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cds/tools/chlorodb added

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Former-commit-id: 0579e878a69b7c285ca71870e9ca5730649a2fda
Former-commit-id: 7cced5b488441d87bf070a9a444317db0e048880
This commit is contained in:
alain viari
2015-11-13 17:41:18 +01:00
parent 0d5f0c1f20
commit e4d6a8484d
585 changed files with 4750 additions and 50 deletions
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27
detectors/cds/bin/go_pass1.sh → detectors/cds/bin/do_exonerate.sh
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@ -1,21 +1,21 @@
#!/bin/csh -f
#
# Annotate CDS - Pass1
# Annotate CDS - Exonerate
#
#========================================================================================
#
# Annotate CDS of chlorodb/core proteins using exonerate
# Annotate CDS using exonerate
#
# pass1.sh <FASTAFILE> <FAMILY> [<OUTDIR>]
# do_exonerate.sh <FASTAGENOM> <FASTAPROT> [<OUTDIR>]
#
# - <FASTAFILE> : The fasta file containing the genome to annotate
# - <FAMILY> : Name of the protein family (defined in chlorodb/core)
# - <FASTAGENOM> : The fasta file containing the genome to annotate
# - <FASTAPROT> : The fasta file containing the protein family
#
# Results are in file : `basename <FASTAFILE>:r`.<FAMILY>.res
# Results are in file : `basename <FASTAGENOM>:r`.`basename <FASTAPROT>:r`.res
#
#========================================================================================
#
# usage: go_pass1.sh fasta family [outdir]
# usage: do_exonerate.sh dna.fasta prot.fasta [outdir]
#
unsetenv ORG_SOURCED
@ -31,12 +31,14 @@ NeedArg 2
set GenoFile = $Argv[1]
set GenoName = `basename $GenoFile:r`
set ProtName = $Argv[2]
set ProtDir = $CDS_DATA_DIR/chlorodb/core
set ProtFile = $ProtDir/$ProtName.fst
set ProtFile = $Argv[2]
set ProtDir = `dirname $ProtFile`
set ProtName = `basename $ProtFile:r`
NeedFile $GenoFile
NeedFile $ProtFile
NeedFile $ProtDir/Annot.lst
set OutDir = .
if ($#Argv >= 3) set OutDir = $3
@ -101,7 +103,7 @@ endif
if ($PASS1_SPEEDUP != 0) then
$PROG_DIR/go_filterbx.sh $GenoFile $ProtFile \
$PROG_DIR/do_filterbx.sh $GenoFile $ProtFile \
$PASS1_BLASTX_FILTER_IDMIN \
$PASS1_BLASTX_FILTER_NBMIN \
$PASS1_BLASTX_FILTER_NBMAX > D_$$
@ -159,8 +161,7 @@ $AwkCmd -v MAX_SPAN=$PASS1_MAX_SPAN \
# get annotations
#
egrep "^$ProtName " $CDS_DATA_DIR/chlorodb/core/Annot.lst |\
awk '{print "c annot", $0}' > T_$$
egrep "^$ProtName " $ProtDir/Annot.lst | awk '{print "c annot", $0}' > T_$$
#
# extend start/stop

2
detectors/cds/bin/go_filterbx.sh → detectors/cds/bin/do_filterbx.sh
View File

@ -5,7 +5,7 @@
#
# output on stdout
#
# usage: go_filterbx.sh dna_fasta prot_fasta [idmin nbmin nbmax]
# usage: do_filterbx.sh dna.fasta prot.fasta [idmin nbmin nbmax]
#
unsetenv ORG_SOURCED

20
detectors/cds/bin/go_cds.sh
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@ -13,7 +13,7 @@
# Results are printed to the standard output
#
#========================================================================================
# usage: go_cds.sh fasta
# usage: go_cds.sh fasta [db_core]
#
unsetenv ORG_SOURCED
@ -22,13 +22,19 @@ source $ORG_HOME/scripts/csh_init.sh
NeedArg 1
set Fasta = $Argv[1]
set Fasta = $Argv[1]; Shift
NeedFile $Fasta
set Genome = `basename $Fasta:r`
NeedFile $CDS_DATA_DIR/chlorodb/core
set DbCore = $CDS_DATA_DIR/chlorodb/core
if ($#Argv > 0) then
set DbCore = $Argv[1]; Shift
endif
NeedFile $DbCore/Annot.lst
#
# run everything into temporary place
@ -44,15 +50,15 @@ endif
# pass1: run exonerate
#
set fams = `ls $CDS_DATA_DIR/chlorodb/core/*.fst`
set fams = `ls $DbCore/*.fst`
Notify "running pass1: exonerate of $Genome"
Notify "running pass1: exonerate of $Genome on $DbCore"
foreach f ($fams)
set prot = `basename $f:r`
$PROG_DIR/go_pass1.sh $Fasta $prot $temp
$PROG_DIR/do_exonerate.sh $Fasta $f $temp
end
#
# pass2: transsplicing
#

8
detectors/cds/test/go_test.sh
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@ -1,5 +1,7 @@
#!/bin/csh -f
setenv Verbose 1
setenv ORG_HOME `dirname $0`/../../..
source $ORG_HOME/scripts/csh_init.sh
@ -8,9 +10,9 @@ echo "+ testing CDS"
setenv TMP_CLEANUP 0
setenv PASS1_SPEEDUP 1
setenv PASS1_SLOWDOWN 0
setenv PASS1_BLASTX_FILTER_NBMAX 10
setenv PASS1_BLASTX_FILTER_NBMAX 5
`dirname $0`/../bin/go_cds.sh test.fst > test.bak
`dirname $0`/../bin/go_cds.sh test.fst test.db > test.bak
diff -q test.bak test.ref >& /dev/null
@ -18,7 +20,7 @@ set stat = $status
if ($stat == 0) then
echo "+ $VTC[3]CDS test Ok$VTC[1]"
\rm -r test.bak test.tmp
\rm -r test.bak test.tmp test.db/*.fst.p??
else
echo "* $VTC[2]CDS test Failure$VTC[1]"
endif

18
detectors/cds/test/test.db/Annot.lst Normal file
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@ -0,0 +1,18 @@
atpf atpF 483 1:80_2:401_3:1_4:1 POLYEX ATP_synthase_CF0_B_subunit
ccsa ccsA 477 1:476_2:1 POLYEX cytochrome_c_biogenesis_protein
ndha ndhA 384 1:9_2:375 POLYEX NADH_dehydrogenase_subunit_1
ndhb ndhB 699 1:5_2:693_3:1 POLYEX NADH_dehydrogenase_subunit_2
ndhd ndhD 383 1:383 MONEX NADH_dehydrogenase_subunit_4
ndhe ndhE 395 1:395 MONEX NADH_dehydrogenase_subunit_4L
ndhf ndhF 384 1:384 MONEX NADH_dehydrogenase_subunit_5
ndhg ndhG 386 1:386 MONEX NADH_dehydrogenase_subunit_6
ndhh ndhH 406 1:400_2:6 POLYEX NADH_dehydrogenase_subunit_7
ndhi ndhI 386 1:386 MONEX NADH_dehydrogenase_subunit_I
psac psaC 498 1:491_2:4_3:3 POLYEX photosystem_I_subunit_VII
rpl2 rpl2 800 1:101_2:698_5:1 POLYEX ribosomal_protein_L2
rpl23 rpl23 787 1:782_2:2_3:1_4:2 POLYEX ribosomal_protein_L23
rpl32 rpl32 474 1:474 MONEX ribosomal_protein_L32
rps15 rps15 480 1:479_2:1 POLYEX ribosomal_protein_S15
rps7 rps7 853 1:853 MONEX ribosomal_protein_S7
ycf1 ycf1 408 1:406_2:2 POLYEX hypothetical_chloroplast_RF1
ycf2 ycf2 654 1:649_2:5 POLYEX Ycf2

50
detectors/cds/test/test.db/atpf.fst Normal file
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@ -0,0 +1,50 @@
>AC_000188@LyesCp071@atpf@11803@13043@R@2@185 ATP_synthase_CF0_B_chain
MKNVTDSFVSLGHWPSAGSFGFNTDILATNPINLSVVLGVLIFFGKGVLS
DLLDNRKQRILNTIRNSEELRGGAIEQLEKARSRLRKVETEAEQFRVNGY
SEIEREKLNLINSTYKTLEQLENYKNETIQFEQQRAINQVRQRVFQQALR
GALGTLNSCLNNELHLRTISANIGMLGTMKEITD
>NC_000925@PopuCp059@atpf@45392@45943@R@1@184 ATP_synthase_CF0_B_subunit
MNSIVNITPIIIILSEHSSEHTFGFNSDIFEANVINILLLLFGLIYVLKQ
SLGSTLNERQLKVLAAIQESEERLEQASSRLSESEKQLAQTQIIINQIKK
EAQLTAEKVRSSILAQGQIDIERLAITGKSNIETAEKQIRRQIQQQIAFL
ALKKVTLQLENQMSSDIQLRIIDNNIAKLGDQL
>NC_000926@GuthCp075@atpf@65505@66053@R@1@183 ATP_synthase_CF0_B_subunit
MDIISGFYNTINLAELSNAKTFGFNPNILEANVLNIAILLSGVIYLGRNF
LTSALESRQQKVTEAIQEAEERLQQANVKLLDAEKQLTQAQTVIEQIKKE
AEKTARTVKETILAQGKLDIERLTNNGKSSIEKAELQIKKQIQQHITDLA
IKKVSAQMETFMTDNLQVKVIDTNIASLGGKI
>NC_000927@NeolCp025@atpf@19121@19651@R@1@177 ATP_synthase_CF0_B_chain
MFHFLALTPLAHSEGFGLNTNILETNILNLAAVFALLAYVGTDFVSSLLK
TRKESILKSLRDADERYQDAVNQLKQALQELETARTNAAEIRRQSEINAE
AIRQRLELLTQEEMARLEEAKETIIKLEEEKAVAEVCTKVISMALVRAEK
KIISSMDEAMHRRVMDMYLNLLREVY
>NC_000932@ArthCp008@atpf@11529@12798@R@2@185 ATP_synthase_CF0_B_subunit
MKNLTDSFVYLGHWPSAGSFGFNTDILATNPINLSVVFGVLIFFGKGVLN
DLLDNRKQRILNTIRNSEELREGAIQQLENARARLRNVETEADKFRVNGY
SEIEREKLNLINSTYKTLKQLENYKNETILFEQQRTINQVRERVFQQALQ
GAIGTLNSCLSNELHLRTINANIGMFGTMKEITD
>NC_001319@MapoCp012@atpf@18468@19609@D@2@185 ATP_synthase_CF0_B_subunit
MENGTYFIISSNFWTIAGSFGLNTNLLETNLINLGVVLGLLVYFGKGVLS
NLLNNRKLTILNTIQDAEERYKEATDKLNQARTRLQQAKQKADDIRINGL
SQMEKEKQDLINAADEDSKRLEDSKNATIRFEKQRAIEQVRQQVSRLALE
RALETLKSRLNSELHLRMIDYHIGLLRAMESTIE
>NC_001320@OrsajCp021@atpf@32741@34111@D@2@181 ATP_synthase_CF0_B_subunit
MKNVTHSFVFLAHWPSAGSFGLNTDILATNLINLTVVVGVLIYFGKGVLK
DLLDNRKQRILSTIRNSEELRRGTIEQLEKARIRLQKVELEADEYRMNGY
SEIEREKANLINATSISLEQLEKSKNETLYFEKQRAMNQVRQRVFQQAVQ
GALGTLNSCLNTELHFRTIRANISILGAME
>NC_001603@EugrCp038@atpf@64813@66970@D@4@184 ATP_synthase_CF0_B_chain
MVIDNFNIFTIISNAKTFGINTNVFETNIINLAIVVGTLFYYGKLTLSDL
LKTRKKTIIKNILDIDEKIRSSQSSLYLAELEFENAAKKASLIRSNGTTF
CLKSFDIIRSSVNEDIKRLKQSKRLILRTEDKKSVREIFKNLYSQACQKA
KATIIKRLNSKIHKKIILKKMEKMSLKKLKPKY
>NC_001631@PithCp015@atpf@11663@12972@R@2@185 ATP_synthase_CF0_B_subunit
MKNVIDPFISLSYWPSAGGFGSNTNILETNIINSSVVLSVLIYFGKGVLS
NLLDNRKQKILETIRNSEELCKGAIDQLEKARACLRNVEMIADEIQVNGN
SQIEREKEDLLNTASDNLEQLEDPKNETIYSEQQRAFDQIRQQVSRQALR
RAIGTLNSRLNTELHLRTIDHNIGLLRTMMNTND
>NC_001666@ZemaCp019@atpf@35097@36479@D@2@184 ATP_synthase_CF0_B_subunit
MKNVTHSFVFLAHWPFAGSFGLNTDILATNLINLTVVVGVLIFFGKGVLK
DLLDNRKQRILSTIRNSEELRKGTLEQLEKARIRLQKVELEADEYRMNGY
SEIEREKENLINATSISLEQLEKSKNETLYFEKQRAMNQVRQQGFQQAVQ
GALGTLNSCLNTELHFRTIRANIGILGAIEWKR

78
detectors/cds/test/test.db/ccsa.fst Normal file
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@ -0,0 +1,78 @@
>AC_000188@LyesCp084@ccsa@115765@116706@D@1@314 cytochrome_c_biogenesis_protein
MIFSTLEHILTHISFSIVSIVITIHLITFLVDEIVKLYDSSEKGIIVTFF
CITGLLVTRWVSSGHFPLSDLYESLIFLSWSFSLIHIIPYFKKNVLILSK
ITGPSAILTQGFATSGILTEIHQSGILVPALQSEWLIMHVSMMILGYAAL
LCGSLLSVALLVITFRKNRKLFSKSNVFLNESFFLGENVVENTSFFCTKN
YYRSQLIQQLDYWSYRVISLGFTFLTIGILSGAVWANEAWGSYWNWDPKE
TWAFITWIVFAIYLHTRTNRNLRGPNSAIVASIGFLIIWICYFGVNLLGI
GLHSYGSFPSTFN
>NC_000925@PopuCp184@ccsa@160407@161366@D@1@320 cytochrome_c_biogenesis_protein
MNLEMMQNSCVNFAFGGLLTAMLVYWSSLAFPRISGLNKLAALITLLVNI
ALALTLSSRWFANGYFPLSNLYESLLFLAWGLTFVHLFIESKTKSRLIGA
VSIPVAMFVTAFASLALPIEMQKASPLVPALKSNWLMMHVSIMMISYSIL
ILGSLLSILFLIITRGQDINLKGSSVGTGSYTVKSLDSNPSFAFSNPSGI
VQEQSNMLINSTRMNLLESIDNLSYRIIGLGFPLLTIGIVAGAVWANEAW
GSYWSWDPKETWALITWLIFAAYLHCRITKSWQGKRPAILASVGFLVVWI
CYLGVNFLGKGLHSYGWLA
>NC_000926@GuthCp037@ccsa@33657@34562@R@1@302 cytochrome_c_biogenesis_protein
MFNVQFDIFNFSNNITFLTLLISLISYWLGLIFKKIKNVFYIGYGSTILA
CITITIILGTRWIESGYFPLSNLYESLMFLTWGLLFSAIYLEYKTNLYLI
GAIVSPISLFIVSFSTLSLPQDMQKAAPLVPALKSNWLMMHVSVMMLSYS
TLIIGSLLAILYLVLIKAQQKKHSLKDFAFANLEFTFPKSTNSTNFNLLE
TLDNLSYRTIGFGFPLLTIGIIAGAVWANEAWGTYWSWDPKETWALITWL
VFAAYLHARITKSWTGERPAYLAALGFVVVWICYLGVNFLGKGLHSYGWL
N
>NC_000927@NeolCp108@ccsa@128438@129259@D@1@274 cytochrome_c_biogenesis_protein
MSTFSILSLVAFATLFVTMLLYFFQRQPLARQSMWIAHTSLAGLLLLRWV
QSGHFPLSNLYESCLFLSWAVTLGHFVVEKDASRAGFLDLGIFTAPMAFF
VYAFATFSLPPTMQEAGPLVPALRSHWLMMHVTLMILSYAALLFGSVLSL
AFLVITTGPRKNSEKLQSLASTFDTLSYRTLGIGFPLLTVGILSGAVWAN
EAWGSYWSWDPKETWALITWLIFAIYLHSRLTYGWNGQKAALIASVGFFL
IWICYLGVNLLGKGLHSYGWLTS
>NC_000927@NeolCp129@ccsa@163667@164488@R@1@274 cytochrome_c_biogenesis_protein
MSTFSILSLVAFATLFVTMLLYFFQRQPLARQSMWIAHTSLAGLLLLRWV
QSGHFPLSNLYESCLFLSWAVTLGHFVVEKDASRAGFLDLGIFTAPMAFF
VYAFATFSLPPTMQEAGPLVPALRSHWLMMHVTLMILSYAALLFGSVLSL
AFLVITTGPRKNSEKLQSLASTFDTLSYRTLGIGFPLLTVGILSGAVWAN
EAWGSYWSWDPKETWALITWLIFAIYLHSRLTYGWNGQKAALIASVGFFL
IWICYLGVNLLGKGLHSYGWLTS
>NC_000932@ArthCp073@ccsa@114461@115447@D@1@329 cytochrome_c_biogenesis_protein
MIFSILEHILTHISFSVVSIVLTIYFLTLLVNLDEIIGFFDSSDKGIIIT
FFGITGLLLTRWIYSGHFPLSNLYESLIFLSWAFSIIHMVSYFNKKQQNK
LNTITAPSVIFIQGFATSGLLNKMPQSAILVPALQSQWLMMHVSMMILGY
GALLCGSLLSIALLVITFRKVGPTFWKKNIKKNFLLNELFSFDVLYYINE
RNSILLQQNINFSFSRNYYRYQLIQQLDFWSFRIISLGFIFLTVGILSGA
VWANETWGSYWNWDPKETWAFITWTIFAIYLHIKTNRNVRGINSAIVALI
GFILIWICYFGVNLLGIGLHSYGSFTSN
>NC_001319@MapoCp078@ccsa@95482@96444@D@1@321 cytochrome_c_biogenesis_protein
MPFITLERILAHTSFFLLFFVTFIYWGKFLYINIKPITILGEISMKIACF
FITTFLLIRWSSSGHFPLSNLYESSMFLSWSFTLIHLILENKSKNTWLGI
ITAPSAMLTHGFATLSLPKEMQESVFLVPALQSHWLMMHVTMMMLSYSTL
LCGSLLAITILIITLTKQKNLPILTSYFNFPFNSFIFKNLLQPMENEILS
YKTQKVFSFINFRKWQLIKELDNWSYRVISLGFPLLTIGILSGAVWANEA
WGSYWNWDPKETWALITWLIFAIYLHTRMIKGWQGKKPAIIASLGFFIVW
ICYLGVNLLGKGLHSYGWLI
>NC_001320@OrsajCp087@ccsa@105236@106201@D@1@322 cytochrome_c_biogenesis_protein
MLFATLEHILTHISFSTISIVITIHLITLLVRELGGLRDSSEKGMIATFF
CITGFLVSRWASSGHFPLSNLYESLIFLSWALYILHMIPKIQNSKNDLST
ITTPSTILTQGFATSGLLTEMHQSTILVPALQSQWLMMHVSMMLLSYATL
LCGSLLSAALLMIRFRKNLDFFSKKKKNVLSKTFFFNEIEYFYAKRSALK
STFFPLFPNYYKYQLIERLDSWSYRVISLGFTLLTIGILCGAVWANEAWG
SYWNWDPKETWAFITWTIFAIYLHSRTNPNWKGTKSAFVASIGFLIIWIC
YFGINLLGIGLHSYGSFTLPI
>NC_001631@PithCp147@ccsa@104925@105887@R@1@321 cytochrome_c_biogenesis_protein
MIFITLEHILAHISFSLILVVTLIYWGTLVYRIEGLSSSGGKGMIVTFLC
TTGLLINRWLYSGHLPLSNLYESFMFLSWSSSVFHILLEVRSRDDRWLGA
ITAPSAMLTHGFATLGLPEEMQRSGMLVPALQSHWSMMHVSMILFSYATL
LCGSLASIALLVIMSGVNRQVIFGAMDNLFSRAILPNENFYSHEKQKSDL
QYTVYFSSTNYRKCQLIKQLDHWSYRAIGLGFSLSTIGTLSGAIWANEAW
GSYWSWDPKETWALITWTIFAIYLHTRMNKGWQGEEPAIVASLGFFIVWI
RYLGVNLLGIGLHSYGWLEP
>NC_001666@ZemaCp085@ccsa@108995@109960@D@1@322 cytochrome_c_biogenesis_protein
MLFATLEHILTHISFSTISIVITIHLITLLVRELRGLRDSSEKGMIATFF
SITGFLVSRWVSSGHFPLSNLYESLIFLSWTLYILHTIPKIQNSKNDLST
ITTPSTILTQGFATSGLLTEMHQSTILVPALQSQWLMMHVSMMLLSYATL
LCGSLLSAALLIIRFRKNFDFFSLKKNVFLKTFFFSEIEYLYAKRSALKN
TSFPVFPNYYKYQLTERLDSWSYRVISLGFTLLTVGILCGAVWANEAWGS
YWNWDPKETWAFITWTIFAIYLHSRKNPNWKGTNSALVASIGFLIIWICY
FGINLLGIGLHSYGSFTLPSK

90
detectors/cds/test/test.db/ndha.fst Normal file
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@ -0,0 +1,90 @@
>AC_000188@LyesCp085@ndha@121113@123337@R@2@364 NADH_dehydrogenase_subunit_1
MIIDTTEIETINSFSKLESLKEVYGIIWMLVPIVTLVLGITIGVLVIVWL
EREISAGIQQRIGPEYAGPLGILQALADGTKLLLKENLIPSTGDTRLFSI
GPSIAVISIFLSYSVIPFGDHLVLADLSIGVFFWIAISSIAPVGLLMSGY
GSNNKYSFLGGLRAAAQSISYEIPLALCVLSISLLSNSLSTVDIVEAQSK
YGFWGWNLWRQPIGFIVFLISSLAECERLPFDLPEAEEELVAGYQTEYSG
IKFGLFYIASYLNLLVSSLFVTVLYLGGWNLSIPYIFVPDIFGINKGGKV
FGTLIGIFITLAKTYLFLFIPIATRWTLPRLRMDQLLNLGWKFLLPISLG
NLLLTTSSQLLSL
>NC_000927@NeolCp116@ndha@144380@145468@D@1@363 NADH_dehydrogenase_subunit_1
MTYVLDLKRSFLDACTWLIGDNFRDLGSVLWVPLPILSLVIVATLGVLVI
VWLERKISAGVQQRVGPEYGGALGLLQPLADGLKLVFKEDVVPAKSDTWL
FTLGPAVVVIPIFLAYLVVPFGQQLIIADLRIGIFFWIAISSIAPIGLLM
SGYGSNNKYSFLGGLRAAAQSISYELPLAICVLSVCLLADSLSTVDIVES
QSSWGILTWNIWRQPIGFVAFLIAALAECERLPFDLPEAEEELVAGYQTE
YTGMKFGLFYVGSYVNLLVSGCFVTVLYLGGWHGPFAIDGILPDSPPFQV
LDAFLGITWTLLKTFLFLFAAILTRWTLPRVRIDQLLDLGWKFLLPVSLG
NLLLTASLKLLF
>NC_000932@ArthCp079@ndha@119847@122009@R@2@361 NADH_dehydrogenase_subunit_1
MIIYATAVQTINSFVKLESLKEVYGLIWIFVPIFSLVLGIITGVLVIVWL
EREISAGIQQRIGPEYAGPLGILQALADGTKLLFKENLRPSRGNTPLFSI
GPSIAVISILLSYSVIPFSNHLVLADLNIGIFLWIAISSIAPIGLLMSGY
GSNNKYSFLGGLRAAAQSISYEIPLTLCVLSISLLSNSLSTVDIVEAQSK
YGFWGWNLWRQPIGFIIFLISSLAECERLPFDLPEAEEELIAGYQTEYSG
IKFGLFYVASYLNLLISSLFVTVLYLGGWNISIPYISILELFQRDQIFGT
TIGIFITLAKTYLFLFVSIATRWTLPRLRMDQLLNLGWKFLLPISLGNLL
LTTSFQLFSL
>NC_001319@MapoCp084@ndha@100382@102200@R@2@369 NADH_dehydrogenase_subunit_1
MISNINLEDKFFSFFFTLGFSKEFFNFLWIIFSILILMLGVTIGVLVLVW
LERKISAAIQQRIGPEYAGPLGIIQALADGIKLFLKEDIVPAQGDVWLFN
IGPILVLIPVFLSYLVIPFEYNVILANFSIGVFFWIAVSSVVPLGLLMAG
YGSNNKYSFLGGLRAAAQSISYEIPLALSVLSIALLSNSLSTVDIVEAQS
KYGFLSWNLWRQPIGFIVFFIASLAECERLPFDLPEAEEELVAGYQTEYS
GMKFAFFYLASYLNLLVSSLFVTILYLGGWHFSIPFFSLFKNFEWNLMSN
GISEVISIIIGIVITLVKSYLFLFISIMTRWTLPRIRIDQLLNLGWKFLL
PIALGNLLLTTSFQLFLL
>NC_001320@OrsajCp093@ndha@110631@112706@R@2@363 NADH_dehydrogenase_subunit_1
MIIDRVQVEAINSFSNLELLKEVYGLIWILPILTLLLGITIEVLVIVWLE
REISASIQQRIGPEYAGPLGLLQAIADGTKLLFKEDILPSRGDIPLFSIG
PSIAVISILLSFLVIPLGYRFVLADLSIGVFLWIAISSIAPIGLLMAGYS
SNNKYSFSGGLRAAAQSISYEIPLTFCVLAISLLSNSSSTVDIVEAQSKY
GFFGWNLWRQPIGFLVFLISSLAECERLPFDLPEAEEELVAGYQTEYSGI
KYGLFYLVSYLNLLVSSLFVTVLYLGGWNLSIPYISFFGFFQMNKMVGIL
EMTMSIFITLTKAYLFLFISITIRWTLPRMRMDQLLNLGWKFLLPISLGN
LLLTTSSQLVSL
>NC_001666@ZemaCp091@ndha@114343@116454@R@2@363 NADH_dehydrogenase_subunit_1
MIIDRVEVETINSFSKSELFKEIYGLIWILPIFALLLGITIEVLVIVWLE
REISASIQQRIGPEYAGPLGLLQAIADGTKLLLKEDILPSRGDIPLFSIG
PSIAVISILLSFLVIPLGYRFVLADLSIGVFLWIAISSIAPIGLLMAGYS
SNNKYSFSGGLRAAAQSISYEIPLTFCVLAISLLSNSSSTVDIVEAQSKY
GFFGWNLWRQPIGFLVFLISSLAECERLPFDLPEAEEELVAGYQTEYSGI
KYGLFYLVSYLNLLVSSLFVTVLYLGGWNFSIPYISFFGFFQMNKIIGIL
EMVIGIFITLTKAYLFLFISITIRWTLPRMRMDQLLNLGWKFLLPISLGN
LLLTTSSQLVSL
>NC_001879@NitaCp088@ndha@121696@123935@R@2@364 NADH_dehydrogenase_subunit_1
MIIDTTEIETINSFSKLESLKEVYGIIWMLFPILTLVLGITIGVLVIVWL
EREISAGIQQRIGPEYAGPLGILQALADGTKLLLKENLIPSTGDTRLFSI
GPSIAVISIFLSYSVIPFGDHLVLADLSIGVFFWIAISSIAPVGLLMSGY
GSNNKYSFLGGLRAAAQSISYEIPLALCVLSISLLSNSLSTVDIVEAQSK
YGFWGWNLWRQPIGFIVFLISSLAECERLPFDLPEAEEELVAGYQTEYSG
IKFGLFYIASYLNLLVSSLFVTVLYLGGWNLSIPYIFVPELFGINKRGKV
FGTLIGIFITLAKTYLFLFIPIATRWTLPRLRMDQLLNLGWKFLLPISLG
NLLLTTSSQLLSL
>NC_002186@MeviCp102@ndha@106489@107592@R@1@368 NADH_dehydrogenase_subunit_1
MLLTINLKDSFLTFFSNLGFSNEFSKALWIPLPILLLIILAVVGVLVVVW
LERKISAAVQQRIGPEYAGPLGVLQPLADGLKLAFKEDIIPSKGDVLLFT
LGPAIVVIPIFLSYLIVPFGENLIVSNINLGIFFWITVSSVAPLGLLMSG
YGSNNKYSFLGGLRATAQSLSYEIPLALCVLSICLLSDSLSTIDIVQKQS
TYGILGWNIWRQPIGFIAFIIAALAECERLPFDLPEAEEELVAGYQTEYT
GMKFGLFYIGSYVNLLVSALFASVLYLGGWSLPIPIEFLLNKMSLNASDS
EVQVISAFLGIGMTLLKTYLFLFLSILTRWTMPRVRIDQLLDLGWKFLLP
ISLGNLLLTASLKIALL
>NC_002202@SpolCp090@ndha@117598@119774@R@2@366 NADH_dehydrogenase_subunit_1
MIIDTTTTKVQAINSFSRLEFLKEVYETIWMLFPILILVLGITIGVLVIV
WLEREISASIQQRIGPEYAGPLGILQALADGTKLLFKENLLPSRGDTYLF
SIGPSIAVISILLGYLIIPFGSRLVLADLSIGVFLWIAVSSIAPIGLLMS
GYGSNNKYSFLGGLRAAAQSISYEIPLTLCVLSISLLSNSSSTVDIVEAQ
SKYGFWGWNLWRQPIGFIVFIISSLAECERLPFDLPEAEEELVAGYQTEY
SGIKFGLFYVASYLNLLISSLFVTVLYLGGWNLSIPYIFISEFFEINKID
GVFGTTIGIFITLAKTFLFLFIPITTRWTLPRLRMDQLLNLGWKFLLPIS
LGNLLLTTSSQLFSL
>NC_002693@OeelhCp102@ndha@125123@127258@R@2@364 NADH_dehydrogenase_subunit_1
MIIDTTAVQDMNSFSRLQSLKEVSGIIWMLVPILSLVLGITLGVLVIVWL
EREISAGIQQRIGPEYAGPMGILQALADGIKLIFKENLLPSRGDTRLFSI
GPSIAVISILLSYSVIPFSSHLVLSDLNIGVFLWIAVSSIAPIGLLMSGY
GSNNKYSFLGGLRAAAQSISYEIPLTLCLLSISLLSNSSSTVDIVEAQSK
YGLWGWNLWRQPIGFLVFLISSLAECERLPFDLPEAEEELVAGYQTEYSG
IKFGLFYVASYLNLLVSSLFVTVLYLGGWNISISYIFVPGLFEITKVGRV
FGTTIGIFTTLAKTYLFLFISITTRWTLPRLRMDQLLNLGWKFLLPISLG
NLLLTTSSQLLSL

