07304
|
||||
143001 10796 12274 8677 7487 4919 6116 11591 10246 19.8673 9.43596 -9.60679 11.1909 -9.3887
|
||||
144001 10752 12307 8705 7451 4912 6172 11637 10194 20.9909 9.99184 -10.0737 11.7958 -10.008
|
||||
145001 10713 12335 8744 7424 4883 6219 11660 10155 22.0516 10.4041 -10.6156 12.4854 -10.462
|
||||
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|
||||
147001 10716 12483 8782 7299 4873 6296 11670 10056 23.9256 11.4049 -11.858 13.3286 -11.1399
|
||||
148001 10703 12519 8763 7292 4869 6311 11654 10067 24.0454 11.4948 -11.9605 13.3449 -11.1765
|
||||
149001 10694 12526 8771 7294 4876 6311 11632 10074 23.9895 11.5328 -12.0605 13.2274 -11.0485
|
||||
150001 10680 12510 8790 7270 4886 6312 11624 10070 24.0983 11.633 -12.3139 13.2087 -10.9223
|
||||
151001 10671 12563 8784 7233 4888 6347 11603 10003 24.7319 11.9897 -12.6064 13.4708 -11.2929
|
||||
152001 10701 12601 8754 7208 4960 6318 11536 10018 23.9702 12.0361 -12.5768 12.5017 -10.7348
|
||||
153001 10752 12620 8709 7216 5011 6304 11470 10021 23.1098 11.7545 -12.2143 11.8324 -10.3295
|
||||
154001 10720 12646 8741 7210 5020 6324 11508 9978 23.752 12.2418 -12.4181 11.9937 -10.7813
|
||||
155001 10659 12646 8780 7210 5019 6310 11528 9992 24.0813 12.6519 -12.7173 11.8754 -10.8203
|
||||
156001 10643 12703 8806 7170 5028 6298 11512 9989 24.4783 13.1201 -13.243 11.6812 -10.7341
|
||||
157001 10654 12696 8784 7172 5060 6269 11479 10037 23.8026 12.9461 -13.1065 11.0682 -10.2312
|
||||
158001 10741 12623 8730 7228 5085 6252 11411 10081 22.2431 11.8528 -12.2699 10.6401 -9.51317
|
||||
159001 10772 12611 8690 7272 5107 6226 11349 10147 21.136 11.3103 -11.8154 10.0129 -8.88505
|
||||
160001 10794 12546 8662 7342 5131 6160 11355 10152 20.0134 10.9216 -10.8867 9.30392 -8.72758
|
||||
161001 10886 12540 8662 7338 5176 6179 11361 10154 19.5559 10.5398 -10.6876 9.22685 -8.48446
|
||||
162001 10878 12532 8713 7342 5143 6192 11376 10140 20.0472 10.6071 -10.9883 9.71159 -8.62104
|
||||
163001 10861 12538 8722 7315 5141 6196 11381 10142 20.3232 10.7812 -11.2611 9.78175 -8.61992
|
||||
164001 10848 12539 8763 7301 5122 6205 11423 10146 20.8438 10.9835 -11.5964 10.1244 -8.76617
|
||||
165001 10865 12513 8733 7332 5110 6225 11422 10157 20.5441 10.5734 -11.2234 10.3301 -8.80836
|
||||
166001 10909 12460 8677 7341 5117 6218 11427 10195 19.7842 9.96844 -10.703 10.2177 -8.54918
|
||||
167001 10948 12432 8658 7383 5107 6199 11424 10200 19.2408 9.54264 -10.2017 10.1568 -8.48014
|
||||
168001 10967 12431 8620 7417 5106 6201 11427 10202 18.8953 9.29401 -9.72881 10.1052 -8.5957
|
||||
169001 10964 12395 8622 7425 5105 6204 11430 10223 18.7301 9.09686 -9.66981 10.1493 -8.45875
|
||||
170001 11002 12339 8564 7484 5109 6192 11398 10278 17.6141 8.28686 -8.91053 9.86442 -8.05489
|
||||
171001 11046 12278 8534 7537 5138 6177 11379 10305 16.5824 7.64506 -8.21481 9.47377 -7.70032
|
||||
172001 11007 12267 8561 7572 5125 6181 11392 10330 16.6862 7.70107 -8.25118 9.54244 -7.74493
|
||||
173001 11034 12259 8557 7587 5118 6179 11397 10323 16.5727 7.51672 -8.05867 9.62742 -7.77972
|
||||
174001 11048 12293 8563 7560 5108 6184 11404 10293 16.9598 7.71264 -8.26192 9.82218 -7.96336
|
||||
175001 11085 12276 8542 7544 5099 6214 11408 10283 17.0417 7.40628 -8.18914 10.2144 -8.01061
|
||||
176001 11101 12261 8543 7530 5090 6214 11416 10294 17.0554 7.27499 -8.25102 10.3532 -7.91793
|
||||
177001 11129 12209 8533 7560 5093 6221 11444 10282 16.8328 6.91568 -7.79777 10.4976 -8.03192
|
||||
178001 11068 12189 8585 7561 5027 6227 11518 10271 17.8399 7.24545 -8.14645 11.2385 -8.54977
|
||||
179001 11004 12196 8651 7555 4976 6221 11555 10288 18.6337 7.67028 -8.73943 11.6576 -8.72372
|
||||
180001 10943 12184 8697 7592 4937 6213 11620 10264 19.2758 8.04287 -8.7566 12.0025 -9.28069
|
||||
181001 10850 12185 8755 7609 4946 6203 11646 10254 19.6923 8.68291 -9.05395 11.826 -9.51657
|
||||
182001 10756 12183 8830 7599 4916 6199 11702 10261 20.5823 9.34242 -9.67124 12.1142 -9.80114
|
||||
183001 10683 12188 8888 7595 4896 6193 11711 10292 21.061 9.76375 -10.2307 12.1859 -9.75053
|
||||
184001 10676 12140 8895 7626 4937 6139 11676 10374 19.9653 9.49415 -10.0414 11.2833 -8.96281
|
||||
185001 10678 12077 8899 7704 4943 6068 11668 10423 18.8953 9.09939 -9.42354 10.5995 -8.54879
|
||||
186001 10648 11979 8900 7800 4970 6008 11663 10482 17.6571 8.66569 -8.66902 9.7796 -8.11695
|
||||
187001 10641 11896 8916 7873 4967 5963 11668 10532 16.8375 8.21062 -8.17832 9.42297 -7.7724
|
||||
188001 10581 11857 8967 7907 4937 5959 11709 10538 17.2217 8.3799 -8.28024 9.69427 -7.98886
|
||||
189001 10494 11845 8997 7948 4885 5977 11771 10557 17.9441 8.66788 -8.38184 10.2189 -8.49559
|
||||
190001 10378 11849 9041 7957 4853 5984 11819 10557 18.836 9.33989 -8.7752 10.4966 -8.96531
|
||||
191001 10350 11754 9057 8030 4839 5966 11836 10604 18.3052 8.88525 -8.34756 10.4518 -8.78687
|
||||
192001 10349 11693 9061 8090 4850 5952 11806 10645 17.5508 8.40921 -7.98207 10.1526 -8.39795
|
||||
193001 10351 11692 9069 8086 4863 5950 11781 10650 17.4026 8.38875 -8.07292 10.0027 -8.20084
|
||||
194001 10295 11700 9075 8146 4841 5949 11784 10694 17.4111 8.46302 -7.97378 9.95897 -8.29221
|
||||
195001 10327 11603 9098 8217 4870 5894 11769 10773 16.0635 7.75323 -7.46254 9.26517 -7.50931
|
||||
196001 10320 11508 9113 8287 4871 5846 11774 10832 15.1552 7.23672 -6.98016 8.85471 -7.08395
|
||||
197001 10332 11464 9115 8299 4886 5791 11755 10908 14.2643 6.9066 -6.86396 8.22582 -6.40247
|
||||
198001 10458 11399 9059 8335 4919 5763 11696 10959 12.6438 5.70511 -6.07832 7.70488 -5.56839
|
||||
199001 10559 11324 8974 8395 4923 5749 11676 10984 11.3886 4.51926 -4.97438 7.54034 -5.26072
|
||||
200001 10663 11234 8927 8449 4947 5727 11643 11047 9.98187 3.29444 -4.12893 7.15579 -4.53113
|
||||
201001 10639 11236 8943 8433 4954 5714 11667 11069 10.0141 3.52959 -4.32076 7.00427 -4.48271
|
||||
202001 10611 11253 8971 8417 4947 5712 11674 11078 10.301 3.81884 -4.66773 7.04463 -4.48479
|
||||
203001 10597 11291 8934 8430 4947 5697 11636 11132 9.90072 3.80325 -4.61553 6.65065 -4.24563
|
||||
204001 10688 11242 8898 8461 4984 5647 11541 11191 8.31809 2.86459 -4.09667 5.82008 -3.21382
|
||||
205001 10773 11192 8813 8504 5031 5577 11484 11247 6.45479 1.97208 -3.10744 4.70705 -2.44188
|
||||
206001 10862 11109 8729 8569 5073 5524 11438 11320 4.6513 0.809163 -1.97717 3.78585 -1.65466
|
||||
207001 10864 11147 8666 8608 5073 5534 11366 11379 4.14146 0.479828 -1.70616 3.48522 -1.36518
|
||||
208001 10947 11156 8614 8601 5126 5519 11326 11392 3.28404 0.0659688 -1.28156 2.87938 -0.920487
|
||||
209001 11004 11170 8580 8607 5148 5502 11286 11405 2.75238 -0.249352 -0.995048 2.485 -0.589964
|
||||
210001 11081 11148 8534 8629 5188 5449 11220 11454 1.9 -0.897975 -0.458751 1.5987 0.193266
|
||||
211001 11131 11090 8502 8677 5210 5421 11176 11493 2.10982 -1.63251 0.14168 1.10759 0.734462
|
||||
212001 11191 11031 8445 8740 5245 5383 11128 11535 2.99288 -2.4678 1.02417 0.37432 1.29547
|
||||
213001 11245 10979 8420 8756 5276 5334 11122 11583 3.82934 -2.99195 1.50224 -0.271278 1.83895
|
||||
214001 11249 10943 8457 8753 5260 5273 11097 11656 4.32619 -3.20599 1.24206 -0.66686 2.53971
|
||||
215001 11252 10924 8447 8730 5305 5266 11065 11642 4.57979 -3.21346 1.26973 -1.07723 2.80633
|
||||
216001 11346 10882 8398 8744 5363 5241 11022 11657 5.80571 -3.92284 1.93088 -1.74463 3.39788
|
||||
217001 11431 10815 8333 8785 5403 5197 10975 11710 7.41468 -4.87947 2.79741 -2.51815 4.12331
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||||
218001 11524 10726 8257 8849 5431 5165 10921 11774 9.26554 -6.13219 3.84046 -3.12401 4.87216
|
||||
219001 11547 10691 8230 8892 5435 5157 10884 11811 10.0429 -6.67431 4.23973 -3.34585 5.20995
|
||||
220001 11540 10694 8220 8919 5435 5154 10845 11824 10.3083 -6.80503 4.34626 -3.51148 5.36024
|
||||
221001 11616 10610 8165 8947 5463 5115 10793 11840 11.7494 -7.72415 5.12165 -4.05706 5.97459
|
||||
222001 11617 10662 8073 8957 5489 5146 10737 11843 12.0611 -7.82273 5.52907 -4.31021 5.92674
|
||||
223001 11614 10655 8077 8961 5504 5157 10702 11858 12.2589 -7.93704 5.45169 -4.40587 6.17666
|
||||
224001 11653 10644 8061 8953 5528 5170 10655 11865 12.7274 -8.27085 5.51696 -4.50963 6.54266
|
||||
225001 11661 10679 8078 8870 5533 5206 10613 11843 12.2681 -8.04072 4.80331 -4.17506 6.73428
|
||||
226001 11663 10749 8095 8820 5537 5247 10600 11783 11.4825 -7.55947 4.31164 -3.80124 6.45467
|
||||
227001 11679 10775 8103 8760 5554 5255 10609 11741 11.0846 -7.24465 4.00956 -3.71666 6.36339
|
||||
228001 11638 10836 8099 8715 5546 5307 10670 11661 9.79871 -6.52076 3.73798 -3.10787 5.46471
|
||||
229001 11644 10861 8112 8686 5538 5370 10720 11595 8.96315 -6.24965 3.53891 -2.32576 4.83185
|
||||
230001 11655 10864 8092 8703 5563 5390 10682 11576 9.19903 -6.39069 3.74805 -2.43378 4.87956
|
||||
231001 11680 10869 8120 8690 5591 5392 10714 11578 9.11684 -6.27747 3.63955 -2.51067 4.91533
|
||||
232001 11722 10883 8143 8668 5629 5448 10741 11535 8.80721 -6.19815 3.51642 -2.15223 4.70666
|
||||
233001 11795 10851 8093 8683 5671 5444 10684 11538 9.82513 -6.8377 4.06925 -2.54873 5.16954
|
||||
234001 11880 10774 8019 8718 5717 5413 10628 11588 11.4946 -7.86352 4.9602 -3.24272 5.93057
|
||||
235001 11954 10710 7985 8785 5766 5377 10616 11624 12.8566 -8.62511 5.86644 -3.9388 6.40078
|
||||
236001 11958 10706 7964 8806 5775 5390 10611 11630 13.0658 -8.77942 6.10376 -3.96857 6.37418
|
||||
237001 11951 10739 7951 8803 5791 5382 10614 11608 12.9154 -8.51143 6.18254 -4.19588 6.20754
|
||||
238001 11966 10757 7920 8802 5776 5388 10613 11624 13.0037 -8.63294 6.29524 -4.10153 6.17386
|
||||
239001 12001 10745 7892 8822 5766 5398 10608 11609 13.3057 -8.96366 6.64872 -3.92823 6.08754
|
||||
240001 11989 10751 7913 8802 5771 5403 10584 11623 13.1906 -8.87642 6.3047 -3.94868 6.31347
|
||||
241001 12011 10761 7893 8803 5762 5392 10586 11630 13.3424 -8.97549 6.45019 -3.98771 6.32094
|
||||
242001 12019 10799 7886 8747 5757 5393 10594 11587 12.8506 -8.6369 6.19763 -3.83893 6.11498
|
||||
243001 12027 10851 7841 8740 5783 5415 10556 11568 12.8736 -8.53777 6.33236 -4.01124 6.0538
|
||||
244001 12097 10833 7785 8741 5825 5434 10528 11515 13.4765 -8.94675 6.92779 -4.10495 6.06022
|
||||
245001 12095 10918 7787 8670 5816 5488 10541 11456 12.4087 -8.36959 6.36665 -3.51313 5.57223
|
||||
246001 12020 10965 7799 8690 5792 5479 10536 11516 12.0559 -8.00648 6.05162 -3.6819 5.57342
|
||||
247001 12035 10936 7772 8725 5846 5419 10496 11584 13.1832 -8.32336 6.51148 -4.77393 6.27117
|
||||
248001 12057 10955 7740 8721 5927 5346 10467 11608 14.054 -8.17913 6.87278 -6.11231 6.78397
|
||||
249001 12040 10972 7742 8728 5909 5325 10458 11647 14.1125 -8.13004 6.76146 -6.27131 6.92955
|
||||
250001 12048 10927 7731 8759 5939 5266 10436 11719 15.1606 -8.47196 7.09394 -7.10949 7.56318
|
||||
251001 12050 10986 7714 8731 5932 5259 10432 11717 14.9229 -8.18817 6.9358 -7.18281 7.4798
|
||||
252001 12044 11024 7749 8704 5950 5240 10447 11730 14.7064 -7.7745 6.55145 -7.44931 7.57767
|
||||
253001 12102 10995 7720 8751 5968 5221 10435 11797 15.7142 -8.40653 7.08583 -7.84331 8.03369
|
||||
254001 12167 10945 7652 8813 5995 5190 10371 11854 17.2677 -9.32358 7.96353 -8.50598 8.68769
|
||||
255001 12186 10916 7610 8854 6053 5141 10332 11875 18.4481 -9.61619 8.63152 -9.49747 9.11903
|
||||
256001 12254 10926 7543 8854 6083 5153 10309 11850 18.9798 -9.96216 9.19609 -9.63675 9.14065
|
||||
257001 12279 10941 7480 8869 6127 5167 10238 11874 19.7623 -10.2992 9.58983 -10.0925 9.52101
|
||||
258001 12314 10988 7443 8862 6179 5128 10188 11866 20.4267 -10.1933 9.85327 -10.9337 9.83433
|
||||
259001 12360 10993 7406 8865 6223 5114 10140 11877 21.1969 -10.4535 10.18 -11.4666 10.2429
|
||||
260001 12420 10930 7348 8888 6261 5110 10103 11874 22.2319 -11.1551 10.9159 -11.7739 10.5849
|
||||
261001 12494 10881 7284 8910 6302 5097 10054 11873 23.3986 -11.8656 11.6833 -12.2051 11.0108
|
||||
262001 12522 10927 7282 8849 6305 5172 10080 11807 22.4604 -11.6045 11.3527 -11.4075 10.5258
|
||||
263001 12520 10949 7292 8834 6311 5160 10081 11805 22.3579 -11.3975 11.1962 -11.5457 10.5505
|
||||
264001 12506 10997 7257 8857 6304 5147 10047 11842 22.6411 -11.3754 11.3364 -11.882 10.6547
|
||||
265001 12568 10917 7230 8911 6340 5108 10007 11907 24.1212 -12.2395 12.0169 -12.5383 11.4198
|
||||
266001 12604 10848 7209 8961 6314 5069 10018 11962 24.957 -12.9255 12.5674 -12.6857 11.7012
|
||||
267001 12630 10772 7215 8997 6319 5034 10018 12032 25.8264 -13.5142 12.8573 -13.0134 12.2355
|
||||
268001 12641 10764 7210 9012 6324 5032 9983 12044 26.1534 -13.7239 12.9381 -13.1377 12.4765
|
||||
269001 12649 10790 7209 8986 6308 5043 9992 12028 25.7916 -13.588 12.7631 -12.8794 12.3206
|
||||
270001 12714 10755 7163 8992 6296 5056 9986 12038 26.2853 -14.2194 13.2031 -12.6341 12.4411
|
||||
271001 12684 10783 7186 8956 6267 5081 10038 11985 25.2739 -13.7324 12.8351 -12.0534 11.8392
|
||||
272001 12610 10829 7238 8902 6244 5135 10090 11932 23.7461 -12.9258 12.026 -11.2971 11.1604
|
||||
273001 12606 10863 7293 8861 6210 5202 10147 11851 22.338 -12.4708 11.4305 -10.1982 10.4311
|
||||
274001 12542 10929 7341 8818 6168 5277 10160 11834 20.903 -11.8856 10.4939 -9.2762 9.97486
|
||||
275001 12538 10883 7341 8857 6174 5232 10159 11877 21.5651 -12.149 10.8023 -9.75184 10.2794
|
||||
276001 12529 10874 7338 8872 6195 5222 10144 11878 21.8195 -12.1591 10.9335 -10.0427 10.3851
|
||||
277001 12552 10825 7311 8907 6202 5213 10135 11902 22.5017 -12.6501 11.4049 -10.2035 10.5887
|
||||
278001 12537 10841 7302 8908 6210 5209 10141 11892 22.4306 -12.4744 11.464 -10.3334 10.4555
|
||||
279001 12501 10846 7333 8912 6225 5201 10168 11851 22.0586 -12.0514 11.3716 -10.4333 10.1577
|
||||
280001 12457 10830 7343 8926 6214 5205 10200 11832 21.7528 -11.8724 11.3996 -10.2901 9.81808
|
||||
281001 12428 10842 7389 8904 6199 5205 10198 11829 21.2606 -11.5801 10.8795 -10.1364 9.83894
|
||||
282001 12427 10812 7417 8876 6207 5202 10200 11788 21.0622 -11.4868 10.683 -10.0345 9.84118
|
||||
283001 12394 10836 7422 8887 6205 5190 10226 11756 20.75 -11.1044 10.7327 -10.1264 9.46157
|
||||
284001 12327 10832 7496 8867 6185 5195 10284 11745 19.8181 -10.548 10.1093 -9.78802 9.13749
|
||||
285001 12282 10820 7544 8878 6185 5179 10306 11762 19.611 -10.2898 9.84431 -9.90756 9.14565
|
||||
286001 12270 10780 7572 8907 6180 5166 10326 11788 19.763 -10.4236 9.88434 -9.94723 9.23448
|
||||
287001 12260 10752 7587 8916 6178 5194 10322 11780 19.6465 -10.5541 9.82618 -9.65843 9.20633
|
||||
288001 12282 10682 7555 8946 6189 5209 10294 11803 20.363 -11.2231 10.2653 -9.64769 9.49944
|
||||
289001 12261 10635 7538 9009 6214 5216 10282 11786 20.8376 -11.4741 10.8166 -9.84943 9.4096
|
||||