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>AC_000188@LyesCp066@ndhb@96224@98435@R@2@511 NADH_dehydrogenase_subunit_2
MIWHVQNENFILDSTRIFMKAFHLLLFDGSLIFPECILIFGLILLLMIDS
TSDQKDIPWLYFISSTSLVMSITALLFRWREEPMISFSGNFQTNNFNEIF
QFLILLCSTLCIPLSVEYIECTEMAITEFLLFVLTATLGGMFLCGANDLI
TIFVAPECFSLCSYLLSGYTKKDVRSNEATMKYLLMGGASSSILVHGFSW
LYGSSGGEIELQEIVNGLINTQMYNSPGISIALIFITVGIGFKLSPAPSH
QWTPDVYEGSPTPVVAFLSVTSKVAASASATRIFNIPFYFSSNEWHLLLE
ILAILSMILGNLIAITQTSMKRMLAYSSIGQIGYVIIGIIVGDSNDGYAS
MITYMLFYISMNLGTFACIVLFGLRTGTDNIRDYAGLYTKDPFLALSLAL
CLLSLGGLPPLAGFFGKLYLFWCGWQAGLYFLVLIGLLTSVVSIYYYLKI
IKLLMTGRNQEITPHVRNYRRSPLRSNNSIELSMIVCVIASTIPGISMNP
IIAIAQDSLF
>AC_000188@LyesCp086@ndhb@142909@145120@D@2@511 NADH_dehydrogenase_subunit_2
MIWHVQNENFILDSTRIFMKAFHLLLFDGSLIFPECILIFGLILLLMIDS
TSDQKDIPWLYFISSTSLVMSITALLFRWREEPMISFSGNFQTNNFNEIF
QFLILLCSTLCIPLSVEYIECTEMAITEFLLFVLTATLGGMFLCGANDLI
TIFVAPECFSLCSYLLSGYTKKDVRSNEATMKYLLMGGASSSILVHGFSW
LYGSSGGEIELQEIVNGLINTQMYNSPGISIALIFITVGIGFKLSPAPSH
QWTPDVYEGSPTPVVAFLSVTSKVAASASATRIFNIPFYFSSNEWHLLLE
ILAILSMILGNLIAITQTSMKRMLAYSSIGQIGYVIIGIIVGDSNDGYAS
MITYMLFYISMNLGTFACIVLFGLRTGTDNIRDYAGLYTKDPFLALSLAL
CLLSLGGLPPLAGFFGKLYLFWCGWQAGLYFLVLIGLLTSVVSIYYYLKI
IKLLMTGRNQEITPHVRNYRRSPLRSNNSIELSMIVCVIASTIPGISMNP
IIAIAQDSLF
>NC_000927@NeolCp033@ndhb@28430@29950@D@1@507 NADH_dehydrogenase_subunit_2
MELSDILASFHASNLIPEGIVACTILLVLLLDLVYSRTCHAWLAWVAMAG
LSLASVLLGQQWYQLMNLPTATMTFGGSFQADSLSLVFRAIIAMSCVLCI
LLSIDYVESTGTAPSEFLVLIATASLGGMLVAGSNDLLMMFVSLETLGLA
SYLLTGYMKRDVRSNEASLKYLLVGAASSGLFLYGISWMYGISGGHMELN
SIAHAIVSLDETKTTTCALALVLMTVGVGFKVAAAPFHQWTPDVYQGSPT
PVVAFLSVGSKAAGFILAVRMCTTLFPSFNTEWHLIFTILSILSMIVGNF
IAVTQTSLKRMLGYSSVGQAGVMMIGMLTDSPDGYASLIVYLLIYLFMNL
GAFACVILFGLRTGTDQIQDYSGLLARDPFLALCLSLCLLSLGGIPPLAG
FFGKMYLFLAAWDAGQYSLVWVGLITSVVSIYYYLSVVKIMLVPATQEMS
LAVREYPRRAWSLEPIQPLEVGIFVCVLGSILVGVAGNSMVNLMTITMSQ
APSLGV
>NC_000932@ArthCp068@ndhb@94941@97164@R@2@513 NADH_dehydrogenase_subunit_2
MIWHVQNENFILDSTRIFMKAFHLLLFDGSFIFPECILIFGLILLLMIDS
TSDQKDIPWLYFISSTSFVMSITALLFRWREEPMISFSGNFQTNNFNEIF
QFLILLCSTLCIPLSVEYIECTEMAITEFLLFILTATLGGMFLCGANDLI
TIFVAPECFSLCSYLLSGYTKKDIRSNEATMKYLLMGGASSSILVHGFSW
LYGSSGGEIELQEIVNGLINTQMYNSPGISIALIFITVGIGFKLSLAPSH
QWTPDVYEGSPTPVVAFLSVTSKVAASASATRIFDIPFYFSSNEWHLLLE
ILAILSMIFGNLIAITQTSMKRMLAYSSIGQIGYVIIGIIVGDSNGGYAS
MITYMLFYIAMNLGTFACIILFGLRTGTDNIRDYAGLYTKDPFLALSLAL
CLLSLGGLPPLAGFFGKLHLFWCGWQAGLYFLVSIGLLTSVLSIYYYLKI
IKLLMTGRNQEITPHMRNYRISPLRSNNSIELSMIVCVIASTIPGISMNP
IIAIAQDTLFSF
>NC_000932@ArthCp086@ndhb@141485@143708@D@2@513 NADH_dehydrogenase_subunit_2
MIWHVQNENFILDSTRIFMKAFHLLLFDGSFIFPECILIFGLILLLMIDS
TSDQKDIPWLYFISSTSFVMSITALLFRWREEPMISFSGNFQTNNFNEIF
QFLILLCSTLCIPLSVEYIECTEMAITEFLLFILTATLGGMFLCGANDLI
TIFVAPECFSLCSYLLSGYTKKDIRSNEATMKYLLMGGASSSILVHGFSW
LYGSSGGEIELQEIVNGLINTQMYNSPGISIALIFITVGIGFKLSLAPSH
QWTPDVYEGSPTPVVAFLSVTSKVAASASATRIFDIPFYFSSNEWHLLLE
ILAILSMIFGNLIAITQTSMKRMLAYSSIGQIGYVIIGIIVGDSNGGYAS
MITYMLFYIAMNLGTFACIILFGLRTGTDNIRDYAGLYTKDPFLALSLAL
CLLSLGGLPPLAGFFGKLHLFWCGWQAGLYFLVSIGLLTSVLSIYYYLKI
IKLLMTGRNQEITPHMRNYRISPLRSNNSIELSMIVCVIASTIPGISMNP
IIAIAQDTLFSF
>NC_001319@MapoCp003@ndhb@1514@3555@D@2@502 NADH_dehydrogenase_subunit_2
MKLELDMFFLYGSTILPECILIFSLLIILIIDLTFPKKDTIWLYFISLTS
LLISIIILLFQYKTDPIISFLGSFQTDSFNRIFQSFIVFCSILCIPLSIE
YIKCAKMAIPEFLIFILTATVGGMFLCGANDLVTIFVSLECLSLCSYLLC
GYTKRDIRSNEAAIKYLLIGGTSSSILAYGFSWLYGLSGGETNIQKITNG
LLNAETYNSSGTFIAFICILVGLAFKLSLVPFHQWTPDIYEGSPTPVVAF
LSVTSKIAGLALATRILNILFSFSPNEWKIFLEILAILSMILGNLVAITQ
TSMKRMLAYSSISQIGYILIGLITGDLKGYTSMTIYVFFYIFMNLGTFAC
IILYSLRTGTDNIRDYAGLYIKDPLLSFSLTLCLLSLGGLPPLTGFFGKL
YLFWCGWQSGFYLLVFIALITSVISLYYYLKIIKLILTKKNNEINPYIQA
YIITSPTFFSKNPIEFVMIFCVLGSTFLGIIINPIFSFFQDSLSLSVFFI
K
>NC_001320@OrsajCp075@ndhb@85395@87639@R@2@511 NADH_dehydrogenase_subunit_2
MIWHVQNENFILDSTRIFMKAFHLLLFQGSFIFPECILIFGLILLLMIDL
TSDQKDRPWFYFISSTSLVISITALLFRWREEPIISFSGNFQTNNFNEIF
QFLILLCSTLCIPLSVEYIECTEMAITEFLLFVLTATLGGMFLCGANDLI
TIFVAPECFSLCSYLLSGYTKRDLRSNEATMKYLLMGGASSSILVHGFSW
LYGSSGGEIELQEIVNGLINTQMYNSPGISIALISITVGLGFKLSPAPFH
QWTPDVYEGSPTPVVAFLSVTSKVAASASATRILDIPFYFSSNEWHLLLE
ILAILSMILGNLLAITQTSMKRMLAYSSIGQIGYVIIGIIVGDSNDGYAS
MITYMLFYISMNLGTFACIVLFGLRTGTDNIRDYAGLYTKDPFLALSLAL
CLLSLGGLPPLAGFFGKLYLFWCGWQAGLYFLVSIGLLTSVLSIYYYLKI
VKLLMTGRNQEITPYVRNYRRSPLRSNNSIELSMTVCVIASTIPGISMNP
ILAIAQDTLF
>NC_001320@OrsajCp104@ndhb@127479@129723@D@2@511 NADH_dehydrogenase_subunit_2
MIWHVQNENFILDSTRIFMKAFHLLLFQGSFIFPECILIFGLILLLMIDL
TSDQKDRPWFYFISSTSLVISITALLFRWREEPIISFSGNFQTNNFNEIF
QFLILLCSTLCIPLSVEYIECTEMAITEFLLFVLTATLGGMFLCGANDLI
TIFVAPECFSLCSYLLSGYTKRDLRSNEATMKYLLMGGASSSILVHGFSW
LYGSSGGEIELQEIVNGLINTQMYNSPGISIALISITVGLGFKLSPAPFH
QWTPDVYEGSPTPVVAFLSVTSKVAASASATRILDIPFYFSSNEWHLLLE
ILAILSMILGNLLAITQTSMKRMLAYSSIGQIGYVIIGIIVGDSNDGYAS
MITYMLFYISMNLGTFACIVLFGLRTGTDNIRDYAGLYTKDPFLALSLAL
CLLSLGGLPPLAGFFGKLYLFWCGWQAGLYFLVSIGLLTSVLSIYYYLKI
VKLLMTGRNQEITPYVRNYRRSPLRSNNSIELSMTVCVIASTIPGISMNP
ILAIAQDTLF
>NC_001666@ZemaCp075@ndhb@89236@91472@R@2@511 NADH_dehydrogenase_subunit_2
MIWHVQNENFILDSTRIFMKAFHLLLFHGSFIFPECILIFGLILLLMIDL
TSDQKDRPWFYFISSTSLVISITALLFRWREEPIISFSGNFQTNNFNEIF
QFLILLCSTLCIPLSVEYIECTEMAITEFLLFVLTATLGGMFLCGANDLI
TIFVAPECFSLCSYLLSGYTKRDLRSNEATMKYLLMGGASSSILVHGFSW
LYGSSGGEIELQEIVNGLINTQMYNSPGISIALIFITVGLGFKLSPAPFH
QWTPDVYEGSPTPVVAFLSVTSKVAASALATRILDIPFYFSSNEWHLLLE
ILAILSMILGNLLAITQTSMKRMLAYSSIGQIGYVIIGIIVGDSNDGYAS
MITYMLFYISMNLGTFACIVLFGLRTGTDNIRDYAGLYTKDPFLALSLAL
CLLSLGGLPPLAGFFGKLYLFWCGWQAGLYFLVSIGLLTSVLSIYYYLKI
IKLLMTGRNQEITPYVRNYRRSPLRSNNSIELSMTVCVIASTIPGISMNP
ILAIAQDTLF
>NC_001666@ZemaCp101@ndhb@131265@133501@D@2@511 NADH_dehydrogenase_subunit_2
MIWHVQNENFILDSTRIFMKAFHLLLFHGSFIFPECILIFGLILLLMIDL
TSDQKDRPWFYFISSTSLVISITALLFRWREEPIISFSGNFQTNNFNEIF
QFLILLCSTLCIPLSVEYIECTEMAITEFLLFVLTATLGGMFLCGANDLI
TIFVAPECFSLCSYLLSGYTKRDLRSNEATMKYLLMGGASSSILVHGFSW
LYGSSGGEIELQEIVNGLINTQMYNSPGISIALIFITVGLGFKLSPAPFH
QWTPDVYEGSPTPVVAFLSVTSKVAASALATRILDIPFYFSSNEWHLLLE
ILAILSMILGNLLAITQTSMKRMLAYSSIGQIGYVIIGIIVGDSNDGYAS
MITYMLFYISMNLGTFACIVLFGLRTGTDNIRDYAGLYTKDPFLALSLAL
CLLSLGGLPPLAGFFGKLYLFWCGWQAGLYFLVSIGLLTSVLSIYYYLKI
IKLLMTGRNQEITPYVRNYRRSPLRSNNSIELSMTVCVIASTIPGISMNP
ILAIAQDTLF

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>AC_000188@LyesCp081@ndhd@116944@118446@R@1@501 NADH_dehydrogenase_subunit_4
MNYFPWLTIIVVFPIFAGSLIFFLPHKGNRVIRWYTICICILELLLTTYA
FCYHFQSDDPLIQLVEDYKWIDFFDFHWRLGIDGLSIGPILLTGFITTLA
TLAAWPVTRDSRLFHFLMLAMYSGQIGLFSSRDLLLFFIMWELELIPVYL
LLAMWGGKKRLYSATKFILYTAGGSVFLLMGVLGVALYGSNEPTLNFETS
VNQSYPVVLEIIFYIGFFIAFAVKSPIIPLHTWLPDTHGEAHYSTCMLLA
GILLKMGAYGLIRINMELLPHAHSIFSPWLMIIGTIQIIYAASTSLGQRN
LKKRIAYSSVSHMGFIIIGISSLTDTGLNGALLQIISHGFIGAALFFLAG
TTYDRIRLVYLDEMGGIAIPMPKMFTMFSSFSMASLALPGMSGFVAELIV
FFGIITGQKYLLMPKLLITFVMAIGIILTPIYSLSMPRQMFYGYKLFNAP
KDSFFDSGPRELFLSISIFLPVIGIGIYPDFVLSLAVDKVEVILSNFFYR
>NC_000927@NeolCp113@ndhd@139299@140801@D@1@501 NADH_dehydrogenase_subunit_4
MTHFPWLSTIVLFPLLASLAIPWLPDRKGTTVRWYALGVGLIDFSLIAYM
FGRYYDFEQTSLQFVEDITWIDRLHLHWSLGVDGLSMPLVLLTGFITTLA
TLAAWPVTKNPRLFYFLMLAMYTGQLGVFVVQDLLLFFLMWELELIPVYL
LVSCWGGKKRLYAATKFILYTALGSIFILLGALTMPFMGIQGVTFDMSTL
AYREYSLPVEILLYTGFLIAYGVKLPAIPVHTWLPDTHGEAHYSTCMLLA
GILLKMGGYALIRINMNMLPHAHALFSPWLIGVGVVNIIYAALTSFAQRN
LKRKIAYSSVSHMGFVLIGIGSLSEAGLNGAMLQMISHGLIGASLFFLAG
TTYDRTRTLVLEEMGGLATFMPKTFALFTACSLASLALPGMSGFFAELLV
FLGLVTSEAYSPTFRAIMTVFEAIGILLTPIYLLSMLRQLFYGRSIGRPK
ALIDAGPREVFVVSCLLVPILGIGIYPKLATAIYVNTTDHVVQHVLSALR
>NC_000932@ArthCp074@ndhd@115665@117167@R@1@501 NADH_dehydrogenase_subunit_4
MNDFPWLTIIVVFPISAGSLMLFLPHRGNKVNKWYTICICILELLLTTYA
FCYNFKMDDPLIQLSEDYKWIDFFDFYWRMGIDGLSIGTILLTGFITTLA
TLAAFPVTRDSRFFHFLMLAMYSGQIGSFSSRDLLLFFIMWELELIPVYL
LLSMWGGKKRLYSATKFILYTAGSSIFLLIGVLGISLYGSNEPTLNLELL
ANKSYPVTLEILFYIGFLIAFAVKSPIIPLHTWLPDTHGEAHYSTCMLLA
GILLKMGAYGLVRINMELLPHAHSMFSPWLLVVGTIQIIYAASTSPGQRN
LKKRIAYSSVSHMGFIIIGISSITDPGLNGAILQIISHGFIGAALFFLAG
TSYDRIRLVYLDEMGGMAISIPKIFTMFTILSMASLALPGMSGFIAEFIV
FFGIITSQKYFLISKIFIIFVMAIGMILTPIYLLSMLRQMFYGYKLINIK
NFSFFDSGPRELFLSISILLPIIGIGIYPDFVLSLASDKVESILSNYFYG
>NC_001319@MapoCp079@ndhd@96665@98164@R@1@500 NADH_dehydrogenase_subunit_4
MNHFPWLTIIVLFPISAGLVIPFLPSTGNKIIRWYTLGVCLLEFLLITYI
FCYHYQFNDHLIQLKEDYNWISFINFHWRLGIDGFSIGLILLTGFITTLA
TLAAWPVTRNPRLFYFLMLAMYSGQIGLFASQDILLFFFMWELELLPVYL
LLAMWGGKRRLYAATKFILYTAAGSLFILIGGLIMAFYNSNEFTFDFQFL
INKKYPLELEIIIYLSFLIAYAVKLPIIPFHTWLPDTHGEAHYSTCMLLA
GILLKMGAYGLIRINMELLPHAHSFFAPWLVIVGAIQIVYAALTSLSQRN
LKRRIAYSSVSHMGFVLIGIGSITNLGLNGAILQMISHGLIGASLFFLAG
ISYDRTRTLVLDQMGGIGNSMPKIFTLFTSCSMASLALPGMSGFIAELMI
FLGVIDNPNYSSLFKIIIIIIQGIGIILTPIYLLSMLRQMFYGYKFSNTL
EPYFMDAGPREIFILICLFFPIISIGIYPNFVLSIWNSKVNFLLSNNFF
>NC_001320@OrsajCp088@ndhd@106398@107900@R@1@501 NADH_dehydrogenase_subunit_4
MSSFPWLTILVVLPIFAGSLIFFLPHRGNKIVRWYTMSICLLEFLLMTYA
FCYHFQLEDPLIQLKEDSKWIDVFNFHWRLGIDGLSLGSILLTGFMTTLA
TLAAWPVTRNSRLFYFLMLAMYSGQIGLFSSRDLLLFFIMWELELIPVYL
LLSMWGGKRRLYSATKFILYTAGGSIFFLIGVLGMGLYGSNEPRLDLERL
INQSYPATLEILFYFGFLIAYAVKLPIIPLHTWLPDTHGEAHYSTCMLLA
GILLKMGAYGLIRINMELLPHAHYLFSPWLVIIGAMQIIYAASTSLGQRN
FKKRIAYSSVSHMGFIIIGIGSITNIGLNGAILQILSHGFIGATLFFLAG
TACDRMRLVYLEELGGASIPMPKIFTMFSSFSMASLALPGMSGFVAELVV
FFGLITSPKFLLMPKMLITFVMAIGMILTPIYLLSMLRQMFYGYKLFHVP
NENFEDSGPRELFLLICIFLPVIGIGIYPDFVLSLSVDRVEALLSNYYPK
>NC_001666@ZemaCp086@ndhd@110138@111640@R@1@501 NADH_dehydrogenase_subunit_4
MSYFPWLTILVVLPIFAGSLIFFLPHKGNKIVRWYTIAICLLEFLLMTYA
FCYHFQLEDPLIQLKEDSKWIDVFDFHWRLGIDPLSLGSILLTGFITTLA
TLAAWPVTRNSQLFYFLMLAMYSGQIGLFSSRDLLLFFIMWELELIPVYL
LLSMWGGKRRLYSATKFILYTAGGSIFFLIGVLGMGLYGSNEPGLDLERL
INQSYPTTWEILLYFGFLIAYAVKLPIIPLHTWLPYTHGEAHYSTCMLLA
GILLKMGAYGLIRVNMELLPHAHYLFSPWLVIIGAVQIIYAASTSLGQRN
FKKRIAYSSVSHMGFIIIGIGSITNIGLNGAILQILSHGFIGATLFFLAG
TACDRMRLVYLEELGGISIPMPKIFTMFSSFSMASLALPGMSGFVAELVV
FFGLITSPKFMLMPKMLITFVMAIGMILTPIYLLSMLRQMFYGYKLFHVP
NKNFVDSGPRELFLLICIFLPVIGIGIYPDLVLSLSVDRVEVLLSNYYTK
>NC_001879@NitaCp083@ndhd@117525@119027@R@1@501 NADH_dehydrogenase_subunit_4
MNYFPWLTIIVVFPIFAGSLIFFLPHKGNRVIRWYTICICILELLLTTYA
FCYHFQSDDPLIQLVEDYKWINFFDFHWRLGIDGLSIGPILLTGFITTLA
TLAAWPVTRDSRLFHFLMLAMYSGQIGSFSSRDLLLFFIMWELELIPVYL
LLCMWGGKKRLYSATKFILYTAGGSVFLLMGVLGLALYGSNEPTLNFETS
VNQSYPVVLEIIFYIGFFIAFAVKSPIIPLHTWLPDTHGEAHYSTCMLLA
GILLKMGAYGLIRINMELLPHAHSIFSPWLMIIGTIQIIYAALTSLGQRN
LKKRIAYSSVSHMGFIIIGISSLTDTGLNGALLQIISHGFIGAALFFLAG
TTYDRIRLVYLDEMGGIAIPMPKMFTMFSSFSMASLALPGMSGFVAELIV
FFGIITGQKYLLIPKILITFVMAIGMILTPIYSLSMSRQMFYGYKLFNAP
KDSFFDSGPRELFLSISIFLPVIGIGIYPDFVLSLAVDKVEVILSNFFYR
>NC_002186@MeviCp085@ndhd@90277@91800@D@1@508 NADH_dehydrogenase_subunit_4
MNNFPWITSIVMLPILAGLLIPFIPDENGKNVRWYALGIGLLDFLLISYI
FGYKYNIQDTSLQLIDDYEWISSINFHWRLGIDGLSIPLILLTGFITTLA
MLGAWPIQKNAKLFYFLMLAMYSGQLGVFASQDLLLFFLMWELELIPIYI
LLIIWGGKKRLYAATKFILYTALGSIFILIAAFGMAFYGENMSFDMQILG
EKEYPINLEILFYICFLIAYAVKLPAFPVHTWLPDTHGEAHYSTCMLLAG
ILLKMGGYALIRINMNMLPNAHIYFAPYLAIIGVINIIYAALTSFAQRNI
KRKIAYSSISHMGFVLIGISSFTDIGLSGAMLQMVSHGLIGASLFFLAGT
TYDRTRTLILEDMGGIAKYMPKIFAMFTTCSLASLALPGMSGFVAELMVF
LGFANSNAYSIEFRGIITFLEAIGIIVTPIYLLSMLRQVFYGSENLKLLK
VNNLIDASAREIFIISCLLVPVIGIGIYPRILTQIYDLKTNAIIEHLEII
RSNSQIM
>NC_002202@SpolCp085@ndhd@113491@114996@R@1@502 NADH_dehydrogenase_subunit_4
MTNSFPWLTTIVVLPIFAGSLIFLFPHRGNKVIRWYTICISMIELLLMTY
VFFYHFQPDDPLIQLVEDYKWINFFDFHWRLGIDGLSIGPILLTGFITTL
ATLAAWPVTRNSQLFHFLMLAMYSAQIGLFSSRDLLLFFIMWELELIPVY
LLLSMWGGKKRLYSATKFILYTAGGSIFLLMGVLGVGLYGSNEPTLNLET
LVNQSYPVALEIIFYIGFFIAFAVKLPIIPLHTWLPDTHGEAHYSTCMLL
AGILLKMGAYGLVRINMELLPHAHSIFSPWLMIIGTMQIIYAASTSPGQR
NLKKRIAYSSVSHMGFIIIGISSITDTGLNGAILQIISHGFIGAALFFLA
GTSYDRIRLVYLDEMGGIAIPMPKIFTLFSSFSMASLALPGMSGFIAELI
VFFGLITSQKYLLIPKLLITFGMAIGMILTPIYLLSMSRQMFYGYKLFNI
SNSSFFDSGPRELFVSTSIFLPVIGIGVYPDLVLSLSVEKVEAILSNYFY
R
>NC_002693@OeelhCp097@ndhd@121124@122647@R@1@508 NADH_dehydrogenase_subunit_4
MNSFPWLTIIVVFPILTGSLIFLLPHRGNKVMKWYTLCICILELLLTTYT
FCYHFQLDDPLTQLTENYKWIHFFDFYWRLGIDGLSIGPILLTGFITTLA
TLAAWPVTRDAQLFHFLMLAMYSGQIGSFSSRDLLLFFLMWEFELIPVYL
LLSMWGGKKRLYSATKFILYTAGGSIFLLIGVLGIGLYGSNEPTLNFETL
ANQSYPVALEVIFYVGFLIAFAVKLPIIPFHTWLPDTHGEAHYSTCMLLA
GILLKMGAYGLVRINMELLPHAHCLFSPGLIIVGAIQIIYAASTSPGQLN
LKKRIAYSSISHMGFIIIGIGSLSDTGLNGAILQIISHGFIGAALFFLAG
TSYDRIRLLYLDEMGGMAIPLPKLFTMLSILSMASLALPGLSGFVAELLV
FFGIITSQKYLLMPKILIAFLMAIGMILTPIYSLSMLRQMFYGYKLFNVP
NYYFFDSGPRELFVSISLLLPIIGIGIYPDFVLSLSVEKVEAIISHFFFS
IVFKKKE

39
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>AC_000188@LyesCp080@ndhe@119061@119366@R@1@102 NADH_dehydrogenase_subunit_4
MILEHVLVLSAYLFSIGIYGLITSRNMVRALMCLELILNAVNINFVTFSD
FFDNRQLKGDIFSIFVIAIAAAEAAIGLAIVSSIYRNRKSTRINQSNLLN
N
>NC_000927@NeolCp119@ndhe@147326@147631@D@1@102 NADH_dehydrogenase_subunit_4L
MIFQSYLLIAASMFCIGLYGLLTSRNVVRVLMSLELLLNAVNLNLLTFSN
FVDSHEMKGQVLALFVIALAAAEAAIGLAIILSIYRNQRTVDPEQFNLLK
W
>NC_000932@ArthCp076@ndhe@117804@118109@R@1@102 NADH_dehydrogenase_subunit_4L
MILEHVLVLSAYLFLIGLYGLITSRNMVRALMCLELILNAVNMNFVTFSD
FFDNSQLKGEIFCIFVIAIAAAEAAIGLAIVSSIYRNRKSIRINQSTLLN
K
>NC_001319@MapoCp081@ndhe@98757@99059@R@1@101 NADH_dehydrogenase_subunit_4L
MLEHILTLSAFLFCIGVFGLITSRNMVRALMCLELIFNAVNINLVAFSNF
LDSSQIKGEIFSIFIIAIAAAEATIGLAIVLAIYRNRKSTRIDQFNLLKW
>NC_001320@OrsajCp090@ndhe@108712@109017@R@1@102 NADH_dehydrogenase_subunit_4L
MMFEHVLFLSVYLFSIGIYGLITSRNMVRALICLELILNSINLNLVTFSD
LFDSRQLKGDIFAIFVIALAAAEAAIGLSILSSIHRNRKSTRINQSNFLN
N
>NC_001666@ZemaCp088@ndhe@112473@112778@R@1@102 NADH_dehydrogenase_subunit_4L
MMFERVLFLSVYLFSIGIYGLITSRNMVRALICLELILNSINLNLVTFSD
LFDSRQLKGDIFAIFVIALAAAEAAIGLSILSSIHRNRKSTRINQSNFLN
N
>NC_001879@NitaCp085@ndhe@119652@119957@R@1@102 NADH_dehydrogenase_subunit_4L
MILEHVLVLSAYLFSIGIYGLITSRNMVRALMCLELILNAVNINFVTFSD
FFDNRQLKGDIFSIFVIAIAAAEAAIGLAIVSSIYRNRKSTRINQSNLLN
N
>NC_002186@MeviCp099@ndhe@104916@105221@R@1@102 NADH_dehydrogenase_subunit_4L
MYIENFLLLASALFCIGIYGLLTSRNIVRVLMCLELCLNAININFIAFSN
FIDYEKINGQVIAIFIMTIAAAEAAIGLALVLTIYRNRETVDIENFDLLK
G
>NC_002202@SpolCp087@ndhe@115663@115968@R@1@102 NADH_dehydrogenase_subunit_4L
MILEHVLVLSAFLFSIGIYGLVTSRNLVRALMCLELILNAVNLNFVTFSD
FFDSRQLKGNIFSIFVIAIAAAEAAIGPAIVSSIYRNRKSIRINQSNLLN
K
>NC_002693@OeelhCp099@ndhe@123298@123603@R@1@102 NADH_dehydrogenase_subunit_4L
MILEHVLVLSAYLFSIGIYGLITSRNMVRALMCLELILNSVNLNFVTFSD
FFDSRQLKGDIFSIFIIAIAAAEAAIGLAIVSSIYRNRKSIRINQSNLLN
K

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>AC_000188@LyesCp073@ndhf@111508@113721@R@1@738 NADH_dehydrogenase_subunit_5
MEQTYEYAWIIPFIPLPVPMLIGAGLILFPTATKRFRRMWAFQSVLLLSI
VMIFSIYLSIQQINSSSVYQYVWSWIINNDFSLDFGYLIDPLTSIMSILI
TTVGIMVLIYSDNYMAHDQGYLRFFAYMSFFSTSMLGLVTSSNLIQIYIF
WELVGLCSYLLIGFWFTRPVAANACQKAFVTNRVGDFGLLLGILGFYWIT
GSFEFRDLFEIFNNLIYNNELNFLFVTLCAVLLFAGAVAKSAQFPLHVWL
PDAMEGPTPISALIHAATMVAAGIFLVARLLPLFRVIPYIMYLISVIGII
TVLLGATLALAQKDIKRGLAYSTMSQLGYMMLALGMGSYRSALFHLITHA
YSKALLFLGSGSIIHSMETIVGYSPAKSQNMGLMGGLRKHVPITKITFLL
GTLSLCGIPPLACFWSKDEILNDSWLYSPIFAIIAWATAGLTAFYMFRIY
LLTFEGHLNAHFQNYGGKQKIPFYSISLWGKNGVKKNSCLLTMNNNESTY
FLSKTKYPIAKNGRKMTRPFMTIAHFKHKAVSSYPYESDNTMLFPIFVLG
LFTLFVGAIGIPFNQEGVNLDILSKWLAPSINLLHPKSNNSLDWNEFLKD
AVVSVSIAYFGIFIASFLYKPIYSSLKNLEFINSFVKKGPKRILWDKILN
GIYDWSYNRAYIDAFYTRFFVGGIRGLAEFTHFVDRRVIDGMTNGVGVIS
FIVGEGIKYIGGGRISSYLFLYLAYVSVFLLVYYLLF
>NC_000927@NeolCp114@ndhf@140837@142783@R@1@649 NADH_dehydrogenase_subunit_5
MEIFHQAIWLIPVLPLSASMLSGIGLLTFRETTSDLRRLHGALAIGAMAL
SFVVSLGVLWNQLHGIAPVRWIIEWMLTDTFRLEIGYWVDPLTSTMLVVV
TSVALLVMIYSDEYMHVDEGYVRFFVYLSIFTTSMLGLVLSPNLVQVYGF
WELVGMCSYLLVGFWFTRPTAAEASQKAFITNRVGDFGLLLGILALYWMT
GSFEFASIADRLGDLLIAIPSLRTIACIACILVFMGPIAKSAQFPLHVWL
PDAMEGPTPISALIHAATMVAAGVFLVARMFPVFDQLPLVMELIAWTGTL
TAFLGATMALTQSDIKKGLAYSTMSQLGYMIMALGTGAYSEALFHLTTHA
YSKALLFLAAGSVIHGMEPVVGFSPMQNQNMHRMGGLRKYMPLTAMTFLL
GTCSICGIPPLACFWSKDAILAEVFATHPTCWLIAWLTAGMTGFYMFRIY
FLTFEGSFRSDLGRAKPKESHLGMVAPLIILAIPTVAIGSLGTPFAPVWE
TFVHAPGQLSSLDEEFDLAEFLEMAGSSVGIGLLGISLSSLMYRNYAIDA
TRISEYFSPLNRLFASKWYIDDLYAQVIVQGTRTIAQTLLIFDQRIIDGA
VNLTAFGTLSAADTLKYWENGRVQFYILSIIFGVLFGSWLLTTHLSSL
>NC_000932@ArthCp071@ndhf@110398@112638@R@1@747 NADH_dehydrogenase_subunit_5
MEHTYQYSWIIPFIPLPVPILLGVGLLLFPTATKNLRRMWTFLSIFLLSI
VMIFSIYLSIQQIFLSCIHQNVWSWTINNEFSFEFGYFIDPLTSIMSILI
TTVGILVLIYSDNYMSHDQGYLRFFAYMGFFNTSMLGLVTSSNLIQVYFF
WELVGMCSYLLIGFWFTRPIAANACQKAFVTNRVGDFGLLLGILGLYWIT
GSFEFQDLFEIFNNLILNNRVNLLFLTLCAFLLFVGPIAKSAQFPLHVWL
PDAMEGPTPISALIHAATMVAAGIFLVARLLPLFIVIPSIMYIISLIGII
TVLLGATLALAQKDIKRGLAYSTMSQLGYMMLALGMGSYRSALFHLITHA
YSKALLFLGSGSIIHSMEAIVGYSPDKSQNMILMGGLTKHVPITKTAFLI
GTLSLCGIPPLACFWSKDEILNDSLLFSPIFAIIACSTAGLTAFYMFRIY
LLTFEGHLNTYFLNYSGKKSGSFYSLSLWGKEEEKKLNKNFGLVPLLTMN
NTKRASFFCNKTYKISNNVRNQIFITVENFGLNTRTFYYPHESDNTILFP
MLILVLFTLFIGAIGIPFNQEGIDFDILSKFFTPSINLLHKNSQNFVDWY
EFLRNATFSVSIAFFGIFIAYCLYKPFYSSLLNLTLLNSFQKWNSKRIHW
EKLINFVYNWSYNRGYIDSFFKTSLIESIRRLAKQTTFFDKRIIDGITNG
VGITSFFVGEVTKYIGGSRISSYLFLYLSYVLIFLMILFFFYFEKF
>NC_001319@MapoCp074@ndhf@91101@93179@R@1@693 NADH_dehydrogenase_subunit_5
MELIFQNVWFVPLFPFLASILLGIGLFFFPNSIKKFRRLSSFISIMFLNI
AMLLSFHFFWQQITGSPIHRYLWSWVLYKNFVLEIGYLLDPLTSIMLVLV
TTVAVMVMIYSDSYMFYDEGYIKFFCYLSLFTASMLGLVLSPNLIQVYIF
WELVGMCSYLLIGFWFTRPSAANACQKAFVTNRIGDFGLLLGILGFYWIT
GSFDFQQLSKRFFELLSYNQINLVFATLCALFLFLGPVAKSAQFPLHIWL
PDAMEGPTPISALIHAATMVAAGIFLVARMFPLFQMLPFVMSIISWTGAI
TALLGATIALAQKDLKKGLAYSTMSQLGYMMLALGIGSYKAGLFHLITHA
YSKALLFLGSGSVIHSMEPIVGYHPNKSQNMIFMGGLRQYMPITAITFLF
GTLSLCGIPPFACFWSKDEILVNSWLHFPILGSIAFFTAGLTAFYMFRIY
FLTFEGDFRGHFFDDVKKLSSISIWGSLEFNKEQFKLDKKSTLYPKEANN
IMLFPLIILTIPTVFIGFIGILFDENKMNVDSLSYWLTLSINSFNYSNSE
KFLEFLFNAIPSVSIAFFGILIAFYLYGPNFSFLKKEKKKLQLKSEIDIV
LKSFSNFIYNWSYYRAYIDGFYSSFFIKGLRFLIKIVSFIDRWIIDGIIN
GIGIFSFFGGESLKYIEGGRISSYLFFIIFCMFLFFLYSYII
>NC_001320@OrsajCp085@ndhf@101433@103637@R@1@735 NADH_dehydrogenase_subunit_5
MEHTYQYAWVIPLLPLPVIMSMGFGLFLVPTATKNLRRIWAFPSVLLLSI
AMVFSVHLSIQQINGSSIYQYLWSWTVNNDFSLEFGYLIDPLTSIMLILI
TTVGILVLIYSDDYMSHDEGYLRFFVYISFFNTSMLGLVTSSNLIQIYFF
WELVGMCSYLLIGFWFTRPIAASACQKAFVTNRVGDFGLLLGILGFFWIT
GSLEFRDLFKIANNWIPNNEINSLLTILCAFLLFLGAVAKSAQFPLHVWL
PDAMEGPTPISALIHATTMVAAGIFLIARLLPLFISLPLIMSFISLIGTL
TLFLGATLALAQRDIKRSLAYSTMSQLGYMMLALGIGSYQAALFHLITHA
YSKALLFLGSGSVIHSMEPLVGYSPDKSQNMVLMGGLRKYIPITRTCFLW
GTLSLCGIPPLACFWSKDEILSNSWLYSPFFGIIASFTAGLTAFYMFRIY
LLTFDGYLRVHFQNYSSTKEDSLYSISLWGKRISKGVNRDFVLSTAKSGV
SFFSQNLSKIHVNTGNRIGSFSTSLGTKNTFVYPHEPGNTMLFPLLILLL
CTLFIGSIGIHFDNEIGELTILSKWLTPSINFFQESSNSSINSYEFITNA
ISSVSLAIFGLFIGIYVLWICLLFFSEFDLINSFVKGGPKKYFFHQLKKK
IYSWSYNRGYIDIFYTRTFTLGIRGLTELTQFFDKGVIDGITNGVGLASF
CIGEEIKYVGGGRISSYLFFFLCYVSVFLFFFLS
>NC_001666@ZemaCp083@ndhf@105072@107288@R@1@739 NADH_dehydrogenase_subunit_5
MEHTYQYAWVIPLLPLPVIMSMGFGLFLIPTATKNLRRIWAFPSILLLSI
AMVFSLHLSIQQINGSSIYQYLWSWTINNDFSLEFGYLVDPLTSIMLILI
TTVGILVLIYSDDYMSHDEGYLRFFVYISFFNTSMLGLVTSSNLIQIYFF
WELVGMCSYLLIGFWFTRPIAASACQKAFVTNRVGDFGLLLGILGFFWIT
GSLEFRDLFKIANNWIPNNGINSLLTTLCAFLLFLGAVAKSAQFPLHVWL
PDAMEGPTPISALIHAATMVAAGIFLLARLLPLFISLPWIMSFISLIGTI
TLFLGATLALAQRDIKRSLAYSTMSQLGYMMLALGIGSYQAALFHLITHA
YSKALLFLGSGSVIHSMEPLVGYSPDKSQNMVLMGGLRKYVPITRTTFLC
GTLSLCGIPPLACFWSKDEILSNSWLYSPFFGIIASFTAGLTAFYMFRIY
LLTFDGYLRVHFQNYSSTKEGSLYSISLWGKSISKGVNRDFVLSTMKSGV
SFFSQNIPKIPANTRNKIGSFSTPFGAKNTFVYPHETGNTMLFPLLILLL
FTLFIGSIGIHFDNGVKDNRILELTILSKWLTPSINLFQENSNSSINSYE
FLTNAISSVSLAIFGLFIAYIFYGSAYSFFQNLNFQNSLVKKNPKKSFLD
EVKKKIYSWSYNRGYIDFFYTRVFILGIRKLAELTHFFDKGVIDGITNGV
GLAGFCIGEEIKYVGGGRISSYLFFFLCYVSLFLFFIP
>NC_001879@NitaCp080@ndhf@112072@114294@R@1@741 NADH_dehydrogenase_subunit_5
MEQTYEYAWIIPFIPLPVPMLIGAGLFLFPTATKSFRRMWAFQSVLLLSI
VMVFSIYLSIQQINSSSFYQYVWSWIINNDFSLDFGYLIDPLTSIMSILI
TTVGIMVLIYSDNYMAHDQGYLRFFAYMSFFSTSMLGLVTSSNLIQIYIF
WELVGLCSYLLIGFWFTRPVAANACQKAFVTNRVGDFGLLLGILGFYWIT
GSFEFRDLFEIFNNLIYNNEVDFLFVTLCAVLLFAGAVAKSAQFPLHVWL
PDAMEGPTPISALIHAATMVAAGIFLVARLLPLFRVIPYIMYLISVIGII
TVLLGATLALAQKDIKRGLAYSTMSQLGYMMLALGMGSYRSALFHLITHA
YSKALLFLGSGSIIHSMETIVGYSPAKSQNMGLMGGLRKHVPISKITFLL
GTLSLCGIPPLACFWSKDEILNDSWLYSPIFAIIAWATAGLTAFYMFRIY
LLTFEGHLNAHFPNYGGKQKTPFYSISLWGKNGVKKNSCLLTMNNNESTY
FFAKTKYPIDKNGRKMTRPFMTIAHFEHKAVYSYPYESDNTMLFPIFVLG
LFTLFVGSIGIPFNQEGGNLDILSKWLAPSINLLHQKSNNSMDWNEFLKD
AVLSVSIAYFGIFIASFLYKPIYSSLKNFELINSFVKKGPKRILWDKIIN
GIYDWSYNRAYIDAFYTRFLVGGIRGLAEFTHFFDRRVIDGMTNGVGVIS
FIVGEGIKYIGGGRISSYLFLYLAYVSIFLLVYYLLFSTL
>NC_002186@MeviCp105@ndhf@109803@111761@D@1@653 NADH_dehydrogenase_subunit_5
MESISQYAWLIPIFPLAGSLLIGIGLISFRRATNILRWRYSFLIIALLGI
SLILSCLILFSQINATPSYQWIFQWIVTNNFLLEIGYFVDPLTAVMLVIV
TTVAILVLIYTDGYMSYDEGYVRFFAYLSLFTTSMLGLVLSPNLLQIYVF
WELVGMCSYLLIGFWFTRPAAADACQKAFVTNRVGDFGLLLGILGFYWMT
GSFEFDVISMKLLQLAEYDNFNTQLAIFFGFLIFLGPVAKSAQFPLHVWL
PDAMEGPTPISALIHAATMVAAGVFLVARMFPIFSQFPFLMDLIAWTGAI
TAIIGATIAVTQVDLKKGLAYSTMSQLGYMIMAMGMGSYTASLFHLMTHA
YSKALLFLSAGSTIHGMEPIVGFNPAKNQNMSLMGGIRKYMPITGNAFLI
GTLSLCGIPPLACFWSKDAILSNAFVHSPLLWFIGWSTAGLTSFYMFRMY
FLVFEGEFRGNSVNQEKIRSNKLPKESNTKMTLPLIILTLFSITIGWIGT
PFNNQFMFLIHTINQEIEPFDINEFLFIAGSSVGIALLGCYTAYLIYIKD
KNTDKFANLLQPFYQLSFNKWYIDDIYEYIFVKGNRQLAQQTLLFDKKII
DGFVNLTGLITLVSSESLRSIENGKIQSYILMIIFTLLTILGISQTYYSL
IL
>NC_002202@SpolCp080@ndhf@107770@109998@R@1@743 NADH_dehydrogenase_subunit_5
MEHIYQYAWIIPFLPLPVPLLIGAGLLFFPTATKNLRRIWAFSSISLLSI
VMIFSMKLAIQQINSNSIYQYLWSWTINNDFSLEFGYLMDPLTSIMSMLI
TTVAILVLIYSDNYMSHDQGYLRFFAYMSFFNTSMLGLVTSSNLIQIYIF
WELVGMCSYLLIGFWFTRPIAANACQKAFVTNRVGDFGLLLGILGLYWIT
GSFEFRDLFEIFNNLIKNNEVNSLFCILCAFLLFAGAVAKSAQFPLHVWL
PDAMEGPTPISALIHAATMVAAGIFLVARLLPLFVVIPYIMYVISFIGII
TVLLGATLALAQKDIKRSLAYYTMSQLGYMMLALGMGSYRTALFHLITHA
YSKALLFLASGSLIHSMGTIVGYSPDKSQNMVLMGGLTKHVPITKTSFLI
GTLSLCGIPPLACFWSKDEILNDSWVYSPIFAIIAYFTAGLTAFYMFRIY
LLTFEGHLNFFCKNYSGKKSSSFYSISLWGKKELKTINQKISLLNLLTMN
NKERASFFSKKPYEINVKLTKLLRSFITITYFENKNISLYPYESDNTMLF
PLIILIMFTLFVGFIGIPFNQEGMDLDILTKWLTPSINLLHSNSENFVDW
YEFVINAIFSISIAFFGIFIAFFFYKPIYSSLKNFDLINSFDKRGQKRIL
GDNIITIIYNWSANRGYIDAFYSTFLIKGIRSLSELVSFFDRRIIDGIPN
GFGVTSFFVGEGIKYVGGGRISSYLFWYLLYVSIFLFIFTFT
>NC_002693@OeelhCp094@ndhf@115809@118142@R@1@778 NADH_dehydrogenase_subunit_5
MEYTYQYSWIIPFIPLPVPILIGMGLLLFPTATKNHRRVWSFPSILLLSM
VMLLSVYLSIQQINRSFIYQYVWSWTINNDFSLEFGHLIDPLASIMLILI
TTVGILVLFYSDNYMSHDQGYLRFFAYLSFFNTSMLGLVTSSNLIQIYIF
WELVGMCSYLLIGFWFTRPIAATACQKAFVTNRVGDFGLLLGILGLYWIT
GSFEFRDLFEIVNNLIDNNNQVHFLFVTLCSFLLFAGAVAKSAQFPLHVW
LPDAMEGPTPISALIHAATMVAAGIFLVARLLPLFVITPYIMNLISLIGI
ITVLLGATLALAQKDIKRSLAYSTMSQLGYMMLALGMGSYRAALFHLITH
AYSKALLFLGSGSIIHSMESIVGYSPDKSQNMVLMGGLKKHVPITKTAFL
VGTLSLCGIPPLACFWSKDEILNDSWLYSPIFAIIACSTAGFTAFYMFRV
YLLTFDGHLNVHFQNYSGQKSSSVYSISLWGKQVPKRIQNPFCLLNLLTM
NNNESTSFFWNNKCKLDGNVKKRIRPFITVTHFPNRKTFSYPHESDNTML
FSLFVLVLFTLFVAAIGIPFNQEGSDCDILSKLLNPSINLLHQNSNNFTD
WYEFVTNASFSVSIALLGIFIATFLYKPIYSSLQNFNLLNSFYKRSANRV
MWDKIQNWIYDWSYNRGYIDSFYTISLTGGIRGLAELSHFFDRRVIDGIL
NGFGLTSFFLGESLKYFGGGRISSYLLLYSIFIFIFLLMDSFFTNLPFFV
LCQFLDSSFSMSISGFLLYENFLYENF

50
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>AC_000188@LyesCp077@ndhg@119590@120120@R@1@177 NADH_degydrogenase_subunit_6
MDLSEPIHDFLLVFLGSGLILGGLGVVLLPNPIYSAFSLGLVLVCTSLFY
ILSNAYFVAAAQLLIYVGAINVLIIFAVMFMNGSEYYKDFHLWTVGDGIT
SMVCISLFISLITTISDTSWYGIIWTTRSNQIIEQDFLSNSQQIGIHLST
DFFLPFELISIILLVALIGAIAVARQ
>NC_000927@NeolCp118@ndhg@146302@146811@D@1@170 NADH_dehydrogenase_subunit_6
MEIVQNFSSAALTTGILLGCLGVIFLPSIVYAAFLLGAVFFCLAGIYVLL
HADFVAAAQVLVYVGAINVLILFAIMLVNPQDAPPRALDSPPLIPGIACI
GLLGVLVQMISTTSWLTPPWTPEPNSLPVLGGHLFSDCLLAFEVMSLVLL
VALVGAIVLARREPVERSS
>NC_000932@ArthCp077@ndhg@118377@118907@R@1@177 NADH_dehydrogenase_subunit_6
MDLPGPIHDFLLVFLGSGLLVGGLGVVLLPNPIFSAFSLGFVLVCISLLY
ILSNSHFVAAAQLLIYVGAINVLIIFAVMFMNDSEYSTDFNLWTIGNGIT
SLVCTTILFLLMSTILDTSWYGVIWTTKLNQILEQDLISNSQQIGIHLST
DFFLPFELISIILLVALIGAISVARQ
>NC_001319@MapoCp082@ndhg@99113@99688@R@1@192 NADH_dehydrogenase_subunit_6
MKLPESFYETIFLFLESGLILGSLGVILLTNIVYSALFLGFVFVCISLLY
LLLNADFVAAAQILIYVGAVNVLIIFAVMLINKKQYSNFFVYWTIGDGIT
LTLCTSIFLLLNNFISNTSWSKIFLMTKPNLVVKDIILINTVRHIGSELL
TEFLLPFELMSIILLVALIGAITLARREKKIELEKNDFFNF
>NC_001320@OrsajCp091@ndhg@109227@109757@R@1@177 NADH_dehydrogenase_subunit_6
MDLPGPIHEILVLFGGFVLLLGGLGVVLLTNPTFSAFSLGLVLVCISLFY
ILLNSYFVAVAQLLIYVGAINVLIIFAVMFVNGSEWSKDKNFWTIGDGFT
SLVCITIPFSLMTTIPDTSWYGILWTTRSNQIVEQGLINNVQQIGIHLAT
DFYLPFELISIILLVSLIGAITMARQ
>NC_001666@ZemaCp089@ndhg@112993@113523@R@1@177 NADH_dehydrogenase_subunit_6
MDLPGPIHEILVLFGGFGLLLGGLGVVLLTNPIYSAFSLGLVLVCISLFY
FLLNSYFVAVAQLLIYVGAINVLIIFAVMFVNGSEWSKDKNYWTIGDGFT
LLLCITIPFSLMTTIPDTSWYGILWTTRSNQIVEQGLINNVQQIGIHLAT
DFYLPFELISLILLVSLIGAITMARQ
>NC_001879@NitaCp086@ndhg@120181@120711@R@1@177 NADH_dehydrogenase_subunit_6
MDLSEPIHDFLLVFLGSGLILGGLGVVLLPNPIYSAFSLGLVLVCTSLFY
ILSNSYFVAAAQLLIYVGAINVLIIFAVMFMNGSEYYKDFHLWTVGDGIT
SMVCISLFISLITTISDTSWYGIIWTTRSNQIIEQDFISNSQQIGIHLST
DFFLPFELISIILLVALIGAIAVARQ
>NC_002186@MeviCp100@ndhg@105252@105821@R@1@190 NADH_dehydrogenase_subunit_6
MSFSEQIQNLSLLLLEIGTIIGALGVVLLPNILYSGFLLGGVLICIAGIY
LLLNAEFIAAAQVLIYVGAINVIILFAIMLVNKIENLNPSNNQMMRNGLS
SFICFSFFILLSNMIFDTQWIDTVGVSTKYSISIIGNHIFSDFLLPFEIV
SVLLLVTLVGAVFIARKEDASEIEISKISFLNLPDPSKK
>NC_002202@SpolCp088@ndhg@116164@116694@R@1@177 NADH_dehydrogenase_subunit_6
MDLPGPIHDFLLVFLGSGLILGALGVVLFTNPIFSAFSLGLVLVCISLFY
ILANSHFVASAQLLIYVGAINVLIIFSVMFMSGPEYDKKFQLWTVGDGVT
SLVCISLFVSLISTILNTSWYGIIWTTKSNQILEQDLINASQQIGIHLST
DFFLPFELISIILLVSLIGAIAVARQ
>NC_002693@OeelhCp100@ndhg@123796@124326@R@1@177 NADH_dehydrogenase_subunit_6
MDLPGPIHDFLLVFLGSGLIVGGLGVVLLTNPIFSAFSLGLVLVCISLFF
SLSNSYFVAAAQLLIYVGAINVLILFAVMFMNGSEYSKDLTLWTVGDGIT
SLVCTSIFISLITTILDTSWYGIIWTTKSNQIIEQDLIGNSQQIGIHLST
DFFLPFELISIILLVSLIGAIAVARQ

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>AC_000188@LyesCp078@ndhh@123339@124520@R@1@394 NADH_dehydrogenase_subunit_7
MTAPTTRKDLMIVNMGPQHPSMHGVLRLIVTLDGEDVVDCEPILGYLHRG
MEKIAENRTIIQYLPYVTRWDYLATMFTEAITINGPEQLGNIQVPKRASY
IRVIMLELSRIASHLLWLGPFMADIGAQTPFFYIFRERELIYDLFEAATG
MRMMHNYFRIGGVAADLPYGWIDKCLDFCDYFLTGVAEYQKLITRNPIFL
ERVEGVGIIGRDEALNWGLSGPMLRASGIEWDLRKVDHYESYDEFDWQVQ
WQREGDSLARYLVRIGEMTESIKIIQQALEGIPGGPYENLEMRRFDRLKD
PEWNDFEYRFISKKPSPTFELSKQELYVRVEAPKGELGIFLIGDQSVFPW
RWKIRPPGFINLQILPQLVKRMKLADIMTILGSIDIIMGEVDR
>NC_000927@NeolCp115@ndhh@143205@144380@D@1@392 NADH_dehydrogenase_subunit_7
MIEAKTDPMIVSMGPHHPSMHGVLRLIVTLDGENVLDCEPVVGYLHRGME
KIAENRTIVQYLPYVTRWDYLATMFTEAITVNAPERLANIEVPRRASYLR
VIMLELSRIASHLLWLGPFMADLGAQTPFFYILREREMIYDLFEAATGMR
MMHNYFRVGGVAADVPYGWIDKCLDFCEYFLPKVDEYEALITRNPIFLKR
VKGVGTISPQQAINWGLSGPMLRASGVSWDLRKVDRYECYEDFHWSVESE
ETGDCLARYLVRIREMRTSTKIVQQALKSIPGGPTENLEARQLSQGRTSP
WNEFDYQFLGKKASPTFKMPRQEHYVRVEAPKGELGVFLIGDDHVFPWRW
KIRPPGFINVQILPNLVQGMKLADIMTILGSIDIIMGEVDR
>NC_000932@ArthCp080@ndhh@122011@123192@R@1@394 NADH_dehydrogenase_subunit_7
MKRPVTGKDLMIVNMGPHHPSMHGVLRLIVTLDGEDVVDCEPILGYLHRG
MEKIAENRAIIQYLPYVTRWDYLATMFTEAITVNGPEQLGNIQVPKRASY
IRVIMLELSRIASHLLWLGPFMADIGAQTPFFYIFREREFVYDLFEAATG
MRMMHNFFRIGGIAADLPYGWIDKCLDFCDYFLTEVVEYQKLITRNPIFL
ERVEGVGIIGGEEAINWGLSGPMLRASGIPWDLRKIDRYESYDEFEWEIQ
WQKQGDSLARYLVRLSEMTESIKIIQQALEGLPGGPYENLESRGFDRKRN
PEWNDFEYRFISKKPSPTFELSKQELYVRVEAPKGELGIFLIGDQSGFPW
RWKIRPPGFINLQILPELVKRMKLADIMTILGSIDIIMGEVDR
>NC_001319@MapoCp085@ndhh@102202@103380@R@1@393 NADH_dehydrogenase_subunit_7
MMILTKNKPMIVSMGPHHPSMHGVLRLIVTLDGEDVLDCEPVLGYLHRGM
EKIAENRTIVQYLPYVTRWDYLATMFTEAITVNAPEKLTNIQVPKRASYI
RIIMLELSRIASHLLWLGPFMADIGAQTPFFYIFREREMIYDLFESATGM
RMMHNYFRIGGVAVDLPYGWIDKCLDFCDYFLPKINEYERLITNNPIFLK
RVEGIGTVTREEAINWGLSGPMLRASGVQWDLRKVDHYECYDELDWKIQW
QKEGDSLARYLVRIGEMKESVKIIQQALKAIPGGPFENLEARRLNQGKNS
EWNLFEYQFISKKPSPTFKLPKQEHYVRVEAPKGELGIFLIGDDSVFPWR
LKIRSPGFINLQILPQLVKGMKLADIMTILGSIDIIMGEVDR
>NC_001320@OrsajCp094@ndhh@112708@113889@R@1@394 NADH_dehydrogenase_subunit_7
MSLPLTRKDLMIVNMGPQHPSMHGVLRLIVTLDGEDVIDCEPILGYLHRG
MEKIAENRTIIQYLPYVTRWDYLATMFTEAITVNAPEFLENIQIPQRASY
IRVIMLELSRIASHLLWLGPFMADLGAQTPFFYIFRERELIYDLFEAATG
MRMMHNYFRIGGVAADLPYGWIDKCLDFCDYFLRGVIEYQQLITQNPIFL
ERVEGVGFISGEEAVNWGLSGPMLRASGIQWDLRKVDLYESYNQFDWKVQ
WQKEGDSLARYLVRIGEMRESIKIIQQAVEKIPGGPYENLEVRRFKKAKN
SEWNDFEYRFLGKKPSPNFELSKQELYARVEAPKGELGIYLVGDDSLFPW
RWKIRPPGFINLQILPQLVKKMKLADIMTILGSIDIIMGEVDR
>NC_001666@ZemaCp092@ndhh@116456@117637@R@1@394 NADH_dehydrogenase_subunit_7
MSLSLKRKDLMIVNMGPQHPSMHGVLRLIVTLDGEDVIDCEPILGYLHRG
MEKIAENRSIIQYLPYVTRWDYLATMFTEAITVNAPEFLENIQIPKRASY
IRVIMLELSRIASHLLWLGPFMADLGAQTPFFYIFRERELIYDLFEAVTG
MRMMHNYFRIGGVAADLPYGWMDKCLDFCDYFLQGVVEYQELITQNPIFL
ERVEGVGFISGEEAVNWGLSGPMLRASGIQWDLRKIDPYESYNQFDWKVQ
WQKEGDSLARYLVRVGEMRESIKIIQQAVEKIPGGPYENLEARRFKKAKN
PEWNDFEYRFLGKKPSPNFELSKQELYVRVEAPKGELGIYLVGDDSLFPW
RWKIRPPGFINLQILPQLVKKMKLADIMTILGSIDIIMGEVDR
>NC_001879@NitaCp089@ndhh@123937@125118@R@1@394 NADH_dehydrogenase_subunit_7
MTAPTTRKDLMIVNMGPQHPSMHGVLRLIVTLDGEDVVDCEPILGYLHRG
MEKIAENRTIIQYLPYVTRWDYLATMFTEAITINGPEQLGNIQVPKRASY
IRVIMLELSRIASHLLWLGPFMADIGAQTPFFYIFRERELIYDLFEAATG
MRMMHNYFRIGGVAADLPYGWIDKCLDFCDYFLTGVAEYQKLITRNPIFL
ERVEGVGIIGGDEALNWGLSGPMLRASGIEWDLRKVDHYESYDEFDWQVQ
WQREGDSLARYLVRIGEMTESIKIIQQALEGIPGGPYENLEIRRFDRLKD
PEWNDFEYRFISKKPSPTFELSKQELYVRVEAPKGELGIFLIGDQSVFPW
RWKIRPPGFINLQILPQLVKRMKLADIMTILGSIDIIMGEVDR
>NC_002186@MeviCp103@ndhh@107611@108792@R@1@394 NADH_dehydrogenase_subunit_7
MTMLQTKTDPMVISMGPHHPSMHGVLRLIVTLDGENVIDCEPVLGYLHRA
MEKIAENRTIVQYLPYVTRWDYLATMFTEAITVNAPEKLANIEVPKRASY
IRVIMLELSRIASHLLWLGPFMADIGAQTPFFYILREREMIYDLFEAATG
MRMMHNYFRIGGVASDLPYGWVDKCLDFSDYFLPKVDEYERLITNNPIFL
KRVRDVGFISREEAINWGLSGPMLRASGVQWDLRKVDNYECYGELDWNVQ
WQSDGDCLARYLVRLGEMRESTKIIQQALKAIPGGPYENLEARRLSKGRK
SEWNNFEYQFVGKKPSPTFKIPKQEHYVRVEAPKGELGVFLMGDDNVFPW
RWKIRSPGFINVQILPELVRGMKLADIMTILGSIDIIMGEVDR
>NC_002202@SpolCp091@ndhh@119776@120957@R@1@394 NADH_dehydrogenase_subunit_7
MAVPTTRKDLMIVNMGPHHPSMHGVLRLIVTLDGEDVIDCEPIVGYLHRG
MEKIAENRTIIQYLPYVTRWDYLATMFTEAITVNGPEQLGNIQVPKRASY
IRVIMLELSRIASHLLWLGPFMADIGAQTPFFYILRERELIYDLFEAATG
MRMMHNYFRIGGVAADLPYGWIDKCLDFCDYFLIGLTEYQKLITRNPIFL
ERVENVGIIGGEEAINWGLSGPMLRASGIQWDLRKVDHYECYDEFDWEVQ
WQKEGDSLARYLIRIGEMAESVKIIQQALEGIPGGPYENLEIRRFNRIKY
PEWNDFEYRFISKKPSPAFELSKQELYVRVEAPKGELGIFLIGDQSVFPW
RWKIRPPGFINLQILPQLVKKMKLADIMTILGSIDIIMGEVDR
>NC_002693@OeelhCp103@ndhh@127260@128441@R@1@394 NADH_dehydrogenase_subunit_7
MNVTTTRKDLMIVNMGPHHPSMHGVLRLILTLDGEDVIDCEPILGYLHRG
MEKIAENRTVIQYLPYVTRWDYLATMFTEAITINGPEQLGNIQVPKRASY
IRIIMLELSRIASHLLWLGPFMADIGAQTPFFYIFRERELVYDLFEAATG
MRMMHNYFRIGGVAADLPYGWIDKCLDFCDYFLTAVSEYQKLITRNPIFL
ERVEGVGIIGGEEAINWGLSGPMLRASGIEWDLRKVDRYECYGELDWEIR
WQKEGDSLARYLVRMSEMTESIKIIQQALEGIPGGPYENLEIRCFDREKD
PEWDGFEYRFISKKPSPTFELPKQELYVRVEAPKGELGIFLIGDQSGFPW
RWKIRPPGFINLQILPQLVKRMKLADIMTILGSIDIIMGEVDR