290001 12239 10620 7532 9033 6214 5236 10286 11770 20.7848 -11.5128 10.9777 -9.70921 9.20243
|
||||
291001 12212 10619 7562 9035 6226 5233 10272 11771 20.6842 -11.3426 10.752 -9.84304 9.31072
|
||||
292001 12184 10617 7562 9058 6225 5230 10278 11731 20.5587 -11.1794 10.9199 -9.86506 9.00653
|
||||
293001 12196 10611 7563 9063 6225 5210 10276 11757 20.8121 -11.2847 10.9594 -10.0508 9.20179
|
||||
294001 12182 10596 7598 9058 6214 5208 10259 11767 20.6961 -11.2874 10.6471 -9.96447 9.3954
|
||||
295001 12189 10587 7609 8999 6195 5196 10259 11747 20.4009 -11.1896 10.2955 -9.76646 9.4662
|
||||
296001 12182 10597 7593 8988 6198 5201 10269 11743 20.3084 -11.0971 10.3257 -9.75932 9.34994
|
||||
297001 12180 10571 7605 8957 6183 5188 10301 11701 20.0002 -10.9745 10.2436 -9.54805 9.13636
|
||||
298001 12134 10624 7638 8928 6127 5205 10379 11651 18.6781 -10.2793 9.79243 -8.8516 8.30453
|
||||
299001 12060 10626 7718 8896 6061 5218 10433 11674 17.509 -9.81499 8.88741 -8.14515 8.0561
|
||||
300001 11967 10701 7809 8811 5999 5222 10493 11650 15.6585 -8.64907 7.56652 -7.50422 7.53769
|
||||
301001 11872 10763 7896 8748 5960 5210 10536 11664 14.3325 -7.62184 6.38919 -7.27238 7.32249
|
||||
302001 11847 10768 7915 8741 5962 5213 10538 11647 14.0686 -7.39657 6.2101 -7.24104 7.22622
|
||||
303001 11845 10806 7955 8704 5976 5199 10554 11612 13.633 -6.8849 5.81905 -7.33707 7.12472
|
||||
304001 11833 10880 7966 8655 5987 5244 10567 11559 12.7348 -6.29238 5.3709 -6.98913 6.69969
|
||||
305001 11739 10926 8037 8602 5960 5279 10618 11513 11.2156 -5.3298 4.44046 -6.37407 6.0858
|
||||
306001 11698 10936 8096 8578 5950 5287 10637 11513 10.6437 -4.92628 3.85175 -6.15674 6.02314
|
||||
307001 11695 10906 8089 8614 5948 5291 10645 11506 10.7642 -5.12414 4.16888 -6.10978 5.90789
|
||||
308001 11681 10921 8155 8572 5939 5293 10713 11474 9.92438 -4.58406 3.6296 -5.7633 5.57586
|
||||
309001 11586 10992 8220 8482 5895 5299 10787 11433 8.31614 -3.37028 2.52866 -5.22278 4.91201
|
||||
310001 11496 11084 8293 8388 5835 5313 10849 11426 6.81934 -2.20015 1.20112 -4.56336 4.40406
|
||||
311001 11448 11090 8313 8358 5788 5316 10912 11376 5.8406 -1.7209 0.919413 -4.01335 3.76813
|
||||
312001 11383 11119 8347 8320 5757 5341 10968 11352 4.88918 -1.09243 0.365339 -3.48011 3.23513
|
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|
||||
808001 11248 11101 5310 5212 8427 7785 11172 10985 3.56269 1.27061 0.591114 -3.12297 0.987906
|
||||
809001 11225 11187 5332 5172 8421 7805 11180 10917 3.56907 2.00968 -0.0117075 -2.91045 0.478118
|
||||
810001 11196 11287 5342 5141 8413 7842 11193 10866 3.85694 2.72758 -0.515309 -2.67591 -0.101373
|
||||
811001 11171 11369 5366 5105 8391 7862 11225 10791 4.38794 3.4802 -1.07783 -2.31463 -0.789301
|
||||
812001 11150 11428 5420 5064 8353 7888 11274 10747 5.03891 4.10478 -1.941 -1.73711 -1.32528
|
||||
813001 11140 11457 5407 5069 8350 7879 11307 10700 5.36967 4.42606 -1.72509 -1.73407 -1.80566
|
||||
814001 11108 11559 5367 5078 8324 7929 11283 10688 5.75123 4.7434 -1.64163 -1.61871 -2.29382
|
||||
815001 11096 11608 5357 5101 8304 7937 11298 10673 6.02489 4.95201 -1.44885 -1.56571 -2.68818
|
||||
816001 11038 11648 5398 5123 8252 7940 11310 10671 6.54716 5.34999 -1.79593 -1.35382 -3.03064
|
||||
817001 11024 11660 5435 5104 8260 7922 11291 10655 6.88842 5.63518 -2.26179 -1.46439 -2.90431
|
||||
818001 10984 11647 5440 5125 8239 7878 11261 10666 6.91818 5.6913 -2.18746 -1.76016 -2.75448
|
||||
819001 10961 11587 5441 5202 8252 7829 11241 10719 6.47403 5.34534 -1.50857 -2.34237 -2.36175
|
||||
820001 10976 11576 5439 5245 8257 7760 11228 10739 6.40876 5.21854 -1.03513 -2.89647 -2.09236
|
||||
821001 10990 11570 5441 5265 8254 7745 11225 10749 6.29075 5.08667 -0.857144 -2.99264 -2.00219
|
||||
822001 10992 11499 5443 5351 8238 7696 11238 10783 5.94124 4.60602 -0.036746 -3.26261 -1.85388
|
||||
823001 10991 11460 5418 5403 8233 7635 11242 10815 6.00362 4.33191 0.690098 -3.73708 -1.68407
|
||||
824001 10971 11493 5429 5397 8229 7618 11235 10825 6.28047 4.60075 0.468471 -3.91488 -1.65277
|
||||
825001 10981 11483 5449 5421 8203 7573 11235 10863 6.22881 4.46081 0.504523 -4.08461 -1.40025
|
||||
826001 11012 11451 5430 5487 8217 7522 11237 10879 6.40383 4.10112 1.36256 -4.55901 -1.2445
|
||||
827001 11026 11472 5430 5495 8294 7449 11145 10900 7.25272 4.19317 1.47177 -5.71463 -0.442901
|
||||
828001 11045 11507 5403 5487 8370 7404 11072 10915 8.10678 4.29353 1.65064 -6.67387 0.142795
|
||||
829001 11107 11484 5366 5539 8401 7372 11096 10886 8.45672 3.96188 2.66659 -6.97915 0.0173064
|
||||
830001 11078 11452 5347 5590 8383 7317 11127 10944 8.93888 3.82346 3.2515 -7.39628 0.0862012
|
||||
831001 11052 11426 5362 5643 8355 7293 11162 10944 9.06346 3.81008 3.59914 -7.39254 -0.161784
|
||||
832001 11022 11396 5375 5681 8314 7279 11236 10922 9.03222 3.90441 3.89799 -7.11592 -0.711291
|
||||
833001 11052 11360 5371 5746 8327 7216 11249 10949 9.63968 3.58675 4.63387 -7.63834 -0.491706
|
||||
834001 11047 11329 5366 5796 8297 7173 11289 10975 9.94127 3.40911 5.14649 -7.77038 -0.58451
|
||||
835001 11060 11295 5360 5865 8263 7116 11323 10997 10.3909 3.10946 5.85632 -7.97423 -0.645764
|
||||
836001 11048 11259 5358 5915 8284 7055 11315 11041 11.1256 2.95306 6.34131 -8.64653 -0.290697
|
||||
837001 11058 11237 5341 5948 8271 6987 11345 11041 11.715 2.88022 6.90972 -9.00455 -0.347186
|
||||
838001 11092 11258 5308 5970 8317 6951 11307 11037 12.5069 2.80617 7.43861 -9.65419 -0.110894
|
||||
839001 11111 11222 5316 6024 8293 6907 11326 11058 12.829 2.49412 7.89695 -9.7979 -0.0381048
|
||||
840001 11088 11205 5317 6082 8264 6857 11311 11115 13.3157 2.29486 8.24618 -10.198 0.206819
|
||||
841001 11105 11158 5321 6134 8244 6800 11297 11167 13.79 1.83846 8.66045 -10.5543 0.622502
|
||||
842001 11094 11129 5325 6172 8237 6745 11305 11213 14.3008 1.70426 8.95667 -10.9835 0.866064
|
||||
843001 11107 11111 5327 6209 8211 6733 11293 11194 14.4 1.47381 9.25488 -10.9043 0.795486
|
||||
844001 11111 11037 5338 6213 8233 6641 11253 11213 15.0767 1.24374 9.39926 -11.6277 1.48658
|
||||
845001 11180 11015 5317 6209 8289 6593 11207 11250 15.8619 0.833933 9.70841 -12.3139 2.23995
|
||||
846001 11189 10998 5330 6229 8306 6522 11192 11319 16.562 0.706331 9.79799 -13.026 2.84973
|
||||
847001 11167 10997 5336 6235 8335 6447 11179 11329 17.2921 0.973171 9.8866 -13.8029 3.13145
|
||||
848001 11184 10947 5342 6315 8352 6384 11192 11364 18.2252 0.62545 10.6232 -14.4033 3.38532
|
||||
849001 11157 10916 5329 6426 8331 6339 11183 11399 19.1236 0.300857 11.5223 -14.8801 3.38267
|
||||
850001 11158 10859 5345 6491 8342 6271 11172 11453 19.9895 -0.0468506 11.9779 -15.53 3.86372
|
||||
851001 11141 10801 5346 6560 8362 6176 11171 11514 21.2087 -0.275717 12.6148 -16.4876 4.33125
|
||||
852001 11147 10781 5339 6632 8351 6109 11182 11529 22.0362 -0.454738 13.3092 -17.0083 4.35558
|
||||
853001 11164 10735 5352 6700 8360 6068 11230 11541 22.6227 -0.690225 13.9191 -17.2905 4.31382
|
||||
854001 11152 10681 5363 6750 8341 6040 11252 11544 22.8957 -0.916975 14.2954 -17.3468 4.25477
|
||||
855001 11178 10674 5362 6761 8333 6014 11253 11533 23.0885 -1.03136 14.4794 -17.4359 4.28399
|
||||
856001 11231 10611 5348 6810 8358 5970 11188 11561 24.0483 -1.75635 15.0809 -17.977 4.96284
|
||||
857001 11261 10578 5330 6872 8379 5941 11176 11562 24.8598 -2.14237 15.8152 -18.368 5.09074
|
||||
858001 11245 10540 5344 6934 8367 5895 11190 11579 25.3738 -2.28968 16.2189 -18.6897 5.12139
|
||||
859001 11278 10508 5360 7002 8416 5845 11191 11602 26.3279 -2.54718 16.7822 -19.3721 5.45425
|
||||
860001 11238 10525 5406 7018 8376 5840 11272 11546 25.7364 -2.01028 16.5984 -18.9913 4.70561
|
||||
861001 11220 10574 5400 7028 8340 5877 11284 11488 25.2634 -1.72878 16.6052 -18.5215 4.05861
|
||||
862001 11211 10585 5409 7032 8314 5912 11313 11440 24.7639 -1.59109 16.5552 -18.0012 3.54942
|
||||
863001 11220 10588 5401 7039 8281 5916 11339 11423 24.6098 -1.63572 16.6858 -17.7181 3.25871
|
||||
864001 11219 10624 5382 7046 8271 5871 11375 11421 24.9681 -1.35909 16.9408 -18.0386 3.02973
|
||||
865001 11273 10647 5382 7053 8291 5850 11425 11410 25.2217 -1.29977 17.1941 -18.1784 2.89047
|
||||
866001 11290 10672 5390 7057 8303 5810 11388 11422 25.5629 -1.24105 17.1505 -18.6406 3.21111
|
||||
867001 11300 10692 5378 7065 8269 5762 11416 11451 25.8181 -1.20415 17.3051 -18.855 3.18507
|
||||
868001 11289 10698 5391 7054 8236 5808 11433 11410 25.1291 -1.11882 17.0674 -18.2002 2.77071
|
||||
869001 11251 10797 5410 7031 8225 5823 11438 11350 24.6429 -0.303341 16.6048 -18.0705 2.21752
|
||||
870001 11200 10878 5420 7005 8148 5877 11559 11226 23.5471 0.627109 16.3184 -16.9524 0.632508
|
||||
871001 11146 10986 5452 6976 8094 5917 11586 11138 22.6492 1.55602 15.6447 -16.3007 -0.305721
|
||||
872001 11116 11078 5504 6924 8063 5948 11649 11044 21.7433 2.54001 14.8315 -15.6503 -1.19048
|
||||
873001 11052 11206 5541 6866 8011 5969 11728 10967 21.0222 3.80173 13.9651 -15.0786 -2.256
|
||||
874001 10985 11323 5588 6816 7972 5991 11788 10879 20.4884 5.03574 13.0952 -14.5742 -3.24411
|
||||
875001 10892 11401 5652 6787 7939 5977 11846 10840 20.2974 6.18137 12.2488 -14.4449 -3.88421
|
||||
876001 10887 11384 5657 6828 7961 5936 11793 10884 20.7388 5.97995 12.4651 -15.0878 -3.36411
|
||||
877001 10889 11391 5663 6844 7987 5890 11792 10858 21.2817 6.1857 12.6764 -15.5773 -3.36183
|
||||
878001 10889 11382 5665 6843 7963 5877 11813 10812 21.2741 6.27085 12.7583 -15.3964 -3.66602
|
||||
879001 10899 11390 5664 6848 7944 5894 11826 10783 21.1334 6.26135 12.8137 -15.0886 -3.94476
|
||||
880001 10902 11401 5654 6877 7940 5853 11839 10781 21.6231 6.32536 13.1637 -15.4276 -4.03151
|
||||
881001 10892 11365 5629 6930 7922 5836 11892 10746 22.124 6.2263 13.9065 -15.386 -4.53711
|
||||
882001 10909 11383 5608 6962 7922 5844 11902 10685 22.476 6.25166 14.3894 -15.2973 -5.00285
|
||||
883001 10921 11379 5593 6968 7919 5831 11908 10644 22.7079 6.25597 14.6641 -15.307 -5.21263
|
||||
884001 10934 11408 5618 6960 7925 5821 11890 10608 22.6704 6.47035 14.4437 -15.3627 -5.23921
|
||||
885001 10938 11445 5603 6964 7916 5831 11909 10557 22.8503 6.68903 14.6158 -15.2015 -5.71685
|
||||
886001 10944 11486 5612 6961 7924 5826 11889 10524 22.9481 6.92888 14.5111 -15.3054 -5.81209
|
||||
887001 10944 11495 5588 6958 7911 5834 11919 10520 23.0323 6.95295 14.682 -15.158 -6.06781
|
||||
888001 10935 11495 5575 7000 7906 5845 11946 10467 23.4147 7.01314 15.1613 -15.017 -6.60963
|
||||
889001 10932 11477 5589 7071 7936 5807 11954 10482 24.0549 6.94947 15.6609 -15.5748 -6.51985
|
||||
890001 10975 11439 5594 7117 7988 5741 11921 10513 24.6885 6.60406 16.151 -16.4401 -5.89752
|
||||
891001 11041 11373 5569 7178 8021 5670 11868 10560 25.4357 5.82766 16.9773 -17.2774 -5.12595
|
||||
892001 11031 11328 5589 7216 8029 5597 11860 10604 25.9173 5.6898 17.1847 -17.95 -4.67097
|
||||
893001 11035 11281 5577 7269 8041 5532 11856 10664 26.6322 5.3445 17.7382 -18.6591 -4.23147
|
||||
894001 11056 11257 5575 7300 8040 5459 11854 10718 27.1852 5.10156 18.0601 -19.3005 -3.78637
|
||||
895001 11047 11232 5582 7356 8027 5411 11869 10736 27.683 4.99035 18.4593 -19.6611 -3.76029
|
||||
896001 11087 11210 5571 7387 8058 5383 11869 10703 28.2417 4.81054 18.9979 -19.9862 -3.75266
|
||||
897001 11094 11268 5513 7419 8074 5438 11809 10703 28.5055 4.6497 19.416 -19.9735 -3.87588
|
||||
898001 11069 11338 5538 7408 8001 5448 11884 10646 28.0743 5.26517 19.0754 -19.3338 -4.7729
|
||||
899001 11028 11326 5566 7432 7953 5433 11956 10588 28.072 5.61083 19.1301 -18.9882 -5.48132
|
||||
900001 10987 11316 5572 7510 7923 5397 11963 10601 28.5788 5.6012 19.5506 -19.2667 -5.65201
|
||||
901001 10992 11266 5570 7588 7939 5340 11957 10654 29.3381 5.20645 20.1876 -19.9572 -5.2715
|
||||
902001 10976 11254 5563 7637 7931 5259 11979 10708 30.113 5.1925 20.6204 -20.7083 -5.07893
|
||||
903001 10978 11234 5567 7697 7965 5186 12005 10750 31.0471 5.15989 21.159 -21.5913 -4.83832
|
||||
904001 10914 11260 5551 7768 7920 5203 11946 10833 31.1313 4.96694 21.2615 -21.6882 -4.69675
|
||||
905001 10879 11284 5578 7797 7920 5196 11920 10821 31.2175 5.22133 21.1323 -21.8649 -4.75588
|
||||
906001 10827 11354 5546 7812 7894 5227 11834 10858 31.161 5.31308 20.9843 -21.92 -4.68489
|
||||
907001 10739 11440 5511 7871 7805 5283 11783 10945 30.8868 5.33094 20.8858 -21.5659 -4.92708
|
||||
908001 10653 11503 5465 7968 7744 5314 11689 11064 31.099 5.08928 21.1125 -21.7423 -4.77304
|
||||
909001 10654 11487 5416 8027 7779 5285 11580 11149 31.9224 4.51634 21.677 -22.6519 -3.95515
|
||||
910001 10681 11456 5339 8100 7792 5254 11481 11224 32.9158 3.66336 22.6137 -23.4083 -3.27116
|
||||
927
src/kimono/lxpack/tests/ref/borbu1.2.ref
Normal file
927
src/kimono/lxpack/tests/ref/borbu1.2.ref
Normal file
@ -0,0 +1,927 @@
|
||||
# input : borbu1.fst
|
||||
# include : borbu1.lst
|
||||
# selector : count
|
||||
# mixer : basic
|
||||
# distance : chi
|
||||
# phase : 2
|
||||
# alphabet : ACGT
|
||||
# excluded : X
|
||||
# seqname : borbu1
|
||||
# seqlength : 910724
|
||||
# unmasked : 284101
|
||||
# valid : 284087
|
||||
# window : 227680
|
||||
# step : 1000
|
||||
#
|
||||
# pos LeftA RightA LeftC
|
||||
1 12255 13322 4686 5089
|
||||
1001 12213 13363 4707 5081
|
||||
2001 12233 13341 4717 5090
|
||||
3001 12265 13363 4727 5077
|
||||
4001 12290 13274 4726 5055
|
||||
5001 12309 13238 4742 5057
|
||||
6001 12269 13241 4763 5044
|
||||
7001 12318 13175 4768 5032
|
||||
8001 12349 13177 4776 5031
|
||||
9001 12344 13178 4778 5019
|
||||
10001 12357 13159 4805 5016
|
||||
11001 12394 13131 4838 5020
|
||||
12001 12408 13102 4857 5013
|
||||
13001 12461 13061 4865 5022
|
||||
14001 12495 13019 4874 5025
|
||||
15001 12520 13002 4883 4999
|
||||
16001 12528 13008 4903 4998
|
||||
17001 12565 13031 4943 4978
|
||||
18001 12600 13013 4968 4974
|
||||
19001 12627 13037 4982 4969
|
||||
20001 12646 13053 4977 4979
|
||||
21001 12600 13104 4959 5020
|
||||
22001 12600 13125 4979 5022
|
||||
23001 12598 13144 4984 5022
|
||||
24001 12635 13125 4990 5000
|
||||
25001 12615 13093 5000 4979
|
||||
26001 12599 13127 5009 4970
|
||||
27001 12622 13143 5023 4953
|
||||
28001 12640 13123 5026 4947
|
||||
29001 12641 13113 5030 4943
|
||||
30001 12668 13106 5004 4931
|
||||
31001 12691 13065 5004 4913
|
||||
32001 12683 13052 5011 4920
|
||||
33001 12676 13094 5003 4923
|
||||
34001 12678 13081 5008 4916
|
||||
35001 12668 13048 5015 4916
|
||||
36001 12638 13048 5036 4905
|
||||
37001 12632 13008 5051 4894
|
||||
38001 12609 13013 5042 4925
|
||||
39001 12615 13017 5013 4958
|
||||
40001 12585 13024 5006 4979
|
||||
41001 12612 12983 4991 4992
|
||||
42001 12616 12965 4968 5003
|
||||
43001 12617 12955 4971 5010
|
||||
44001 12592 12991 4955 5014
|
||||