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>AC_000188@LyesCp076@ndhi@120525@121028@R@1@168 NADH_dehydrogenase_subunit_I
MLPMITEFINYGQQTIRAARYIGQGFMITLSHANRLPVTIQYPYEKLITS
ERFRGRIHFEFDKCIACEVCVRVCPIDLPVVDWKLETDIRKKRLLNYSID
FGICIFCGNCVEYCPTNCLSMTEEYELSTYDRHELNYNQIALGRLPMSVI
DDYTIRTISNLPQINNE
>NC_000927@NeolCp117@ndhi@145747@146268@D@1@174 NADH_dehydrogenase_subunit_I
MFDFLTSLQTYRQEAAQAAQYIGQGFGVTFDHMSRRPITIHYPYEKLIPS
ERFRGRIHFEFDKCIACEVCVRVCPINLPVVDWDYQKSVKKKQLRSYSID
FGVCIFCGNCVEYCPTNCLSMTEEYELSVYDRHELNFDHVALGRVPTSVV
QDTLVTPVLGLGYLPKGELSSLP
>NC_000932@ArthCp078@ndhi@119244@119762@R@1@173 NADH_dehydrogenase_subunit_I
MLPMITGFMNYGQQTLRAARYIGQGFMITLSHTNRLPVTIQYPYEKLITS
ERFRGRIHFEFDKCIACEVCVRVCPIDLPVVDWKLETNIRKKRLLNYSID
FGICIFCGNCVEYCPTNCLSMTEEYEFSTYDRHELNYNQIALGRLPMSVI
DDYTIRTIWNSPQTKNGVNPLI
>NC_001319@MapoCp083@ndhi@99779@100330@R@1@184 NADH_dehydrogenase_subunit_I
MFSIINGLKNYNQQAIQAARYIGQGFLVTLDHMNRLPTTIQYPYEKLIPS
ERFRGRIHFEFDKCIACEVCVRVCPINLPVVDWELKKTIKKKQLKNYSID
FGVCIFCGNCVEYCPTNCLSMTEEYELSTYNRHELNYDQIALGRLPISII
EDSTIENIFNLTSLPKGKIEGHIYSRNITNIVN
>NC_001320@OrsajCp092@ndhi@110000@110536@R@1@179 NADH_dehydrogenase_subunit_I
MFPMVTGFMGQQTIRAARYIGQSFIITLSHTNRLPITIHYPYEKSITSER
FRGRIHFEFDKCIACEVCVRVCPIDLPLVDWRFEKDIKRKQLLNYSIDFG
VCIFCGNCVEYCPTNCLSMTEEYELSTYDRHELNYNQIALSRLPISIMGD
YTIQTIRNSTQSKIDEEKSWNSRTITDY
>NC_001666@ZemaCp090@ndhi@113707@114249@R@1@181 NADH_dehydrogenase_subunit_I
MFPMLTGFISYGQQTIRAARYIGQSFIITLSHTNRLPITIHYPYEKSITS
ERFRGRIHFEFDKCIACEVCVRVCPIDLPLVDWRFEKDIKRKQLLNYSID
FGVCIFCGNCVEYCPTNCLSMTEEYELSTYDRHELNYNQIALSRLPISIM
GDYTIQTIRNSPQSKIDEEKSWNSRTITDY
>NC_001879@NitaCp087@ndhi@121108@121611@R@1@168 NADH_dehydrogenase_subunit_I
MLPMITEFINYGQQTIRAARYIGQGFMITLSHANRLPVTIQYPYEKLITS
ERFRGRIHFEFDKCIACEVCVRVCPIDLPVVDWKLETDIRKKRLLNYSID
FGICIFCGNCVEYCPTNCLSMTEEYELSTYDRHELNYNQIALGRLPMSVI
DDYTIRTISNLPQIKNE
>NC_002186@MeviCp101@ndhi@105946@106476@R@1@177 NADH_dehydrogenase_subunit_I
MFNFIDNVQTYSKEALQAAKYIGQGFMVTFDHMNRRAITIQYPYEKLIPS
ERFRGRIHFEFDKCIACEVCVRVCPINLPVVNWEFQKEKKKKQLQTYSID
FGVCIFCGNCVEYCPTNCLSMTEEYELSVYDRHELNYDNFALGRLPTMVN
NDSMVKGIKGLGYLPKGIIEGHIDNQ
>NC_002202@SpolCp089@ndhi@116981@117493@R@1@171 NADH_dehydrogenase_subunit_I
MFPMVTGFINYGQQTIRAARYIGQSFMITLSHANRLPVTIQYPYEKLITS
ERFRGRIHFEFDKCIACEVCVRACPIDLPVVDWKLETDIRKKRLLNYSID
FGICIFCGNCVEYCPTNCLSMTEEYELSTYDRHELNYNQIALGRLPISIT
DDYTIRTILNSPQTKEKACD
>NC_002693@OeelhCp101@ndhi@124541@125038@R@1@166 NADH_dehydrogenase_subunit_I
MFPMVTGFMNYGQQTVRAARYIGQGFMITLSHANRLPVTIQYPYEKLITS
ERFRGRIHFEFDKCIACEVCVRVCPIDLPVVDWKLETGVRKKRLLNYSID
FGVCIFCGNCVEYCPTNCLSMTEEYELSTYDRHELNYNQIALGRLPMSVI
DDYTIRTILNSAQIK

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>AC_000188@LyesCp065@psac@118564@118809@R@1@82 photosystem_I_subunit_VII
MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRTEDCVG
CKRCESACPTDFLSVRVYLWHETTRSMGLAY
>NC_000925@PopuCp189@psac@164452@164697@R@1@82 photosystem_I_subunit_VII
MAHSVKVYDTCIGCTQCVRACPCDVLEMVPWDGCKAKQIASAPRTEDCIG
CKRCETACPTDFLSVRVYLGAETTRSMGLAY
>NC_000926@GuthCp035@psac@33008@33253@D@1@82 photosystem_I_subunit_VII
MSHSVKVYDTCIGCTQCVRACPCDVLEMVAWDGCKAGQIASAPRTEDCIG
CKRCETACPTDFLSVRVYLGGETTRSMGLAY
>NC_000927@NeolCp112@psac@138977@139222@D@1@82 photosystem_I_subunit_VII
MSHSVKIYDTCIGCTQCVRACPTDVLEMVPWGGCKAAQIASAPRTEDCVG
CKRCESACPTDFLSVRVYLGAETTRSMGLAY
>NC_000932@ArthCp075@psac@117318@117563@R@1@82 photosystem_I_subunit_VII
MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRTEDCVG
CKRCESACPTDFLSVRVYLWHETTRSMGLAY
>NC_001319@MapoCp080@psac@98289@98534@R@1@82 photosystem_I_subunit_VII
MAHAVKIYDTCIGCTQCVRACPTDVLEMIPWDGCKANQIASAPRTEDCVG
CKRCESRCPTDFLSVRVYLGNETTRSMGLSY
>NC_001320@OrsajCp089@psac@108020@108265@R@1@82 photosystem_I_subunit_VII
MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRTEDCVG
CKRCESACPTDFLSVRVYLGPETTRSMALSY
>NC_001603@EugrCp046@psac@74937@75893@R@3@82 photosystem_I_subunit_VII
MSHSVKIYNTCIGCTQCVRACPTDVLEMVPWDGCKAGQIASSPRTEDCVG
CKRCESACPTDFLSVRVYLGSETSRSMGLAY
>NC_001631@PithCp145@psac@103521@103766@D@1@82 photosystem_I_subunit_VII
MAHSVKIYDTCIGCTQCVRACPTDVLEMIPWEGCKAKQIASAPRTEDCAG
CKRCESACPTDFLSVRVYLWHETTRSMGLAY
>NC_001666@ZemaCp087@psac@111760@112005@R@1@82 photosystem_I_subunit_VII
MSHSVKIYDTCIGCTHCVRACPTDVLEMIPWDGCKAKQIASAPRTEDCVG
CKRCESACPTDFLSVRVYLGPETTRSMALSY

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>AC_000188@LyesCp030@rpl2@86038@87528@R@2@275 ribosomal_protein_L2
MAIHLYKTSTPSTRNGTVDSQVKSNPRNNLIYGQRRCGKGRNARGIITAR
HRGGGHKRLYRKIDFRRNEKDIYGRIVTIEYDPNRNAYICLIHYGDGEKR
YILHPRGAIIGDTIVSGTEVPIKMGNALPLTDMPLGTAIHNIEITLGKGG
QLARAAGAVAKLIAKEGKSATLKLPSGEVRLISKNCSATVGQVGNVGVNQ
KSLGRAGSKRWLGKRPVVRGVVMNPVDHPHGGGEGRAPIGRKKPTTPWGY
PALGRRSRKRNKYSDNLILRRRSK
>AC_000188@LyesCp087@rpl2@153816@155306@D@2@275 ribosomal_protein_L2
MAIHLYKTSTPSTRNGTVDSQVKSNPRNNLIYGQRRCGKGRNARGIITAR
HRGGGHKRLYRKIDFRRNEKDIYGRIVTIEYDPNRNAYICLIHYGDGEKR
YILHPRGAIIGDTIVSGTEVPIKMGNALPLTDMPLGTAIHNIEITLGKGG
QLARAAGAVAKLIAKEGKSATLKLPSGEVRLISKNCSATVGQVGNVGVNQ
KSLGRAGSKRWLGKRPVVRGVVMNPVDHPHGGGEGRAPIGRKKPTTPWGY
PALGRRSRKRNKYSDNLILRRRSK
>NC_000925@PopuCp126@rpl2@103379@104263@R@1@295 ribosomal_protein_L2
MAIRLYRAYTPGTRNRTVSTFSEITTDKPEKSLINKHHFCKGRNNRGVIT
CRHKGGGHKQRYRLIDFKRNRHNIIAKVASIEYDPNRNARIALLHYLDGE
KRYILHPRSLSVGAIVVSGPMAPIEVGNALPLSTIPLGTAVHNIELRPYC
GGQIVRSAGTYAQIVAKEGNFVTVKLPSSEVRMIRKECYATIGQVGNIDA
SNITLGKAGRSRWLGKRPTVRGVVMNPVDHPHGGGGEGKSPIGRSRPVTP
WGKPALGVKTRNPNKYSNPYVLLVVNKVYLTYNLILKYNVEINT
>NC_000926@GuthCp113@rpl2@100540@101367@D@1@276 ribosomal_protein_L2
MGIRIYKSYTPGTRNRSSSDFVEITKSKPEKSLLRKKLSCAGRNNRGLIT
VRHKGGGHKQRYRLVDFKRNKLDIPAIVASVEYDPNRNARIALLHYQDGE
KRYILHPKKLAVGDKIYSGINVPIEIGNAMPLYNVPLGTAVHNVELIPGR
GGQIVRSAGTSAQVVAKDGQVVTIKMPSNEVRMIYKNCYATIGEVGNADI
KNIRLGKAGRKRWLGIRPSVRGVVMNPCDHPHGGGEGRSPIGRAKPVTPW
GKPALGVKTRRQNKYSDFCIIRSRN
>NC_000927@NeolCp022@rpl2@15904@16731@R@1@276 ribosomal_protein_L2
MGIRFYRAHTPGTRNRSVSDFHEITTSTPTKSLTHANHRARGRNHSGSIT
TRWRGGGHKRLYRQIDFRRDKVGVLARVATVEYDPNRSARIALLHYQDGS
KRYILHPQGLAIGAEVMSSPEAPISIGNALPLVNMPLGTEVHNIELRPYN
GGQLVRAAGAVAQLVAKEGGFGTLRMPSGEVRLVAKDCWATVGQVGHVES
INLTLGKAGRSRWLDRRPRVRGSVMNACDHPHGGGEGRCPIGHPGPLTPW
GKPALGQRTRARKKYSDALLVRRRK
>NC_000932@ArthCp064@rpl2@84337@85843@R@2@275 ribosomal_protein_L2
MAIHLYKTSTPSTRNGAVDSQVKSNPRNNLICGQHHCGKGRNARGIITAR
HRGGGHKRLYRKIDFRRNAKDIYGRIVTIEYDPNRNAYICLIHYGDGEKR
YILHPRGAIIGDTIVSGTEVPIKMGNALPLTDMPLGTAIHNIEITLGRGG
QLARAAGAVAKLIAKEGKSATLKLPSGEVRLISKNCSATVGQVGNVGVNQ
KSLGRAGSKCWLGKRPVVRGVVMNPVDHPHGGGEGRAPIGRKKPVTPWGY
PALGRRTRKRKKYSETLILRRRSK
>NC_000932@ArthCp085@rpl2@152806@154312@D@2@275 ribosomal_protein_L2
MAIHLYKTSTPSTRNGAVDSQVKSNPRNNLICGQHHCGKGRNARGIITAR
HRGGGHKRLYRKIDFRRNAKDIYGRIVTIEYDPNRNAYICLIHYGDGEKR
YILHPRGAIIGDTIVSGTEVPIKMGNALPLTDMPLGTAIHNIEITLGRGG
QLARAAGAVAKLIAKEGKSATLKLPSGEVRLISKNCSATVGQVGNVGVNQ
KSLGRAGSKCWLGKRPVVRGVVMNPVDHPHGGGEGRAPIGRKKPVTPWGY
PALGRRTRKRKKYSETLILRRRSK
>NC_001319@MapoCp072@rpl2@79137@80514@R@2@278 ribosomal_protein_L2
MAIRLYRAYTPGTRNRSVPKFDEIVKCQPQKKLTYNKHIKKGRNNRGIIT
SQHRGGGHKRLYRKIDFQRNKKYITGKIKTIEYDPNRNTYICLINYEDGE
KRYILYPRGIKLDDTIISSEEAPILIGNTLPLTNMPLGTAIHNIEITPGK
GGQLVRAAGTVAKIIAKEGQLVTLRLPSGEIRLISQKCLATIGQIGNVDV
NNLRIGKAGSKRWLGKRPKVRGVVMNPIDHPHGGGEGRAPIGRKKPLTPW
GHPALGKRSRKNNKYSDTLILRRRKNS
>NC_001320@OrsajCp069@rpl2@81180@82664@R@2@274 ribosomal_protein_L2
MAKHLYKTPIPSTRKGTIDRQVKSNPRNNLIHGRHRCGKGRNSRGIITAR
HRGGGHKRLYRKIDFRRNQKDISGRIVTIEYDPNRNAYICLIHYGDGEKG
YILHPRGAIIGDTIVSGTKVPISMGNALPLTDMPLGTAIHNIEITRGRGG
QLARAAGAVAKLIAKEGKSATLRLPSGEVRLVSQNCLATVGQVGNVGVNQ
KSLGRAGSKCWLGKRPVVRGVVMNPVDHPHGGGEGKAPIGRKKPTTPWGY
PALGRRTRKRKKYSDSFILRRRK
>NC_001320@OrsajCp109@rpl2@132454@133938@D@2@274 ribosomal_protein_L2
MAKHLYKTPIPSTRKGTIDRQVKSNPRNNLIHGRHRCGKGRNSRGIITAR
HRGGGHKRLYRKIDFRRNQKDISGRIVTIEYDPNRNAYICLIHYGDGEKG
YILHPRGAIIGDTIVSGTKVPISMGNALPLTDMPLGTAIHNIEITRGRGG
QLARAAGAVAKLIAKEGKSATLRLPSGEVRLVSQNCLATVGQVGNVGVNQ
KSLGRAGSKCWLGKRPVVRGVVMNPVDHPHGGGEGKAPIGRKKPTTPWGY
PALGRRTRKRKKYSDSFILRRRK

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>AC_000188@LyesCp026@rpl23@87547@87828@R@1@94 ribosomal_protein_L23
MDGIKYAVFTDKSIRLLGKNQYTSNVESGSTRTEIKHWVELFFGVKVIAM
NSHRLPGKSRRMGPIMGHTMHYRRMIITLQPGYSIPPLRKKRT
>AC_000188@LyesCp083@rpl23@153516@153797@D@1@94 ribosomal_protein_L23
MDGIKYAVFTDKSIRLLGKNQYTSNVESGSTRTEIKHWVELFFGVKVIAM
NSHRLPGKSRRMGPIMGHTMHYRRMIITLQPGYSIPPLRKKRT
>NC_000925@PopuCp127@rpl23@104311@104613@R@1@101 ribosomal_protein_L23
MDSIDSRDLLDLVKYPIITDKTTKLLEENQYCFAVDPNATKINIKAAIQY
IFNVQVTGVNTCHPPKKKRSIGRFIGKRPHYKKAIITLASKDSINLFPET
>NC_000926@GuthCp112@rpl23@100237@100524@D@1@96 ribosomal_protein_L23
MHALIDLVKYPLITDKATRLLELNQYTFLTSRVATKTDIKNAIEFLFNVK
VISINTCLLPLKRKRLGKFVGSKPRYKKAVVTLEKNNTINLFSEN
>NC_000927@NeolCp023@rpl23@16871@17149@R@1@93 ribosomal_protein_L23
MIIDLVKRPVITEKATRILEKNQYTFDVELSLTKPKIKALIEKAFKVEVV
SVNTHRPPRRKRRLGTTQGYLPRYKRAIITLKRGFMIPLTPF
>NC_000932@ArthCp065@rpl23@85862@86143@R@1@94 ribosomal_protein_L23
MDGIKYAVFTDKSIRLLGKNQYTFNVESGSTRTEIKHWVELFFGVKVIAM
NSHRLPGKVKRMGPILGHTMHYRRMIITLQPGYSIPPLRKKRT
>NC_000932@ArthCp084@rpl23@152506@152787@D@1@94 ribosomal_protein_L23
MDGIKYAVFTDKSIRLLGKNQYTFNVESGSTRTEIKHWVELFFGVKVIAM
NSHRLPGKVKRMGPILGHTMHYRRMIITLQPGYSIPPLRKKRT
>NC_001319@MapoCp073@rpl23@80550@80825@R@1@92 ribosomal_protein_L23
MNQVKYPVLTEKTIRLLEKNQYSFDVNIDSNKTQIKKWIELFFNVKVISV
NSHRLPKKKKKIGTTTGYTVRYKRMIIKLQSGYSIPLFSNK
>NC_001320@OrsajCp071@rpl23@82683@82964@R@1@94 ribosomal_protein_L23
MDGIKYAVFTEKSLRLLGKNQYTFNVESGFTKTEIKHWVELFFGVKVVAV
NSHRLPGKGRRMGPILGHTMHYRRMIITLQPGYSIPLLDREKN
>NC_001320@OrsajCp108@rpl23@132154@132435@D@1@94 ribosomal_protein_L23
MDGIKYAVFTEKSLRLLGKNQYTFNVESGFTKTEIKHWVELFFGVKVVAV
NSHRLPGKGRRMGPILGHTMHYRRMIITLQPGYSIPLLDREKN

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>AC_000188@LyesCp036@rpl32@114504@114671@D@1@56 ribosomal_protein_L32
MAVPKKRTSTSKKRIRKNIWKRKGYWVALKAFSLAKSLSTGNSKSFFVRQ
TKINK
>NC_000925@PopuCp022@rpl32@16239@16418@D@1@60 ribosomal_protein_L32
MAVPKKRTSKAKKNARKANWKNQAKTEAQKALSLAKSVLTGKSNGFVYNT
LEVADAIVE
>NC_000926@GuthCp026@rpl32@24770@24931@D@1@54 ribosomal_protein_L32
MAVPKKRTSRSKTNSRFANWLNKSNLQAQRAISKAKSITNKKNTVNDETI
ETE
>NC_000927@NeolCp122@rpl32@149220@149447@D@1@76 ribosomal_protein_L32
MAVPKKRKSKSRANSQNHVWKREIVKQARRAVSLAKALLGGNTNFLLVSP
GPTTPIKPNPKKQTGRRPRSQRRRT
>NC_000932@ArthCp072@rpl32@113449@113607@D@1@53 ribosomal_protein_L32
MAVPKKRTSISKKRIRKKIWKRKGYWTSLKAFSLGKSLSTGNSKSFFVQQ
NK
>NC_001319@MapoCp076@rpl32@93886@94095@D@1@70 ribosomal_protein_L32
MAVPKKRTSKSKTRIRKAIWKNKANKSALRAFSLAKSILTNRSKSFYYTI
NDKLLNSSKSISTSKLDES
>NC_001320@OrsajCp086@rpl32@104352@104543@D@1@64 ribosomal_protein_L32
MAVPKKRTSMSKKRIRKNLWKKKTYFSIVQSYSLAKSRSFSGVSEHPKPK
GFSRQQTNNRVLG
>NC_001603@EugrCp047@rpl32@75928@76092@R@1@55 ribosomal_protein_L32
MAVPKKKMSKSRRNSRKSNWKKKVLKKVLFALSLGKSFEANTNVNFSFGD
KLPQ
>NC_001631@PithCp150@rpl32@107399@107611@R@1@71 ribosomal_protein_L32
MAVPKKRTSRSKKKIRKNVRKGKAYRAAIKAFSLAKSISTGHSKSFYCIV
NDDSSGSSESKLTAIDLDDP
>NC_001666@ZemaCp084@rpl32@108127@108306@D@1@60 ribosomal_protein_L32
MAVPKKRTSMSKKRIRKNLWKKKTYFSIVQSYSLAKSRSFSRGNEHPKPK
GFSGQQANK

30
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>AC_000188@LyesCp029@rps15@124632@124895@R@1@88 ribosomal_protein_S15
MVKNSVISVISQEEKKGSVEFQVFNFTNKIRRLTSHLELHKKDYLSQRGL
KKILGKRQRLLAYLAKKNRVRYKELINRLDIRETKTR
>NC_000932@ArthCp081@rps15@123296@123562@R@1@89 ribosomal_protein_S15
MIKNIVISFEEQKEESRGSVEFQVFSFTNKIRRLTSHLELHRKDYLSQRG
LRKILGKRQRLLAYLSKKNRVRYKELINQLNIRELKTR
>NC_001319@MapoCp086@rps15@103433@103699@R@1@89 ribosomal_protein_S15
MSKNLFMDLSSISEKEKGSVEFQIFRLTNRVVKLTYHFKKHGKDYSSQRG
LWKILGKRKRLLAYLFKTNFVSYENLIIQLGIRGLKKN
>NC_001320@OrsajCp083@rps15@100818@101090@D@1@91 ribosomal_protein_S15
MKKKGGRKIFGFMVKEEKEENWGSVEFQVFSFTNKIRRLASHLELHKKDF
SSERGLRRLLGKRQRLLAYLAKKNRVRYKKLISQLDIRER
>NC_001320@OrsajCp095@rps15@114028@114300@R@1@91 ribosomal_protein_S15
MKKKGGRKIFGFMVKEEKEENWGSVEFQVFSFTNKIRRLASHLELHKKDF
SSERGLRRLLGKRQRLLAYLAKKNRVRYKKLISQLDIRER
>NC_001631@PithCp139@rps15@101136@101402@D@1@89 ribosomal_protein_S15
MINNLSISSSLIPDKQRGSVESQVFYLTNRVLRLTQHLQLHGRDYSSQRG
LWKILSKRKQLLVYLSKRDKLRYDDLIGQLGIRGLKTR
>NC_001666@ZemaCp082@rps15@104729@104965@D@1@79 ribosomal_protein_S15
MVKEEKQENRGSVEFQVFSFTNKIRRLASHLELHKKDFSSERGLRRLLGK
RQRLLAYLAKKNRVRYKKLISQLDIREK
>NC_001666@ZemaCp093@rps15@117772@118008@R@1@79 ribosomal_protein_S15
MVKEEKQENRGSVEFQVFSFTNKIRRLASHLELHKKDFSSERGLRRLLGK
RQRLLAYLAKKNRVRYKKLISQLDIREK
>NC_001879@NitaCp090@rps15@125230@125493@R@1@88 ribosomal_protein_S15
MVKNSVISVISQEEKRGSVEFQVFNFTNKIRRLTSHLELHKKDYLSQRGL
KKILGKRQRLLAYLSKKNRVRYKELINQLDIRETKTR
>NC_002186@MeviCp104@rps15@109145@109417@R@1@91 ribosomal_protein_S15
MLKKKIIKTHANHTNDTGSTQVQVSLLSSRVAQLTKHLNNHKNDYSSQRG
LKKLLGQRKRLLKYLFVKDPLGYNNLIIQLGIRPGKSLVN

50
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>AC_000188@LyesCp008@rps7@98721@99188@R@1@156 ribosomal_protein_S7
MSRRGTAEKKTAKSDPIYRNRLVNMLVNRILKHGKKSLAYQIIYRAVKKI
QQKTETNPLSVLRQAIRGVTPDITVKARRVGGSTHQVPIEIGSTQGKALA
IRWLLAASRKRPGRNMAFKLSSELVDAAKGSGDAIRKKEETHRMAEANRA
FAHFR
>AC_000188@LyesCp022@rps7@142156@142623@D@1@156 ribosomal_protein_S7
MSRRGTAEKKTAKSDPIYRNRLVNMLVNRILKHGKKSLAYQIIYRAVKKI
QQKTETNPLSVLRQAIRGVTPDITVKARRVGGSTHQVPIEIGSTQGKALA
IRWLLAASRKRPGRNMAFKLSSELVDAAKGSGDAIRKKEETHRMAEANRA
FAHFR
>NC_000925@PopuCp103@rps7@92209@92679@R@1@157 ribosomal_protein_S7
MSRRNTAKKRFASPDPLYKSRLVSMLTVRILKSGKKTLAQRIIYQALDIV
KERTETDPLNVLEKAIRNITPLVEVKARRVGGSTYQVPIEVRAYRGTNLA
LRWITRFSRERSGKSMSMKLANEIMDAANETGNSIRKREETHRMAEANKA
FAHYRY
>NC_000926@GuthCp136@rps7@111745@112215@D@1@157 ribosomal_protein_S7
MSRRSTTKKKLALPDPIYNSRLVNMLTVRILKEGKKHLAQRIIYNAFDII
KQRTGEDAILVFESAIKKVTPLVEVKARRIGGSTYQVPMEVRAFRGTNLA
LRWITKYARERAGKSMSMKLANEIMDAANETGSSIRKREEIHRMAEANKA
FAHYRF
>NC_000927@NeolCp044@rps7@48318@48788@D@1@157 ribosomal_protein_S7
MSRRNTAVKRSISSDPVYNSQLIHMMISHILKEGKKALAYRLMYDAMKRI
EKTTQQDPILVVERAVRNATPTIEVKARRMGGSIYQVPLEVKPERGTALA
LRWILLAARNRTGRDMVAKLSNELMDASNRIGNAVRKRDEMHRMAEANKA
FAHIRV
>NC_000932@ArthCp069@rps7@97478@97945@R@1@156 ribosomal_protein_S7
MSRRGTAEEKTAKSDPIYRNRLVNMLVNRILKHGKKSLAYQIIYRALKKI
QQKTETNPLSVLRQAIRGVTPDIAVKARRVGGSTHQVPIEIGSTQGKALA
IRWLLGASRKRPGRNMAFKLSSELVDAAKGSGDAIRKKEETHRMAEANRA
FAHFR
>NC_000932@ArthCp088@rps7@140704@141171@D@1@156 ribosomal_protein_S7
MSRRGTAEEKTAKSDPIYRNRLVNMLVNRILKHGKKSLAYQIIYRALKKI
QQKTETNPLSVLRQAIRGVTPDIAVKARRVGGSTHQVPIEIGSTQGKALA
IRWLLGASRKRPGRNMAFKLSSELVDAAKGSGDAIRKKEETHRMAEANRA
FAHFR
>NC_001319@MapoCp002@rps7@892@1359@D@1@156 ribosomal_protein_S7
MSRKSIAEKQVAKPDPIYRNRLVNMLVNRILKNGKKSLAYRILYKAMKNI
KQKTKKNPLFVLRQAVRKVTPNVTVKARRIDGSTYQVPLEIKSTQGKALA
IRWLLGASRKRSGQNMAFKLSYELIDAARDNGIAIRKKEETHKMAEANRA
FAHFR
>NC_001320@OrsajCp076@rps7@87944@88414@R@1@157 ribosomal_protein_S7
MSRRGTAEKRTAKSDPIFRNRLVNMVVNRIMKDGKKSLAYQILYRAVKKI
QQKTETNPLLVLRQAIRRVTPNIGVKTRRNKKGSTRKVPIEIGSKQGRAL
AIRWLLEASQKRPGRNMAFKLSSELVDAAKGGGGAIRKKEATHRMAEANR
ALAHFR
>NC_001320@OrsajCp103@rps7@126704@127174@D@1@157 ribosomal_protein_S7
MSRRGTAEKRTAKSDPIFRNRLVNMVVNRIMKDGKKSLAYQILYRAVKKI
QQKTETNPLLVLRQAIRRVTPNIGVKTRRNKKGSTRKVPIEIGSKQGRAL
AIRWLLEASQKRPGRNMAFKLSSELVDAAKGGGGAIRKKEATHRMAEANR
ALAHFR

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>AC_000188@LyesCp019@ycf1@125297@130972@R@1@1892 ycf1_protein
MIFQSFLLGNLVSLCMKIINSVVVVGLYYGFLTTFSIGPSYLFLLRALVM
EEGTEKKVSATTGFITGQLMMFISIYYAPLHLALGRPHTITVLALPYLLF
HFFWNNHKHFFDYGSTTRNSMRNLSIQCVFLNNLIFQLFNHFILPSSMLA
RLVNIYLFRCNNKILFVTSGFVGWLIGHILFMKWLGLVLVWIRQNHSIRS
NKYIRSNKYLVLELRNSMARIFSILLFITCVYYLGRIPSPILTKKLKEAS
KTEERVESEEERDVEIETASEMKGTKQEQEGSTEEDPYPSPSLFSEEGWD
PDKIDETEEIRVNGKDKIKDKFHSHLTETGYNNINTSNSPIYDYQDSYLN
NNNTGNLENCKLQLLDKKNENQEQDLFWFQKPLVSLLFDYNRWNRPFRYI
KNNRFEQAVRTEMSQYFFDTCKSDGKQKISFTYPPSLSTFWKMIKRKIPL
LSLQKTLPNELDTQWVSTNKEKSNNLNKEFLNRLEILDKESLSLDILETR
TRFCNDDTKKEYVPKMYDPLLNGLYRGTIKKGVSSSIINNTLLENWEKRV
RLNRIHTIFLPNIDYQEFEQKAYTIDKKPLSTEIDEFLTLINELGNEAKS
SLNLKGLSLFSDQEQRRANSEKRTKFVKFVFNALDPNETKSGKKSIGIKE
ISKKVPRWSHKLITELDQQMGEFKDRASMDHQLRSRKAKRVVIFTDNKAT
KDAEEEVALISYSQQSDFRRGIITGSMRAQRRKTFISKLFQANVHSPLFV
DRITPLRLFSFDISELIKPILKNWTDKEGEFKILESREEQTKREEKKEKD
KKEDNKRKEQARIAIEEAWDTIPLAQIIRGYMLITQSILRKYILLPALII
AKNIGRMLFLQLPEWSEDLQEWNREMQIKCTYNGVQLSETEFPKNWLRDG
IQIKILFPFCLKPWHISKLYPSRRELMKKQKQKDDFCFLTVWGMEAELPF
GSPRKRPSFFEPIFKELEKKIGKFKKKYFLTLKILKGKTKLFRKVSKETT
KLFIKSIGFLKKIKKELSKVNLIVLFRFKEISESNETKKEKDYLISNQII
NESFRQIESGNWPNSSLIETKMKDLTNRTSTIKNKIERITKEKKKVTPEI
DINPNKTNNIKKFESPKKIFQILKSRNTRVIWKFHYFLKLFIQRLYINLF
LSIINIPRITTQLFLKSTNKLIEKFISNNEINQEKINNKKKIHFMFISTI
KKSLYNISKKNSHILCDLSYLSQAYVFYKLSQTQVINFSKFRSVLQYNTT
SCFLKTKIKDYFKTLGIFHSELKHKKLQSYRINQWKNWLRWHYQYDLSQI
RWSRLMPKKWRTRVNQSCMAQNKNRNLNKWNSYEKDQLLHYKKENDSELY
SLSNEKDNFKKCYGYGLLAYKSINYENKSDSFFSRLPFEVQVKKNLEISY
NSNTSKHNFVDMPGNLHINNYLRKGNILDRERNLDRKYFDWKIIHFSLRQ
KGDIEAWVKIDTNSNPNTKIGINNYQIIDKIEKKGVFYLTTHQNPEKTQK
NSKKFFFDWMGMNEKIFNRPILNLEFWFFPEFVLLYNVYKIKPWIIPSKF
LLFNLNTNKNVSQNKNQNFFLPSNKKIKIKNRSQEAKEPPSQRERGSDIE
NKGNLSPVFSKHQTDLEKDYVESDTKKGKNKKQYKSNTEAELDLFLKRYL
LFQLRWNGALNQRMFENIKVYCLLLRLINPTKITISSIQRREMSLDIMLI
QANLPLTDLMKKGVLIIEPIRLSVKDNGQFIMYQTIGISLIHKSKHQTNQ
RYREQRYVDKKNFDEFILQPQTQRINTEKTHFGLLVPENILWSRRRRELR
IRSFFNSWNWNVVDRNSVFCNETNVKNWSQFLGERKPLYKDKNELIKFKF
FFWPNYRLEDLACMNRYWFDTNNGSRFSILRIHMYPRLKIN
>NC_000932@ArthCp070@ycf1@109405@110436@D@1@344 hypothetical_protein
MMVFQSFILGNLVSLCMKIINSVVVVGLYYGFLTTFSIGPSYLFLLRARV
MDEGEEGTEKKVSATTGFIAGQLMMFISIYYAPLHLALGRPHTITVLALP
YLLFHFFWNNHKHFFDYGSTTRNEMRNLRIQCVFLNNLIFQLFNHFILPS
SMLARLVNIYMFRCNNKMLFVTSSFVGWLIGHILFMKWVGLVLVWIQQNN
SIRSNVVIRSNKYKFLVSELRNSMARIFSILLFITCVYYLGRIPSPIFTK
KLKGTSETGGTKQDQEVSTEEAPFPSLFSEEGEDLDKIDEMEEIRVNGKD
KINKDDEFHVRTYYNYKTVSENLYGNKENSNLEFFKIKKKEDH
>NC_000932@Arthcp087@ycf1@123884@129244@R@1@1787 Ycf1
MMVFQSFILGNLVSLCMKIINSVVVVGLYYGFLTTFSIGPSYLFLLRARV
MDEGEEGTEKKVSATTGFIAGQLMMFISIYYAPLHLALGRPHTITVLALP
YLLFHFFWNNHKHFFDYGSTTRNEMRNLRIQCVFLNNLIFQLFNHFILPS
SMLARLVNIYMFRCNNKMLFVTSSFVGWLIGHILFMKWVGLVLVWIQQNN
SIRSNVVIRSNKYKFLVSELRNSMARIFSILLFITCVYYLGRIPSPIFTK
KLKGTSETGGTKQDQEVSTEEAPFPSLFSEEGEDLDKIDEMEEIRVNGKD
KINKDDEFHVRTYYNYKTVSENLYGNKENSNLEFFKIKKKEDHFLWFEKP
FVTLVFDYKRWNRPNRYIKNDKIENIVRNEMSQYFFYTCQSDGKERISFT
YPPNLSTFFEMIQKRIPSFTKEKKTFDQVSTYWSLIHEEKRENLKKEFLN
RIEALDKEWSVENILEKTTRFCYNEAKKEYLPKIYDPFLHGISRGRIKKL
PPFQIITETYRKNNLGGSWINKIHGLLLKINYKKFEQTIEKFNRKSLSIE
KKLSFFSEPQQEEKINSEEEIKTFKFLFDIVRTDSNDQTLIKNFMDFPEI
NKKVPRWSYKLISELEELEGENEENVPMEPGIRSRKAKRVVVFTDKEPHG
EIYTNLKDNQNSDQNDEMALIRYSQQSDFRREIIKGSMRSQRRKTVIWEF
FQAKVHSPLFFDRIDKLFFFSFDIWGLKKKIIKNFIWKKKIDKKEEEQSK
REETRRIEIAETWDSFLFAQIIRGSLLVTQSILRKYIILPLLIIIKNSVR
MLLFQFPEWSQDLKDWKREMHVKCTYNGVQLSETEFPRNWLTDGIQIKIL
FPFYLKPWHKSKFQASQKARLKKTKDKGEKNDFCFLTVWGMETELPFGSA
QRKPSFFEPISKELKKRIKKLKKKSFVVLKIFKERAPIFLKVAKETKNWI
LKNFIFIKGISKRNLIPLFGPREIYELNEPKKDSIISNQMIHELSVQNKS
LEWTNSSLSEKKIKNLIDRKKTIRNQIEEISKEKQNLTNSCTKLRYDSKI
IESSKKIWQTFKRKNTRLIRKSIFFFKFCIEQMSIAIFLGIINIPRITTQ
LFFESTKKILDKYIYKNEENGEKKKNTLYFISTIKNLISNKKKMSYDLCS
LSQAYVFYKLSQIKVSNFCKLKAVLEYNICITSFFVKNKIKVFFQEHGIF
HYELKNKTFLNSEVNQWKNWLRSQYQYNLPQISWARLVTQNWKNKINKDS
LVLNPSLTKEDSYEKKKFDNYKKQKFFEADSLLNPKHNVKKDSIYNLFCY
KSIHSTEKNFDMSIGIALDNCLVSSFLEKYNIRGMGEIRHRKYLDWRILN
FWFTKKVTIEPWVDTKSKKKYINTKVQNYQKIDKITQTDLANKKRNFFDW
MGMNEEILNQRITNFEFFFFPEFFLFSSTYKMKPWVIPIKLLLLNFNENI
NVNKKIIRKKKGFIPSNEKESLRFYNLNKEEKESAGQVELESDKETKRNP
EAARLNQEKNIEENFAESTIKKRKNKKQYKSNTEAELDLFLTRYSRFQLR
WNCFFNQKILNNVKVYCLLVRLNNPNEIAVSSIERGEMSLDILMIEKNFT
FAKLMKKGILIIEPVRLSVQNDGQLIIYRTIGISLVHKNKHKISKRYKKK
SYINKKFFEKSITKYQNKTVNKKKNNYDFFVPEKILSPKRRREFRILICF
NLKKKNARDTNSRFDKNIQNLTTVLHKKKDLDLDKDKNNLINLKSFLWPN
FKLEDLACMNRYWFNTTNGNHFSMIRIRMYTRFPIP
>NC_001879@NitaCp151@ycf1@125891@131599@R@1@1903 Ycf1
MMIFQSFLLGNLVSLCMKIINSVVVVGLYYGFLTTFSIGPSYLFLLRALV
MEEGTEKKVSATTGFITGQLMMFISIYYAPLHLALGRPHTITVLALPYLL
FHFFWNNHKHFFDYGSTTRNSMRNLSIQCVFLNNLIFQLFNHFILPSSML
ARLVNIYLFRCNSKILFVTSGFVGWLIGHILFMKWLGLVLVWIRQNHSIR
SNKYIRSNKYLVLELRNSMARIFSILLFITCVYYLGRIPSPILTKKLKEA
SKTEERVESEEERDVEIETASEMKGTKQEQEGSTEEDPYPSPSLFSEERW
DPDKIDETEEIRVNGKDKIKDKFHSHLTETGYNNINTSNSPIYDYEDSYL
NNNNTGNTEIFKLQLLDKKNENKDLFWFQQPLVSLLFDYNRWNRPFRYIK
NNRFEQAIRTEMSQYFFNTCKSDGKQRISFTYPPSLSTFWKMIKRRIPLL
SLQKTLPNELDNQWISTNKEKSNNLNKEFLNRLEVLDKESFSLDILETRT
RLCNDDTKKEYVPKMYDPLLNGPYRGTIKKKFSPSIINNTSLENLKERVR
INRIHTIFLPNTDYQELEQKVDTVAKKPLSTEIDEFLTLINEFGNEPKSS
LNLKDLSLFSDQEQGRVNSEKRTKFVKFVFNAIAPNGTTSEKKSIGIKEI
SKKIPRWSHKLITELEQQSGDYQEGVPLDHQIRSRKAKRVVIFTANNQNN
DPDTKDTDTADQDQTKEVALIRYSQQPDFRRGIIKGSMRAQRRKTVIWKL
FQANVHSPLFLDRITPPFLFSFDISGLIKPIFRNWSGKEGEFKILESREE
QTKREEKKEKDKKGENKRKEKARIEIAEAWDTIPFAQIIRGYMLITQSIL
RKYIVLPSLIIAKNLGRMLVLQLPEWSEDLQEWNREMHIKCTYNGVQLSE
TEFPKNWLKDGIQIKILFPFCLKPWHISKLYSSRGELMKKKKQKDDFCFL
TVWGMEAELPFGSPRKRPSFFEPIFKELEKKIGKFKKKYFITLKVFKGKI
KLFRRISKETKKWLIKSSLFIKKMKKELSKVNPIVLFRLKEIDESNETKK
EKDSLMSNQIINESFSQIESGNWPNSSLIESKMKDLTDRTSTIKNQIERI
TKEKKKVTPEIDISPNKTNNIKKFESPKKIFQILKRRNTRLIWKFHYFLK
LFIQRLYIDLFLSIINIPRINTQLFLESTNKLIDKYISNNEINQEKINNQ
KKIHFISTIKKSLYNISKKNSHIFFDLSYLSQAYVFYKLSQPQVINLSKL
RSVLQYNRTSFFLKTKIKDYFRTLGIFHSELKHKKLQSYRINQWKNWLRR
HYQYDLSQIRWSRLMPQKWRNRVNQGCMAQNRNLNKWNSYEKDQLIHYKK
ENDSELYSLANQKDNFQKCYRYDLLAYKSINYEKKNDSFISRLPFQVNKN
LEISSNSNTSKHNLFDMLGNLHINNYLRKGNILYIERNLDRKYFDWKIIH
FSLRQKEDIEAWVKIDTNSNPNTKIGINNYQIIDKIDKKGFFYLTIHQNP
ENNQKNSKKAFFDWMGMNEKILNRPILNLEFWFFPEFVPLYNVYKIKPWI
IPSKLLLLNLNTNENVSQNKNINKNQKQNFFLRSNKKIKNRIQEAKEPAS
QGEKERGSDIENKGNLGPVLSKHQNALKKDYAESDTKKGKKKKQYKSNTE
AELDLFLKRYLLFQLRWNDALNQRMIENIKVYCLLLRLINPSKIAISSIQ
RREMSLDIMLIQKNLTLTELMKKGILIIEPIRLSVKNNGQFIMYQTIGIS
LVHKSKHQTNQRYPEQRYVDKKNFDEFILQPQTQRINTDKNHFDLLVPEN
ILWSRRRRELRIRSLFNSLNWNGIDRNSVFCNENNVKNWSQFLDERKPLY
KEKNELIKLKFFLWPNYRLEDLACMNRYWFDTNNGSRFSILRIHMYPQLK
IN
>NC_002202@SpolCp093@ycf1@121596@127097@R@1@1834 ycf1_protein
MIFQSFLLGNLVSLCMKIINSVVVVGLYYGFLTTFSIGPSYLFLLRAQVM
EEGEEGTEKKVSGTTGFIMGQLMMFISIYYTPLHLALGRPHTITVLALPY
LLFHFFWNNHKHFFDYGSTSRNSMRNLSIQCVFLNNLIFQLFNYFILPSS
MLARLVNIYMFRCNNKMLFVTSSFVGWLIGHILFMKWVGLVLVWIQQNNS
IRSNKYLVSELRNSMARIFSILFFITCVYYLGRMPSPIFTNKLKQMLETN
EIEEETNLEIEKTSETKETKQEEEGFTEEDPSPSLFSEEKEDPDKIDETE
KIRVNGKDKTKDEFHLKEACYKNSPTSYSGNQDISKLEILKKEKKILFWF
QKPLIFLLFDYKRWNRPMRYIKNNRFENAVRNEMSQYFFYTCQNDGKQRI
SFTYPPSLSIFWEMIQRKISLATTEKFLYDDELYNYWIYTNEQKKNSLSN
EFANRITVLDKGLFYIDVLDKKTRLCKSKNEYLQKDHDPLLNGSYRGIIK
KTLLPFINNDETTVKKLIDEIFINKIHSVLGNCNNYQEFEYKKDPFKKNP
ISSKIRHFVTLMSQFDGESTFNQKGISLLSEHKQICSEDPEIFFKFLVDT
IIADSFTQTIPKESIGIKEISKKVPHWSYQLIDESEQEEMENEKQVSWPH
QIRSRSGKEVVFFTDKQENTDNPTPNTADISEQADEVVLTRYPQESDFRR
DIIKGSMRSQRRKIVIWELFQANIHSPLFLDRTNKSSFFSITFSRLIKRI
FKNYMGKNPELDISNYKEEELKKKEKAKEHKKDKEKKQEQIRLDIAETWD
TIPGAQIIRSLILLTQSILRKYILLPLLITGKNIGRILLFQLPEWSDDFK
EWTSEMHIKCTYNGVQLSEKEFPKNWLTDGMQIKILSPFCLKPWHKSMIR
PYHQDKKKKEQNQIDAFCFLTVVGLETDIPFGPPRKRPSFFQPIFKQLDK
KIEKLIKGNFQVRKRLKEKILFFLKLQNETNNWIIEIFPFFKKIIRKMST
VNTIGVFGLKEASSEIKSEKDSRIKNHMIHESSVQIRFLNQTNSSVTEKK
MKDLANRTRIIKNKIEKISNDKLKMSPKKTRYGTKNLGQILKRRNARLIR
NSNYILKFFRERIYGDIFLYIINIPKINTQLFLESTKNGIDKSIYNNESI
TKTNKNRIQFISTINKKFLPFLSTSKNNSKIISDFSFLSQAYVFYKLSQA
KILNLYKLRLVLQYRGISLFLKNEIKDFFGTQGITNSELKTKKLPNSGMN
QWKNWLKLKNNYQYNLSQLKWSRLVPQKWRNRVTEHCEVENTNLYQNEEL
INSKKHLLLLPDQKYNFQKNYRYDVLSYKFFNYKNKNDSYRYSYGLPFQV
NKNQEFSYTYNYNINNNKFIDMWWNIPISNFSYLEKTKIMDIDKNIDRKY
LDFKILDFSLRNKIDIEDWIDISTSINENTKTEPRNYQIVEKINKKSLVY
STIYQEIKQSDQKNKLFDWMGMNEKILSRPISNLEFWFFSEFFSFYNAYK
MKPWVIPINLLFSNSNVSEKFSKNKSINRKKKTNPFIPSNEKKSFELENR
NQDEKELVSKEDLGSYVQENYEKDIEEDYISFIDIKKPIKQKQPKSVIEA
EFDLFLKRYLLFQLKWADSLNEKLMDNIQVYCLVLRLINPIEILISSIER
KELSMDIMLDRKDFNCPNWKQKRVLIIEPIRLSIRGDGQFLLYQTIGISL
VHKSKHQNNQKRYSENVDKKFLGERNKNNFDLLAPENLLSPRRRRELRIL
LCLNSRNNNGVNTNPMENRVKNCNQFFDEKKDLDRDKNTLRNLKFFLWPN
YRLEDLACMNRFWFDTNNGSRFSILRIHMYPQF
>NC_002693@OeelhCp105@ycf1@129224@136615@R@1@2464 Ycf1
MVNLVYVCMKINNSVVMVGLYYGFISAFSIGSSYLFLLRPRFLNDDPDAI
EKKASETAGFFTGQLLIFISILYGPLHLALGRPHTILLLLAPYFFFHYLF
SNSGQWPSQRFAFPLLTKSMRNRRFQLVFLNNLLFQLFSLSLLGRPMLTR
LSYIYIFRCNNKMLFVLSSFVGWLIGHILVLKWAGLVFVWLLQVIRSKTM
KYITCNVLIPATKYIIEKWRNSFVAGLIREILAMKQVESALVRIKNSKLL
DDARWWIRGSSLISGLKINIRFYARLILRGFENVYVGAKFRQDMEHLFSI
ILFAIFLLYLDQTPLLYADPADKKLQLQRKLSNETQAARAEKKLEERLTK
KFEAQRRAQRAAQRQALQEFKQGVVESYLAKQVAKDANQIQAQKDEKQIQ
AEQKARRIRAEQVVQYTFWLIEAQRREMEIEAARAMQEAYKGMLAAQEGY
VEEGVQEKQEGFPEELISPSPIFHSEEREENPKLLILKEKISILKKKISI
LKKKISILKEKNDLFSFEIPIITSLFDPQKPLRPLRYIKTCAGVEKAVKN
EMSQYFFYACRSDGKQRICFTYPPSLATFWEMIQRKMASRFPRIYAKAKW
RALRWSAPGSYRQWISRNKKKKNSLSTEFQNRIKTLDKKKSLLNVLARRK
RSSLLNVLARRKRSSLQNVLETRKRLCNYKTNKTKKEYLPEKEYLPEIAD
PFLTGALRGKSDPEVDDGGRKTSDLIKVVFLKNNITMATLRNKNDDDLRE
QKNAIALLSRMKNPVNKLHLLFVNERDYPFVKTLVNRINGPAVPKKKKKI
SKSKQKNVKSKQKNVKSKQKNVKSKQKNVKSKQNEIKRKVNEIKRKVNEI
KRKQNESYPRGVKFGATPKTEINPHGIRFDAATIEKYSFATGYSYSPPSF
DDILFHAFVTEPQRNKKAVIELEEEINKKVPRWSYQLIDELEQLEGAEGE
TQFSDHEIRILPFKRVAVFTEKDSKKRKPLIDEQGNFVRHRKTYAIRFLG
HMSDFRRGLIKGSARQDRRKAYVCRTTQVNARSPLFALGPRTFLDGLVNL
AVQVKFFYETRIKGEKIVDDDDDNEKDEFKVMIPDTKSIVAETREMLKQA
GAEDGQSYEDVEDDIRIENVTEMWENIDYGQVIRTFILLLHIFLRKKVVF
PAFIIGKNIARMLLLQATEWKIDFARLKRERYAICTYNGMKVSEKIAFDQ
FPPDWADDGIQILVTNPFYLKPWYRSKTRSIQKDPKKEKDPKKEKGPKKE
PWYRFKTRFIQKDPKKEKGPKKEKGPKKEPWYRRFFFQKDPKKEKGPKKG
KAQFEGDRGVRFLTSFGILTDRPFGDLITPDWGVFFNPIRNELKKKIRQF
EKKHSIILSKRFRNVLKKTKKWFIKSFLFLKRARLKRHPIELSGGRETPE
FTRSQKDIDNLKNEQDFRMSRNPRISESLLQGPVRALKDDSLPEEKVADP
EKEPSDLDNELRAVWDEIDKVTKERKKIVFTPKPDSPDKLVQAKKNILKK
LERIKSRRHKFYFLRIRKSYYVLLFFIKRISRNIKRIYLNPLERAISIRK
IHPQRFFEFSKKMIEKSIGIGKTETNKETVYKTKKKKKKKNPFISIFKES
LYDKDIRISENDIKLGDTWNGYKYKRKKATDTSDLASMSQAYVFYKLYQT
QQTQLIHLDKLRYVLQYDGTSRFLKKELKDYFEAQELFHSKLKHKNSLNS
GKNQWKNWLKAQHQYSVSPIIWNSLSPQKWRTKVNQERMDENTDLNKRYS
NEKRKQFFEANSLDDEENVVETYLGQRAGDIKNSIKSYSYDLFSYQSINS
EDKYVCINNKQKNSYNYNRRKVNLVDSPEGIALSNQFLVQNDLLDLYTFP
DRKYVPWRLFPGSLIGGNDKDKDRFVKMWTATNSGNAVKYWTAANGNTSI
KPGVFWTFQNSQRTKKQNPLFDWRGMNTELPNRCISDLKGWFFFSELLKL
DLRYQVKPWILSKNLLFENLIFENQEENPNLIQNPIEDGRKNVIQNENEN
DPIEDGRQNVIQNENENAIQNLIDFFLEKKNSPKDTNQELHAQAKARIWD
ALVASLKQKREQKERKNKRIAQLIEKKKQKEIEKQKRKIEKQKRKKEKIE
NAKKKIENEKKKIETEEEKIEKEKRKKERKKEKLKKKVAKNIEKLKNKVA
KNVAKNIEKLKKQRAKNIARMEEEDKKARKKRKRKVQVQENKIPYTAFGS
DKWQRPIAEYPKSGDIRNFQVILPEDDDEDDEEDRLDELKLNAYELSRIQ
KITDEKRMKRNLLSSIKRERLKMEFSTRNNSLATIMLTHGIFSIEPLRIS
RQNQDASFLIYQLIKISLVEQLDPYDHNDSFELTEKYRARRNFFMPKTNA
ETMHKSDSDLFVPETILSTKRRRELRILISFYSRRGKRKNRIYKNPVFWK
YVKNCGEVVDNSEKKKKKLIKSFLWPNYRLEDLACMNRYWFNAQNGSRFS
MLRIRMYPRLKIR
>NC_002694@LocoCp080@ycf1@120497@125878@R@1@1794 hypothetical_protein
MIFQSFILDNLVSLCLKIINSVIVVGLYYGFMTTFSTGPSYLFLLRAHVM
EEGTEKKISATTGFITGQLVMFISIYYAPLHIALDRPHTITVITLPYLLL
YFLGNNQKNFLNYVYKNQNSIRHFSIQRIFFQNLFFQLLNPFFLPSSILM
RLANIYIFQSNNKVLFLTSSFVGWLIGHVFFMKWIGLMLVWIQEKNNSIK
STVAIRSNKGVLAKFRKSMFQIFLIFFFITCLYYLGRIPPIYFFTPKMSE
IKERGEIEKREGEIDIEINSQRAGSKQEQKITAEEKLSPYLFSKKNNNLD
KIKEENDIFGFQKPLVTILFDYNRWNRPLRYIKNDRFENVVRNEISQFFF
FTCQSDGKERISFTYPPNLSTFQKMMEMKISLFTRDIISYEELSNSWRST
NEEKKKKLTNEFLNRVEVLDKESLPVDIFENRIRLCNDEKKQKYLTKEYD
PFLNGPCRGQIQKWFSPPIQKETYKKNSLFINKIHGILFSNTNNYPKFEQ
KKNIFDRKSLLTDINFFFNLITKFSRKSVSSLNFEGLYLFPKDNKGKMSS
KKKKFLFDTIRPDLNDNKIVNLQKCIGINEIVKKLPRWSYNLIDELEQLE
GKKKVEYHQIRSRKAKRVVLLTKNSQNDDNYDETTDTDNTEKKKELALIR
YSQQPDFRRDIIKGSIRAQRRKTVTCKLFQRSVDSPLFLEKMEKTSFFCF
DILDSSKIFFMFKNWIRKKKELKNSDYTDEKAKESQKKEEEKIKKNEKEE
KRRIEIGEAWDSIIFAQVIRGCLLITQSILRKYILLPSLIITKNIVRILL
FQFPEWSEDFRDWQREMYIKCTYNGVQLSETEFPKKWLTDGIQIKILFPF
RLKPWHRSKLRFTEKKKDPLKNKKVKKKNFCFLTIFGMEVELPFSGYPRN
RFSFFDPILKELKKKMKKLKNNFFLILKIVNERTKNFITTLKETSKRIIQ
SILKKVLFLNKKIKKLYNYLFLFRFKKIDELNQNKKNFPITKNNPIIYES
TILIQAINKTNCSLTEKKIKAINAKTKKIIKKIERMTKENKGGFLISEIN
SNSKKTSSNTKGLELEKKILQILQRRNVQLTHKLYSFFKFLLNFMKKVYT
DIFLCIVSVPRINVQFFLESTKKIINQSIYNKKTNEEIIDKTNQSIIHFI
SIINKSSNTKNTNSAANSYEVSALSQAYVFFKISQIQVLNVYKYKFKYVF
DYDGRSFFIKDEIKDYFFGIQGIIHSKLRHKNSPVSLKNQWTNWLKVHYQ
YDLSQNRWSRLVQKNLKNRINKHRLDQNKDLTKCDSYKKTQLIVSKNKKQ
QVDFLVNLLIQKKIKKQSRYDLLLYKFINYAEKKELSIYGYRSPFQANKK
RAISYDYNTQKKEFFDRMDDISIKNYIAEDAIRYIEQNRDRKYFDWVVMD
VKIQNNSISNLQFSFFFKFLRFYDAYRNKPWIIPIKFLFLHFSVNQNFNK
IKNIIEKKRRIDIFKPWKKKKILEVELETPNRAKKEYTSRVDLNKPSLSN
QEKDIEEDYGESDSKKGGKDKNKKKYKNKIEAEVNLLLRKYLNFHLNWKG
SLNKRVINNVKVYCLLIRLKNIKQIAISSIQRGELSLDIMMIQNEKDSTL
TGFRKKKEFIEKGIFIIEPVRLSRKNNEQFFMYETARLLLIHKSKRQINQ
RNPEKSDLDKQIFYKNIPPKRDQRITQNKEKKHYALVVIENILSARRRRE
LRILICFNPRSINSMPRKTIFDNENKINNCCQVFAKNKDLDKEKKILMNL
KLILWPNYRLEDLACINRYWFDTYNGSRFSIVRIHMYPRLKMR
>NC_003119@MetrCp012@ycf1@13390@18672@R@1@1761 hypothetical_chloroplast_RF1
MIYQLFILDRLVGLWLKILNSAIVMGLYYGFLTTFSIGPSYLFLIRARVM
DKGTETEIAATTGFITGQLMMFISIYYAPLHLALIRPHTITVLTLPYLFF
NFVYKNNKHYYSADSHFYLDLDYGYKNPNSIRKFRIYKVFFNNLFFQLSN
PLLFPSSILLRLMNIYLFRSNNKLLFLTSSFLGWLIGHIFLMKCIGLILL
VWSKQKNSIKSKLTMRFDKYILLQLRNYVGQIFVVFSFVIVVHYLGRTPV
PYLYTYTDEILEYDEKQKDEINGETEIDVEIDSEQEQNGSIEDEEDILSY
LFPKKDKTLENIEQDNNLLALEKPLVTTLFDYRKWNRPLRYIKNDHFERV
VRDENSQFFFHICQSDGKERISFTYPPDLSSFLKIMEKKMDLFTKDKISY
NDNELSNYWSSNNKEKRKKLSNEFFKRAKVLDKKYKKYKKFIPVDVFENR
IRLSNDKRKIKYLTKIYDPFLNGPFRGQSFSPSIQNETYTTNSILINKIH
GLLLINSNYPEFDNSNYPEFDNSNYPEFEQKIDQFDRKFLLTEIGFFFNL
ISQFSEKSVSSFNFDGLYLFPEHEQVKIYSEEKKRKKKFLFEAIRTDQNN
QTIFNRKKCTGINEISKQVPRWSYELIDELEQMTERLTKEFQIRSAKAER
MVIFNGNTDSLTLNIGPRNDNDAIPEVDLNHEFFLVNFLREPDFDRDIIK
GSMRPLRRKIATTKLSQGNAQPHSPIFLEMIDPLYFIFGDLFDDLSQIFK
EMFRKPGTDNSEFVEFQERLEHKYEEDAKDDAEIRRLKIEEDWESILYGL
IIRSFVLLIQSFFRKYILLPSLIITKNIIRILLFQNPEWSEDFRDWSREV
HIKCTYQGIPVSDKELPKNWFDEGIQIRILNPFVLKAWHKSKVQSTEKKK
KKRSTEKKYTENKNFWFLTGYGTLVESYLDEGFPRDPLSIFGPVLKTIRK
QLKKDLKKHFFLVLKFLNERKKWFPTMLKKIENWNIKRILKSILFRFKII
DELSESKKTSTISKNNSKIEVIEVIEESPVKMESINWTNSSFTEKRIKDL
NVKTKTIIKQIETMTEEKKEGILTSEINLNSNKTTYDAKRLELQKNNLQI
LQRRFVRLIRKSYSFFKIFIEGVYIDILLCISSIARIHRQRFLDFLESTD
KILNVKKPIYDKKKKMEEMEERFENLSVSRLISILEKSENITNMNSQNSW
DVSSLSSLSQEYVFYKLSQIQFSNGSKFKIRSILESPGRSFFLKNEIKDY
FFRMQGTYNSKLRHKKRSDSLMNPWTNWFKVLYQYDLPEKRWSRLVSQNW
RNRINEHRVAQNKDLVEYDSYEKNQLIWKELILSKKQEQEGDLLKIEIKN
KIKKQYRYDLFSYQYLNFANKKKSSIYGYRSPNKNQAISYNYNISIQNYL
EEYDILDMEKNLEKNLDRKYFNWMGMNVKRKKTSRPKDKFLIPGFWFFSK
LSKLYCAYKMNPWILPIKFFVLQLDNLELTTEEYVNTVDEDLKSVSYYYK
GSDSKYRTDLKGERDFLLSKYLGFYLHCDSSDEEIGMDNTNLFCLLLRMK
KFNKIVIMSIKKLELDIEMLVDSRTKDFCYTECRDTEDLKERLIFFIEPI
RLPRKKHEQSLLYQTIRLPLIHKSKTRKSWSWKKKKSRVDQKITENKDKN
LYDLFVPENLLSTRRRRELRILTCFNPRNRNTVHRKTINDNENQIKNVSQ
VLTKNKDLDSETKKLMNFKLFLWPNYRLEDLACINRYWFNTHNGSHFSIL
RIHMYPRLKD
>NC_003386@PsnuCp088@ycf1@112439@117550@R@1@1704 hypothetical_protein
MIGRLYMKKLKNLFLFLSSLCPVFPWISQISLVMPFGLYYGFLTALPIGP
SQILSIRTFFLEGNRSGIICILGSMMGQFVILLSIYCSPLYVMLVKPHLM
TLLVIPYMFYYWYRTKNPSRYYILHPIKSLTHAHTRNLLLDSFIFQLLNP
ILLPNPVLTRLLNLFLFRYSSNVFFLTSSLLGWLCGHILFINSIKLLLFR
IEHDSPIIYILMKRSISRTFSILISITFFLYLGRSPVPLITKKFADEITL
SDQKIKENLWEESLWLYRPWPTSFFDQYRWNRPIRYIPNSKSSHNGFVKK
QVSKFFYDECITDGKNAISFASQPSLSIFKKQLMNYLHNSDISISTKDSY
KGWIETKREKRDALNNEFKDRIQFVYNSSTIEEAMENKTGFSHDRNHFLV
KVNDPFLSGSSRIRIPNKKYSSSLLKLHDSKDQTMKISKKTKRKHTRNKM
RNWIFNKHKKWQHNKFPLPWEPIPTKAEKVFWRILNESENPIILEMLTTL
NSIKEKNYQFRITWEHIFQLPRIEKAIFLFRSKQEIEDSIFRYPSHLSLK
NLTLFNIFTRSKNIFYSAKIAVSPILQIEEMQKELPRYNSRLRSDRIDAV
NVDVDIRQRKIKNLGPRKGKLEDKEKEKEKAAQTQTEVKKEREKEKEERV
IKRFQNQSDFRRKLVKGSIRARRRKTGIWRLYQSGTHSPFFLRMKEIPIS
FQSSINALRLNKMKDERAILGIGKELRPFNLYKKRSKADRLTIAARFDFP
IAHAGRGVLLIIQSNIRKYVILPILIICKNIGRIMLFQSPEWKEDWAEWN
QEIHIKCTYDGIEVSHRHLPAHWFKEGLQIKILYPFHLKPWHIHRTNNIN
DLRNEAQIQKEISDFGKQRKLSFSYLTIWGYQTSSVFGSMKKRPSFWRPI
ANALKKKLQRNLFSKLTWISHFFYEIILLSRTFIISKKPNNIPEMSIQSN
ELRYDVSDYELIQKYPNSNEKNDYVVMNEISIESNNRNGKEISHESQDQY
KDNFNNIRSFNDIETLLTDISGTSVEESYRDRIETYLRLNKKNHRYAINI
RLIWNKQLVQTQQEFSRFRRIIMQFMHKGYRLAKRFLTKFYREIFRRFTF
SIQLSIQLVLRLTKNITKLSEKNKVYQNLNLLKKNEQNLKIDSSRNKPVL
SQAYVFQKLWHARTRTKIDVHYLVQSLEREIVNSIENNELKASKLKDLKW
NEHNYLNDHIKDLLEIQGLLKETQTFTEKNWKEWLHCFTRYQISSKIEYG
IVPQKWKNEVKKRWKSNTNKLDKNKEYKTLEKENKYSLYETNNMLKQRIN
NRNNYCEFYNLLYSFIDSTKASNIIKLPIQQKGKEDPIQYINDINKIHEN
IHLNSKKKYKRPQFQSISTEKGDIDSNLMLWLLPNLLDTKPESVTNSLDS
YSFEMYLSQNEDKDSLKKEIRFNAKKLNLDTKEPTSDAMKPTSDTKELIS
DTNEPTSDIKSDDQSENQNKPLKEKSIRERKHHRPIPQVKWKSKSVEKKM
QRINNLTSFLSVIEDRKNMENYIISFCMKMGIDIDLLNSFFTNTEDELSI
QLLDDSAHRLPRLLNDQTLVRKMVSILLNFEKQFEEGITSKISSQSISSI
YRTEKKYSVNSYNLEDIMLSRRYRELRILNSLILEKQYVNFDHWIDKSEK
YPFLNLPSQVQIIKRFLWPTYRLEDLACMNRFWFNTNNGSRFAMLKLRMY
CPD
>NC_004115@ChglCp095@ycf1@114383@118735@R@1@1451 hypothetical_chloroplast_RF1
MITTYSTFLFNFLSQFQYLVNIPEPLILFGLYYGFLTTLPISFSHIVVIR
NRLIEGKTSSVMAFCGLITGQLCMIGTIYYTPLYKLFIKPHLILLLSIIY
SFFYWQRLRNNQNYDDLREAQSLINVRNFFSFFDSFVFQILNPILLPTPI
FFRLNNVFLFRYSNNLNFFLSFFIGSLIGNFLFFNALNWIRYRFEQDSNV
IYPVLKLLINKSIIPIVFCICLIPIAKYSHIPFCTMKQKEGQSSYSFDKN
WPNIIFDSNQPHRPIRIFSETKTDDNLNINDNLSKKQTSQFFFKECISDG
NVRISYTYPSTLANFQTDLSSSFQDFSLSEQSFDNLYSNWKLEKLSRKDN
LNNLLLTKIKLLNNKKEWFYKHFQNKFGTFIKDDNNYNKFVKKSNDVRLK
QSSKIQIKKSKLLTSDIRDISTTQSGFYDLKKNKLKSFISQKFKMNSNNS
TLPVWNHLNKQLLQNELKRIKKQLQDKTKNIKENDFNNLKLLKSNIETID
NTINDIHHNKIKQITSVDLIKIFATNNKTLLLETLAFNKKITQKDNFNFN
KLFQHKNKKFTTNSGNENTYLNLNDIFKNIKRLPKWRTFSKHVVYDEVSD
IRRRAIKSNSKLKIANKDSDIIIFEYKKSLNFRARLPKGSLRARRKNKFT
WKLFHNNLNSPFFIRSKQLLNKTDIPFLKYNENYLNFFKNFISPDKNINY
LNNDISEMRRQELLFKWDKTNVHILRSMVLVGQAFFRKYIKLPIFIFFKN
LSRQLLYQPSEWTKDWSNWMNEWYIFCYYDGTELAKDQWPEMWLQRGIQI
KLINPFYIKPWYIQKSFIKNKQNKKTRTSYLTVFGSQQELPFGKKIRMPS
FWKPVRREVSKSIKLKLYFPFLTLQKNTIILFEKVFNKKRINEDNKTIEK
SILNKKNEQLILKKDEVIPNNKSIAGKLSKLDFHNQNITKTSIKNATKQI
LIKNEYNSLLKENKNLFTKNKIVFLKIKNILNKLNLKLIKVKINFTYKIK
TVLKIISRNLLKFYSIIQFQLENLGRNNSNDLSYKNQLSYQKDFPNFNNF
CLNQANIIQNLCKNNILKHKKLNQNFQINSKNLNQTNIIDVNPENIKAQD
FKNLLENIYTFTPTINLWDKLSTNNWKISVQNNWKQKSYNNYDLTKKALV
SKNLNFISYFYQNNLINNLNKKIKHTKIFNLSKNYLSLNNLNQNQIKNFD
FQNSLNNNITYKKNIKNFTIRQNVPSQLRRWDWKNNKIKKFVNRLLQKNT
ILLKEEVFNLIPFFDRFTIQNPMIRNWSHPISSILDDEIFTYELLDTFLQ
INKNIDFLHTKQIEDNLSSNSNQAIASLPLSSTTAENFLYYLTTVEDLIS
IEDKKELKILNSLNFNKSTPNYIKTNVVEKSLNENLSKNLQSILSKETLD
SINNTQILKKFLWASYRCEDLACMNRFWFSTNNGSRFGTLRLRLYPNLKN