45001 12599 12964 4921 5024
|
||||
46001 12593 12978 4942 5032
|
||||
47001 12514 13062 4931 5041
|
||||
48001 12431 13109 4946 5026
|
||||
49001 12402 13103 4932 5010
|
||||
50001 12410 13092 4913 5009
|
||||
51001 12397 13107 4900 4998
|
||||
52001 12407 13157 4916 4995
|
||||
53001 12394 13173 4896 4988
|
||||
54001 12397 13173 4879 4992
|
||||
55001 12364 13168 4883 5008
|
||||
56001 12364 13151 4872 5017
|
||||
57001 12356 13194 4859 5037
|
||||
58001 12378 13183 4860 5022
|
||||
59001 12384 13180 4845 5017
|
||||
60001 12416 13191 4829 5015
|
||||
61001 12438 13201 4819 5024
|
||||
62001 12427 13223 4804 5018
|
||||
63001 12437 13257 4822 5012
|
||||
64001 12501 13242 4826 5017
|
||||
65001 12570 13215 4817 5009
|
||||
66001 12561 13229 4838 4980
|
||||
67001 12561 13199 4841 4984
|
||||
68001 12588 13170 4841 4991
|
||||
69001 12583 13159 4858 4980
|
||||
70001 12548 13203 4865 4973
|
||||
71001 12554 13215 4882 4978
|
||||
72001 12642 13159 4867 5015
|
||||
73001 12662 13154 4890 5032
|
||||
74001 12712 13135 4922 5025
|
||||
75001 12784 13071 4923 5020
|
||||
76001 12789 13035 4932 5029
|
||||
77001 12825 12991 4958 5029
|
||||
78001 12842 13016 4970 5029
|
||||
79001 12847 13008 4974 5032
|
||||
80001 12832 12954 4967 5017
|
||||
81001 12766 13006 4979 5019
|
||||
82001 12738 13022 4992 5014
|
||||
83001 12750 13047 4993 5006
|
||||
84001 12741 13077 4991 5028
|
||||
85001 12735 13119 5007 5035
|
||||
86001 12728 13157 4998 5055
|
||||
87001 12734 13183 4980 5070
|
||||
88001 12766 13162 4998 5058
|
||||
89001 12794 13119 4999 5057
|
||||
90001 12806 13103 5019 5080
|
||||
91001 12821 13125 5028 5081
|
||||
92001 12819 13146 5020 5091
|
||||
93001 12811 13119 5012 5070
|
||||
94001 12794 13152 4994 5083
|
||||
95001 12778 13191 4976 5086
|
||||
96001 12776 13240 4960 5090
|
||||
97001 12754 13269 4943 5099
|
||||
98001 12742 13306 4933 5097
|
||||
99001 12707 13369 4900 5111
|
||||
100001 12748 13406 4923 5116
|
||||
101001 12797 13448 4930 5136
|
||||
102001 12791 13498 4934 5161
|
||||
103001 12804 13547 4958 5148
|
||||
104001 12805 13602 4956 5133
|
||||
105001 12807 13633 4920 5143
|
||||
106001 12860 13602 4889 5133
|
||||
107001 12936 13619 4892 5153
|
||||
108001 12956 13568 4914 5158
|
||||
109001 13036 13517 4938 5171
|
||||
110001 13133 13497 4982 5192
|
||||
111001 13241 13523 5021 5198
|
||||
112001 13240 13526 5026 5206
|
||||
113001 13211 13549 5048 5207
|
||||
114001 13346 13520 5098 5191
|
||||
115001 13356 13516 5084 5191
|
||||
116001 13342 13526 5088 5192
|
||||
117001 13346 13522 5072 5222
|
||||
118001 13270 13588 5053 5242
|
||||
119001 13236 13639 5053 5240
|
||||
120001 13237 13688 5044 5239
|
||||
121001 13185 13734 5032 5248
|
||||
122001 13167 13737 5022 5261
|
||||
123001 13179 13736 5013 5267
|
||||
124001 13154 13713 5013 5268
|
||||
125001 13123 13719 5020 5245
|
||||
126001 13097 13730 5004 5248
|
||||
127001 13056 13722 5021 5237
|
||||
128001 13013 13725 5022 5238
|
||||
129001 12995 13689 5003 5258
|
||||
130001 13019 13693 5001 5286
|
||||
131001 13030 13693 4980 5284
|
||||
132001 13027 13644 4977 5274
|
||||
133001 13031 13592 4979 5299
|
||||
134001 13058 13584 4981 5331
|
||||
135001 13108 13576 5022 5306
|
||||
136001 13138 13572 5019 5314
|
||||
137001 13145 13564 5018 5308
|
||||
138001 13126 13553 5003 5334
|
||||
139001 13096 13597 4975 5335
|
||||
140001 13128 13602 4970 5344
|
||||
141001 13147 13597 4946 5365
|
||||
142001 13128 13566 4947 5390
|
||||
143001 13118 13542 4940 5396
|
||||
144001 13099 13569 4933 5415
|
||||
145001 13059 13591 4916 5433
|
||||
146001 13065 13578 4921 5438
|
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||||
576001 12434 12208 4820 4835
|
||||
577001 12434 12190 4837 4820
|
||||
578001 12430 12197 4811 4851
|
||||
579001 12436 12149 4798 4867
|
||||
580001 12490 12121 4834 4866
|
||||
581001 12504 12159 4842 4865
|
||||
582001 12508 12129 4878 4835
|
||||
583001 12481 12129 4891 4812
|
||||
584001 12474 12117 4891 4815
|
||||
585001 12443 12157 4885 4833
|
||||
586001 12395 12125 4902 4841
|
||||
587001 12413 12110 4915 4822
|
||||
588001 12379 12129 4923 4831
|
||||
589001 12374 12125 4931 4811
|
||||
590001 12364 12122 4938 4808
|
||||
591001 12388 12133 4929 4834
|
||||
592001 12396 12138 4941 4830
|
||||
593001 12384 12142 4935 4846
|
||||
594001 12372 12152 4939 4824
|
||||
595001 12386 12148 4959 4808
|
||||
596001 12449 12144 4977 4814
|
||||
597001 12480 12177 4982 4819
|
||||
598001 12449 12169 5006 4814
|
||||
599001 12446 12194 5004 4798
|
||||
600001 12434 12240 5017 4783
|
||||
601001 12339 12293 5008 4769
|
||||
602001 12296 12313 5029 4742
|
||||
603001 12273 12319 5041 4716
|
||||
604001 12296 12278 5052 4728
|
||||
605001 12306 12223 5028 4760
|
||||
606001 12337 12227 5019 4785
|
||||
607001 12391 12247 5025 4807
|
||||
608001 12418 12269 5020 4819
|
||||
609001 12462 12282 5063 4831
|
||||
610001 12455 12283 5021 4849
|
||||
611001 12492 12229 4988 4886
|
||||
612001 12473 12267 4968 4893
|
||||
613001 12472 12273 4962 4893
|
||||
614001 12463 12279 4946 4900
|
||||
615001 12454 12278 4922 4930
|
||||
616001 12453 12267 4909 4952
|
||||
617001 12454 12245 4885 4970
|
||||
618001 12445 12253 4870 4972
|
||||
619001 12428 12279 4839 5010
|
||||
620001 12442 12270 4841 5002
|
||||
621001 12487 12228 4840 4979
|
||||
622001 12489 12237 4815 4983
|
||||
623001 12501 12220 4805 4987
|
||||
624001 12501 12220 4804 4981
|
||||
625001 12526 12192 4795 4985
|
||||
626001 12516 12186 4812 4948
|
||||
627001 12501 12198 4842 4931
|
||||
628001 12474 12248 4851 4925
|
||||
629001 12441 12262 4841 4914
|
||||
630001 12437 12288 4836 4921
|
||||
631001 12414 12280 4842 4910
|
||||
632001 12366 12231 4863 4875
|
||||
633001 12317 12238 4889 4879
|
||||
634001 12295 12221 4889 4886
|
||||
635001 12239 12253 4899 4874
|
||||
636001 12188 12270 4912 4876
|
||||
637001 12113 12340 4895 4884
|
||||
638001 12148 12273 4874 4872
|
||||
639001 12137 12285 4882 4868
|
||||
640001 12160 12262 4881 4864
|
||||
641001 12188 12235 4879 4856
|
||||
642001 12212 12249 4906 4850
|
||||
643001 12227 12247 4892 4862
|
||||
644001 12234 12208 4880 4886
|
||||
645001 12266 12223 4862 4915
|
||||
646001 12296 12236 4879 4924
|
||||
647001 12343 12245 4893 4933
|
||||
648001 12383 12263 4900 4944
|
||||
649001 12370 12255 4882 4947
|
||||
650001 12373 12236 4903 4963
|
||||
651001 12345 12239 4883 4994
|
||||
652001 12344 12241 4878 4991
|
||||
653001 12347 12248 4869 5025
|
||||
654001 12350 12245 4849 5038
|
||||
655001 12428 12231 4884 5027
|
||||
656001 12445 12220 4904 5013
|
||||
657001 12471 12203 4898 5009
|
||||
658001 12444 12201 4898 4999
|
||||
659001 12391 12202 4890 5011
|
||||
660001 12380 12160 4892 5003
|
||||
661001 12359 12124 4886 4984
|
||||
662001 12400 12107 4908 4987
|
||||
663001 12373 12120 4912 4972
|
||||
664001 12337 12142 4895 5012
|
||||
665001 12356 12150 4878 5031
|
||||
666001 12378 12177 4865 5062
|
||||
667001 12399 12180 4863 5093
|
||||
668001 12421 12201 4831 5111
|
||||
669001 12376 12233 4778 5129
|
||||
670001 12371 12228 4747 5142
|
||||
671001 12389 12254 4757 5159
|
||||
672001 12373 12250 4750 5194
|
||||
673001 12383 12266 4756 5189
|
||||
674001 12384 12300 4774 5201
|
||||
675001 12369 12362 4786 5209
|
||||
676001 12336 12381 4828 5178
|
||||
677001 12272 12460 4837 5159
|
||||
678001 12236 12523 4838 5131
|
||||
679001 12257 12546 4842 5140
|
||||
680001 12343 12532 4854 5149
|
||||
681001 12361 12491 4853 5133
|
||||
682001 12352 12502 4844 5141
|
||||
683001 12314 12552 4842 5139
|
||||
684001 12286 12608 4858 5098
|
||||
685001 12243 12641 4861 5073
|
||||
686001 12232 12618 4849 5073
|
||||
687001 12226 12610 4838 5091
|
||||
688001 12212 12635 4823 5104
|
||||
689001 12194 12677 4815 5079
|
||||
690001 12203 12662 4829 5058
|
||||
691001 12179 12652 4821 5059
|
||||
692001 12188 12653 4855 5033
|
||||
693001 12145 12686 4871 5000
|
||||
694001 12129 12698 4862 4965
|
||||
695001 12155 12705 4861 4957
|
||||
696001 12133 12710 4826 4957
|
||||
697001 12119 12696 4815 4969
|
||||
698001 12140 12706 4826 4975
|
||||
699001 12162 12696 4836 4952
|
||||
700001 12116 12674 4842 4919
|
||||
701001 12100 12671 4825 4916
|
||||
702001 12143 12644 4833 4894
|
||||
703001 12128 12632 4808 4910
|
||||
704001 12119 12614 4809 4909
|
||||
705001 12157 12593 4838 4905
|
||||
706001 12131 12600 4840 4890
|
||||
707001 12135 12585 4845 4886
|
||||
708001 12159 12568 4817 4889
|
||||
709001 12144 12577 4811 4874
|
||||
710001 12165 12543 4814 4876
|
||||
711001 12179 12549 4818 4867
|
||||
712001 12163 12575 4813 4853
|
||||
713001 12198 12541 4798 4894
|
||||
714001 12249 12540 4778 4931
|
||||
715001 12275 12589 4757 4941
|
||||
716001 12323 12580 4733 4938
|
||||
717001 12303 12600 4721 4936
|
||||
718001 12266 12647 4738 4905
|
||||
719001 12216 12727 4761 4878
|
||||
720001 12221 12766 4783 4857
|
||||
721001 12271 12771 4817 4824
|
||||
722001 12277 12766 4821 4831
|
||||
723001 12292 12772 4833 4787
|
||||
724001 12268 12789 4853 4798
|
||||
725001 12222 12806 4890 4788
|
||||
726001 12266 12792 4896 4781
|
||||
727001 12277 12821 4893 4771
|
||||
728001 12282 12819 4903 4780
|
||||
729001 12285 12830 4932 4748
|
||||
730001 12259 12872 4961 4729
|
||||
731001 12247 12927 4968 4730
|
||||
732001 12252 12939 4983 4760
|
||||
733001 12280 12937 5009 4778
|
||||
734001 12257 12968 4993 4778
|
||||
735001 12226 12955 4984 4767
|
||||
736001 12236 12958 4983 4783
|
||||
737001 12222 12940 4983 4799
|
||||
738001 12218 12966 4987 4781
|
||||
739001 12178 12982 4979 4786
|
||||
740001 12187 12991 4940 4793
|
||||
741001 12206 12962 4935 4796
|
||||
742001 12254 12938 4922 4812
|
||||
743001 12282 12914 4922 4842
|
||||
744001 12281 12881 4918 4853
|
||||
745001 12264 12915 4897 4889
|
||||
746001 12234 12940 4874 4885
|
||||
747001 12228 12888 4881 4864
|
||||
748001 12215 12831 4885 4877
|
||||
749001 12264 12792 4870 4894
|
||||
750001 12273 12786 4882 4888
|
||||
751001 12314 12785 4880 4913
|
||||
752001 12284 12795 4867 4927
|
||||
753001 12280 12815 4869 4912
|
||||
754001 12265 12827 4864 4903
|
||||
755001 12237 12818 4857 4905
|
||||
756001 12248 12798 4849 4880
|
||||
757001 12246 12815 4864 4841
|
||||
758001 12208 12850 4888 4827
|
||||
759001 12219 12835 4918 4807
|
||||
760001 12232 12826 4918 4792
|
||||
761001 12247 12800 4935 4771
|
||||
762001 12265 12795 4939 4763
|
||||
763001 12258 12851 4948 4767
|
||||
764001 12232 12936 4970 4737
|
||||
765001 12243 12985 4990 4717
|
||||
766001 12244 12973 4995 4732
|
||||
767001 12248 12978 5029 4717
|
||||
768001 12244 12990 5036 4711
|
||||
769001 12232 12958 5023 4717
|
||||
770001 12216 12935 5008 4729
|
||||
771001 12205 12936 5006 4723
|
||||
772001 12199 12938 4998 4730
|
||||
773001 12194 12955 5014 4702
|
||||
774001 12156 12954 5000 4700
|
||||
775001 12123 12966 4994 4714
|
||||
776001 12107 12995 4981 4732
|
||||
777001 12134 13020 4990 4746
|
||||
778001 12140 13029 5022 4741
|
||||
779001 12143 13022 5032 4749
|
||||
780001 12177 13029 5065 4738
|
||||
781001 12188 13021 5099 4743
|
||||
782001 12203 13053 5113 4772
|
||||
783001 12221 13061 5125 4794
|
||||
784001 12229 13031 5147 4793
|
||||
785001 12252 12998 5166 4780
|
||||
786001 12251 12990 5201 4753
|
||||
787001 12264 12971 5185 4778
|
||||
788001 12310 12924 5200 4786
|
||||
789001 12368 12852 5210 4807
|
||||
790001 12385 12790 5175 4806
|
||||
791001 12474 12721 5147 4807
|
||||
792001 12528 12624 5133 4788
|
||||
793001 12548 12528 5142 4759
|
||||
794001 12519 12403 5147 4721
|
||||
795001 12499 12378 5135 4720
|
||||
796001 12502 12385 5142 4713
|
||||
797001 12554 12236 5134 4683
|
||||
798001 12618 12214 5099 4705
|
||||
799001 12642 12238 5080 4711
|
||||
800001 12620 12269 5072 4730
|
||||
801001 12616 12289 5095 4727
|
||||
802001 12626 12312 5098 4749
|
||||
803001 12672 12272 5078 4762
|
||||
804001 12668 12319 5059 4762
|
||||
805001 12648 12354 5053 4779
|
||||
806001 12654 12343 5031 4784
|
||||
807001 12695 12359 4990 4811
|
||||
808001 12689 12401 4962 4847
|
||||
809001 12701 12406 4957 4862
|
||||
810001 12704 12464 4960 4869
|
||||
811001 12689 12504 4971 4876
|
||||
812001 12701 12531 4965 4885
|
||||
813001 12691 12526 4950 4906
|
||||
814001 12679 12564 4920 4947
|
||||
815001 12668 12600 4914 4965
|
||||
816001 12641 12636 4892 4979
|
||||
817001 12631 12635 4908 4971
|
||||
818001 12606 12605 4908 4959
|
||||
819001 12597 12595 4903 4981
|
||||
820001 12593 12603 4893 4986
|
||||
821001 12581 12634 4890 4986
|
||||
822001 12572 12610 4888 5005
|
||||
823001 12576 12599 4876 5011
|
||||
824001 12540 12622 4878 5026
|
||||
825001 12551 12640 4861 5026
|
||||
826001 12579 12645 4859 5028
|
||||
827001 12534 12666 4900 5005
|
||||
828001 12545 12690 4934 5002
|
||||
829001 12587 12682 4939 5010
|
||||
830001 12579 12678 4945 4996
|
||||
831001 12608 12674 4931 5013
|
||||
832001 12659 12661 4891 5023
|
||||
833001 12733 12633 4870 5039
|
||||
834001 12768 12627 4854 5052
|
||||
835001 12770 12618 4828 5039
|
||||
836001 12773 12616 4822 5011
|
||||
837001 12777 12590 4787 5008
|
||||
838001 12792 12618 4801 4984
|
||||
839001 12808 12608 4784 4977
|
||||
840001 12800 12615 4776 4973
|
||||
841001 12827 12589 4772 4950
|
||||
842001 12830 12590 4764 4923
|
||||
843001 12838 12583 4745 4946
|
||||
844001 12869 12506 4731 4929
|
||||
845001 12933 12419 4737 4950
|
||||
846001 12944 12396 4761 4931
|
||||
847001 12936 12398 4776 4907
|
||||
848001 12976 12395 4784 4904
|
||||
849001 12945 12409 4777 4908
|
||||
850001 12961 12393 4782 4892
|
||||
851001 12946 12390 4794 4881
|
||||
852001 12972 12364 4779 4882
|
||||
853001 12998 12359 4794 4873
|
||||
854001 12986 12353 4793 4861
|
||||
855001 12960 12377 4794 4855
|
||||
856001 12947 12367 4814 4840
|
||||
857001 12906 12424 4845 4830
|
||||
858001 12881 12437 4860 4819
|
||||
859001 12935 12432 4892 4807
|
||||
860001 12940 12429 4872 4823
|
||||
861001 12877 12509 4867 4820
|
||||
862001 12824 12568 4879 4822
|
||||
863001 12788 12566 4899 4833
|
||||
864001 12778 12570 4895 4837
|
||||
865001 12807 12593 4920 4841
|
||||
866001 12790 12583 4922 4858
|
||||
867001 12829 12545 4905 4865
|
||||
868001 12823 12566 4901 4881
|
||||
869001 12808 12646 4909 4868
|
||||
870001 12805 12655 4870 4898
|
||||
871001 12826 12722 4841 4922
|
||||
872001 12847 12776 4824 4923
|
||||
873001 12830 12793 4805 4934
|
||||
874001 12833 12826 4786 4960
|
||||
875001 12797 12849 4765 4969
|
||||
876001 12797 12844 4768 4974
|
||||
877001 12867 12829 4760 4967
|
||||
878001 12951 12763 4734 4977
|
||||
879001 12990 12730 4717 4996
|
||||
880001 12973 12747 4729 4993
|
||||
881001 12982 12736 4715 4990
|
||||
882001 12991 12735 4705 5013
|
||||
883001 12950 12725 4721 4992
|
||||
884001 12932 12733 4728 4984
|
||||
885001 12931 12772 4727 5001
|
||||
886001 12939 12795 4734 5001
|
||||
887001 12957 12807 4701 5016
|
||||
888001 12944 12822 4696 5028
|
||||
889001 12964 12819 4712 5023
|
||||
890001 12989 12819 4741 5006
|
||||
891001 13026 12783 4742 4991
|
||||
892001 13031 12773 4743 4976
|
||||
893001 13017 12773 4753 4957
|
||||
894001 13024 12757 4741 4942
|
||||
895001 13029 12738 4744 4929
|
||||
896001 13062 12704 4781 4902
|
||||
897001 13047 12762 4790 4927
|
||||
898001 13024 12797 4797 4932
|
||||
899001 13004 12794 4776 4936
|
||||
900001 12982 12805 4761 4956
|
||||
901001 12970 12802 4778 4952
|
||||
902001 12908 12806 4789 4918
|
||||
903001 12862 12865 4819 4882
|
||||
904001 12772 12942 4803 4897
|
||||
905001 12711 12970 4806 4919
|
||||
906001 12630 13041 4789 4944
|
||||
907001 12499 13147 4752 4987
|
||||
908001 12395 13244 4724 5017
|
||||
909001 12385 13230 4723 5028
|
||||
910001 12367 13224 4709 5052
|
||||
927
src/kimono/lxpack/tests/ref/borbu1.3.ref
Normal file
927
src/kimono/lxpack/tests/ref/borbu1.3.ref
Normal file
@ -0,0 +1,927 @@
|
||||
# input : borbu1.fst
|
||||
# include : borbu1.lst
|
||||
# selector : count
|
||||
# mixer : basic
|
||||
# distance : chi
|
||||
# phase : 7
|
||||
# alphabet : ACGT
|
||||
# excluded : X
|
||||
# seqname : borbu1
|
||||
# seqlength : 910724
|
||||
# unmasked : 849408
|
||||
# valid : 849367
|
||||
# window : 227680
|
||||
# step : 1000
|
||||
#
|
||||
# pos LeftA RightA LeftC
|
||||
1 33401 42069 12563 18275
|
||||
1001 33398 42133 12544 18312
|
||||
2001 33527 42158 12573 18285
|
||||
3001 33656 42179 12640 18272
|
||||
4001 33781 41887 12627 18205
|
||||
5001 33914 41776 12674 18264
|
||||
6001 33937 41760 12733 18283
|
||||
7001 34058 41589 12793 18251
|
||||
8001 34178 41618 12871 18245
|
||||
9001 34278 41568 12834 18281
|
||||
10001 34470 41433 12833 18374
|
||||
11001 34641 41316 12853 18448
|
||||
12001 34784 41230 12868 18468
|
||||
13001 35025 41076 12871 18543
|
||||
14001 35196 40931 12868 18625
|
||||
15001 35342 40865 12836 18647
|
||||
16001 35424 40868 12886 18681
|
||||
17001 35664 40831 12955 18712
|
||||
18001 35814 40796 13016 18690
|
||||
19001 35974 40847 13095 18623
|
||||
20001 36056 40878 13110 18638
|
||||
21001 35998 41046 13082 18697
|
||||
22001 35998 41205 13190 18628
|
||||
23001 36018 41226 13266 18664
|
||||
24001 36116 41165 13319 18658
|
||||
25001 36070 41094 13450 18538
|
||||
26001 36047 41144 13553 18547
|
||||
27001 36161 41151 13570 18579
|
||||
28001 36241 41084 13613 18611
|
||||
29001 36263 41009 13713 18629
|
||||
30001 36354 40982 13707 18629
|
||||
31001 36456 40902 13719 18660
|
||||
32001 36496 40858 13778 18715
|
||||
33001 36511 40947 13839 18721
|
||||
34001 36540 40883 13912 18703
|
||||
35001 36535 40854 13983 18694
|
||||
36001 36547 40829 14074 18710
|
||||
37001 36591 40759 14151 18715
|
||||
38001 36624 40746 14204 18716
|
||||
39001 36673 40756 14251 18717
|
||||
40001 36670 40764 14291 18776
|
||||
41001 36766 40670 14317 18835
|
||||
42001 36822 40637 14378 18863
|
||||
43001 36880 40620 14467 18865
|
||||
44001 36852 40717 14535 18823
|
||||
45001 36869 40737 14569 18774
|
||||
46001 36899 40759 14645 18752
|
||||
47001 36728 40994 14672 18746
|
||||
48001 36638 41131 14683 18775
|
||||
49001 36635 41113 14699 18774
|
||||
50001 36682 41088 14709 18798
|
||||
51001 36648 41134 14787 18775
|
||||
52001 36681 41225 14941 18708
|
||||
53001 36663 41324 15037 18669
|
||||
54001 36670 41358 15099 18631
|
||||
55001 36689 41320 15198 18644
|
||||
56001 36734 41300 15266 18591
|
||||
57001 36720 41410 15330 18576
|
||||
58001 36813 41324 15356 18581
|
||||
59001 36832 41373 15398 18562
|
||||
60001 36884 41405 15451 18553
|
||||
61001 36945 41458 15548 18538
|
||||
62001 36975 41481 15617 18539
|
||||
63001 37055 41543 15690 18501
|
||||
64001 37226 41519 15710 18562
|
||||
65001 37372 41411 15732 18638
|
||||
66001 37392 41389 15770 18643
|
||||
67001 37445 41292 15834 18678
|
||||
68001 37595 41148 15862 18759
|
||||
69001 37667 41076 15911 18808
|
||||
70001 37691 41119 15963 18791
|
||||
71001 37722 41153 15995 18794
|
||||
72001 37968 41086 15993 18824
|
||||
73001 38156 41028 15995 18867
|
||||
74001 38377 40982 16017 18882
|
||||
75001 38617 40791 15999 18894
|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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|
||||
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||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
506001 33856 34322 14485 12473
|
||||
507001 33842 34380 14421 12469
|
||||
508001 33876 34310 14328 12505
|
||||
509001 33853 34272 14231 12491
|
||||
510001 33989 34251 14165 12505
|
||||
511001 34034 34255 14085 12484
|
||||
512001 34115 34201 13997 12502
|
||||
513001 34107 34193 13883 12519
|
||||
514001 34102 34162 13753 12574
|
||||
515001 34140 34073 13645 12643
|
||||
516001 34164 33978 13536 12640
|
||||
517001 34192 33936 13403 12700
|
||||
518001 34246 33895 13267 12739
|
||||
519001 34335 33804 13159 12771
|
||||
520001 34485 33749 13059 12786
|
||||
521001 34599 33663 12935 12795
|
||||
522001 34732 33579 12824 12820
|
||||
523001 34877 33351 12773 12798
|
||||
524001 34890 33371 12710 12780
|
||||
525001 34929 33372 12749 12777
|
||||
526001 34889 33399 12686 12775
|
||||
527001 34882 33474 12640 12772
|
||||
528001 34755 33538 12605 12782
|
||||
529001 34646 33565 12579 12752
|
||||
530001 34542 33569 12576 12677
|
||||
531001 34422 33596 12653 12603
|
||||
532001 34258 33694 12630 12599
|
||||
533001 34087 33870 12525 12646
|
||||
534001 33938 33942 12368 12693
|
||||
535001 33840 33952 12229 12712
|
||||
536001 33808 33953 12175 12776
|
||||
537001 33815 33863 12177 12786
|
||||
538001 33736 33806 12133 12845
|
||||
539001 33723 33780 12166 12876
|
||||
540001 33566 33755 12184 12836
|
||||
541001 33316 33900 12128 12851
|
||||
542001 33218 33973 12081 12879
|
||||
543001 33092 34068 12059 12888
|
||||
544001 33045 33992 11974 12940
|
||||
545001 33073 33899 11890 12984
|
||||
546001 33099 33844 11815 12989
|
||||
547001 33088 33749 11728 13078
|
||||
548001 32902 33822 11637 13158
|
||||
549001 32823 33831 11641 13131
|
||||
550001 33125 33741 11804 13041
|
||||
551001 33390 33730 11995 12972
|
||||
552001 33581 33835 12131 12954
|
||||
553001 33865 33837 12207 12987
|
||||
554001 34060 33894 12292 13007
|
||||
555001 34412 33716 12413 12973
|
||||
556001 34549 33667 12442 12974
|
||||
557001 34561 33648 12380 13011
|
||||
558001 34711 33660 12404 12999
|
||||
559001 34927 33655 12525 13002
|
||||
560001 35188 33671 12648 12979
|
||||
561001 35200 33711 12612 12941
|
||||
562001 35131 33646 12585 12915
|
||||
563001 35096 33616 12534 12925
|
||||
564001 35015 33538 12509 12962
|
||||
565001 34873 33557 12517 12979
|
||||
566001 34764 33739 12460 13003
|
||||
567001 34761 33726 12341 13071
|
||||
568001 34735 33677 12244 13121
|
||||
569001 34769 33567 12139 13141
|
||||
570001 34748 33549 12019 13182
|
||||
571001 34728 33466 11999 13191
|
||||
572001 34618 33432 11986 13219
|
||||
573001 34508 33425 12053 13168
|
||||
574001 34479 33433 12114 13128
|
||||
575001 34462 33359 12139 13130
|
||||
576001 34422 33421 12154 13136
|
||||
577001 34394 33428 12235 13052
|
||||
578001 34375 33473 12211 13105
|
||||
579001 34361 33449 12192 13111
|
||||
580001 34515 33423 12218 13092
|
||||
581001 34593 33472 12187 13108
|
||||
582001 34675 33378 12212 13095
|
||||
583001 34719 33331 12174 13087
|
||||
584001 34748 33289 12110 13132
|
||||
585001 34692 33397 12081 13164
|
||||
586001 34660 33352 12052 13252
|
||||
587001 34695 33271 12069 13270
|
||||
588001 34663 33293 12037 13292
|
||||
589001 34681 33236 12045 13303
|
||||
590001 34644 33230 12080 13293
|
||||
591001 34706 33297 12029 13316
|
||||
592001 34738 33317 11998 13305
|
||||
593001 34699 33320 12005 13320
|
||||
594001 34685 33364 12015 13294
|
||||
595001 34728 33403 12053 13261
|
||||
596001 34879 33389 12069 13277
|
||||
597001 34994 33419 12084 13266
|
||||
598001 34968 33398 12135 13240
|
||||
599001 34987 33405 12168 13224
|
||||
600001 34996 33466 12210 13222
|
||||
601001 34826 33536 12191 13263
|
||||
602001 34748 33573 12212 13233
|
||||
603001 34712 33611 12244 13202
|
||||
604001 34745 33576 12273 13210
|
||||
605001 34709 33544 12292 13204
|
||||
606001 34725 33599 12332 13194
|
||||
607001 34840 33662 12414 13167
|
||||
608001 34848 33715 12401 13199
|
||||
609001 34993 33755 12450 13219
|
||||
610001 34940 33756 12423 13243
|
||||
611001 34967 33682 12392 13294
|
||||
612001 34890 33753 12369 13317
|
||||
613001 34873 33762 12364 13304
|
||||
614001 34821 33782 12352 13302
|
||||
615001 34757 33836 12392 13258
|
||||
616001 34652 33880 12439 13237
|
||||
617001 34571 33875 12469 13218
|
||||
618001 34460 33909 12503 13179
|
||||
619001 34332 34045 12482 13219
|
||||
620001 34330 34053 12472 13207
|
||||
621001 34377 33964 12467 13191
|
||||
622001 34286 34019 12493 13149
|
||||
623001 34270 34044 12496 13150
|
||||
624001 34255 34055 12501 13142
|
||||
625001 34255 34025 12478 13146
|
||||
626001 34204 34019 12508 13078
|
||||
627001 34200 34022 12522 13048
|
||||
628001 34152 34096 12584 13003
|
||||
629001 34054 34111 12641 12949
|
||||
630001 34003 34199 12656 12927
|
||||
631001 33919 34240 12718 12862
|
||||
632001 33883 34079 12729 12815
|
||||
633001 33786 34088 12778 12808
|
||||
634001 33745 34051 12788 12805
|
||||
635001 33646 34104 12806 12790
|
||||
636001 33560 34151 12830 12805
|
||||
637001 33344 34341 12806 12845
|
||||
638001 33389 34169 12767 12820
|
||||
639001 33378 34210 12770 12804
|
||||
640001 33410 34180 12781 12822
|
||||
641001 33466 34134 12785 12817
|
||||
642001 33561 34143 12798 12818
|
||||
643001 33568 34216 12751 12792
|
||||
644001 33557 34192 12666 12781
|
||||
645001 33631 34239 12583 12802
|
||||
646001 33711 34291 12604 12795
|
||||
647001 33865 34310 12647 12793
|
||||
648001 33958 34381 12716 12771
|
||||
649001 33922 34382 12717 12772
|
||||
650001 33947 34407 12783 12743
|
||||
651001 33852 34484 12806 12727
|
||||
652001 33797 34523 12857 12661
|
||||
653001 33779 34572 12871 12657
|
||||
654001 33780 34567 12840 12716
|
||||
655001 33956 34488 12866 12773
|
||||
656001 34002 34397 12893 12782
|
||||
657001 34042 34349 12885 12838
|
||||
658001 33962 34333 12945 12820
|
||||
659001 33863 34323 12973 12865
|
||||
660001 33830 34230 13008 12902
|
||||
661001 33726 34212 13083 12814
|
||||
662001 33844 34155 13151 12791
|
||||
663001 33803 34142 13107 12804
|
||||
664001 33741 34227 13038 12834
|
||||
665001 33742 34312 12958 12829
|
||||
666001 33832 34342 12951 12834
|
||||
667001 33860 34389 13004 12837
|
||||
668001 33868 34462 13019 12807
|
||||
669001 33703 34558 12972 12848
|
||||
670001 33657 34537 12980 12844
|
||||
671001 33665 34602 13024 12828
|
||||
672001 33655 34622 12989 12835
|
||||
673001 33660 34690 13007 12766
|
||||
674001 33683 34761 12967 12776
|
||||
675001 33661 34902 12920 12805
|
||||
676001 33690 34897 12931 12737
|
||||
677001 33601 34983 12936 12744
|
||||
678001 33520 35067 12958 12742
|
||||
679001 33562 35089 12972 12706
|
||||
680001 33736 35073 13016 12675
|
||||
681001 33722 35042 13091 12647
|
||||
682001 33670 35080 13125 12652
|
||||
683001 33562 35163 13150 12660
|
||||
684001 33531 35199 13174 12672
|
||||
685001 33481 35177 13183 12701
|
||||
686001 33451 35143 13216 12671
|
||||
687001 33435 35115 13160 12694
|
||||
688001 33416 35138 13134 12664
|
||||
689001 33374 35158 13126 12664
|
||||
690001 33428 35109 13111 12661
|
||||
691001 33416 35035 13049 12690
|
||||
692001 33455 34998 13111 12730
|
||||
693001 33448 34938 13111 12773
|
||||
694001 33437 34893 13092 12769
|
||||
695001 33457 34863 13113 12786
|
||||
696001 33372 34852 13082 12793
|
||||
697001 33307 34808 13108 12829
|
||||
698001 33344 34830 13155 12889
|
||||
699001 33412 34803 13185 12864
|
||||
700001 33321 34683 13264 12770
|
||||
701001 33236 34677 13276 12759
|
||||
702001 33306 34583 13297 12771
|
||||
703001 33232 34580 13299 12813
|
||||
704001 33229 34490 13296 12831
|
||||
705001 33356 34436 13325 12833
|
||||
706001 33310 34462 13313 12821
|
||||
707001 33307 34460 13316 12822
|
||||
708001 33396 34417 13280 12830
|
||||
709001 33392 34398 13266 12783
|
||||
710001 33415 34327 13272 12795
|
||||
711001 33414 34354 13263 12806
|
||||
712001 33387 34423 13240 12780
|
||||
713001 33414 34394 13217 12824
|
||||
714001 33474 34417 13227 12844
|
||||
715001 33488 34546 13244 12821
|
||||
716001 33593 34499 13219 12800
|
||||
717001 33594 34499 13206 12805
|
||||
718001 33574 34514 13210 12803
|
||||
719001 33544 34636 13190 12778
|
||||
720001 33602 34664 13188 12748
|
||||
721001 33714 34658 13185 12727
|
||||
722001 33732 34671 13203 12728
|
||||
723001 33764 34651 13216 12673
|
||||
724001 33738 34702 13257 12650
|
||||
725001 33664 34738 13301 12625
|
||||
726001 33773 34683 13318 12616
|
||||
727001 33763 34758 13305 12610
|
||||
728001 33808 34744 13298 12631
|
||||
729001 33854 34770 13245 12596
|
||||
730001 33871 34843 13249 12569
|
||||
731001 33882 34938 13213 12568
|
||||
732001 33913 35008 13188 12618
|
||||
733001 34049 34985 13217 12645
|
||||
734001 34018 35047 13196 12653
|
||||
735001 33969 35033 13190 12617
|
||||
736001 34021 35018 13150 12643
|
||||
737001 34059 34971 13146 12674
|
||||
738001 34049 34999 13152 12650
|
||||
739001 33994 35011 13138 12676
|
||||
740001 34019 35038 13065 12703
|
||||
741001 34040 35021 13053 12723
|
||||
742001 34094 35012 12996 12745
|
||||
743001 34161 35017 12969 12770
|
||||
744001 34206 34963 12916 12776
|
||||
745001 34187 35024 12839 12826
|
||||
746001 34080 35072 12812 12883
|
||||
747001 34079 34963 12818 12857
|
||||
748001 34040 34893 12804 12883
|
||||
749001 34115 34878 12786 12914
|
||||
750001 34170 34849 12816 12886
|
||||
751001 34284 34866 12833 12913
|
||||
752001 34189 34926 12813 12941
|
||||
753001 34202 34942 12810 12918
|
||||
754001 34187 34986 12820 12902
|
||||
755001 34132 34921 12821 12917
|
||||
756001 34153 34852 12811 12915
|
||||
757001 34228 34807 12781 12919
|
||||
758001 34197 34840 12782 12966
|
||||
759001 34230 34763 12807 12982
|
||||
760001 34282 34694 12791 13022
|
||||
761001 34329 34565 12789 13068
|
||||
762001 34371 34536 12766 13071
|
||||
763001 34395 34596 12779 13088
|
||||
764001 34422 34675 12747 13054
|
||||
765001 34490 34774 12713 13032
|
||||
766001 34541 34768 12652 13045
|
||||
767001 34572 34765 12665 13005
|
||||
768001 34560 34771 12725 12982
|
||||
769001 34472 34771 12770 12971
|
||||
770001 34389 34771 12783 13005
|
||||
771001 34356 34748 12839 12983
|
||||
772001 34332 34743 12815 13003