466
detectors/cds/test/test.db/ycf2.fst Normal file
View File

@ -0,0 +1,466 @@
>AC_000188@LyesCp004@ycf2@88196@95032@D@1@2279 Ycf2_protein
MRGHQFKSWIFELREILREIKNSHHFLDSWTQFNSVGSFIHIFFHQERFL
KLFDPRIWSILLSRNSQGSPSNRYFTIKGVILFVVAVLIYRINNRNMVER
KNLYLIGLLPIPMNSIGPRNDTLEESVGSSNINRLIVSLLYLPKGKKISE
SCFLNPKESTWVLPITKKCSMPESNWGSRWWRNWIGKKRDSSCKISNETV
AGIEILFKEKDLKYLEFLFVYYMDDPIRKDHDWELFDRLSLRKSRNRINL
NSGPLFEILVKHWISYLMSAFREKIPIEVEGFFKQQGAGSTIQSNDIEHV
SHLFSRNKWAISLQNCAQFHMWQFRQDLFVSWGKNPPESDFLRNVSRENW
IWLDNVWLVNKDRFFSKVQNVSSNIQYDSTRSSFVQVTDSSQLKGSSDQS
RDHLDSISNEDSEYHTLINQREIQQRKERSILWDPSFLQTERKEIESGRF
PKCLSGYSSMSRLFTEREKQMINHLFPEEIEEFLGNPTRSVRSFFSDRWS
ELHLGSNPTERSTRDQKLLKKQQDLSFVPSRRSEKKEMVNIFKIITYLQN
TVSIHPISSDPGCDMVPKDEPDMDSSNKISFLNKNPFFDLFHLFHDRNRG
GYTLHYDFASEERFQEMADLFTLSITEPDLVYHKGFAFSIDSCGLDQKQF
LNEARDESKKKSLLVLPPIFYEENESFSRRIRKKWVRISCGNDLEDPKPK
IVVFASNNIMEAVTQYRLIRNLIQIQYSTYGYIRNVLNRFFLMNRSDRNF
EYGIQRDQIGKDTLNHRTIMKYTINQYLSNLKKSQKKWFEPLILISRTER
SMNRDPDAYRYKWSNGSKSFQEHLEQSVSKQKSRFQVVFDRLRINQYSID
WSEVIDKKDLSKSLRFFLSKSLLFLSKLLLFLSNSLPFFCVSFGNIPIHR
SEIYIYEELKGPNDQLCNQLLESIGLQIVHLKKLKPFLLDDHDTSQKSKF
LINGGTISPFLFNKIPKWMIDSFHTRNNRRKSFDNPDSYFSMIFHDQDNW
LNPVKPFHRSSLISSFYKANRLRFLNNPHHFCFYWNTRFPFSVEKARINN
SDFTYGQFLNILFIRNKIFSLCVGKKKHAFWGRDTISPIESQVSNIFIPN
DFPQSGDETYNLYKSFHFPSRSDPFVRRAIYSIADISGTPLTEGQIVNFE
RTYCQPLSDMNLSDSEGKNLHQYLNFNSNMGLIHTPCSEKDLSSEKRKKW
SLCLKKCVEKGQTYRTFQRDSAFSTLSKWNLFQTYMPWFLTSTGYKYLNL
IFLDTFSDLLPILSSSQKFVSIFPDIMHGSGISWRILQKKLCLPQWNLIS
EISSKCLHNLLLSEEMIHRNNESPLISTHLRSPNAREFLYSILFLLLVAG
YLVRTHLLFVSRASSELQTEFERVKSLMTPSSMIELRKLLDRYPTSEPNS
FWLKNLFLVALEQLGDSLEEIRGSASGGNMLGPAYGVKSIRSKKKDWNIN
LIEIIDLIPNPINRITFSRNTRHLSHTSKEIYSLIRKRKNVNGDWIDEKI
ESWVANSDSIDDEEREFLVQFSTLTTENRIDQILLSLTHSDHLSKNDSGY
QMIEQPGAIYLRYLVDIHKKHLMNYEFNPSCLAERRIFLAHYQTITYSQT
SCGENSFHFPSHGKPFSLRLALSPSRGILVIGSIGTGRSYLVKYLATNSY
VPFITVFLNKFLDNKSKGFLLDEIDIDDSDDIDDSDNLDASDDIDRDLDT
ELELLTRMNGLTVDMMPEIDRFYITLQFELAKAMSPCIIWIPNIHDLDVN
ESNDLSLGLLVNHLSRDCERCSTRNILVIASTHIPQKVDPALIAPNKLNT
CIKIRRLLIPQQRKHFFTLSYTRGFHLEKKMFHTNGFGSITMGSNARDLV
ALTNEVLSISITQKKSIIDTNTIRSALHRQTWDLRSQVRSVQDHGILFYQ
IGRAVAQNVLLSNCPIDPISIYMKKKSCNEGDSYLYKWYFELGTSMKRLT
ILLYLLSCSAGSVAQDLWSLSVPDEKNGITSYGLVENDSDLVHGLLEVEG
ALVGSSRTEKDCSQFDNDRVTLLLRPEPRNPLDMMQKGSWSILDQRFLYE
KYESEFEEGEGEGALDPQEDLFNHIVWAPRIWRPWGFLFDCIERPNELGF
PYWSRSFRGKRIIYDEEDELQENDSGFLQSGTMQYQTRDRSQGLFRISQF
IWDPADPLFFLFKDQPPGSVFSHRELFADEEMSKGLLTSQTDPPTSLYKR
WFIKNTQEKHFELLINRQRWLRTNSSLSNGSFRSNTLSESYQYLSNLFLS
NGTLLDQMPKTLLRKRWLFPDEMKIGFM
>AC_000188@LyesCp055@ycf2@146312@153148@R@1@2279 Ycf2_protein
MRGHQFKSWIFELREILREIKNSHHFLDSWTQFNSVGSFIHIFFHQERFL
KLFDPRIWSILLSRNSQGSPSNRYFTIKGVILFVVAVLIYRINNRNMVER
KNLYLIGLLPIPMNSIGPRNDTLEESVGSSNINRLIVSLLYLPKGKKISE
SCFLNPKESTWVLPITKKCSMPESNWGSRWWRNWIGKKRDSSCKISNETV
AGIEILFKEKDLKYLEFLFVYYMDDPIRKDHDWELFDRLSLRKSRNRINL
NSGPLFEILVKHWISYLMSAFREKIPIEVEGFFKQQGAGSTIQSNDIEHV
SHLFSRNKWAISLQNCAQFHMWQFRQDLFVSWGKNPPESDFLRNVSRENW
IWLDNVWLVNKDRFFSKVQNVSSNIQYDSTRSSFVQVTDSSQLKGSSDQS
RDHLDSISNEDSEYHTLINQREIQQRKERSILWDPSFLQTERKEIESGRF
PKCLSGYSSMSRLFTEREKQMINHLFPEEIEEFLGNPTRSVRSFFSDRWS
ELHLGSNPTERSTRDQKLLKKQQDLSFVPSRRSEKKEMVNIFKIITYLQN
TVSIHPISSDPGCDMVPKDEPDMDSSNKISFLNKNPFFDLFHLFHDRNRG
GYTLHYDFASEERFQEMADLFTLSITEPDLVYHKGFAFSIDSCGLDQKQF
LNEARDESKKKSLLVLPPIFYEENESFSRRIRKKWVRISCGNDLEDPKPK
IVVFASNNIMEAVTQYRLIRNLIQIQYSTYGYIRNVLNRFFLMNRSDRNF
EYGIQRDQIGKDTLNHRTIMKYTINQYLSNLKKSQKKWFEPLILISRTER
SMNRDPDAYRYKWSNGSKSFQEHLEQSVSKQKSRFQVVFDRLRINQYSID
WSEVIDKKDLSKSLRFFLSKSLLFLSKLLLFLSNSLPFFCVSFGNIPIHR
SEIYIYEELKGPNDQLCNQLLESIGLQIVHLKKLKPFLLDDHDTSQKSKF
LINGGTISPFLFNKIPKWMIDSFHTRNNRRKSFDNPDSYFSMIFHDQDNW
LNPVKPFHRSSLISSFYKANRLRFLNNPHHFCFYWNTRFPFSVEKARINN
SDFTYGQFLNILFIRNKIFSLCVGKKKHAFWGRDTISPIESQVSNIFIPN
DFPQSGDETYNLYKSFHFPSRSDPFVRRAIYSIADISGTPLTEGQIVNFE
RTYCQPLSDMNLSDSEGKNLHQYLNFNSNMGLIHTPCSEKDLSSEKRKKW
SLCLKKCVEKGQTYRTFQRDSAFSTLSKWNLFQTYMPWFLTSTGYKYLNL
IFLDTFSDLLPILSSSQKFVSIFPDIMHGSGISWRILQKKLCLPQWNLIS
EISSKCLHNLLLSEEMIHRNNESPLISTHLRSPNAREFLYSILFLLLVAG
YLVRTHLLFVSRASSELQTEFERVKSLMTPSSMIELRKLLDRYPTSEPNS
FWLKNLFLVALEQLGDSLEEIRGSASGGNMLGPAYGVKSIRSKKKDWNIN
LIEIIDLIPNPINRITFSRNTRHLSHTSKEIYSLIRKRKNVNGDWIDEKI
ESWVANSDSIDDEEREFLVQFSTLTTENRIDQILLSLTHSDHLSKNDSGY
QMIEQPGAIYLRYLVDIHKKHLMNYEFNPSCLAERRIFLAHYQTITYSQT
SCGENSFHFPSHGKPFSLRLALSPSRGILVIGSIGTGRSYLVKYLATNSY
VPFITVFLNKFLDNKSKGFLLDEIDIDDSDDIDDSDNLDASDDIDRDLDT
ELELLTRMNGLTVDMMPEIDRFYITLQFELAKAMSPCIIWIPNIHDLDVN
ESNDLSLGLLVNHLSRDCERCSTRNILVIASTHIPQKVDPALIAPNKLNT
CIKIRRLLIPQQRKHFFTLSYTRGFHLEKKMFHTNGFGSITMGSNARDLV
ALTNEVLSISITQKKSIIDTNTIRSALHRQTWDLRSQVRSVQDHGILFYQ
IGRAVAQNVLLSNCPIDPISIYMKKKSCNEGDSYLYKWYFELGTSMKRLT
ILLYLLSCSAGSVAQDLWSLSVPDEKNGITSYGLVENDSDLVHGLLEVEG
ALVGSSRTEKDCSQFDNDRVTLLLRPEPRNPLDMMQKGSWSILDQRFLYE
KYESEFEEGEGEGALDPQEDLFNHIVWAPRIWRPWGFLFDCIERPNELGF
PYWSRSFRGKRIIYDEEDELQENDSGFLQSGTMQYQTRDRSQGLFRISQF
IWDPADPLFFLFKDQPPGSVFSHRELFADEEMSKGLLTSQTDPPTSLYKR
WFIKNTQEKHFELLINRQRWLRTNSSLSNGSFRSNTLSESYQYLSNLFLS
NGTLLDQMPKTLLRKRWLFPDEMKIGFM
>NC_000932@ArthCp066@ycf2@86474@93358@D@1@2295 Ycf2
MKGHQFKSWIFELREIVREIKNAHYFLDSWTQFNSVGSFIHIFFHQERFR
KLLDPRIFSILLLRNSQGSTSNRYFTIKGVVLFVVAALLYRINNRNMVES
KNLYLKGLLPIPMNSIGPRNDTSEESFGSCNINRLIVSLLYLTKGKKISE
SCFRDPKESTWVLPITQKCIMPESNWSSRWWRNWIGKKRGFCCKISNETV
AGIDISFKEKDIKYLEFLFVYYMDDPIRKGHDWELFDRLSPSKRRNIINL
NSGQLFEILVKDWICYLMFAFREKIPIEVEGFCKQQGAGSTIQSNDIEHV
SHLFSRNKWAISLQNCAQFHMWQFHQDLFVSWGKNPHESDFFRKISRENW
IWLDNVWLVNKDRFFSKVRNVSSNIQYDSTRSSFVQVTDSSQLNGSSDQF
IDPFDSISNEDSEYHYHTLINQREIQQLKERSILLDPSFIQTEGREIESD
RFPKYLSGYSSMPRLFTEREKRMNNHLLPEESEEFLGNPTRAIRSFFSDR
WSELHLGSNPTERSTRDQKLLKKEQDVSFVPSRRSENKEIVNIFKIITYL
QNTVSIHPISSDLGCDMVPKDELDMDSSNKISFLNKNPFFDLFHLFHERK
RGGYTLRHESEERFQEMADLFTLSITEPDLVYHKGFAFSIDSYGLDQRQF
LKEVFNFRDESKKKSLLVLPPIFYEENESFYRRLRKIWVRISCGNYLEDQ
KRVVFASNNIMEAVNQYRLIRNMIQIQFQYSPYGYIRNVLNRFFLMKRPD
RNFEYGIQRDLIGNDTLNHRTIMKDTINQHLSNLKKSQKKWFDPLIFLSQ
TERSINRDPNAYRYKWSNGSKNFQEHLEHFVSERKSRFQVVFDQLCINQY
SIDWSEVIDKKDLSKSLRFFLSKLLRFFLSKLLLFLSKLLLFLSNSLPFF
FVSFENIPIHRSEIHIYELKGPNDQLCNQLLESIGLQIVHLKKLKPFLLD
DHNTSQKSKFLINGGTISPFLFNKIPKWMIDSFHTRKNRRKSFDNTDSAY
FSIVSHDQDNWLNPVKPFQRSSLISSFSKANRLRFLNNPHHFCFYCNKRF
PFYVEKARLNNSDFTFTYGQFLTILFIHNKTFSSCGGKKKHAFLERDTIS
PSSIESQVSNIFISNDFPQSGDERYNLYKSFHFPIRSDPLVRRAIYSIAD
ISGTPLIEGQRVNFERTYCQTLSDMNLSDSEEKSLHQYLNFNSNMGLIHT
PCSEKYLQRKKRSLCLKKCVDKGQMDRTFQRDSAFSTLSKWNLFQTYMPW
FFTSTGYKYLNLIFLDTFSDLLRILSSSQKFVSIFHDIMHGLDISWRILQ
KKLCLPQRNLISEISSKSLHNLLLSEEMIHRNNESSLISTHLRSPNVREV
LYSILFLLLVAGYIVRTHLLFVSRAYSELQTEFEKIKSLMIPSYMIELRK
LLDRYPTSELNSFWLKNLFLVALEQLGDCLEEIRGSGGNMLWGGDPAYGV
KSIRSKKKDLKINFIDIIDLISIIPNPINRITFSRNTRHLSHTSKEIYSL
IRKRKNVSGDWIDDKIESWVANSDSIDDKEREFLVQFSTLRAEKRIDQIL
LSLTHSDHLSKNDSGYQMIEQPGTIYLRYLVDIHKKYLMNYEFNTSCLAE
RRIFLAHYQTITYSQTSCGANSFHFPSHGKPFSLRLALSPSRSILVIGSI
GTGRSYLVKYLATNSYVPFITVFLNKFLDNKPKGFFIDDIDIDDSDDIDA
SNDIDRELDTELELLTMMNALTMDMMLEIDRFYITLQFELAKAMSPCIIW
IPNIHDLDVNESSYLALGLLVNSLSRDCERCSTRNILVIASTHIPQKVDP
ALIAPNKLNTCIKIRRLLIPQQRKHFFTLSYTRGFHLEKKMFHTNGFESI
TMGSSARDLVALTNEALSISITQKKSIIDTNTIRSALHRQTWDLRSQVRS
VQDHGILFYQIGRAVAQNVLISNCPIDPISIYMKKKSCNEGDSYLYKWYF
ELGTSMKKFTILLYLLSCSAGSVAQDLWSLPVPDEKNRITSYGFVENDSD
LVHGLLEVQGALVGSSRTEKDCSQFDNDRVTLLFRSEPRDPLYMMQDGSC
SIVDQRFLYEKYESEFEEGEGEGVLDPQQIEEDLFNHIVWAPRIWRPRGF
LFDCIERPNELGFPYSAGSFRGKRIIYDEKYELQENDSEFLQSGTMQYQR
RDRSSKEQGFFRISQFIWDPADPLFFLFKDQPFVSVFSHREFFADEEMSK
GLLTSQTDPPTSIYKRWFIKNTQEKHFELLIQRQRWLRTNSSLSNGFFRS
NTRSESYQYLSNLFISNGTLLDRMTKTLLKKRWLFSDEMKIGFM
>NC_000932@ArthCp083@ycf2@145291@152175@R@1@2295 Ycf2
MKGHQFKSWIFELREIVREIKNAHYFLDSWTQFNSVGSFIHIFFHQERFR
KLLDPRIFSILLLRNSQGSTSNRYFTIKGVVLFVVAALLYRINNRNMVES
KNLYLKGLLPIPMNSIGPRNDTSEESFGSCNINRLIVSLLYLTKGKKISE
SCFRDPKESTWVLPITQKCIMPESNWSSRWWRNWIGKKRGFCCKISNETV
AGIDISFKEKDIKYLEFLFVYYMDDPIRKGHDWELFDRLSPSKRRNIINL
NSGQLFEILVKDWICYLMFAFREKIPIEVEGFCKQQGAGSTIQSNDIEHV
SHLFSRNKWAISLQNCAQFHMWQFHQDLFVSWGKNPHESDFFRKISRENW
IWLDNVWLVNKDRFFSKVRNVSSNIQYDSTRSSFVQVTDSSQLNGSSDQF
IDPFDSISNEDSEYHYHTLINQREIQQLKERSILLDPSFIQTEGREIESD
RFPKYLSGYSSMPRLFTEREKRMNNHLLPEESEEFLGNPTRAIRSFFSDR
WSELHLGSNPTERSTRDQKLLKKEQDVSFVPSRRSENKEIVNIFKIITYL
QNTVSIHPISSDLGCDMVPKDELDMDSSNKISFLNKNPFFDLFHLFHERK
RGGYTLRHESEERFQEMADLFTLSITEPDLVYHKGFAFSIDSYGLDQRQF
LKEVFNFRDESKKKSLLVLPPIFYEENESFYRRLRKIWVRISCGNYLEDQ
KRVVFASNNIMEAVNQYRLIRNMIQIQFQYSPYGYIRNVLNRFFLMKRPD
RNFEYGIQRDLIGNDTLNHRTIMKDTINQHLSNLKKSQKKWFDPLIFLSQ
TERSINRDPNAYRYKWSNGSKNFQEHLEHFVSERKSRFQVVFDQLCINQY
SIDWSEVIDKKDLSKSLRFFLSKLLRFFLSKLLLFLSKLLLFLSNSLPFF
FVSFENIPIHRSEIHIYELKGPNDQLCNQLLESIGLQIVHLKKLKPFLLD
DHNTSQKSKFLINGGTISPFLFNKIPKWMIDSFHTRKNRRKSFDNTDSAY
FSIVSHDQDNWLNPVKPFQRSSLISSFSKANRLRFLNNPHHFCFYCNKRF
PFYVEKARLNNSDFTFTYGQFLTILFIHNKTFSSCGGKKKHAFLERDTIS
PSSIESQVSNIFISNDFPQSGDERYNLYKSFHFPIRSDPLVRRAIYSIAD
ISGTPLIEGQRVNFERTYCQTLSDMNLSDSEEKSLHQYLNFNSNMGLIHT
PCSEKYLQRKKRSLCLKKCVDKGQMDRTFQRDSAFSTLSKWNLFQTYMPW
FFTSTGYKYLNLIFLDTFSDLLRILSSSQKFVSIFHDIMHGLDISWRILQ
KKLCLPQRNLISEISSKSLHNLLLSEEMIHRNNESSLISTHLRSPNVREV
LYSILFLLLVAGYIVRTHLLFVSRAYSELQTEFEKIKSLMIPSYMIELRK
LLDRYPTSELNSFWLKNLFLVALEQLGDCLEEIRGSGGNMLWGGDPAYGV
KSIRSKKKDLKINFIDIIDLISIIPNPINRITFSRNTRHLSHTSKEIYSL
IRKRKNVSGDWIDDKIESWVANSDSIDDKEREFLVQFSTLRAEKRIDQIL
LSLTHSDHLSKNDSGYQMIEQPGTIYLRYLVDIHKKYLMNYEFNTSCLAE
RRIFLAHYQTITYSQTSCGANSFHFPSHGKPFSLRLALSPSRSILVIGSI
GTGRSYLVKYLATNSYVPFITVFLNKFLDNKPKGFFIDDIDIDDSDDIDA
SNDIDRELDTELELLTMMNALTMDMMLEIDRFYITLQFELAKAMSPCIIW
IPNIHDLDVNESSYLALGLLVNSLSRDCERCSTRNILVIASTHIPQKVDP
ALIAPNKLNTCIKIRRLLIPQQRKHFFTLSYTRGFHLEKKMFHTNGFESI
TMGSSARDLVALTNEALSISITQKKSIIDTNTIRSALHRQTWDLRSQVRS
VQDHGILFYQIGRAVAQNVLISNCPIDPISIYMKKKSCNEGDSYLYKWYF
ELGTSMKKFTILLYLLSCSAGSVAQDLWSLPVPDEKNRITSYGFVENDSD
LVHGLLEVQGALVGSSRTEKDCSQFDNDRVTLLFRSEPRDPLYMMQDGSC
SIVDQRFLYEKYESEFEEGEGEGVLDPQQIEEDLFNHIVWAPRIWRPRGF
LFDCIERPNELGFPYSAGSFRGKRIIYDEKYELQENDSEFLQSGTMQYQR
RDRSSKEQGFFRISQFIWDPADPLFFLFKDQPFVSVFSHREFFADEEMSK
GLLTSQTDPPTSIYKRWFIKNTQEKHFELLIQRQRWLRTNSSLSNGFFRS
NTRSESYQYLSNLFISNGTLLDRMTKTLLKKRWLFSDEMKIGFM
>NC_001568@EpviCp27@ycf2@22045@28695@D@1@2217 Ycf2
MKEHPFPYKSWILELREIKNSHYFLDSWTKFNSVGSYINIFSHQERFIKL
FDPRILSILLSRNSQGSTSNRYFTIKGVILFVVAVLIYRINNRNMVEIKN
IYWRGLLPIPMNSIGPRNDTLEELVGSYNINRFIVSLLYLTKGKNISESF
FLNLKESTLVLPITKKCSMPESNWGSRWWRNWTGKNRDYSCKISNETVAG
IEILFKEKDKKYLEFIFFYYMDDPIRKDRDWELFDRLSPSKRLNKINFYS
GPLFEILVKRRIYYLMSAFREKIPIEVVKGFFKQQKVGSTIQSNDIEHVS
HFFSRNKRAISLKNSAQFNMWQFRQDLLVSWGENPHESDFLRNVSRANWI
WLNNVWLVNKYRFCRKVRNVSSNIKYKYDSTRSRSSFVQVTDSSQLKGSY
YKSSGHFYSVISNEDSEYHTLINQREIKPLKSIFFDPSFLQTEATEIESD
QLQKRPSGYSSTLFTEHEKQMINHMLPEEIEEFIGNPTRLVHSFLSDRWS
ELHLGSNPTERSTRDHKLLKKQQDLSFVPSRRSENKELVNILKIITYLKN
TVSIHPISSDPGCDGVLKDEPDMDSSNKISVFNKNTFIYLFHLFHDWNRV
GYTLNLHHDFELEERFQEKADLFTLSITEPDLVYHKGFSFSIYMDQKQKM
VVFASNNIMEAVNQSRFIRNMIKIQYSTYGYIRNVLHRFFLMNRSDHNLE
YEIKRDQIGKDTLNHRTIIKYMINQHLSNFKKSQNKWFNPILFFSRTERS
VNRNPDAYRYKRSNGSNNFLEHLEHFVSEQKSHFKFKIVFDLIRFNQYSI
DWSAFIDTKDLSKPLRFFLSKLLFFLSNSLPFFCVSFGNIPIHRSEIYIY
ELKDPNDQLCNQFLEPIDLKIVHLKKRKPFLLGYHGTSRKLKLLITGGRP
FLFNKIPRCMIDSFHTINNRSKSFDNTDSYLSMIFHNKDNWLNLVKPFHR
SSLISYFYKANRLQFLNNPHNFCFYCNTRLPFYVEKAHIHNYYFTYGQFL
NILFIRNKIFSLCVDKKKHAFWGGRDTISPIESQVSKIFIPKNFPQSGDE
TYNLSQPFHFPSRYDPFVRLIANIYGTPLTEGQIVNLGRTYCQPLSDMNL
SDSEGKNFHQYLNFNSNMGLIHTPCSDKYLPSEKRKKRSLCINKYKCVEK
GQMYRTFQRKVAFSTLSKWNLFQTYMPWFLTSAGYKYINLIFLDTFSELL
SILSSSKKFVSIFNNIMHGSGISWRIINKKRCLPQWNLISEISSKCLHNL
LLSEETIRQNNESPLISTHLRSPNVREFLYSILFLLLVVGYLVRTHLLFV
SRASSELQTEFKRVKSLMIPSSMIELRKLLNRYPTPASNSFWLKNLFIVA
MEQLVYSLEEIRASGGNLLGPAYGVKSICSKNKYFNINLIDLIPNPINRI
IFSRNMRHLSHTSKEIYSLIRKRKNVNGDWIDDIIESWVANSDSIDDEER
EFLVQFSALTTEKRIYQILLSLTHSDHLSKNDSGYKMIEQPGAIYLRYLV
DIHKKYLLNYECNTSCLVERRVFLAHSQTITYSQTSRGTNTLHFPSQGKP
FSISLALSPSKGILVIGSIGTGRSFLVKYLATNSYVPFITVFLNKFLDNK
PKGFLVDDNDDNDSSDDIYASDDINSDLDTELELITMMNALTMDMMLELD
RFFTTLQLELAKAMSPWIIWIPNIHDLDVNESNYLSFGLLVNHLSERCST
NNIIVIASTHIPKKVDPALLAPNKLNTCIKIRRLLIPQQRKHFCTLSYTR
GFHLENKIFHTNGFGSITMGSSARDLVALTNEALSISITQNKSILDTNTI
RSALHRQTWDLRSGVRSFQDNGILSYQIGRAITQNVLLSNCPIDPISIYM
KKKSCTCNGGDYYFYKWYFGLGTSMKKLTILLYLLSCSAGSVAQDLWSLP
GPAEKNGITSYGLVENDSDLVRGLLEVEGALVGSSRTEKDCSPFDNDRVI
FTLILRPEPGNPLDIIKKGSCSIFDHRFIYEKYESEFEEGYGEGALDPQQ
IEEDLFNHIVWAPRIWRPWGFIFYCIERPNELGFPYWSRSFRGKRIVYDK
DEEGELQENDSELLKSGTVQYQTRDRSSKEQGLLKINQFIWDPADPLFFL