|
||||
773001 34301 34751 12885 12948
|
||||
774001 34227 34746 12884 12933
|
||||
775001 34211 34787 12823 12954
|
||||
776001 34153 34864 12778 12990
|
||||
777001 34182 35018 12836 12952
|
||||
778001 34242 35031 12837 12965
|
||||
779001 34297 35044 12829 12976
|
||||
780001 34359 35074 12831 12969
|
||||
781001 34421 35047 12831 12974
|
||||
782001 34457 35128 12807 12997
|
||||
783001 34516 35143 12836 12986
|
||||
784001 34533 35058 12845 12978
|
||||
785001 34600 34978 12826 12986
|
||||
786001 34633 34937 12834 12962
|
||||
787001 34680 34932 12756 12989
|
||||
788001 34777 34861 12780 13001
|
||||
789001 34915 34753 12803 13019
|
||||
790001 34893 34614 12729 13014
|
||||
791001 35006 34507 12745 13059
|
||||
792001 35074 34261 12738 12989
|
||||
793001 35092 34050 12702 12910
|
||||
794001 35062 33729 12670 12813
|
||||
795001 35052 33678 12637 12749
|
||||
796001 35076 33709 12657 12661
|
||||
797001 35167 33357 12665 12547
|
||||
798001 35203 33412 12683 12539
|
||||
799001 35176 33528 12713 12570
|
||||
800001 35139 33673 12669 12652
|
||||
801001 35127 33789 12687 12632
|
||||
802001 35107 33947 12648 12681
|
||||
803001 35145 33950 12677 12735
|
||||
804001 35113 34070 12668 12798
|
||||
805001 35019 34200 12694 12874
|
||||
806001 34989 34294 12745 12830
|
||||
807001 34941 34483 12767 12842
|
||||
808001 34865 34665 12774 12867
|
||||
809001 34867 34809 12791 12867
|
||||
810001 34839 35043 12803 12864
|
||||
811001 34815 35223 12823 12861
|
||||
812001 34814 35365 12880 12848
|
||||
813001 34790 35424 12854 12890
|
||||
814001 34700 35674 12774 12965
|
||||
815001 34668 35832 12754 13023
|
||||
816001 34581 35984 12776 13100
|
||||
817001 34567 36027 12831 13082
|
||||
818001 34488 36004 12831 13089
|
||||
819001 34450 35995 12833 13201
|
||||
820001 34454 36036 12824 13271
|
||||
821001 34450 36113 12826 13327
|
||||
822001 34420 36070 12824 13466
|
||||
823001 34395 36048 12784 13552
|
||||
824001 34334 36164 12801 13578
|
||||
825001 34359 36244 12801 13627
|
||||
826001 34425 36278 12785 13714
|
||||
827001 34399 36352 12829 13714
|
||||
828001 34435 36457 12843 13718
|
||||
829001 34546 36493 12815 13788
|
||||
830001 34481 36514 12806 13833
|
||||
831001 34493 36541 12806 13932
|
||||
832001 34530 36530 12782 14006
|
||||
833001 34639 36545 12766 14086
|
||||
834001 34660 36595 12747 14157
|
||||
835001 34668 36639 12730 14211
|
||||
836001 34664 36692 12715 14256
|
||||
837001 34667 36684 12668 14300
|
||||
838001 34708 36786 12644 14320
|
||||
839001 34749 36803 12622 14405
|
||||
840001 34707 36879 12612 14475
|
||||
841001 34765 36852 12611 14536
|
||||
842001 34749 36877 12615 14576
|
||||
843001 34789 36888 12586 14665
|
||||
844001 34818 36712 12579 14665
|
||||
845001 34971 36625 12582 14682
|
||||
846001 35010 36630 12619 14703
|
||||
847001 34980 36647 12647 14697
|
||||
848001 35067 36643 12664 14803
|
||||
849001 35008 36690 12631 14951
|
||||
850001 35020 36668 12654 15035
|
||||
851001 34978 36664 12671 15107
|
||||
852001 35002 36704 12652 15202
|
||||
853001 35058 36728 12694 15278
|
||||
854001 35020 36732 12711 15337
|
||||
855001 35018 36813 12721 15357
|
||||
856001 35027 36805 12743 15395
|
||||
857001 35005 36897 12772 15461
|
||||
858001 34957 36948 12785 15553
|
||||
859001 35073 36989 12843 15628
|
||||
860001 35063 37034 12877 15682
|
||||
861001 34948 37239 12867 15703
|
||||
862001 34893 37362 12888 15743
|
||||
863001 34856 37403 12913 15781
|
||||
864001 34830 37472 12894 15831
|
||||
865001 34930 37607 12925 15868
|
||||
866001 34923 37666 12937 15913
|
||||
867001 34977 37695 12905 15966
|
||||
868001 34972 37749 12911 15993
|
||||
869001 34913 37992 12935 15985
|
||||
870001 34848 38155 12911 16005
|
||||
871001 34813 38413 12929 16012
|
||||
872001 34811 38613 12972 15987
|
||||
873001 34756 38801 12990 15944
|
||||
874001 34696 39013 13019 15938
|
||||
875001 34552 39180 13067 15936
|
||||
876001 34544 39226 13077 16000
|
||||
877001 34610 39260 13082 16015
|
||||
878001 34694 39207 13056 16030
|
||||
879001 34779 39215 13035 16085
|
||||
880001 34778 39307 13038 16137
|
||||
881001 34785 39307 12996 16212
|
||||
882001 34786 39409 12971 16275
|
||||
883001 34766 39444 12970 16263
|
||||
884001 34762 39548 13010 16254
|
||||
885001 34750 39676 12985 16322
|
||||
886001 34742 39811 13010 16331
|
||||
887001 34766 39874 12946 16386
|
||||
888001 34732 39955 12918 16466
|
||||
889001 34777 39992 12947 16565
|
||||
890001 34880 39984 12983 16620
|
||||
891001 35028 39895 12950 16696
|
||||
892001 35021 39881 12975 16732
|
||||
893001 35027 39886 12981 16782
|
||||
894001 35082 39900 12972 16804
|
||||
895001 35073 39925 12980 16875
|
||||
896001 35147 39917 13009 16887
|
||||
897001 35106 40119 12954 16970
|
||||
898001 35048 40294 12989 16986
|
||||
899001 34991 40318 12992 17036
|
||||
900001 34926 40392 12969 17169
|
||||
901001 34940 40382 12990 17263
|
||||
902001 34833 40464 13002 17290
|
||||
903001 34800 40553 13040 17338
|
||||
904001 34589 40772 13006 17458
|
||||
905001 34480 40881 13052 17504
|
||||
906001 34272 41103 12988 17577
|
||||
907001 33991 41422 12892 17731
|
||||
908001 33703 41733 12803 17898
|
||||
909001 33693 41764 12737 18004
|
||||
910001 33657 41779 12642 18125
|
||||
927
src/kimono/lxpack/tests/ref/borbu1.4.ref
Normal file
927
src/kimono/lxpack/tests/ref/borbu1.4.ref
Normal file
@ -0,0 +1,927 @@
|
||||
# input : borbu1.fst
|
||||
# exclude : borbu1.lst
|
||||
# selector : count
|
||||
# mixer : basic
|
||||
# distance : chi
|
||||
# phase : 7
|
||||
# alphabet : ACGT
|
||||
# excluded : X
|
||||
# seqname : borbu1
|
||||
# seqlength : 910724
|
||||
# unmasked : 61316
|
||||
# valid : 61314
|
||||
# window : 227680
|
||||
# step : 1000
|
||||
#
|
||||
# pos LeftA RightA LeftC
|
||||
1 3196 2425 788 676
|
||||
1001 3288 2409 804 679
|
||||
2001 3286 2409 800 679
|
||||
3001 3233 2421 784 681
|
||||
4001 3292 2677 795 800
|
||||
5001 3259 2678 784 800
|
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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|
||||
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||||
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|
||||
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|
||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
358001 2102 5050 554 3092
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
386001 1721 5632 486 3223
|
||||
387001 1721 5633 486 3223
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
394001 1725 5543 489 3185
|
||||
395001 1741 5527 497 3177
|
||||
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|
||||
397001 1896 5399 543 3134
|
||||
398001 1925 5368 561 3116
|
||||
399001 1925 5368 561 3116
|
||||
400001 1922 5397 559 3122
|
||||
401001 1922 5397 559 3122
|
||||
402001 1927 5387 562 3118
|
||||
403001 1918 5428 557 3129
|
||||
404001 1896 5428 551 3129
|
||||
405001 1881 5428 548 3129
|
||||
406001 1917 5372 570 3100
|
||||
407001 1917 5372 570 3100
|
||||
408001 1930 5346 582 3085
|
||||
409001 2018 5255 649 3018
|
||||
410001 2018 5253 649 3013
|
||||
411001 2187 5083 702 2960
|
||||
412001 2194 5076 702 2960
|
||||
413001 2187 5101 699 2965
|
||||
414001 2224 5073 710 2951
|
||||
415001 2226 5081 708 2955
|
||||
416001 2250 5057 716 2947
|
||||
417001 2315 4988 724 2931
|
||||
418001 2301 5037 714 2951
|
||||
419001 2324 5149 721 2983
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
428001 2585 5271 791 3013
|
||||
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|
||||
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|
||||
431001 2606 5340 792 3025
|
||||
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|
||||
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|
||||
434001 2532 5491 768 3110
|
||||
435001 2517 5493 759 3110
|
||||
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|
||||
437001 3020 5004 1272 2601
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
442001 4077 4034 2454 1445
|
||||
443001 4146 3965 2463 1436
|
||||
444001 4319 3734 2513 1373
|
||||
445001 4531 3495 2692 1184
|
||||
446001 4782 3244 2975 901
|
||||
447001 4906 3120 3033 843
|
||||
448001 4938 3084 3035 839
|
||||
449001 4805 3098 3005 835
|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
906001 2045 3547 504 939
|
||||
907001 2320 3248 582 857
|
||||
908001 2663 2881 664 767
|
||||
909001 2814 2744 682 759
|
||||
910001 2954 2670 718 746
|
||||
927
src/kimono/lxpack/tests/ref/borbu1.5.ref
Normal file
927
src/kimono/lxpack/tests/ref/borbu1.5.ref
Normal file
@ -0,0 +1,927 @@
|
||||
# input : borbu1.fst
|
||||
# include : <none>
|
||||
# selector : cumul
|
||||
# mixer : basic
|
||||
# distance : chi
|
||||
# phase : 7
|
||||
# alphabet : GC
|
||||
# excluded : X
|
||||
# seqname : borbu1
|
||||
# seqlength : 910724
|
||||
# unmasked : 910724
|
||||
# valid : 260406
|
||||
# window : 227680
|
||||
# step : 1000
|
||||
#
|
||||
# pos G-C/G+C
|
||||
1 -0.0131973
|
||||
1001 -0.0271626
|
||||
2001 -0.041181
|
||||
3001 -0.0566452
|
||||
4001 -0.0739519
|
||||
5001 -0.0937391
|
||||
6001 -0.115266
|
||||
7001 -0.138618
|
||||
8001 -0.163833
|
||||
9001 -0.190044
|
||||
10001 -0.218113
|
||||
11001 -0.248402
|
||||
12001 -0.280177
|
||||
13001 -0.31381
|
||||
14001 -0.349193
|
||||
15001 -0.385367
|
||||
16001 -0.423263
|
||||
17001 -0.462602
|
||||
18001 -0.503178
|
||||
19001 -0.544475
|
||||
20001 -0.58725
|
||||
21001 -0.631494
|
||||
22001 -0.677426
|
||||
23001 -0.727306
|
||||
24001 -0.779324
|
||||
25001 -0.833779
|
||||
26001 -0.890698
|
||||
27001 -0.950176
|
||||
28001 -1.01161
|
||||
29001 -1.07601
|
||||
30001 -1.14239
|
||||
31001 -1.21137
|
||||
32001 -1.28293
|
||||
33001 -1.35671
|
||||
34001 -1.43248
|
||||
35001 -1.50889
|
||||
36001 -1.58832
|
||||
37001 -1.66917
|
||||
38001 -1.75101
|
||||
39001 -1.83431
|
||||
40001 -1.92052
|
||||
41001 -2.00927
|
||||
42001 -2.10023
|
||||
43001 -2.19319
|
||||
44001 -2.2871
|
||||
45001 -2.3821
|
||||
46001 -2.47837
|
||||
47001 -2.57673
|
||||
48001 -2.6782
|
||||
49001 -2.78169
|
||||
50001 -2.88799
|
||||
51001 -2.99698
|
||||
52001 -3.10867
|
||||
53001 -3.22322
|
||||
54001 -3.34097
|
||||
55001 -3.46201
|
||||
56001 -3.58429
|
||||
57001 -3.70745
|
||||
58001 -3.83238
|
||||
59001 -3.95946
|
||||
60001 -4.08804
|
||||
61001 -4.21914
|
||||
62001 -4.35289
|
||||
63001 -4.48783
|
||||
64001 -4.62468
|
||||
65001 -4.76293
|
||||
66001 -4.90319
|
||||
67001 -5.04565
|
||||
68001 -5.1909
|
||||
69001 -5.33903
|
||||
70001 -5.48814
|
||||
71001 -5.63755
|
||||
72001 -5.78723
|
||||
73001 -5.93694
|
||||
74001 -6.08738
|
||||
75001 -6.23924
|
||||
76001 -6.3923
|
||||
77001 -6.54679
|
||||
78001 -6.70215
|
||||
79001 -6.85952
|
||||
80001 -7.01926
|
||||
81001 -7.17986
|
||||
82001 -7.34095
|
||||
83001 -7.50369
|
||||
84001 -7.6678
|
||||
85001 -7.83239
|
||||
86001 -7.99843
|
||||
87001 -8.16523
|
||||
88001 -8.333
|
||||
89001 -8.50148
|
||||
90001 -8.6698
|
||||
91001 -8.83788
|
||||
92001 -9.00605
|
||||
93001 -9.1757
|
||||
94001 -9.34679
|
||||
95001 -9.5196
|
||||
96001 -9.69379
|
||||
97001 -9.86967
|
||||
98001 -10.0466
|
||||
99001 -10.2239
|
||||
100001 -10.4031
|
||||
101001 -10.5831
|
||||
102001 -10.7637
|
||||
103001 -10.9459
|
||||
104001 -11.1298
|
||||
105001 -11.3165
|
||||
106001 -11.5065
|
||||
107001 -11.6968
|
||||
108001 -11.8864
|
||||
109001 -12.0763
|
||||
110001 -12.2671
|
||||
111001 -12.4592
|
||||
112001 -12.6531
|
||||
113001 -12.8494
|
||||
114001 -13.0472
|
||||
115001 -13.2445
|
||||
116001 -13.4407
|
||||
117001 -13.6363
|
||||
118001 -13.8329
|
||||
119001 -14.0304
|
||||
120001 -14.2266
|
||||
121001 -14.4216
|
||||
122001 -14.6161
|
||||
123001 -14.8112
|
||||
124001 -15.0079
|
||||
125001 -15.206
|
||||
126001 -15.4054
|
||||
127001 -15.6053
|
||||
128001 -15.8063
|
||||
129001 -16.0076
|
||||
130001 -16.2085
|
||||
131001 -16.4102
|
||||
132001 -16.6122
|
||||
133001 -16.8115
|
||||
134001 -17.0086
|
||||
135001 -17.2051
|
||||
136001 -17.4002
|
||||
137001 -17.5948
|
||||
138001 -17.7902
|
||||
139001 -17.9845
|
||||
140001 -18.1783
|
||||
141001 -18.3724
|
||||
142001 -18.5659
|
||||
143001 -18.7574
|
||||
144001 -18.9472
|
||||
145001 -19.1365
|
||||
146001 -19.3255
|
||||
147001 -19.5139
|
||||
148001 -19.7022
|
||||
149001 -19.891
|
||||
150001 -20.0792
|
||||
151001 -20.2667
|
||||
152001 -20.4535
|
||||
153001 -20.6395
|
||||
154001 -20.825
|
||||
155001 -21.0113
|
||||
156001 -21.1969
|
||||
157001 -21.3821
|
||||
158001 -21.567
|
||||
159001 -21.752
|
||||
160001 -21.9377
|
||||
161001 -22.1226
|
||||
162001 -22.308
|
||||
163001 -22.4928
|
||||
164001 -22.6773
|
||||
165001 -22.8616
|
||||
166001 -23.046
|
||||
167001 -23.232
|
||||
168001 -23.4181
|
||||
169001 -23.6042
|
||||
170001 -23.7906
|
||||
171001 -23.9768
|
||||
172001 -24.1632
|
||||
173001 -24.3502
|
||||
174001 -24.5364
|
||||
175001 -24.7213
|
||||
176001 -24.906
|
||||
177001 -25.0904
|
||||
178001 -25.2765
|
||||
179001 -25.464
|
||||
180001 -25.6532
|
||||
181001 -25.8421
|
||||
182001 -26.0319
|
||||
183001 -26.2223
|
||||
184001 -26.4128
|
||||
185001 -26.6059
|
||||
186001 -26.8004
|
||||
187001 -26.9965
|
||||
188001 -27.1937
|
||||
189001 -27.3916
|
||||
190001 -27.5905
|
||||
191001 -27.7911
|
||||
192001 -27.9923
|
||||
193001 -28.1937
|
||||
194001 -28.3955
|
||||
195001 -28.599
|
||||
196001 -28.8042
|
||||
197001 -29.0103
|
||||
198001 -29.2155
|
||||
199001 -29.4211
|
||||
200001 -29.6267
|
||||
201001 -29.8331
|
||||
202001 -30.0397
|
||||
203001 -30.2467
|
||||
204001 -30.4536
|
||||
205001 -30.6604
|
||||
206001 -30.8673
|
||||
207001 -31.0736
|
||||
208001 -31.2787
|
||||
209001 -31.4832
|
||||
210001 -31.6881
|
||||
211001 -31.8934
|
||||
212001 -32.0989
|
||||
213001 -32.305
|
||||
214001 -32.5127
|
||||
215001 -32.7187
|
||||
216001 -32.9236
|
||||
217001 -33.1282
|
||||
218001 -33.3326
|
||||
219001 -33.5371
|
||||
220001 -33.7417
|
||||
221001 -33.9464
|
||||
222001 -34.1497
|
||||
223001 -34.3522
|
||||
224001 -34.5539
|
||||
225001 -34.7542
|
||||
226001 -34.9533
|
||||
227001 -35.1509
|
||||
228001 -35.3467
|
||||
229001 -35.5412
|
||||
230001 -35.7354
|
||||
231001 -35.929
|
||||
232001 -36.1208
|
||||
233001 -36.3113
|
||||
234001 -36.5011
|
||||
235001 -36.6905
|
||||
236001 -36.8796
|
||||
237001 -37.0674
|
||||
238001 -37.2548
|
||||
239001 -37.4417
|
||||
240001 -37.6276
|
||||
241001 -37.8135
|
||||
242001 -37.9987
|
||||
243001 -38.1825
|
||||
244001 -38.3648
|
||||
245001 -38.5452
|
||||
246001 -38.7268
|
||||
247001 -38.908
|
||||
248001 -39.0887
|
||||
249001 -39.2698
|
||||
250001 -39.4513
|
||||
251001 -39.6324
|
||||
252001 -39.814
|
||||
253001 -39.9954
|
||||
254001 -40.1771
|
||||
255001 -40.3595
|
||||
256001 -40.541
|
||||
257001 -40.7212
|
||||
258001 -40.9014
|
||||
259001 -41.0809
|
||||
260001 -41.2594
|
||||
261001 -41.4366
|
||||
262001 -41.6123
|
||||
263001 -41.7882
|
||||
264001 -41.9649
|
||||
265001 -42.1423
|
||||
266001 -42.3211
|
||||
267001 -42.5009
|
||||
268001 -42.6809
|
||||
269001 -42.8606
|
||||
270001 -43.0403
|
||||
271001 -43.2196
|
||||
272001 -43.3988
|
||||
273001 -43.5785
|
||||
274001 -43.7576
|
||||
275001 -43.9376
|
||||
276001 -44.1173
|
||||
277001 -44.297
|
||||
278001 -44.4763
|
||||
279001 -44.6556
|
||||
280001 -44.8352
|
||||
281001 -45.0156
|
||||
282001 -45.1964
|
||||
283001 -45.3775
|
||||
284001 -45.5592
|
||||
285001 -45.7421
|
||||
286001 -45.9266
|
||||
287001 -46.1109
|
||||
288001 -46.2954
|
||||
289001 -46.4794
|
||||
290001 -46.663
|
||||
291001 -46.8469
|
||||
292001 -47.0311
|
||||
293001 -47.2155
|
||||
294001 -47.4006
|
||||
295001 -47.5865
|
||||
296001 -47.7717
|
||||
297001 -47.9575
|
||||
298001 -48.1446
|
||||
299001 -48.3328
|
||||
300001 -48.522
|
||||
301001 -48.7127
|
||||
302001 -48.9036
|
||||
303001 -49.0943
|
||||
304001 -49.283
|
||||
305001 -49.4712
|
||||
306001 -49.6592
|
||||
307001 -49.8476
|
||||
308001 -50.0362
|
||||
309001 -50.2254
|
||||
310001 -50.4158
|
||||
311001 -50.6067
|
||||
312001 -50.7976
|
||||
313001 -50.9873
|
||||
314001 -51.1763
|
||||
315001 -51.3637
|
||||
316001 -51.5501
|
||||
317001 -51.7368
|
||||
318001 -51.9249
|
||||
319001 -52.1147
|
||||
320001 -52.306
|
||||
321001 -52.4986
|
||||
322001 -52.6919
|
||||
323001 -52.886
|
||||
324001 -53.0813
|
||||
325001 -53.2775
|
||||
326001 -53.4749
|
||||
327001 -53.6733
|
||||
328001 -53.8713
|
||||
329001 -54.0699
|
||||
330001 -54.269
|
||||
331001 -54.4685
|
||||
332001 -54.6687
|
||||
333001 -54.8697
|
||||
334001 -55.0713
|
||||
335001 -55.2738
|
||||
336001 -55.476
|
||||
337001 -55.678
|
||||
338001 -55.881
|
||||
339001 -56.0843
|
||||
340001 -56.288
|
||||
341001 -56.4917
|
||||
342001 -56.6958
|
||||
343001 -56.9003
|
||||
344001 -57.1051
|
||||
345001 -57.3084
|
||||
346001 -57.5099
|
||||
347001 -57.7098
|
||||
348001 -57.9084
|
||||
349001 -58.1052
|
||||
350001 -58.299
|
||||
351001 -58.4904
|
||||
352001 -58.6792
|
||||
353001 -58.8664
|
||||
354001 -59.053
|
||||
355001 -59.2381
|
||||
356001 -59.4219
|
||||
357001 -59.6053
|
||||
358001 -59.7882
|
||||
359001 -59.969
|
||||
360001 -60.149
|
||||
361001 -60.3294
|
||||
362001 -60.5101
|
||||
363001 -60.69
|
||||
364001 -60.8703
|
||||
365001 -61.0481
|
||||
366001 -61.2242
|
||||
367001 -61.3992
|
||||
368001 -61.5729
|
||||
369001 -61.7456
|
||||
370001 -61.9171
|
||||
371001 -62.088
|
||||
372001 -62.2579
|
||||
373001 -62.4265
|
||||
374001 -62.5929
|
||||
375001 -62.7581
|
||||
376001 -62.9203
|
||||
377001 -63.0797
|
||||
378001 -63.2368
|
||||
379001 -63.3921
|
||||
380001 -63.546
|
||||
381001 -63.6994
|
||||
382001 -63.8505
|
||||
383001 -63.9987
|
||||
384001 -64.1437
|
||||
385001 -64.2859
|
||||
386001 -64.4253
|
||||
387001 -64.5617
|
||||
388001 -64.6946
|
||||
389001 -64.8254
|
||||
390001 -64.9533
|
||||
391001 -65.0786
|
||||
392001 -65.2018
|
||||
393001 -65.3229
|
||||
394001 -65.4402
|
||||
395001 -65.5538
|
||||
396001 -65.6641
|
||||
397001 -65.7711
|
||||
398001 -65.8758
|
||||
399001 -65.9787
|
||||
400001 -66.0791
|
||||
401001 -66.1771
|
||||
402001 -66.2736
|
||||
403001 -66.3683
|
||||
404001 -66.4597
|
||||
405001 -66.549
|
||||
406001 -66.6357
|
||||
407001 -66.7195
|
||||
408001 -66.8002
|
||||
409001 -66.8783
|
||||
410001 -66.953
|
||||
411001 -67.0255
|
||||
412001 -67.0954
|
||||
413001 -67.1621
|
||||
414001 -67.2257
|
||||
415001 -67.2881
|
||||
416001 -67.3501
|
||||
417001 -67.4111
|
||||
418001 -67.4717
|
||||
419001 -67.5291
|
||||
420001 -67.5837
|
||||
421001 -67.6362
|
||||
422001 -67.6862
|
||||
423001 -67.7338
|
||||
424001 -67.7789
|
||||
425001 -67.8226
|
||||
426001 -67.8657
|
||||
427001 -67.9079
|
||||
428001 -67.9477
|
||||
429001 -67.9854
|
||||
430001 -68.02
|
||||
431001 -68.0523
|
||||
432001 -68.0821
|
||||
433001 -68.1101
|
||||
434001 -68.1365
|
||||
435001 -68.1627
|
||||
436001 -68.1883
|
||||
437001 -68.2134
|
||||
438001 -68.2379
|
||||
439001 -68.2597
|
||||
440001 -68.2793
|
||||
441001 -68.2968
|
||||
442001 -68.3124
|
||||
443001 -68.327
|
||||
444001 -68.3395
|
||||
445001 -68.3514
|
||||
446001 -68.362
|
||||
447001 -68.3712
|
||||
448001 -68.3796
|
||||
449001 -68.3862
|
||||
450001 -68.3918
|
||||
451001 -68.3972
|
||||
452001 -68.4024
|
||||
453001 -68.4067
|
||||
454001 -68.4092
|
||||
455001 -68.411
|
||||
456001 -68.4116
|
||||
457001 -68.411
|
||||
458001 -68.4085
|
||||
459001 -68.4056
|
||||
460001 -68.404
|
||||
461001 -68.4002
|
||||
462001 -68.3953
|
||||
463001 -68.3898
|
||||
464001 -68.3823
|
||||
465001 -68.372
|
||||
466001 -68.3588
|
||||
467001 -68.3431
|
||||
468001 -68.3258
|
||||
469001 -68.3065
|
||||
470001 -68.2854
|
||||
471001 -68.2642
|
||||
472001 -68.2421
|
||||
473001 -68.2192
|
||||
474001 -68.1939
|
||||
475001 -68.1667
|
||||
476001 -68.1377
|
||||
477001 -68.1071
|
||||
478001 -68.0743
|
||||
479001 -68.0398
|
||||
480001 -68.0025
|
||||
481001 -67.9631
|
||||
482001 -67.9214
|
||||
483001 -67.8773
|
||||
484001 -67.8326
|
||||
485001 -67.7864
|
||||
486001 -67.7395
|
||||
487001 -67.6911
|
||||
488001 -67.6414
|
||||
489001 -67.5915
|
||||
490001 -67.541
|
||||
491001 -67.4886
|
||||
492001 -67.4346
|
||||
493001 -67.3794
|
||||
494001 -67.3213
|
||||
495001 -67.2609
|
||||
496001 -67.1982
|
||||
497001 -67.1333
|
||||
498001 -67.0668
|
||||
499001 -66.999
|
||||
500001 -66.9292
|
||||
501001 -66.8596
|
||||
502001 -66.7899
|
||||
503001 -66.7187
|
||||
504001 -66.6458
|
||||
505001 -66.5714
|
||||
506001 -66.4951
|
||||
507001 -66.4167
|
||||
508001 -66.3369
|
||||
509001 -66.2538
|
||||
510001 -66.1678
|
||||
511001 -66.079
|
||||
512001 -65.9875
|
||||
513001 -65.8935
|
||||
514001 -65.7973
|
||||
515001 -65.7001
|
||||
516001 -65.6008
|
||||
517001 -65.4996
|
||||
518001 -65.3966
|
||||
519001 -65.2908
|
||||
520001 -65.1821
|
||||
521001 -65.0706
|
||||
522001 -64.9556
|
||||
523001 -64.8386
|
||||
524001 -64.7188
|
||||
525001 -64.5967
|
||||
526001 -64.472
|
||||
527001 -64.3452
|
||||
528001 -64.2164
|
||||
529001 -64.0858
|
||||
530001 -63.9536
|
||||
531001 -63.8205
|
||||
532001 -63.688
|
||||
533001 -63.5531
|
||||
534001 -63.4159
|
||||
535001 -63.2768
|
||||
536001 -63.1368
|
||||
537001 -62.9963
|
||||
538001 -62.8556
|
||||
539001 -62.7152
|
||||
540001 -62.5743
|
||||
541001 -62.4325
|
||||
542001 -62.29
|
||||
543001 -62.1466
|
||||
544001 -62.0028
|
||||
545001 -61.8577
|
||||
546001 -61.7104
|
||||
547001 -61.5621
|
||||
548001 -61.4128
|
||||
549001 -61.2618
|
||||
550001 -61.1086
|
||||
551001 -60.953
|
||||
552001 -60.7953
|
||||
553001 -60.6355
|
||||
554001 -60.4731
|
||||
555001 -60.308
|
||||
556001 -60.1407
|
||||
557001 -59.9727
|
||||
558001 -59.8033
|
||||
559001 -59.6325
|
||||
560001 -59.4588
|
||||
561001 -59.2818
|
||||
562001 -59.1035
|
||||
563001 -58.9231
|
||||
564001 -58.7417
|
||||
565001 -58.56
|
||||
566001 -58.3767
|
||||
567001 -58.1915
|
||||
568001 -58.0055
|
||||
569001 -57.8176
|
||||
570001 -57.6268
|
||||
571001 -57.434
|
||||
572001 -57.2406
|
||||
573001 -57.0474
|
||||
574001 -56.855
|
||||
575001 -56.6635
|
||||
576001 -56.4719
|
||||
577001 -56.2801
|
||||
578001 -56.0885
|
||||
579001 -55.8967
|
||||
580001 -55.7046
|
||||
581001 -55.5119
|
||||
582001 -55.3194
|
||||
583001 -55.1257
|
||||
584001 -54.9314
|
||||
585001 -54.737
|
||||
586001 -54.543
|
||||
587001 -54.3504
|
||||
588001 -54.1571
|
||||
589001 -53.964
|
||||
590001 -53.7711
|
||||
591001 -53.5771
|
||||
592001 -53.3816
|
||||
593001 -53.1866
|
||||
594001 -52.9911
|
||||
595001 -52.7949
|
||||
596001 -52.5982
|
||||
597001 -52.4004
|
||||
598001 -52.2032
|
||||
599001 -52.0071
|
||||
600001 -51.8116
|
||||
601001 -51.6175
|
||||
602001 -51.4235
|
||||
603001 -51.229
|
||||
604001 -51.0352
|
||||
605001 -50.8422
|
||||
606001 -50.65
|
||||
607001 -50.4574
|
||||
608001 -50.2647
|
||||
609001 -50.0721
|
||||
610001 -49.8805
|
||||
611001 -49.6902
|
||||
612001 -49.5004
|
||||
613001 -49.3105
|
||||
614001 -49.1203
|
||||
615001 -48.9308
|
||||
616001 -48.7421
|
||||
617001 -48.5546
|
||||
618001 -48.368
|
||||
619001 -48.1823
|
||||
620001 -47.9958
|
||||
621001 -47.8088
|
||||
622001 -47.6221
|
||||
623001 -47.4352
|
||||
624001 -47.2482
|
||||
625001 -47.0608
|
||||
626001 -46.8729
|
||||
627001 -46.6839
|
||||
628001 -46.4956
|
||||
629001 -46.3077
|
||||
630001 -46.1194
|
||||
631001 -45.9315
|
||||
632001 -45.7443
|
||||
633001 -45.558
|
||||
634001 -45.3718
|
||||
635001 -45.1852
|
||||
636001 -44.9986
|
||||
637001 -44.8126
|
||||
638001 -44.6264
|
||||
639001 -44.4396
|
||||
640001 -44.2533
|
||||
641001 -44.0677
|
||||
642001 -43.8816
|
||||
643001 -43.6936
|
||||
644001 -43.5036
|
||||
645001 -43.3118
|
||||
646001 -43.1189
|
||||
647001 -42.9268
|
||||
648001 -42.735
|
||||
649001 -42.5434
|
||||
650001 -42.3519
|
||||
651001 -42.1602
|
||||
652001 -41.9675
|
||||
653001 -41.774
|
||||
654001 -41.5807
|
||||
655001 -41.3875
|
||||
656001 -41.195
|
||||
657001 -41.004
|
||||
658001 -40.8151
|
||||
659001 -40.6278
|
||||
660001 -40.4422
|
||||
661001 -40.2565
|
||||
662001 -40.0701
|
||||
663001 -39.8828
|
||||
664001 -39.6948
|
||||
665001 -39.5047
|
||||
666001 -39.3133
|
||||
667001 -39.1221
|
||||
668001 -38.931
|
||||
669001 -38.7408
|
||||
670001 -38.5511
|
||||
671001 -38.3623
|
||||
672001 -38.1719
|
||||
673001 -37.98
|
||||
674001 -37.7867
|
||||
675001 -37.5922
|
||||
676001 -37.3969
|
||||
677001 -37.2025
|
||||
678001 -37.0089
|
||||
679001 -36.8141
|
||||
680001 -36.6191
|
||||
681001 -36.4254
|
||||
682001 -36.2329
|
||||
683001 -36.041
|
||||
684001 -35.8505
|
||||
685001 -35.662
|
||||
686001 -35.4745
|
||||
687001 -35.2863
|
||||
688001 -35.0967
|
||||
689001 -34.9082
|
||||
690001 -34.7188
|
||||
691001 -34.5287
|
||||
692001 -34.3408
|
||||
693001 -34.1552
|
||||
694001 -33.97
|
||||
695001 -33.7865
|
||||
696001 -33.6033
|
||||
697001 -33.4214
|
||||
698001 -33.2414
|
||||
699001 -33.0611
|
||||
700001 -32.8819
|
||||
701001 -32.7035
|
||||
702001 -32.5259
|
||||
703001 -32.3498
|
||||
704001 -32.1742
|
||||
705001 -31.9984
|
||||
706001 -31.8216
|
||||
707001 -31.6447
|
||||
708001 -31.468
|
||||
709001 -31.2904
|
||||
710001 -31.1126
|
||||
711001 -30.9347
|
||||
712001 -30.7562
|
||||
713001 -30.5773
|
||||
714001 -30.3981
|
||||
715001 -30.2191
|
||||
716001 -30.0388
|
||||
717001 -29.8587
|
||||
718001 -29.679
|
||||
719001 -29.4977
|
||||
720001 -29.3161
|
||||
721001 -29.1335
|
||||
722001 -28.9514
|
||||
723001 -28.7685
|
||||
724001 -28.5852
|
||||
725001 -28.402
|
||||
726001 -28.2188
|
||||
727001 -28.0358
|
||||
728001 -27.8535
|
||||
729001 -27.6692
|
||||
730001 -27.4836
|
||||
731001 -27.2961
|
||||
732001 -27.1084
|
||||
733001 -26.9204
|
||||
734001 -26.7315
|
||||
735001 -26.5418
|
||||
736001 -26.3505
|
||||
737001 -26.1593
|
||||
738001 -25.9675
|
||||
739001 -25.7761
|
||||
740001 -25.5847
|
||||
741001 -25.3932
|
||||
742001 -25.2007
|
||||
743001 -25.0077
|
||||
744001 -24.8141
|
||||
745001 -24.6193
|
||||
746001 -24.4258
|
||||
747001 -24.2323
|
||||
748001 -24.0396
|
||||
749001 -23.8475
|
||||
750001 -23.6552
|
||||
751001 -23.4627
|
||||
752001 -23.2705
|
||||
753001 -23.0783
|
||||
754001 -22.8865
|
||||
755001 -22.6955
|
||||
756001 -22.5053
|
||||
757001 -22.3151
|
||||
758001 -22.1253
|
||||
759001 -21.936
|
||||
760001 -21.7469
|
||||
761001 -21.5594
|
||||
762001 -21.3713
|
||||
763001 -21.183
|
||||
764001 -20.9932
|
||||
765001 -20.802
|
||||
766001 -20.609
|
||||
767001 -20.4147
|
||||
768001 -20.2211
|
||||
769001 -20.0281
|
||||
770001 -19.8365
|
||||
771001 -19.6462
|
||||
772001 -19.4557
|
||||
773001 -19.2661
|
||||
774001 -19.0763
|
||||
775001 -18.886
|
||||
776001 -18.6947
|
||||
777001 -18.5025
|
||||
778001 -18.3099
|
||||
779001 -18.1163
|
||||
780001 -17.9216
|
||||
781001 -17.7263
|
||||
782001 -17.5309
|
||||
783001 -17.3357
|
||||
784001 -17.1411
|
||||
785001 -16.9458
|
||||
786001 -16.7502
|
||||
787001 -16.5527
|
||||
788001 -16.3549
|
||||
789001 -16.1568
|
||||
790001 -15.9583
|
||||
791001 -15.7621
|
||||
792001 -15.5665
|
||||
793001 -15.3698
|
||||
794001 -15.1727
|
||||
795001 -14.9744
|
||||
796001 -14.7746
|
||||
797001 -14.5747
|
||||
798001 -14.3769
|
||||
799001 -14.1819
|
||||
800001 -13.9884
|
||||
801001 -13.7954
|
||||
802001 -13.6022
|
||||
803001 -13.4115
|
||||
804001 -13.2235
|
||||
805001 -13.0389
|
||||
806001 -12.8561
|
||||
807001 -12.6747
|
||||
808001 -12.4939
|
||||
809001 -12.3136
|
||||
810001 -12.1335
|
||||
811001 -11.9546
|
||||
812001 -11.7769
|
||||
813001 -11.6
|
||||
814001 -11.4233
|
||||
815001 -11.2477
|
||||
816001 -11.0751
|
||||
817001 -10.9039
|
||||
818001 -10.7346
|
||||
819001 -10.5681
|
||||
820001 -10.4045
|
||||
821001 -10.2426
|
||||
822001 -10.0839
|
||||
823001 -9.92776
|
||||
824001 -9.7727
|
||||
825001 -9.62004
|
||||
826001 -9.46954
|
||||
827001 -9.32056
|
||||
828001 -9.17234
|
||||
829001 -9.025
|
||||
830001 -8.87994
|
||||
831001 -8.73758
|
||||
832001 -8.59697
|
||||
833001 -8.45889
|
||||
834001 -8.3232
|
||||
835001 -8.19003
|
||||
836001 -8.05847
|
||||
837001 -7.92891
|
||||
838001 -7.7995
|
||||
839001 -7.67252
|
||||
840001 -7.5485
|
||||
841001 -7.42736
|
||||
842001 -7.30856
|
||||
843001 -7.19243
|
||||
844001 -7.07855
|
||||
845001 -6.96517
|
||||
846001 -6.85438
|
||||
847001 -6.74539
|
||||
848001 -6.63987
|
||||
849001 -6.53748
|
||||
850001 -6.43794
|
||||
851001 -6.34213
|
||||
852001 -6.24945
|
||||
853001 -6.16003
|
||||
854001 -6.07333
|
||||
855001 -5.98908
|
||||
856001 -5.90644
|
||||
857001 -5.82624
|
||||
858001 -5.74908
|
||||
859001 -5.6741
|
||||
860001 -5.60186
|
||||
861001 -5.53028
|
||||
862001 -5.45992
|
||||
863001 -5.39177
|
||||
864001 -5.32623
|
||||
865001 -5.26266
|
||||
866001 -5.20101
|
||||
867001 -5.14201
|
||||
868001 -5.08347
|
||||
869001 -5.02581
|
||||
870001 -4.9691
|
||||
871001 -4.91389
|
||||
872001 -4.85983
|
||||
873001 -4.80686
|
||||
874001 -4.75492
|
||||
875001 -4.70474
|
||||
876001 -4.65606
|
||||
877001 -4.60877
|
||||
878001 -4.56261
|
||||
879001 -4.51743
|
||||
880001 -4.47457
|
||||
881001 -4.4337
|
||||
882001 -4.39383
|
||||
883001 -4.35545
|
||||
884001 -4.3178
|
||||
885001 -4.28119
|
||||
886001 -4.24533
|
||||
887001 -4.21051
|
||||
888001 -4.17654
|
||||
889001 -4.14544
|
||||
890001 -4.11702
|
||||
891001 -4.09076
|
||||
892001 -4.06695
|
||||
893001 -4.04528
|
||||
894001 -4.026
|
||||
895001 -4.00913
|
||||
896001 -3.99324
|
||||
897001 -3.9769
|
||||
898001 -3.96318