LKDQPPGSVFSHRRFFADEEMSKGLLTSQKDPPTSIYKRWFIKNTQEQHF
ELLINRQRWLRTKSSLSKSNGSFRSNTLFESYQYLSTLFLSNGTLFDKMT
KTLLIKRWLFPDEMQM
>NC_001568@EpviCp32@ycf2@61133@67783@R@1@2217 Ycf2
MKEHPFPYKSWILELREIKNSHYFLDSWTKFNSVGSYINIFSHQERFIKL
FDPRILSILLSRNSQGSTSNRYFTIKGVILFVVAVLIYRINNRNMVEIKN
IYWRGLLPIPMNSIGPRNDTLEELVGSYNINRFIVSLLYLTKGKNISESF
FLNLKESTLVLPITKKCSMPESNWGSRWWRNWTGKNRDYSCKISNETVAG
IEILFKEKDKKYLEFIFFYYMDDPIRKDRDWELFDRLSPSKRLNKINFYS
GPLFEILVKRRIYYLMSAFREKIPIEVVKGFFKQQKVGSTIQSNDIEHVS
HFFSRNKRAISLKNSAQFNMWQFRQDLLVSWGENPHESDFLRNVSRANWI
WLNNVWLVNKYRFCRKVRNVSSNIKYKYDSTRSRSSFVQVTDSSQLKGSY
YKSSGHFYSVISNEDSEYHTLINQREIKPLKSIFFDPSFLQTEATEIESD
QLQKRPSGYSSTLFTEHEKQMINHMLPEEIEEFIGNPTRLVHSFLSDRWS
ELHLGSNPTERSTRDHKLLKKQQDLSFVPSRRSENKELVNILKIITYLKN
TVSIHPISSDPGCDGVLKDEPDMDSSNKISVFNKNTFIYLFHLFHDWNRV
GYTLNLHHDFELEERFQEKADLFTLSITEPDLVYHKGFSFSIYMDQKQKM
VVFASNNIMEAVNQSRFIRNMIKIQYSTYGYIRNVLHRFFLMNRSDHNLE
YEIKRDQIGKDTLNHRTIIKYMINQHLSNFKKSQNKWFNPILFFSRTERS
VNRNPDAYRYKRSNGSNNFLEHLEHFVSEQKSHFKFKIVFDLIRFNQYSI
DWSAFIDTKDLSKPLRFFLSKLLFFLSNSLPFFCVSFGNIPIHRSEIYIY
ELKDPNDQLCNQFLEPIDLKIVHLKKRKPFLLGYHGTSRKLKLLITGGRP
FLFNKIPRCMIDSFHTINNRSKSFDNTDSYLSMIFHNKDNWLNLVKPFHR
SSLISYFYKANRLQFLNNPHNFCFYCNTRLPFYVEKAHIHNYYFTYGQFL
NILFIRNKIFSLCVDKKKHAFWGGRDTISPIESQVSKIFIPKNFPQSGDE
TYNLSQPFHFPSRYDPFVRLIANIYGTPLTEGQIVNLGRTYCQPLSDMNL
SDSEGKNFHQYLNFNSNMGLIHTPCSDKYLPSEKRKKRSLCINKYKCVEK
GQMYRTFQRKVAFSTLSKWNLFQTYMPWFLTSAGYKYINLIFLDTFSELL
SILSSSKKFVSIFNNIMHGSGISWRIINKKRCLPQWNLISEISSKCLHNL
LLSEETIRQNNESPLISTHLRSPNVREFLYSILFLLLVVGYLVRTHLLFV
SRASSELQTEFKRVKSLMIPSSMIELRKLLNRYPTPASNSFWLKNLFIVA
MEQLVYSLEEIRASGGNLLGPAYGVKSICSKNKYFNINLIDLIPNPINRI
IFSRNMRHLSHTSKEIYSLIRKRKNVNGDWIDDIIESWVANSDSIDDEER
EFLVQFSALTTEKRIYQILLSLTHSDHLSKNDSGYKMIEQPGAIYLRYLV
DIHKKYLLNYECNTSCLVERRVFLAHSQTITYSQTSRGTNTLHFPSQGKP
FSISLALSPSKGILVIGSIGTGRSFLVKYLATNSYVPFITVFLNKFLDNK
PKGFLVDDNDDNDSSDDIYASDDINSDLDTELELITMMNALTMDMMLELD
RFFTTLQLELAKAMSPWIIWIPNIHDLDVNESNYLSFGLLVNHLSERCST
NNIIVIASTHIPKKVDPALLAPNKLNTCIKIRRLLIPQQRKHFCTLSYTR
GFHLENKIFHTNGFGSITMGSSARDLVALTNEALSISITQNKSILDTNTI
RSALHRQTWDLRSGVRSFQDNGILSYQIGRAITQNVLLSNCPIDPISIYM
KKKSCTCNGGDYYFYKWYFGLGTSMKKLTILLYLLSCSAGSVAQDLWSLP
GPAEKNGITSYGLVENDSDLVRGLLEVEGALVGSSRTEKDCSPFDNDRVI
FTLILRPEPGNPLDIIKKGSCSIFDHRFIYEKYESEFEEGYGEGALDPQQ
IEEDLFNHIVWAPRIWRPWGFIFYCIERPNELGFPYWSRSFRGKRIVYDK
DEEGELQENDSELLKSGTVQYQTRDRSSKEQGLLKINQFIWDPADPLFFL
LKDQPPGSVFSHRRFFADEEMSKGLLTSQKDPPTSIYKRWFIKNTQEQHF
ELLINRQRWLRTKSSLSKSNGSFRSNTLFESYQYLSTLFLSNGTLFDKMT
KTLLIKRWLFPDEMQM
>NC_001879@NitaCp068@ycf2@88885@95727@D@1@2281 Ycf2
MRGHQFKSWIFELREILREIKNSHHFLDSWTQFNSAGSFIHIFFHQERFL
KLFDPRIWSILLSRNSQGSTSNRYFTIKGVILFVVAVLIYRINNRNMVER
KNLYLIGLLPIPMNSIGPRNDTLEESVGSSNINRLIVSLLYLPKGKKISE
SCFLNPKESTWVLPITKKCSMPESNWGSRWWRNWIGKKRDSSCKISNETV
AGIEILFKEKDLKYLEFLFVYYMDDPIRKDHDWELFDRLSLRKSRNRINL
NSGPLFEILVKHWISYLMSAFREKIPIEVEGFFKQQGAGSTIQSNDIEHV
SHLFSRNKWAISLQNCAQFHMWQFRQDLFVSWGKNPPESDFLRNVSRENW
IWLDNVWLVNKDRFFSKVQNVSSNIQYDSTRSSFVQVTDSSQLKGSSDQS
RDHLDSISNEDSEYHTLINQREIQQRKERSILWDPSFLQTERKEIESGRF
PKCLSGYSSMSRLFTEREKQMINHLFPEEIEEFLGNPTRSVRSFFSDRWS
ELHLGSNPTERSTRDQKLLKKQQDLSFVPSKRSENKEMVNIFKIITYLQN
TVSIHPISSDPGCDMVPKDEPDMDSSNKISFLNKNPFFDLFHLFHDRNRG
GYTLHYDFESEERFQEMADLFTLSITEPDLVYHKGFAFSIDSCGLDQKQF
LNEARDESKKKSLLVLPPIFYEENESFSRRIRKKWVRISCGNDLEDPKPK
IVVFASNNIMEAVTQYRLIRNLIQIQYSTYGYIRNVLNRFFLMNRSDRNF
EYGIQRDQIGKDTLNHRTIMKYTINQYLSNLKKSQKKWFEPLILISRTER
SMNRDPDAYRYKWSNGSKNFQEHLEQSVSEQKSRFQVVFDRLRINQYSID
WSEVIDKKDLSKPLRFFLSKSLLFLSKLLFFLSNSLPFFCVSFGNIPIHR
SEIYIYELKGPNDQLCNQLLESIGLQIVHLKKWKPFLLDDHDTSQKSKFL
INGGTISPFLFNKIPKWMIDSFHTRNNRRKSFDNPDSYFSMIFHDQDNWL
NPVKPFHRSSLISSFYKANRLRFLNNPHHFCFYWNTRFPFSVEKARINNS
DFTYGQFLNILFIRNKIFSLCVGKKKHAFWGRDTISPIESQVSNIFIPND
FPQSGDETYNLYKSFHFPSRSDPFVRRAIYSIADISGTPLTEGQIVNFER
TYCQPLSDMNLSDSEGKNLHQYLNFNSNMGLIHTPCSEKDLSSEKRKKRS
LCLKKCVEKGQMYRTFQRDSAFSTLSKWNLFQTYMPWFLTSTGYKYLNLI
FLDTFSDLLPILSSSQKFVPIFHDIMHGSGISWRILQKKLCLPQWNLISE
ISSKCLHNLLLSEEMIHRNNESPLISTHLRSPNAREFLYSILFLLLVAGY
LVRTHLLFVSRASSELQTEFEKVKSLMIPSSMIELRKLLDRYPTSEPNSF
WLKNLFLVALEQLGDSLEEIRGSASGGNMLGPAYGVKSIRSKKKDWNINL
IEIIDLIPNPINRITFSRNTRHLSHTSKEIYSLIRKRKNVNGDWIDDKIE
SWVANSDSIDDEEREFLVQFSTLTTENRIDQILLSLTHSDRLSKNDSGYQ
MIEQPGAIYLRYLVDIHKKHLMNYEFNPSCLAERRIFLAHYQTITYSQTS
CGENSFHFPSHGKPFSLRLALSPSRGILVIGSIGTGRSYLVKYLATNSYV
PFITVFLNKFLDNKPKGFLLDEIDIDDSDDIDDSDNLDASDDIDRDLDTE
LKLLTRMNGLTMDMMPEIDRFYITLQFELAKAMSPCIIWIPNIHDLDVNE
SNDLALGLLVNHLSRDCERCSTRNILVIASTHIPQKVDPALIAPNKLNTC
IKIRRLLLPQQRKHFFTLSYTRGFHLEKKMFHTNGFGSITMGSNARDLVA
LTNEVLSISITQKKSIIDTNTIRSALHRQTWDLRSQVRSVQDHGILFYQI
GRAVAQNVLLSNCPIDPISIYMKKKSCNEGDSYLYKWYFELGTSMKRLTI
LLYLLSCSAGSVAQDLWSLSGPDEKNGITSYGLVENDSDLVHGLLEVEGA
LVGSSRTEKDCSQFDNDRVTLLLRPEPRNPLDMMQNGSCSILDQRFLYEK
YESEFEEGEGEGALDPQEDLFNHIVWAPRIWRPWGFLFDCIERPNELGFP
YWSRSFRGKRIIYDEEDELQENDSEFLQSGTMQYQTRDRSSKEQGLFRIS
QFIWDPADPLFFLFKDQPPGSVFSHRELFADEEMSKGLLTSQTDPPTSIY
KRWFIKNTQEKHFELLINRQRWLRTNSSLSNGSFRSNTLSESYQYLSNLF
LSNGTLLDQMTKTLLRKRWLFPDEMKIGFM
>NC_001879@NitaCp102@ycf2@146903@153745@R@1@2281 Ycf2
MRGHQFKSWIFELREILREIKNSHHFLDSWTQFNSAGSFIHIFFHQERFL
KLFDPRIWSILLSRNSQGSTSNRYFTIKGVILFVVAVLIYRINNRNMVER
KNLYLIGLLPIPMNSIGPRNDTLEESVGSSNINRLIVSLLYLPKGKKISE
SCFLNPKESTWVLPITKKCSMPESNWGSRWWRNWIGKKRDSSCKISNETV
AGIEILFKEKDLKYLEFLFVYYMDDPIRKDHDWELFDRLSLRKSRNRINL
NSGPLFEILVKHWISYLMSAFREKIPIEVEGFFKQQGAGSTIQSNDIEHV
SHLFSRNKWAISLQNCAQFHMWQFRQDLFVSWGKNPPESDFLRNVSRENW
IWLDNVWLVNKDRFFSKVQNVSSNIQYDSTRSSFVQVTDSSQLKGSSDQS
RDHLDSISNEDSEYHTLINQREIQQRKERSILWDPSFLQTERKEIESGRF
PKCLSGYSSMSRLFTEREKQMINHLFPEEIEEFLGNPTRSVRSFFSDRWS
ELHLGSNPTERSTRDQKLLKKQQDLSFVPSKRSENKEMVNIFKIITYLQN
TVSIHPISSDPGCDMVPKDEPDMDSSNKISFLNKNPFFDLFHLFHDRNRG
GYTLHYDFESEERFQEMADLFTLSITEPDLVYHKGFAFSIDSCGLDQKQF
LNEARDESKKKSLLVLPPIFYEENESFSRRIRKKWVRISCGNDLEDPKPK
IVVFASNNIMEAVTQYRLIRNLIQIQYSTYGYIRNVLNRFFLMNRSDRNF
EYGIQRDQIGKDTLNHRTIMKYTINQYLSNLKKSQKKWFEPLILISRTER
SMNRDPDAYRYKWSNGSKNFQEHLEQSVSEQKSRFQVVFDRLRINQYSID
WSEVIDKKDLSKPLRFFLSKSLLFLSKLLFFLSNSLPFFCVSFGNIPIHR
SEIYIYELKGPNDQLCNQLLESIGLQIVHLKKWKPFLLDDHDTSQKSKFL
INGGTISPFLFNKIPKWMIDSFHTRNNRRKSFDNPDSYFSMIFHDQDNWL
NPVKPFHRSSLISSFYKANRLRFLNNPHHFCFYWNTRFPFSVEKARINNS
DFTYGQFLNILFIRNKIFSLCVGKKKHAFWGRDTISPIESQVSNIFIPND
FPQSGDETYNLYKSFHFPSRSDPFVRRAIYSIADISGTPLTEGQIVNFER
TYCQPLSDMNLSDSEGKNLHQYLNFNSNMGLIHTPCSEKDLSSEKRKKRS
LCLKKCVEKGQMYRTFQRDSAFSTLSKWNLFQTYMPWFLTSTGYKYLNLI
FLDTFSDLLPILSSSQKFVPIFHDIMHGSGISWRILQKKLCLPQWNLISE
ISSKCLHNLLLSEEMIHRNNESPLISTHLRSPNAREFLYSILFLLLVAGY
LVRTHLLFVSRASSELQTEFEKVKSLMIPSSMIELRKLLDRYPTSEPNSF
WLKNLFLVALEQLGDSLEEIRGSASGGNMLGPAYGVKSIRSKKKDWNINL
IEIIDLIPNPINRITFSRNTRHLSHTSKEIYSLIRKRKNVNGDWIDDKIE
SWVANSDSIDDEEREFLVQFSTLTTENRIDQILLSLTHSDRLSKNDSGYQ
MIEQPGAIYLRYLVDIHKKHLMNYEFNPSCLAERRIFLAHYQTITYSQTS
CGENSFHFPSHGKPFSLRLALSPSRGILVIGSIGTGRSYLVKYLATNSYV
PFITVFLNKFLDNKPKGFLLDEIDIDDSDDIDDSDNLDASDDIDRDLDTE
LKLLTRMNGLTMDMMPEIDRFYITLQFELAKAMSPCIIWIPNIHDLDVNE
SNDLALGLLVNHLSRDCERCSTRNILVIASTHIPQKVDPALIAPNKLNTC
IKIRRLLLPQQRKHFFTLSYTRGFHLEKKMFHTNGFGSITMGSNARDLVA
LTNEVLSISITQKKSIIDTNTIRSALHRQTWDLRSQVRSVQDHGILFYQI
GRAVAQNVLLSNCPIDPISIYMKKKSCNEGDSYLYKWYFELGTSMKRLTI
LLYLLSCSAGSVAQDLWSLSGPDEKNGITSYGLVENDSDLVHGLLEVEGA
LVGSSRTEKDCSQFDNDRVTLLLRPEPRNPLDMMQNGSCSILDQRFLYEK
YESEFEEGEGEGALDPQEDLFNHIVWAPRIWRPWGFLFDCIERPNELGFP
YWSRSFRGKRIIYDEEDELQENDSEFLQSGTMQYQTRDRSSKEQGLFRIS
QFIWDPADPLFFLFKDQPPGSVFSHRELFADEEMSKGLLTSQTDPPTSIY
KRWFIKNTQEKHFELLINRQRWLRTNSSLSNGSFRSNTLSESYQYLSNLF
LSNGTLLDQMTKTLLRKRWLFPDEMKIGFM
>NC_002202@SpolCp103@ycf2@142690@149085@R@1@2132 Ycf2
MKGHQFKSWIFELREILREIKNSHYFLDSWTQFNSVGSFIHIFFYQERFL
KLFDPRIWSILLSPNSQGSTSNRYFTIKGVVLFVVVVLIYRITNRNMVER
KNLYLIGLFPIPMNSIGPRNDTLEKSFGSSNINRLIVSLLYLPKGKKISE
SYFLDPKESTWFLPITKKCIMPESNRGSRWWRNWIGKRRDSSCKISNETV
AGIEISFKEKDIQYLEFPFVYYMDDPIRKDHDWELFDCLSLFLRNVSREN
WIWLDNVRLVNKDRFFSKVRNVSSNIQYDFTRSSFVQVTDSSQLKESSDQ
SRDRSNSISNADSEYHTLINKREIQQLKERSILRDPSFLQTEGTEIESDR
FPKCLSGYSSMPRLFTAREKQMIIHLLPEEIEQLLENPTRSIRSFFSGRW
SELHLGSNPTERSTRDPQLLKKQQDVSFAPSRQSENKEMVNIFKIIKYLQ
NTVSIHPISSDPGCDMVPKDELDMDSSDKISFLNKNSFFDLFHLFHDRNR
GGYALHHDFESEEKFQEMADLFTLSITDPDLVYHRGFSFSIDSCGLDQKQ
FLNEVFNSRDESKKKSLLVLSPIFYEENESFYRRIRKKGVRISRNVLNRF
FLINRSDRSFEYGIQRDQIGNDTLNHRTIRKYMINQDFSNLKKSQKKWFD
PLIFLSRTERFMNRDPDAYRYKWFNGSKNFQEHLEHFVSEQKSRFQVVFD
QLRINQYSIDWSEVIDKKDLSKSLRFFLSKSLRFFLSKLLLFLSNSLPFF
FVSFGNIPINRSEIRIYELKGPNDQLYNPLVESIGLQIVHLKKWKAFLLD
DHDTFQKSKFLINGGTISPFLFNKIPKWMIDSFHTRNNSGKSFDNTDSYF
SMISHDQNNWLNPVKPFHRSSLISSFYKANQLRFLNNPHHFCFYCNKRFP
FYMEKARINNSDFTYRQFLNILFIHNKLFSLCVGKKKHAFLERDTISPIE
SQVSNIFLPNDFPIRSDLLVRRTIYSIADISGTPLTEGQLVHFERTYCQP
LSDMNLSDSEKKNLHQYLNFNSNMGFIYTPCSEKYLLSEKRKKRSLCLKK
CVEKGQMYRTFQRDSAFSTLSKWNLFQTYMPWFLTSTGYKYLNFLFLDTF
SDLLPILSSSQKFLSILHDIMHGSGISWRILQKKLCLPPWNLISEISSKC
LHNLLLPEEMIHRNNESPLIWTHLASPNVREFFYSILFLLFVAGYLVRTH
LLFVFRASSELQTEFERVKSLMIPSYMIELRKLLDRYPTSEPNSFWLKNL
FLVALEQLGDSLEEIRGSASGDNMLLGGGPGPAYGFKSIRSKKKYLNINL
IDILDLISIIPNPINRITFSRNTRHLSHTSKEIYSLIRKRKRVNGDWIDD
KIESWVASSDSIDDEEREFLVQFSTLTTEKRIDQILLSLTHSDHLSKNDS
GYQLIEQPGAIYLRYLVDIHKKYLMNYEFNTSCLAERRVFLAHYQTITYS
QTSCGANSFHFPSHGKPFSLRLALSPSRGILVIGSIGTGRSYLVKYLATN
SYVPFITVFLNKFLDNKPKGSLIDASDDIDRDLDTELELLTMMNALTMDM
MPEIDQFSITLQFELAKAMSPCIIWIPNIHDLDVNESNYLSLGLFVNYLS
RDCERGSTRNILVIASTHIPQKVDPALIAPNQLNTCIKIRRLRIPQQRKH
FFTLSYTRGFHLEKKMFHTNGFGSITMGSNVRDLVAFINEALSISITQKK
SIIDTNTIRSALHRQTWDLRSQVRSVQDHGILFYQIGRAVAQNVLLSNCP
IDPISTYMKKKSCNEGDSYLYKWYFELGTSMKKLTILLYLLSCSAGSVAQ
DLWSLPGPDEKNGITSYGLVENDSYLVHGLLEVEGALVGSSRIEKACSQN
DRVTLFLRPELRNPLDMMQNGSCSILDHRFLYEKYESELEEGEGALDPQQ
IEEDLFNHIVWAPRIWNPWGFLFDCIERPNELGFPYWARSFRGKRSIYDK
EDELQENDSEFLQSGTMQYQTRDRSSKEQGFFRISQFIWDPADPLFFLFK
DQPFVSVFSHREFFADEEISKGLLTSQMNPPISIFQRWFIKNTQEKHFEL
LINRQRWLRTNSSLSNGSFRSNTLSESYQYLSNLFLSNGTLLDQMTKTLL
RKRWLFPDEMKIGFMQEEKDFPFLSRKDMWP
>NC_002693@OeelhCp081@ycf2@92143@99165@D@1@2341 Ycf2
MGNQRNRVNLNPFRFWVFELREILREIKNSRYPFNSVGSFIHIFVHQERF
LKLLDPRIWSVLRSQGSTGVVLFLVAVLIYRINNRNMIERKNIYLTGLLP
IPTNFAGPRNETLEESFLSSNINRLIVSLLHLPKGKRLSESCFLDPKEST
RVLPITKWRNWIGKRRDSSQLKGSSDQSRDHFDSIGTEDSEYHTLINQRE
IQQRKERSSLLDPSFLQTERTEIESDRFSKGLSGSSSKSRLFTEGEKEMN
NHLPPEEIEEFLGNPTRSILSFFSDEWSELHLGSNPTERSTVDQKLLKKE
QEVSFAPFRRSETKEIVNLFKTMAYLQKTVSIHPISSDPGCDMVPKDELD
SEERFQEMADLFTLSITEPDLVYHKGFAFSIDSSVLDQKQFLAEARDESK
KKSLLVLPPVFYQENESFYRRIRKRGVQISCGNDLEDPKPKIVVFASNNI
VEAVNQYRWIRNLIQIQYSTHGYIRNVLNRFFLMNRSDRNFEYGIQRDQI
GNDTLNHRTFMKYTINQHLSNLKKSQKKGSDPLILISRTERSVNRDPNAY
RYKWSKGSKNFQEHLEHFVSEQKSRFQVVFDRYRSIRNRYRSIRNRYRSR
INQYSSDRSEVSDKKDNRYRSRINQYSSDRSEVSDQKNLAKFRSFVFSKL
LLFLSNSLPFFFVSFGNTPPIQRSEIRVSELKGPNDRLCNQFLESIGLQL
VYLKKLKPFLLDDHETSQKSKLLFNKKPEGMIDSFHTRNNRGKSLDSYFS
MISHDQDNWLNPVKPFHRSSLISSFYKANRLRFLNNPHDFGFFCNKRFPF
YVDIKNLDFTYGQFLNILFIRNTKFSLCGDKKKHAFLERDTISSIESQVS
NLFKDFPQSGDERYNFYKYFHLAMRSDPLVRRAIYSIADISGTPLTEGQR
VNFERTYCQPLSDMNLSDSEGKNLYQYLNFNSNMGLIYSEKCFSSEKRKK
KKPEKRKEKKPEKRKEKKPEKRKEKKPEKRKEKKPEKRKEKKPEKRKEKK
PEKRKEKKQSLYLKQWVEKVQMDRALQGERVSLILSNWNLFKTYVMPFSL
TSTGYNLLKLMFLDTLGSYVMPLLRSSPKFVSICYAISDPCGISWRILQK
KLCLLQWNWISAISNKCFHKLLLSEESIHRNNESPSMTDLRWPNLGAFLY
SILFLLFVAGHLVFSHLLFLSQDFSELQRDFARAQSLMIPSYIVELRELL
DMYPAPRSFKKLFLAAREKLVNYLRWGGGRKSFLIHLFELLNITPNPIDR
IAFLKNTRHLSHTSKELYSLITELGDFSSLCSGQRYRYDQIIENVNGPCC
LIDDKIESWISNCDAIEDKEREFLVPFCNFTRETRIDQILLSLTHSDHLS
NNDSASQMSEEPGAFYLRHLVDIHKKGLMNYECNTSCLAERRIFLAHYQT
ITYSPCGDNRSHFPSHGKTFSLRLPLHPSRATLVIGSIGSGRSYLVKSLA
TNSYVPLITVVLNKFLKNWTPQGFDIHESGVYDEYGDDAEEANDYGASFF
DFLDNDSDDYEDRDSDDYDEPGASDDYEDRDMEDFVDSEMTEWLTKTNVP
LVYQLLDDEIDEFYITLQFELAKAMSPCILWIPNIHDLDAKESDYLSLGL
LVNHLSRDCGRRSTKNEILVIASTHIPQKVDPSLIGPDGLSTCIKTRRLL
VPQQQQCLFTLSYTRGFHLENKMFHTHTNEFESTILGPSVPDLVALTNEA
LSISITQKKSIIDTTTIRYALHRKTWDLEADRNLSPAKEHGTLFYQVGRA
FAHTVLLRNCPIDPISIYIKKNLCEAGDSSLYKWYFELGTSMKKLTILLY
LLTCSAGSIAQDLLSPPGPDEQNLITSYGLVENDSDLVHGLSDIVHGLLE
LEGALVGSSPTEEEVEGTEEEVEGTEEEVEGTEEEVEGTEEEVEGTEEEV
EGTEEEVEGTEDEEGEGTEEEVEGTEDEEGEGTEEEVEGTEDEEGEGTEE
EVEGTEDEEGEGTEDEEGEGTEEEVEGTEEEVEGTEDEEGEGTEKDSSQF
DNDRVTLLLRPKPRNPLDIQRLIYQHQKYESELEEDDDDDEDVFAPQKML
EDLFSELVWSPRIWHPWDFILDCEAEIPAEEIPEEEDPLPEEALETEVAV
WGEEEEGEADDEEDERLEAQQEDELLEEEDEELKEEEDELHEEEEEEEEE
EEEEEEDELHEEEEEEEEEDELQENDSEFFRSETQQPQARDGFSEEEGCF
RISQFMWVPGDPLSFLYKDTPFVEVLSYPEEATEISKELLRLLNPKTKRD
APKRARQRWWTKKKQDKHYELVLDRQRWLITKSSLSKSNGFFRSNTPSES
YQYLSNLFLSNRRLLDQITKTFFRKKWLFPDEMKIGFMEQ