|
||||
899001 -3.95229
|
||||
900001 -3.94465
|
||||
901001 -3.93979
|
||||
902001 -3.93766
|
||||
903001 -3.93744
|
||||
904001 -3.93928
|
||||
905001 -3.9432
|
||||
906001 -3.94814
|
||||
907001 -3.95509
|
||||
908001 -3.96367
|
||||
909001 -3.97366
|
||||
910001 -3.98531
|
||||
927
src/kimono/lxpack/tests/ref/borbu1.6.ref
Normal file
927
src/kimono/lxpack/tests/ref/borbu1.6.ref
Normal file
@ -0,0 +1,927 @@
|
||||
# input : borbu1.fst
|
||||
# include : borbu1.lst
|
||||
# selector : codon
|
||||
# mixer : basic
|
||||
# distance : chi
|
||||
# phase : 7
|
||||
# alphabet : ACGT
|
||||
# excluded : X
|
||||
# seqname : borbu1
|
||||
# seqlength : 910724
|
||||
# unmasked : 284128
|
||||
# valid : 284088
|
||||
# window : 227680
|
||||
# step : 1000
|
||||
#
|
||||
# pos LeftTotalCodon RightTotalCodon LeftA0
|
||||
1 35051 36273 10243 11968
|
||||
1001 34984 36282 10218 11960
|
||||
2001 34991 36278 10180 12054
|
||||
3001 35055 36271 10195 12127
|
||||
4001 35031 36073 10190 12174
|
||||
5001 35042 36071 10173 12237
|
||||
6001 35053 36080 10185 12283
|
||||
7001 35074 36008 10142 12359
|
||||
8001 35115 36004 10132 12429
|
||||
9001 35083 36022 10104 12459
|
||||
10001 35081 36024 10077 12516
|
||||
11001 35080 36031 10058 12565
|
||||
12001 35082 36035 10072 12613
|
||||
13001 35136 36026 10088 12692
|
||||
14001 35128 36021 10098 12745
|
||||
15001 35127 36020 10092 12786
|
||||
16001 35105 36059 10049 12838
|
||||
17001 35253 36048 10064 12937
|
||||
18001 35319 35986 10062 13024
|
||||
19001 35382 35974 10075 13126
|
||||
20001 35379 35980 10067 13179
|
||||
21001 35290 36086 10033 13190
|
||||
22001 35340 36074 10045 13245
|
||||
23001 35319 36111 10050 13291
|
||||
24001 35330 36089 10079 13335
|
||||
25001 35328 35956 10055 13384
|
||||
26001 35313 35995 10034 13422
|
||||
27001 35333 35997 10072 13476
|
||||
28001 35340 35989 10050 13546
|
||||
29001 35338 35983 10002 13609
|
||||
30001 35316 36003 10001 13654
|
||||
31001 35317 35994 10022 13698
|
||||
32001 35290 36017 9951 13762
|
||||
33001 35302 36037 9942 13814
|
||||
34001 35301 35987 9906 13872
|
||||
35001 35278 35970 9904 13896
|
||||
36001 35272 35976 9852 13970
|
||||
37001 35272 35969 9786 14061
|
||||
38001 35274 35943 9746 14152
|
||||
39001 35270 35939 9740 14232
|
||||
40001 35214 35985 9712 14280
|
||||
41001 35217 35983 9707 14329
|
||||
42001 35212 35986 9677 14410
|
||||
43001 35259 35974 9676 14497
|
||||
44001 35259 35965 9673 14550
|
||||
45001 35260 35914 9705 14616
|
||||
46001 35247 35936 9677 14668
|
||||
47001 35129 36043 9661 14646
|
||||
48001 35067 36107 9640 14656
|
||||
49001 35068 36107 9654 14693
|
||||
50001 35041 36120 9669 14731
|
||||
51001 35009 36147 9657 14767
|
||||
52001 35080 36127 9687 14824
|
||||
53001 35073 36133 9681 14874
|
||||
54001 35049 36131 9666 14940
|
||||
55001 35052 36117 9616 15028
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
927
src/kimono/lxpack/tests/ref/borbu1.7.ref
Normal file
927
src/kimono/lxpack/tests/ref/borbu1.7.ref
Normal file
@ -0,0 +1,927 @@
|
||||
# input : borbu1.fst
|
||||
# include : borbu1.lst
|
||||
# selector : genes
|
||||
# mixer : basic
|
||||
# distance : chi
|
||||
# phase : 7
|
||||
# alphabet : DR
|
||||
# excluded : X
|
||||
# seqname : borbu1
|
||||
# seqlength : 910724
|
||||
# unmasked : 850
|
||||
# valid : 850
|
||||
# window : 227680
|
||||
# step : 1000
|
||||
#
|
||||
# pos LeftDirect RightDirect LeftReverse
|
||||
1 63 42 36 73
|
||||
1001 64 42 35 74
|
||||
2001 64 42 35 73
|
||||
3001 64 42 34 74
|
||||
4001 64 41 34 73
|
||||
5001 63 41 34 74
|
||||
6001 63 41 33 76
|
||||
7001 62 41 33 76
|
||||
8001 62 41 33 77
|
||||
9001 63 40 33 77
|
||||
10001 64 39 33 77
|
||||
11001 66 37 32 79
|
||||
12001 67 36 30 80
|
||||
13001 69 34 29 81
|
||||
14001 69 34 28 82
|
||||
15001 69 34 27 82
|
||||
16001 70 33 28 80
|
||||
17001 70 33 27 81
|
||||
18001 70 34 27 81
|
||||
19001 70 34 27 80
|
||||
20001 70 34 27 79
|
||||
21001 69 35 26 80
|
||||
22001 67 35 27 79
|
||||
23001 65 34 29 77
|
||||
24001 64 34 29 78
|
||||
25001 63 34 30 79
|
||||
26001 62 33 31 78
|
||||
27001 61 32 31 78
|
||||
28001 60 32 32 77
|
||||
29001 59 32 33 77
|
||||
30001 60 31 34 77
|
||||
31001 59 32 34 78
|
||||
32001 60 31 34 79
|
||||
33001 59 31 35 79
|
||||
34001 59 31 35 80
|
||||
35001 58 32 34 80
|
||||
36001 58 32 35 79
|
||||
37001 58 32 36 79
|
||||
38001 58 33 36 80
|
||||
39001 58 34 37 79
|
||||
40001 58 33 38 79
|
||||
41001 59 32 38 79
|
||||
42001 58 32 39 78
|
||||
43001 57 33 41 77
|
||||
44001 57 34 41 77
|
||||
45001 56 36 41 77
|
||||
46001 56 36 42 76
|
||||
47001 55 37 44 74
|
||||
48001 56 35 45 73
|
||||
49001 56 35 45 73
|
||||
50001 57 35 46 73
|
||||
51001 55 35 47 73
|
||||
52001 53 35 48 72
|
||||
53001 53 35 49 72
|
||||
54001 53 35 50 72
|
||||
55001 52 35 50 72
|
||||
56001 51 36 51 72
|
||||
57001 50 36 53 70
|
||||
58001 50 36 54 70
|
||||
59001 50 36 54 70
|
||||
60001 49 36 55 70
|
||||
61001 48 36 57 69
|
||||
62001 48 36 58 69
|
||||
63001 48 36 58 70
|
||||
64001 47 35 58 70
|
||||
65001 47 34 58 71
|
||||
66001 48 32 58 73
|
||||
67001 47 32 58 73
|
||||
68001 48 31 58 74
|
||||
69001 47 31 58 75
|
||||
70001 45 32 58 75
|
||||
71001 45 31 58 75
|
||||
72001 45 31 57 75
|
||||
73001 46 31 56 75
|
||||
74001 47 31 55 76
|
||||
75001 48 30 55 78
|
||||
76001 50 28 54 80
|
||||
77001 51 30 54 81
|
||||
78001 51 30 54 81
|
||||
79001 50 30 53 82
|
||||
80001 50 30 55 81
|
||||
81001 51 29 55 81
|
||||
82001 52 30 55 81
|
||||
83001 51 30 55 81
|
||||
84001 51 31 56 80
|
||||
85001 51 31 55 80
|
||||
86001 51 31 56 79
|
||||
87001 51 31 57 78
|
||||
88001 51 31 57 78
|
||||
89001 51 31 57 79
|
||||
90001 51 32 58 77
|
||||
91001 51 33 58 77
|
||||
92001 50 34 58 76
|
||||
93001 50 35 59 75
|
||||
94001 49 35 60 74
|
||||
95001 49 36 62 73
|
||||
96001 49 37 62 73
|
||||
97001 48 37 63 72
|
||||
98001 48 38 64 71
|
||||
99001 49 38 65 70
|
||||
100001 49 38 65 70
|
||||
101001 50 37 64 70
|
||||
102001 50 38 65 69
|
||||
103001 49 38 65 68
|
||||
104001 48 39 66 67
|
||||
105001 47 39 66 67
|
||||
106001 47 40 68 67
|
||||
107001 47 41 69 66
|
||||
108001 47 41 69 66
|
||||
109001 46 41 68 65
|
||||
110001 44 42 68 65
|
||||
111001 44 42 68 66
|
||||
112001 42 42 71 63
|
||||
113001 42 42 73 62
|
||||
114001 41 42 73 63
|
||||
115001 42 41 74 63
|
||||
116001 42 42 73 65
|
||||
117001 42 42 73 64
|
||||
118001 41 43 73 65
|
||||
119001 41 44 75 63
|
||||
120001 41 44 76 62
|
||||
121001 41 44 76 61
|
||||
122001 41 44 77 60
|
||||
123001 40 44 77 59
|
||||
124001 39 44 77 61
|
||||
125001 37 44 79 61
|
||||
126001 35 44 80 61
|
||||
127001 34 44 81 61
|
||||
128001 34 44 82 60
|
||||
129001 34 45 82 61
|
||||
130001 33 45 80 61
|
||||
131001 33 45 81 61
|
||||
132001 34 45 81 61
|
||||
133001 34 46 80 61
|
||||
134001 35 45 80 60
|
||||
135001 35 47 79 60
|
||||
136001 35 47 78 60
|
||||
137001 34 47 77 61
|
||||
138001 34 47 78 61
|
||||
139001 34 48 79 60
|
||||
140001 33 49 78 60
|
||||
141001 32 49 78 60
|
||||
142001 32 51 78 59
|
||||
143001 32 52 78 58
|
||||
144001 31 52 77 58
|
||||
145001 31 51 78 57
|
||||
146001 31 52 78 56
|
||||
147001 31 52 79 55
|
||||
148001 31 52 79 54
|
||||
149001 32 51 80 53
|
||||
150001 32 51 79 54
|
||||
151001 33 51 80 52
|
||||
152001 33 51 79 52
|
||||
153001 34 51 79 52
|
||||
154001 33 52 79 51
|
||||
155001 32 52 79 51
|
||||
156001 32 52 78 52
|
||||
157001 33 51 77 52
|
||||
158001 34 50 77 52
|
||||
159001 36 48 77 53
|
||||
160001 36 47 76 54
|
||||
161001 37 47 73 54
|
||||
162001 35 47 73 54
|
||||
163001 36 47 74 54
|
||||
164001 35 47 73 54
|
||||
165001 35 47 73 54
|
||||
166001 35 47 73 55
|
||||
167001 35 47 72 55
|
||||
168001 35 47 72 56
|
||||
169001 35 47 72 57
|
||||
170001 36 46 72 56
|
||||
171001 36 46 70 57
|
||||
172001 36 45 70 56
|
||||
173001 36 45 69 57
|
||||
174001 36 45 69 57
|
||||
175001 36 45 69 58
|
||||
176001 36 45 69 59
|
||||
177001 35 45 70 58
|
||||
178001 34 45 71 59
|
||||
179001 34 45 72 59
|
||||
180001 32 45 73 60
|
||||
181001 32 45 73 61
|
||||
182001 31 45 74 61
|
||||
183001 32 44 75 61
|
||||
184001 32 43 75 63
|
||||
185001 31 43 75 64
|
||||
186001 31 42 75 65
|
||||
187001 32 40 75 66
|
||||
188001 31 40 76 65
|
||||
189001 29 40 78 65
|
||||
190001 29 39 81 64
|
||||
191001 30 37 81 64
|
||||
192001 30 37 81 66
|
||||
193001 30 37 81 66
|
||||
194001 30 36 81 66
|
||||
195001 30 35 81 67
|
||||
196001 30 34 81 68
|
||||
197001 30 34 81 69
|
||||
198001 31 33 80 70
|
||||
199001 31 33 80 71
|
||||
200001 31 33 79 71
|
||||
201001 31 33 78 73
|
||||
202001 31 33 78 73
|
||||
203001 32 32 79 73
|
||||
204001 32 32 77 74
|
||||
205001 33 31 76 76
|
||||
206001 34 30 76 78
|
||||
207001 35 30 75 79
|
||||
208001 35 31 73 79
|
||||
209001 36 30 73 78
|
||||
210001 37 29 73 80
|
||||
211001 37 29 72 80
|
||||
212001 38 28 71 81
|
||||
213001 38 27 70 84
|
||||
214001 38 27 70 85
|
||||
215001 37 28 70 85
|
||||
216001 38 28 69 85
|
||||
217001 38 28 68 86
|
||||
218001 39 27 67 86
|
||||
219001 39 27 67 86
|
||||
220001 40 26 67 85
|
||||
221001 41 25 66 86
|
||||
222001 41 26 66 86
|
||||
223001 41 26 65 86
|
||||
224001 42 25 65 86
|
||||
225001 42 26 65 85
|
||||
226001 42 26 63 85
|
||||
227001 42 27 62 85
|
||||
228001 42 28 63 84
|
||||
229001 41 29 64 82
|
||||
230001 42 29 65 81
|
||||
231001 42 29 64 81
|
||||
232001 43 29 65 81
|
||||
233001 44 28 63 81
|
||||
234001 44 28 62 83
|
||||
235001 44 28 60 84
|
||||
236001 44 28 60 84
|
||||
237001 44 28 59 84
|
||||
238001 44 28 61 83
|
||||
239001 44 28 61 82
|
||||
240001 44 28 61 82
|
||||
241001 44 28 61 82
|
||||
242001 44 29 60 83
|
||||
243001 45 28 61 82
|
||||
244001 45 29 60 82
|
||||
245001 45 30 60 81
|
||||
246001 45 29 61 81
|
||||
247001 46 28 61 81
|
||||
248001 45 29 60 82
|
||||
249001 47 27 60 82
|
||||
250001 47 27 60 82
|
||||
251001 47 27 61 82
|
||||
252001 47 27 60 83
|
||||
253001 48 26 60 84
|
||||
254001 49 25 60 85
|
||||
255001 50 25 60 86
|
||||
256001 51 25 59 86
|
||||
257001 52 25 58 86
|
||||
258001 52 26 58 86
|
||||
259001 52 25 57 86
|
||||
260001 52 26 56 86
|
||||
261001 52 27 55 87
|
||||
262001 52 28 54 87
|
||||
263001 51 28 53 87
|
||||
264001 52 27 54 87
|
||||
265001 51 27 52 87
|
||||
266001 51 27 52 88
|
||||
267001 51 26 52 89
|
||||
268001 52 25 51 89
|
||||
269001 52 25 51 90
|
||||
270001 52 25 52 90
|
||||
271001 51 26 52 90
|
||||
272001 49 27 52 90
|
||||
273001 48 28 53 89
|
||||
274001 47 28 54 88
|
||||
275001 47 28 54 89
|
||||
276001 47 28 54 90
|
||||
277001 47 27 54 90
|
||||
278001 47 27 54 91
|
||||
279001 47 27 54 90
|
||||
280001 47 27 55 89
|
||||
281001 47 27 55 90
|
||||
282001 47 27 56 89
|
||||
283001 47 27 57 89
|
||||
284001 46 27 57 90
|
||||
285001 46 27 56 90
|
||||
286001 45 27 57 89
|
||||
287001 45 27 57 89
|
||||
288001 45 27 57 88
|
||||
289001 45 27 58 86
|
||||
290001 45 27 59 84
|
||||
291001 45 27 58 84
|
||||
292001 45 27 59 84
|
||||
293001 45 27 59 84
|
||||
294001 45 27 60 84
|
||||
295001 45 27 61 86
|
||||
296001 45 27 61 86
|
||||
297001 44 28 61 86
|
||||
298001 43 28 63 84
|
||||
299001 43 28 64 83
|
||||
300001 42 29 65 83
|
||||
301001 40 29 66 82
|
||||
302001 40 29 65 83
|
||||
303001 40 30 64 82
|
||||
304001 38 32 64 80
|
||||
305001 37 32 64 80
|
||||
306001 37 32 66 79
|
||||
307001 37 32 66 78
|
||||
308001 36 33 66 78
|
||||
309001 35 35 67 77
|
||||
310001 34 36 68 76
|
||||
311001 34 37 69 76
|
||||
312001 33 38 70 75
|
||||
313001 33 39 71 74
|
||||
314001 33 39 71 74
|
||||
315001 33 41 72 72
|
||||
316001 33 41 73 71
|
||||
317001 32 41 73 71
|
||||
318001 31 41 74 70
|
||||
319001 30 41 76 68
|
||||
320001 30 41 78 66
|
||||
321001 30 40 79 65
|
||||
322001 31 39 79 66
|
||||
323001 30 39 79 65
|
||||
324001 29 39 80 64
|
||||
325001 29 39 80 64
|
||||
326001 27 39 81 63
|
||||
327001 27 39 84 60
|
||||
328001 27 39 85 59
|
||||
329001 28 38 85 60
|
||||
330001 28 37 85 61
|
||||
331001 28 38 86 61
|
||||
332001 27 38 86 61
|
||||
333001 27 38 85 62
|
||||
334001 26 38 85 63
|
||||
335001 26 39 86 63
|
||||
336001 26 40 86 63
|
||||
337001 26 40 86 63
|
||||
338001 25 40 86 64
|
||||
339001 26 39 85 65
|
||||
340001 26 39 85 65
|
||||
341001 27 38 85 65
|
||||
342001 28 37 84 65
|
||||
343001 29 37 81 66
|
||||
344001 29 36 81 66
|
||||
345001 29 37 82 65
|
||||
346001 29 37 81 65
|
||||
347001 28 40 82 64
|
||||
348001 28 40 83 63
|
||||
349001 28 42 84 62
|
||||
350001 28 42 84 61
|
||||
351001 28 43 83 61
|
||||
352001 28 43 83 59
|
||||
353001 28 43 81 59
|
||||
354001 28 43 82 59
|
||||
355001 28 43 82 58
|
||||
356001 29 42 83 59
|
||||
357001 28 42 82 60
|
||||
358001 29 41 82 62
|
||||
359001 30 41 81 63
|
||||
360001 29 41 81 62
|
||||
361001 28 42 81 63
|
||||
362001 28 42 82 62
|
||||
363001 27 42 82 62
|
||||
364001 27 42 82 62
|
||||
365001 27 43 82 62
|
||||
366001 27 44 83 60
|
||||
367001 25 44 85 57
|
||||
368001 25 44 85 57
|
||||
369001 26 43 86 57
|
||||
370001 25 43 86 57
|
||||
371001 25 44 86 57
|
||||
372001 26 44 86 57
|
||||
373001 25 46 86 57
|
||||
374001 26 46 86 57
|
||||
375001 27 46 87 56
|
||||
376001 28 48 87 56
|
||||
377001 28 49 87 56
|
||||
378001 27 49 87 55
|
||||
379001 27 50 87 55
|
||||
380001 26 50 88 54
|
||||
381001 25 51 89 54
|
||||
382001 25 52 90 53
|
||||
383001 25 54 90 53
|
||||
384001 25 55 90 52
|
||||
385001 26 56 90 51
|
||||
386001 27 58 90 51
|
||||
387001 28 58 89 51
|
||||
388001 28 60 88 51
|
||||
389001 28 63 90 49
|
||||
390001 28 65 90 49
|
||||
391001 27 68 90 48
|
||||
392001 27 70 91 47
|
||||
393001 27 70 90 46
|
||||
394001 27 74 89 46
|
||||
395001 27 74 90 45
|
||||
396001 27 76 89 44
|
||||
397001 27 77 89 43
|
||||
398001 27 78 90 41
|
||||
399001 27 78 90 41
|
||||
400001 27 79 89 42
|
||||
401001 27 80 88 42
|
||||
402001 27 81 88 41
|
||||
403001 27 83 86 41
|
||||
404001 27 83 84 41
|
||||
405001 27 83 83 41
|
||||
406001 27 83 84 39
|
||||
407001 27 83 85 37
|
||||
408001 27 83 85 35
|
||||
409001 27 83 86 33
|
||||
410001 27 84 86 32
|
||||
411001 28 84 85 31
|
||||
412001 28 84 84 31
|
||||
413001 28 85 83 31
|
||||
414001 29 84 83 30
|
||||
415001 29 84 82 31
|
||||
416001 29 84 83 31
|
||||
417001 30 83 82 30
|
||||
418001 32 81 80 32
|
||||
419001 32 82 79 33
|
||||
420001 32 83 79 32
|
||||
421001 32 85 78 32
|
||||
422001 33 85 78 32
|
||||
423001 35 83 77 32
|
||||
424001 36 83 76 32
|
||||
425001 37 82 76 31
|
||||
426001 38 82 75 32
|
||||
427001 39 81 74 34
|
||||
428001 40 80 73 34
|
||||
429001 41 80 72 35
|
||||
430001 41 82 70 35
|
||||
431001 41 83 71 34
|
||||
432001 41 83 69 34
|
||||
433001 41 83 67 34
|
||||
434001 41 83 66 34
|
||||
435001 40 83 65 35
|
||||
436001 39 83 66 36
|
||||
437001 39 83 65 36
|
||||
438001 39 83 64 37
|
||||
439001 39 85 64 37
|
||||
440001 39 86 63 37
|
||||
441001 39 87 60 37
|
||||
442001 38 88 59 37
|
||||
443001 38 88 60 36
|
||||
444001 37 88 61 36
|
||||
445001 38 87 61 36
|
||||
446001 38 87 61 36
|
||||
447001 38 87 63 35
|
||||
448001 39 86 63 36
|
||||
449001 39 86 63 36
|
||||
450001 40 85 63 36
|
||||
451001 40 84 63 36
|
||||
452001 40 84 65 35
|
||||
453001 39 85 65 35
|
||||
454001 39 86 65 35
|
||||
455001 38 87 65 34
|
||||
456001 37 89 65 34
|
||||
457001 37 88 66 33
|
||||
458001 36 89 66 33
|
||||
459001 36 88 65 33
|
||||
460001 38 86 65 33
|
||||
461001 40 85 64 34
|
||||
462001 40 85 62 35
|
||||
463001 42 83 62 36
|
||||
464001 42 84 61 37
|
||||
465001 43 85 60 37
|
||||
466001 43 85 59 37
|
||||
467001 43 86 59 37
|
||||
468001 43 87 59 36
|
||||
469001 43 87 58 36
|
||||
470001 42 88 60 33
|
||||
471001 41 88 60 33
|
||||
472001 41 89 62 32
|
||||
473001 41 89 63 31
|
||||
474001 41 90 62 31
|
||||
475001 42 90 62 30
|
||||
476001 42 89 62 30
|
||||
477001 42 90 62 31
|
||||
478001 42 91 61 31
|
||||
479001 43 91 62 30
|
||||
480001 44 90 59 30
|
||||
481001 44 90 57 30
|
||||
482001 44 90 57 30
|
||||
483001 43 91 57 29
|
||||
484001 42 91 57 29
|
||||
485001 43 89 57 29
|
||||
486001 44 89 57 30
|
||||
487001 45 87 57 30
|
||||
488001 46 87 56 30
|
||||
489001 47 86 56 30
|
||||
490001 48 84 56 30
|
||||
491001 49 83 55 31
|
||||
492001 49 83 55 31
|
||||
493001 50 82 55 31
|
||||
494001 51 82 54 32
|
||||
495001 51 83 54 31
|
||||
496001 52 82 53 31
|
||||
497001 54 80 53 32
|
||||
498001 56 79 52 33
|
||||
499001 56 79 51 33
|
||||
500001 57 76 51 33
|
||||
501001 58 75 51 33
|
||||
502001 61 71 51 34
|
||||
503001 64 68 49 35
|
||||
504001 66 66 49 35
|
||||
505001 68 65 48 36
|
||||
506001 70 63 47 36
|
||||
507001 71 62 46 36
|
||||
508001 74 59 45 36
|
||||
509001 75 59 45 37
|
||||
510001 76 59 44 37
|
||||
511001 77 58 42 37
|
||||
512001 78 58 41 37
|
||||
513001 78 59 41 37
|
||||
514001 79 58 42 36
|
||||
515001 80 57 42 36
|
||||
516001 81 56 41 37
|
||||
517001 83 55 41 38
|
||||
518001 83 55 41 38
|
||||
519001 83 57 40 38
|
||||
520001 83 57 39 38
|
||||
521001 83 58 37 38
|
||||
522001 83 58 34 38
|
||||
523001 84 58 33 39
|
||||
524001 84 58 32 39
|
||||
525001 84 59 31 39
|
||||
526001 84 60 31 39
|
||||
527001 84 59 30 39
|
||||
528001 84 59 30 39
|
||||
529001 84 60 31 38
|
||||
530001 84 60 31 38
|
||||
531001 82 61 30 39
|
||||
532001 81 62 33 37
|
||||
533001 83 60 33 37
|
||||
534001 84 59 32 37
|
||||
535001 85 59 32 38
|
||||
536001 85 58 32 37
|
||||
537001 82 58 32 38
|
||||
538001 83 57 32 38
|
||||
539001 82 57 31 38
|
||||
540001 82 56 32 38
|
||||
541001 81 58 34 36
|
||||
542001 80 58 34 36
|
||||
543001 80 57 35 35
|
||||
544001 82 55 35 36
|
||||
545001 83 54 34 37
|
||||
546001 83 55 34 37
|
||||
547001 83 55 34 37
|
||||
548001 83 56 34 38
|
||||
549001 83 56 35 36
|
||||
550001 83 56 36 36
|
||||
551001 83 56 36 36
|
||||
552001 83 56 37 36
|
||||
553001 85 54 37 36
|
||||
554001 87 52 37 36
|
||||
555001 87 52 37 37
|
||||
556001 88 51 37 37
|
||||
557001 88 51 36 37
|
||||
558001 87 51 35 37
|
||||
559001 87 51 36 36
|
||||
560001 87 52 36 37
|
||||
561001 87 52 35 36
|
||||
562001 86 53 37 33
|
||||
563001 86 53 36 33
|
||||
564001 85 53 36 33
|
||||
565001 84 53 35 33
|
||||
566001 85 52 35 34
|
||||
567001 85 52 35 35
|
||||
568001 86 51 35 36
|
||||
569001 87 51 34 37
|
||||
570001 89 50 34 37
|
||||
571001 88 50 33 37
|
||||
572001 89 49 33 37
|
||||
573001 88 49 33 39
|
||||
574001 86 48 34 38
|
||||
575001 85 49 34 39
|
||||
576001 84 49 35 38
|
||||
577001 83 51 36 37
|
||||
578001 84 50 37 36
|
||||
579001 85 50 37 36
|
||||
580001 85 51 37 36
|
||||
581001 86 50 36 36
|
||||
582001 87 50 36 37
|
||||
583001 87 50 36 37
|
||||
584001 88 50 33 38
|
||||
585001 88 50 34 37
|
||||
586001 89 49 32 37
|
||||
587001 89 48 31 38
|
||||
588001 90 50 31 39
|
||||
589001 90 49 30 39
|
||||
590001 89 50 30 40
|
||||
591001 90 50 31 39
|
||||
592001 90 51 30 39
|
||||
593001 91 51 30 39
|
||||
594001 90 51 30 39
|
||||
595001 90 51 30 39
|
||||
596001 91 51 29 39
|
||||
597001 91 51 29 39
|
||||
598001 91 52 29 39
|
||||
599001 89 52 29 40
|
||||
600001 88 51 30 40
|
||||
601001 88 50 30 42
|
||||
602001 87 51 30 42
|
||||
603001 86 51 30 42
|
||||
604001 84 52 30 42
|
||||
605001 83 53 31 41
|
||||
606001 83 53 31 41
|
||||
607001 82 53 32 40
|
||||
608001 82 53 32 40
|
||||
609001 82 52 31 40
|
||||
610001 82 52 32 39
|
||||
611001 80 53 32 40
|
||||
612001 79 53 33 39
|
||||
613001 78 53 33 39
|
||||
614001 76 54 33 39
|
||||
615001 74 55 33 39
|
||||
616001 71 56 34 38
|
||||
617001 68 56 35 37
|
||||
618001 66 58 35 38
|
||||
619001 64 57 36 37
|
||||
620001 63 58 36 37
|
||||
621001 61 59 36 37
|
||||
622001 59 60 37 36
|
||||
623001 59 60 37 36
|
||||
624001 59 62 37 36
|
||||
625001 58 63 37 36
|
||||
626001 58 65 37 36
|
||||
627001 59 67 36 36
|
||||
628001 58 67 36 36
|
||||
629001 57 68 37 36
|
||||
630001 55 68 37 36
|
||||
631001 55 68 38 35
|
||||
632001 56 68 38 35
|
||||
633001 57 68 38 35
|
||||
634001 57 68 38 35
|
||||
635001 58 69 38 35
|
||||
636001 58 69 38 35
|
||||
637001 58 69 39 34
|
||||
638001 59 69 39 34
|
||||
639001 59 69 39 34
|
||||
640001 60 69 39 34
|
||||
641001 59 71 39 34
|
||||
642001 59 71 38 34
|
||||
643001 60 71 38 34
|
||||
644001 60 72 38 33
|
||||
645001 61 71 38 32
|
||||
646001 61 71 37 31
|
||||
647001 60 72 37 31
|
||||
648001 59 72 37 31
|
||||
649001 59 72 38 31
|
||||
650001 58 73 37 31
|
||||
651001 58 74 38 30
|
||||
652001 57 75 38 30
|
||||
653001 57 75 38 30
|
||||
654001 57 74 37 29
|
||||
655001 58 73 36 30
|
||||
656001 58 73 35 31
|
||||
657001 56 73 35 31
|
||||
658001 55 73 36 32
|
||||
659001 55 72 37 31
|
||||
660001 55 72 37 31
|
||||
661001 55 73 37 32
|
||||
662001 56 72 38 31
|
||||
663001 56 73 37 31
|
||||
664001 56 75 36 31
|
||||
665001 56 76 36 31
|
||||
666001 55 76 36 30
|
||||
667001 53 76 36 30
|
||||
668001 52 76 36 30
|
||||
669001 52 76 37 31
|
||||
670001 51 77 37 32
|
||||
671001 51 77 37 32
|
||||
672001 51 78 36 31
|
||||
673001 51 78 36 31
|
||||
674001 52 78 37 30
|
||||
675001 52 78 35 30
|
||||
676001 53 78 33 30
|
||||
677001 53 77 33 31
|
||||
678001 53 77 33 32
|
||||
679001 53 78 34 32
|
||||
680001 52 79 34 31
|
||||
681001 52 79 35 30
|
||||
682001 51 79 36 30
|
||||
683001 51 78 37 30
|
||||
684001 50 77 37 31
|
||||
685001 50 77 37 32
|
||||
686001 49 77 38 32
|
||||
687001 49 78 39 32
|
||||
688001 48 79 38 32
|
||||
689001 49 78 39 32
|
||||
690001 49 79 38 33
|
||||
691001 52 76 37 34
|
||||
692001 50 76 36 35
|
||||
693001 50 75 36 35
|
||||
694001 51 74 36 36
|
||||
695001 50 74 36 38
|
||||
696001 50 73 37 38
|
||||
697001 50 73 37 39
|
||||
698001 50 72 38 39
|
||||
699001 49 72 37 40
|
||||
700001 49 72 38 40
|
||||
701001 47 72 39 40
|
||||
702001 49 69 39 41
|
||||
703001 49 69 40 41
|
||||
704001 51 68 40 42
|
||||
705001 51 69 39 42
|
||||
706001 51 71 39 42
|
||||
707001 51 71 39 42
|
||||
708001 51 72 39 42
|
||||
709001 51 74 39 42
|
||||
710001 51 75 39 42
|
||||
711001 51 75 39 42
|
||||
712001 52 75 39 42
|
||||
713001 52 75 40 41
|
||||
714001 51 76 40 40
|
||||
715001 50 76 42 38
|
||||
716001 51 76 42 38
|
||||
717001 51 75 42 38
|
||||
718001 52 75 42 40
|
||||
719001 53 74 41 40
|
||||
720001 53 74 41 40
|
||||
721001 52 74 40 40
|
||||
722001 52 73 40 40
|
||||
723001 52 74 40 40
|
||||
724001 52 74 39 40
|
||||
725001 53 74 40 39
|
||||
726001 52 74 39 39
|
||||
727001 53 73 39 39
|
||||
728001 54 73 39 39
|
||||
729001 55 73 39 39
|
||||
730001 56 73 38 39
|
||||
731001 56 74 37 39
|
||||
732001 58 72 38 38
|
||||
733001 57 72 37 38
|
||||
734001 58 73 37 38
|
||||
735001 59 74 37 38
|
||||
736001 59 73 36 38
|
||||
737001 61 71 36 38
|
||||
738001 62 70 36 38
|
||||
739001 63 69 36 38
|
||||
740001 65 68 36 38
|
||||
741001 67 65 36 38
|
||||
742001 67 66 36 38
|
||||
743001 68 66 36 37
|
||||
744001 68 67 36 37
|
||||
745001 68 66 35 37
|
||||
746001 68 65 35 37
|
||||
747001 68 66 35 38
|
||||
748001 69 66 35 38
|
||||
749001 69 66 35 38
|
||||
750001 69 67 34 38
|
||||
751001 69 66 34 38
|
||||
752001 69 66 34 38
|
||||
753001 69 68 34 38
|
||||
754001 69 68 34 38
|
||||
755001 71 67 34 39
|
||||
756001 71 67 34 40
|
||||
757001 71 66 33 41
|
||||
758001 72 65 33 41
|
||||
759001 71 65 32 42
|
||||
760001 71 64 31 42
|
||||
761001 72 63 31 42
|
||||
762001 72 64 31 43
|
||||
763001 72 64 31 42
|
||||
764001 73 63 31 42
|
||||
765001 74 62 30 42
|
||||
766001 75 62 30 42
|
||||
767001 75 62 30 42
|
||||
768001 74 62 29 43
|
||||
769001 73 62 30 42
|
||||
770001 73 62 31 41
|
||||
771001 73 62 31 42
|
||||
772001 73 62 32 40
|
||||
773001 72 62 31 41
|
||||
774001 72 62 31 41
|
||||
775001 73 62 32 41
|
||||
776001 72 62 31 41
|
||||
777001 73 62 31 40
|
||||
778001 75 60 31 40
|
||||
779001 76 59 30 40
|
||||
780001 76 60 30 40
|
||||
781001 76 60 30 40
|
||||
782001 76 60 30 40
|
||||
783001 76 60 31 38
|
||||
784001 77 59 32 38
|
||||
785001 77 59 32 38
|
||||
786001 78 59 31 39
|
||||
787001 79 59 31 39
|
||||
788001 78 60 30 39
|
||||
789001 77 60 30 39
|
||||
790001 78 59 30 39
|
||||
791001 77 59 31 38
|
||||
792001 77 61 32 38
|
||||
793001 78 62 32 38
|
||||
794001 79 61 31 38
|
||||
795001 79 63 31 37
|
||||
796001 79 63 30 37
|
||||
797001 78 64 30 36
|
||||
798001 77 64 31 35
|
||||
799001 77 64 32 35
|
||||
800001 77 64 32 34
|
||||
801001 79 63 32 34
|
||||
802001 79 63 32 34
|
||||
803001 78 63 32 33
|
||||
804001 78 62 33 33
|
||||
805001 76 62 34 33
|
||||
806001 76 63 35 33
|
||||
807001 75 64 36 32
|
||||
808001 74 66 37 31
|
||||
809001 74 67 38 30
|
||||
810001 73 69 38 29
|
||||
811001 73 69 39 28
|
||||
812001 72 69 39 27
|
||||
813001 72 70 40 28
|
||||
814001 72 70 40 27
|
||||
815001 71 70 40 27
|
||||
816001 69 70 41 27
|
||||
817001 68 70 41 27
|
||||
818001 68 69 42 27
|
||||
819001 70 66 42 28
|
||||
820001 71 65 42 29
|
||||
821001 71 64 42 29
|
||||
822001 72 63 42 30
|
||||
823001 74 62 42 31
|
||||
824001 75 61 42 31
|
||||
825001 75 60 42 32
|
||||
826001 75 59 42 33
|
||||
827001 75 60 41 34
|
||||
828001 76 60 39 34
|
||||
829001 75 60 38 35
|
||||
830001 76 59 38 35
|
||||
831001 75 59 39 35
|
||||
832001 75 58 40 34
|
||||
833001 74 58 40 35
|
||||
834001 74 58 40 36
|
||||
835001 73 58 40 36
|
||||
836001 73 58 40 37
|
||||
837001 74 58 40 38
|
||||
838001 74 59 39 38
|
||||
839001 74 58 39 39
|
||||
840001 74 57 39 41
|
||||
841001 73 57 39 41
|
||||
842001 73 56 39 41
|
||||
843001 73 56 39 42
|
||||
844001 73 55 39 45
|
||||
845001 73 56 38 45
|
||||
846001 72 56 38 45
|
||||
847001 72 57 38 46
|
||||
848001 72 55 38 47
|
||||
849001 74 53 38 48
|
||||
850001 73 53 38 49
|
||||
851001 72 52 38 50
|
||||
852001 70 52 38 50
|
||||
853001 68 51 38 51
|
||||
854001 68 50 38 53
|
||||
855001 66 50 38 54
|
||||
856001 67 49 38 55
|
||||
857001 66 49 37 56
|
||||
858001 67 48 37 57
|
||||
859001 66 48 37 58
|
||||
860001 65 48 37 59
|
||||
861001 66 48 38 58
|
||||
862001 65 47 38 58
|
||||
863001 66 48 38 58
|
||||
864001 66 47 38 58
|
||||
865001 66 48 38 58
|
||||
866001 66 46 38 58
|
||||
867001 68 45 38 58
|
||||
868001 67 45 38 58
|
||||
869001 67 45 39 57
|
||||
870001 67 46 40 56
|
||||
871001 66 47 41 55
|
||||
872001 65 49 41 55
|
||||
873001 65 50 42 54
|
||||
874001 64 51 42 54
|
||||
875001 63 51 42 54
|
||||
876001 64 50 42 54
|
||||
877001 64 50 42 55
|
||||
878001 63 51 42 55
|
||||
879001 62 52 42 55
|
||||
880001 62 51 42 55
|
||||
881001 62 51 42 56
|
||||
882001 62 51 42 55
|
||||
883001 62 51 42 56
|
||||
884001 62 51 41 57
|
||||
885001 62 51 41 57
|
||||
886001 62 51 40 57
|
||||
887001 62 51 41 58
|
||||
888001 62 51 41 59
|
||||
889001 62 50 41 58
|
||||
890001 62 50 41 59
|
||||
891001 62 49 40 61
|
||||
892001 60 49 40 62
|
||||
893001 59 49 40 62
|
||||
894001 60 48 40 63
|
||||
895001 60 48 40 64
|
||||
896001 60 49 39 65
|
||||
897001 60 49 38 65
|
||||
898001 59 50 38 64
|
||||
899001 58 50 38 65
|
||||
900001 59 49 39 65
|
||||
901001 59 48 39 66
|
||||
902001 60 47 39 66
|
||||
903001 60 47 39 68
|
||||
904001 59 47 39 69
|
||||
905001 59 47 39 68
|
||||
906001 62 45 39 68
|
||||
907001 62 44 38 68
|
||||
908001 62 43 38 69
|
||||
909001 63 42 37 71
|
||||
910001 63 42 37 73
|
||||
52
src/kimono/lxpack/tests/test.csh
Executable file
52
src/kimono/lxpack/tests/test.csh
Executable file
@ -0,0 +1,52 @@
|
||||
#!/bin/csh -f
|
||||
|
||||
set path = (. ../src $path); rehash
|
||||
|
||||
set out = "tst"
|
||||
#set out = "ref" # for recording
|
||||
|
||||
echo borbu1.0.$out
|
||||
kimono borbu1.fst | awk '{print $1, $2, $3, $4, $5}' > borbu1.0.$out
|
||||
diff borbu1.0.$out ref/borbu1.0.ref
|
||||
if (($out != "ref") && ($status != 0)) exit $status
|
||||
|
||||
echo borbu1.1.$out
|
||||
kimono -i borbu1.lst -p 1 borbu1.fst | awk '{print $1, $2, $3, $4, $5}' > borbu1.1.$out
|
||||
diff borbu1.1.$out ref/borbu1.1.ref
|
||||
if (($out != "ref") && ($status != 0)) exit $status
|
||||
|
||||
echo borbu1.2.$out
|
||||
kimono -i borbu1.lst -p 2 borbu1.fst | awk '{print $1, $2, $3, $4, $5}' > borbu1.2.$out
|
||||
diff borbu1.2.$out ref/borbu1.2.ref
|
||||
if (($out != "ref") && ($status != 0)) exit $status
|
||||
|
||||
echo borbu1.3.$out
|
||||
kimono -i borbu1.lst -p 123 borbu1.fst | awk '{print $1, $2, $3, $4, $5}' > borbu1.3.$out
|
||||
diff borbu1.3.$out ref/borbu1.3.ref
|
||||
if (($out != "ref") && ($status != 0)) exit $status
|
||||
|
||||
echo borbu1.4.$out
|
||||
kimono -x borbu1.lst borbu1.fst | awk '{print $1, $2, $3, $4, $5}' > borbu1.4.$out
|
||||
diff borbu1.4.$out ref/borbu1.4.ref
|
||||
if (($out != "ref") && ($status != 0)) exit $status
|
||||
|
||||
echo borbu1.5.$out
|
||||
kimono -a gc -c cumul borbu1.fst | awk '{print $1, $2, $3, $4, $5}' > borbu1.5.$out
|
||||
diff borbu1.5.$out ref/borbu1.5.ref
|
||||
if (($out != "ref") && ($status != 0)) exit $status
|
||||
|
||||
echo borbu1.6.$out
|
||||
kimono -c codon -e 0 -i borbu1.lst borbu1.fst | awk '{print $1, $2, $3, $4, $5}' > borbu1.6.$out
|
||||
diff borbu1.6.$out ref/borbu1.6.ref
|
||||
if (($out != "ref") && ($status != 0)) exit $status
|
||||
|
||||
echo borbu1.7.$out
|
||||
kimono -c genes -i borbu1.lst borbu1.fst | awk '{print $1, $2, $3, $4, $5}' > borbu1.7.$out
|
||||
diff borbu1.7.$out ref/borbu1.7.ref
|
||||
if (($out != "ref") && ($status != 0)) exit $status
|
||||
|
||||
echo "+ all test ok"
|
||||
|
||||
if ($out != "ref") \rm -f *.$out
|
||||
|
||||
exit 0
|
||||
BIN
src/ncbiblast/.DS_Store
vendored
Normal file
BIN
src/ncbiblast/.DS_Store
vendored
Normal file
Binary file not shown.
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user