31
detectors/cds/test/test.ref
View File

@ -45,28 +45,27 @@ FT AAAQSISYEIPLALCVLSISLRVIR"
FT gene 42910..45121
FT /gene="ndhB"
FT /locus_tag=""
FT CDS join(42910..43780,44367..45121)
FT CDS join(42910..43685,44365..45121)
FT /codon_start=1
FT /transl_table=11
FT /gene="ndhB"
FT /locus_tag=""
FT /product="NADH dehydrogenase subunit 2"
FT /inference="similar to DNA sequence:NC_008535:CoarCp067"
FT /inference="similar to DNA sequence:AC_000188:LyesCp066"
FT /translation="MIWHVQNENFILDSTRIFMKAFHLLLFDGSLIFPECILIFGLILL
FT LMIDSTSDQKDIPWLYFISSTSLVMSITALLFRWREEPMISFSGNFQTNNFNEIFQFLI
FT LLCSTLCIPLSVEYIECTEMAITEFLLFVLTATLGGMFLCGANDLITIFVAPECFSLCS
FT YLLSGYTKKDVRSNEATMKYLLMGGASSSILVHGFSWLYGSSGGEIELQEIVNGLINTQ
FT MYNSPGISIALIFITVGIGFKLSPAPSHQWTPDVYEGVRFVREIPTSLSISEMFGFFKT
FT PWTCRREMLSPTPVVAFLSVTSKVAASASATRIFNIPFYFSSNEWHLLLEILAILSMIL
FT GNLIAITQTSMKRMLAYSSIGQIGYVIIGIIVGDSNDGYASMITYMLFYISMNLGTFAC
FT IVLFGLRTGTDNIRDYAGLYTKDPFLALSLALCLLSLGGLPPLAGFFGKLYLFWCGWQA
FT GLYFLVLIGLLTSVVSIYYYLKIIKLLMTGRNQEITPHVRNYRRSPLRSNNSIELSMIV
FT CVIASTIPGISMNPIIAIAQDSLF"
FT exon 42910..43780
FT MYNSPGISIALIFITVGIGFKLSPAPSHQWTPDVYEGSPTPVVAFLSVTSKVAASASAT
FT RIFNIPFYFSSNEWHLLLEILAILSMILGNLIAITQTSMKRMLAYSSIGQIGYVIIGII
FT VGDSNDGYASMITYMLFYISMNLGTFACIVLFGLRTGTDNIRDYAGLYTKDPFLALSLA
FT LCLLSLGGLPPLAGFFGKLYLFWCGWQAGLYFLVLIGLLTSVVSIYYYLKIIKLLMTGR
FT NQEITPHVRNYRRSPLRSNNSIELSMIVCVIASTIPGISMNPIIAIAQDSLF"
FT exon 42910..43685
FT /gene="ndhB"
FT /locus_tag=""
FT /number=1
FT exon 44367..45121
FT exon 44365..45121
FT /gene="ndhB"
FT /locus_tag=""
FT /number=2
@ -79,7 +78,7 @@ FT /transl_table=11
FT /gene="ndhD"
FT /locus_tag=""
FT /product="NADH dehydrogenase subunit 4"
FT /inference="similar to DNA sequence:NC_007898:LyesC2p017"
FT /inference="similar to DNA sequence:AC_000188:LyesCp081"
FT /translation="MNYFPWLTIIVVFPIFAGSLIFFLPHKGNRVIRWYTICICILELL
FT LTTYAFCYHFQSDDPLIQLVEDYKWIDFFDFHWRLGIDGLSIGPILLTGFITTLATLAA
FT WPVTRDSRLFHFLMLAMYSGQIGLFSSRDLLLFFIMWELELIPVYLLLAMWGGKKRLYS
@ -98,7 +97,7 @@ FT /transl_table=11
FT /gene="ndhE"
FT /locus_tag=""
FT /product="NADH dehydrogenase subunit 4L"
FT /inference="similar to DNA sequence:NC_001879:NitaCp085"
FT /inference="similar to DNA sequence:AC_000188:LyesCp080"
FT /translation="MILEHVLVLSAYLFSIGIYGLITSRNMVRALMCLELILNAVNINF
FT VTFSDFFDNRQLKGDIFSIFVIAIAAAEAAIGLAIVSSIYRNRKSTRINQSNLLNN"
FT gene complement(11509..13722)
@ -178,7 +177,7 @@ FT /transl_table=11
FT /gene="psaC"
FT /locus_tag=""
FT /product="photosystem I subunit VII"
FT /inference="similar to DNA sequence:NC_023792:CP89_p014"
FT /inference="similar to DNA sequence:AC_000188:LyesCp065"
FT /translation="MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRT
FT EDCVGCKRCESACPTDFLSVRVYLWHETTRSMGLAY"
FT gene 53817..55307
@ -190,7 +189,7 @@ FT /transl_table=11
FT /gene="rpl2"
FT /locus_tag=""
FT /product="ribosomal protein L2"
FT /inference="similar to DNA sequence:NC_007898:LyesC2p002"
FT /inference="similar to DNA sequence:AC_000188:LyesCp030"
FT /translation="MAIHLYKTSTPSTRNGTVDSQVKSNPRNNLIYGQRRCGKGRNARG
FT IITARHRGGGHKRLYRKIDFRRNEKDIYGRIVTIEYDPNRNAYICLIHYGDGEKRYILH
FT PRGAIIGDTIVSGTEVPIKMGNALPSTDMPLGTAIHNIEITLGKGGQLARAAGAVAKLI
@ -213,7 +212,7 @@ FT /transl_table=11
FT /gene="rpl23"
FT /locus_tag=""
FT /product="ribosomal protein L23"
FT /inference="similar to DNA sequence:NC_007898:LyesC2p003"
FT /inference="similar to DNA sequence:AC_000188:LyesCp026"
FT /translation="MDGIKYAVFTDKSIRLLGKNQYTSNVESGSTRTEIKHWVELFFGV
FT KVIAMNSHRLPGKSRRMGPIMGHTMHYRRMIITLQPGYSIPPLRKKRT"
FT gene 14505..14672
@ -249,7 +248,7 @@ FT /transl_table=11
FT /gene="rps7"
FT /locus_tag=""
FT /product="ribosomal protein S7"
FT /inference="similar to DNA sequence:NC_007898:LyesC2p007"
FT /inference="similar to DNA sequence:AC_000188:LyesCp008"
FT /translation="MSRRGTAEKKTAKSDPIYRNRLVNMLVNRILKHGKKSLAYQIIYR
FT AVKKIQQKTETNPLSVLRQAIRGVTPDITVKARRVGGSTHQVPIEIGSTQGKALAIRWL
FT LAASRKRPGRNMAFKLSSELVDAAKGSGDAIRKKEETHRMAEANRAFAHFR"

254
detectors/cds/tools/chlorodb/go_chlorodb.sh Executable file
View File

@ -0,0 +1,254 @@
#!/bin/csh -f
#
# make ChloroDB's
#
# usage: copy genbank/embl files into 'DB_DIR/download'
# usage: [create a paramter.sh file in 'DB_DIR']
# usage: go_chlorodb [DB_DIR]
#
unsetenv ORG_SOURCED
setenv ORG_HOME `dirname $0`/../../../..
source $ORG_HOME/scripts/csh_init.sh
#
# which DB to process
#
set DB_BASE = $DATA_DIR/cds/chlorodb # default location
if ($#Argv > 0) then
set DB_BASE = $Argv[1]; Shift
endif
set DB_BASE = `cd $DB_BASE && pwd -P`
NeedDir $DB_BASE/download
if (! -d $DB_BASE/info) mkdir $DB_BASE/info
if (! -d $DB_BASE/fasta) mkdir $DB_BASE/fasta
cd $DB_BASE/info
#
# params
#
if (! -e $DB_BASE/parameters.sh) then
@ n = `find $DB_BASE/download -depth 1 -type f -print | wc -l`
@ cor_cutoff = $n / 2
@ atg_cutoff = $n / 10
@ dbs_cutoff = $n / 4
if ($cor_cutoff == 0) @ cor_cutoff = 1
if ($atg_cutoff == 0) @ atg_cutoff = 1
if ($dbs_cutoff == 0) @ dbs_cutoff = 1
echo "# sourced file" > $DB_BASE/parameters.sh
echo "" >> $DB_BASE/parameters.sh
echo "set CORE_NCDS_CUTOFF = $cor_cutoff" >> $DB_BASE/parameters.sh
echo "set CORE_START_ATG_CUTOFF = $atg_cutoff" >> $DB_BASE/parameters.sh
echo "set CORE_START_DFT_CUTOFF = $atg_cutoff" >> $DB_BASE/parameters.sh
echo "set CORE_START_OTH_CUTOFF = 10" >> $DB_BASE/parameters.sh
echo "set CORE_STOP_CUTOFF = $cor_cutoff" >> $DB_BASE/parameters.sh
echo "set CORE_SPLICE_CUTOFF = $atg_cutoff" >> $DB_BASE/parameters.sh
echo "" >> $DB_BASE/parameters.sh
echo "set SHEL_NCDS_CUTOFF = 10" >> $DB_BASE/parameters.sh
echo "" >> $DB_BASE/parameters.sh
echo "set CORE_DELTA = Inf" >> $DB_BASE/parameters.sh
echo "set CORE_COVMIN = 30" >> $DB_BASE/parameters.sh
echo "set CORE_PMAX = 1e-6" >> $DB_BASE/parameters.sh
echo "set CORE_IDMIN = 30" >> $DB_BASE/parameters.sh
echo "set CORE_SIZMIN = $cor_cutoff" >> $DB_BASE/parameters.sh
echo "" >> $DB_BASE/parameters.sh
echo "set SHEL_DELTA = 0.5" >> $DB_BASE/parameters.sh
echo "set SHEL_COVMIN = 30" >> $DB_BASE/parameters.sh
echo "set SHEL_PMAX = 1e-6" >> $DB_BASE/parameters.sh
echo "set SHEL_IDMIN = 30" >> $DB_BASE/parameters.sh
echo "set SHEL_SIZMIN = $dbs_cutoff" >> $DB_BASE/parameters.sh
echo "" >> $DB_BASE/parameters.sh
echo "set DUST_DELTA = 0.5" >> $DB_BASE/parameters.sh
echo "set DUST_COVMIN = 30" >> $DB_BASE/parameters.sh
echo "set DUST_PMAX = 1e-6" >> $DB_BASE/parameters.sh
echo "set DUST_IDMIN = 30" >> $DB_BASE/parameters.sh
echo "set DUST_SIZMIN = 10" >> $DB_BASE/parameters.sh
endif
source $DB_BASE/parameters.sh
##set CMIN_COD = 0
##set FMIN_COD = 0.01
#
# temporarily uncompress
#
set ff = `find $DB_BASE/download -depth 1 -name \*.gz -print`
if ($#ff != 0) then
Notify "uncompressing $#ff entries"
foreach f ($ff)
gunzip -f $f
end
endif
#
# convert gbk/embl to fasta
#
set ff = `find $DB_BASE/download -depth 1 \( -name \*.gbk -or -name \*.embl \) -print`
Notify "convert $#ff gbk/embl entries to fasta"
foreach f ($ff)
set nom = `basename $f:r`
set typ = $f:e
$AwkCmd -f $LIB_DIR/$typ.tofasta.awk $f > $DB_BASE/fasta/$nom.fst
end
#
# get gbk/embl info
#
Notify "get gbk/embl info for $#ff entries"
echo "" | awk -v HEADONLY=1 -f $LIB_DIR/gbk.info.awk > db.info.txt # just get header
foreach f ($ff)
set nom = `basename $f:r`
set typ = $f:e
$AwkCmd -f $LIB_DIR/$typ.oneliner.awk $f |\
$AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/$typ.info.awk |\
egrep -v '^#' >> db.info.txt
end
#
# get cds info
#
Notify "get gbk/embl cds for $#ff entries"
echo "" | awk -v HEADONLY=1 -f $LIB_DIR/gbk.cds_long.awk > db.cds.txt # just get header
foreach f ($ff)
set nom = `basename $f:r`
set typ = $f:e
$AwkCmd -f $LIB_DIR/$typ.oneliner.awk $f |\
$AwkCmd -v FASTA=$DB_BASE/fasta/$nom.fst -f $LIB_DIR/libutil.awk \
-f $LIB_DIR/$typ.cds_long.awk |\
egrep -v '^#' >> db.cds.txt
end
#
# get fasta for prots
#
Notify "get prots"
$AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/cds2fasta.awk db.cds.txt > db.prot.fst
#
# get introns
#
Notify "get gbk/embl introns for $#ff entries"
echo "" | awk -v HEADONLY=1 -f $LIB_DIR/gbk.intron.awk > db.intron.txt # just get header
foreach f ($ff)
set nom = `basename $f:r`
set typ = $f:e
$AwkCmd -f $LIB_DIR/$typ.oneliner.awk $f |\
$AwkCmd -v FASTA=$DB_BASE/fasta/$nom.fst -f $LIB_DIR/libutil.awk \
-f $LIB_DIR/$typ.intron.awk |\
egrep -v '^#' >> db.intron.txt
end
#
# make models
#
Notify "Making models"
echo -n "" > db.models.params.txt
echo "CORE_NCDS_CUTOFF <- $CORE_NCDS_CUTOFF" >> db.models.params.txt
echo "CORE_START_ATG_CUTOFF <- $CORE_START_ATG_CUTOFF" >> db.models.params.txt
echo "CORE_START_DFT_CUTOFF <- $CORE_START_DFT_CUTOFF" >> db.models.params.txt
echo "CORE_START_OTH_CUTOFF <- $CORE_START_OTH_CUTOFF" >> db.models.params.txt
echo "CORE_STOP_CUTOFF <- $CORE_STOP_CUTOFF" >> db.models.params.txt
echo "CORE_SPLICE_CUTOFF <- $CORE_SPLICE_CUTOFF" >> db.models.params.txt
echo "SHEL_NCDS_CUTOFF <- $SHEL_NCDS_CUTOFF" >> db.models.params.txt
$LIB_DIR/make.models.r |& Cat
GetStatus
OnError then
Error 2 "model parameter too stringent"
endif
#
# add matrices
#
cp -f $PROG_DIR/matrices/* models
#
# make subDBs
#
if (-e db.core.pat.txt) then
Notify "Making core DB (take some time... please wait)"
$PROG_DIR/subdb/go_subdb.sh db.prot.fst db.core.pat.txt \
$CORE_DELTA $CORE_COVMIN $CORE_PMAX $CORE_IDMIN $CORE_SIZMIN
endif
if (-e db.shell.pat.txt) then
Notify "Making shell DB (take some time... please wait)"
$PROG_DIR/subdb/go_subdb.sh db.prot.fst db.shell.pat.txt \
$SHEL_DELTA $SHEL_COVMIN $SHEL_PMAX $SHEL_IDMIN $SHEL_SIZMIN
endif
if (-e db.dust.pat.txt) then
Notify "Making dust DB (take some time... please wait)"
$PROG_DIR/subdb/go_subdb.sh db.prot.fst db.dust.pat.txt \
$DUST_DELTA $DUST_COVMIN $DUST_PMAX $DUST_IDMIN $DUST_SIZMIN
endif
#
# recompress entries
#
set ff = `find $DB_BASE/download -depth 1 -type f -print`
if ($#ff != 0) then
Notify "recompressing $#ff entries"
foreach f ($ff)
gzip -f $f
end
endif
# compress fasta
set ff = `find $DB_BASE/fasta -depth 1 -name \*.fst -print`
if ($#ff != 0) then
Notify "compressing $#ff fasta entries"
foreach f ($ff)
gzip -f $f
end
endif
# install everything in proper directory
foreach dir ("core" "shell" "dust")
if (-e $DB_BASE/$dir) \rm -r $DB_BASE/$dir
if ((-d db.$dir.pat.db) && (-e db.$dir.pat.db/Annot.lst)) then
Notify "installing $DB_BASE/$dir"
\mv -f db.$dir.pat.db $DB_BASE/$dir
endif
end
if (-e $DB_BASE/models) \rm -r $DB_BASE/models
if (-d models) \mv -f models $DB_BASE
Notify "Done"
exit 0

29
detectors/cds/tools/chlorodb/matrices/blosum62.mat Normal file
View File

@ -0,0 +1,29 @@
#
# blosum62 substitution matrix
# with larger penalty for stops
#
A R N D C Q E G H I L K M F P S T W Y V B Z X *
A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -50
R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -50
N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -50
D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -50
C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -50
Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -50
E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -50
G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -50
H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -50
I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 -3 -1 -50
L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 -3 -1 -50
K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -50
M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -50
F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -50
P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -50
S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -50
T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 0 -50
W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2 -50
Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -50
V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -50
B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -50
Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -50
X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -50
* -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 1

195
detectors/cds/tools/chlorodb/subdb/go_subdb.sh Executable file
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@ -0,0 +1,195 @@
#!/bin/csh -f
#
# usage: go_subdb.sh prot.fst pat.txt [deltalen covmin pmax idmin sizmin]
# usage: prot.fst : proteins fasta file
# usage: pat.txt : text file containing patterns and names for families to extract
# usage: output directory containig subdbs : basename <pat:r>.db
#
unsetenv ORG_SOURCED
setenv ORG_HOME `dirname $0`/../../../../..
source $ORG_HOME/scripts/csh_init.sh
NeedArg 2
set ProtFile = $Argv[1]; Shift
set PatFile = $Argv[1]; Shift
NeedFile $ProtFile
NeedFile $PatFile
#
# parameters
#
set Delta = 0.5
set Covmin = 30
set Pmax = 1e-6
set Idmin = 30
set Sizmin = 5
if ($#Argv > 0) then
set Delta = $Argv[1]; Shift
endif
if ($#Argv > 0) then
set Covmin = $Argv[1]; Shift
endif
if ($#Argv > 0) then
set Pmax = $Argv[1]; Shift
endif
if ($#Argv > 0) then
set Idmin = $Argv[1]; Shift
endif
if ($#Argv > 0) then
set Sizmin = $Argv[1]; Shift
endif
#
# output directory
#
set OutDir = `basename $PatFile:r`.db
if (-d $OutDir) \rm -r $OutDir
mkdir $OutDir
set OutLog = `basename $PatFile:r`.log
echo -n '' > $OutLog
alias Report 'egrep "^>" \!:1 | wc -l | awk -v P=`basename \!:1` -v H=\!:2 '"'{print H,P,"'$1}'"'"' >> $OutLog'
#
# remove entries with bad symbols
#
Notify "cleanup $ProtFile"
Report $ProtFile "init_size"
$AwkCmd -f $LIB_DIR/db.filter.sym.awk $ProtFile > P_$$
Report $ProtFile "cleanup_size"
#
# select by name pattern
#
Notify "select by patterns"
mkdir D_$$
mkdir E_$$
mkdir F_$$
set noms = `awk '{print $1}' $PatFile`
foreach nom ($noms)
set pat = `egrep "^$nom " $PatFile | awk '{print $2}'`
$AwkCmd -f $LIB_DIR/db.filter.pat.awk -v PAT="$pat" P_$$ > D_$$/$nom.fst
set n = `egrep '^>' D_$$/$nom.fst | wc -l`
Notify " pattern : $nom : $n"
Report D_$$/$nom.fst "pattern_filter"
if ($n <= $Sizmin) \rm -f D_$$/$nom.fst
end
set ok = `ls D_$$ | wc -l`
if ($ok == 0) goto fin
#
# select by length
#
Notify "select by length"
foreach f (D_$$/*.fst)
set nom = `basename $f:r`
$AwkCmd -f $LIB_DIR/db.getlen.awk $f > L_$$
$LIB_DIR/db.filter.len.r L_$$ $Delta |\
$AwkCmd '($NF == "TRUE") {print $2}' > M_$$
$AwkCmd -v FILE=M_$$ -f $LIB_DIR/db.subdb.awk $f > E_$$/$nom.fst
Report E_$$/$nom.fst "length_filter"
set n = `egrep '^>' E_$$/$nom.fst | wc -l`
Notify " length filter : $nom : $n"
if ($n <= $Sizmin) \rm -f E_$$/$nom.fst
end
set ok = `ls E_$$ | wc -l`
if ($ok == 0) goto fin
#
# select by similarity
#
Notify "select by similarity"
foreach f (E_$$/*.fst)
set nom = `basename $f:r`
Notify " blasting $nom"
makeblastdb -dbtype 'prot' -in $f >>& db.log
blastp -db $f -query $f -outfmt 7 > $f.blast.out
\rm -f $f.p??
$AwkCmd -v COVMIN=$Covmin -v PMAX=$Pmax -v IDMIN=$Idmin \
-f $LIB_DIR/db.blastlink.awk $f.blast.out |\
$AwkCmd -f $LIB_DIR/db.todl.awk > G_$$
($LIB_DIR/db.cc.r G_$$ > $f.cc.txt) >>& db.log
awk -v NAME=$nom -f $LIB_DIR/db.reportcc.awk $f.cc.txt >> $OutLog
$AwkCmd -f $LIB_DIR/db.selcc.awk $f.cc.txt > S_$$
$AwkCmd -v FILE=S_$$ -f $LIB_DIR/db.subdb.awk $f > F_$$/$nom.fst
Report F_$$/$nom.fst "similarity_filter"
set n = `egrep '^>' F_$$/$nom.fst | wc -l`
Notify " blast filter : $nom : $n"
if ($n <= $Sizmin) \rm -f F_$$/$nom.fst
end
set ok = `ls D_$$ | wc -l`
if ($ok == 0) goto fin
#
# annotations
#
echo -n "" > J_$$
foreach f (F_$$/*.fst)
$AwkCmd -f $LIB_DIR/db.annot.awk $f >> J_$$
end
awk '(NF >= 3) {print $1, $NF}' $PatFile | sort > A_$$
sort J_$$ | egrep -v '^ *$' > B_$$
join A_$$ B_$$ > F_$$/Annot.lst
#
# copy files
#
set n = `ls F_$$/* | wc -l`
Notify "copy $n files to $OutDir"
\mv -f F_$$/* $OutDir
#
# end
#
fin:
Notify "output directory : $OutDir"
\rm -r ?_$$
exit 0

39
detectors/cds/tools/chlorodb/subdb/lib/db.annot.awk Normal file
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@ -0,0 +1,39 @@
#
/^>/ {
N++
na = split($1, a, "@")
if (a[na-1] > NEXMAX) NEXMAX = a[na-1]
NEX[a[na-1]]++
ANNOT[$NF]++
}
END {
na = split(FILENAME, a, "/")
na = split(a[na], a, "\\.")
printf("%s %d ", a[1], N)
s = ""
for (i = 1 ; i <= NEXMAX ; i ++) {
if (NEX[i] != 0)
s = s "" i ":" NEX[i] "_"
}
gsub("_+$", "", s)
printf("%s ", s)
s = (NEXMAX == 1) ? "MONEX" : "POLYEX"
printf("%s ", s)
nmax = 0
amax = "none"
for (e in ANNOT) {
if (ANNOT[e] > nmax) {
nmax = ANNOT[e]
amax = e
}
}
print amax
}

48
detectors/cds/tools/chlorodb/subdb/lib/db.blastlink.awk Normal file
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@ -0,0 +1,48 @@
#
function min(x, y) {
return ((x < y) ? x : y)
}
BEGIN {
if (COVMIN == "") COVMIN = 50
if (PMAX == "") PMAX = 1e-6
if (IDMIN == "") IDMIN = 30
}
/^#/ {
hitnum = 0;
next;
}
{
if ($1 == $2) next
hitnum++;
na = split($1, a, "@");
if (na < 2) {
print "query file not properly formatted" > "/dev/stderr"
exit(1);
}
len1 = a[na];
na = split($2, a, "@");
if (na < 2) {
print "bank file not properly formatted" > "/dev/stderr"
exit(1);
}
len2 = a[na];
id = $3 + 0.0;
ali = $4;
covmin = ali * 100. / min(len1, len2);
proba = $11 + 0.0;
if ((covmin > COVMIN) && ((proba < PMAX) || (proba == 0)) && (id > IDMIN)) {
print $1, $2, hitnum, id, covmin, proba, ali, len1, len2;
}
}

18
detectors/cds/tools/chlorodb/subdb/lib/db.cc.r Executable file
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@ -0,0 +1,18 @@
#!/usr/bin/env Rscript
#
require(igraph, warn.conflicts=F)
args <- commandArgs(T)
path <- if(length(args) > 0) args[1] else 'graph.dl'
g <- read.graph(path, format='dl')
cc <- clusters(g)
res <- cbind(V(g)$name, membership(cc))
write.table(res, quote=FALSE, row.names=FALSE, col.names=FALSE)
quit(save="no")

19
detectors/cds/tools/chlorodb/subdb/lib/db.filter.len.r Executable file
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@ -0,0 +1,19 @@
#!/usr/bin/env Rscript
#
args <- commandArgs(T)
path <- if(length(args) > 0) args[1] else 'len.txt'
delta <- if(length(args) > 1) args[2] else 0.5
tab <- read.table(path, header=T)
lmed <- median(tab$len)
dlen <- lmed * as.numeric(delta)
tab$ok <- (abs(tab$len-lmed)/lmed) <= delta
write.table(tab, quote=F)
quit(save='no')

10
detectors/cds/tools/chlorodb/subdb/lib/db.filter.pat.awk Normal file
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@ -0,0 +1,10 @@
#
/^>/ {
split($1, a, "@")
ok = a[3] ~ PAT
}
ok {
print $0
}

30
detectors/cds/tools/chlorodb/subdb/lib/db.filter.sym.awk Normal file
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@ -0,0 +1,30 @@
#
#
#
function Check(seq) {
if (seq == "") return 0
gsub("[ACDEFGHIKLMNPQRSTVWXY\n]+", "", seq)
return (length(seq) == 0)
}
/^>/ {
if (Check(Seq)) {
print Name
printf("%s", Seq)
}
Name = $0
Seq = ""
next
}
{
Seq = Seq "" $0 "\n"
}
END {
if (Check(Seq)) {
print Name
printf("%s", Seq)
}
}

10
detectors/cds/tools/chlorodb/subdb/lib/db.getlen.awk Normal file
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@ -0,0 +1,10 @@
#
BEGIN {
print "id len"
}
/^>/ {
na = split($1, a, "@")
print substr($1, 2), a[na]
}

15
detectors/cds/tools/chlorodb/subdb/lib/db.reportcc.awk Normal file
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@ -0,0 +1,15 @@
#
#
{
cnt[$NF]++
}
END {
n = asort(cnt)
printf("cc_size %s", NAME)
for (i = n ; i >= 1 ; i--)
printf(" %d", cnt[i])
print ""
}

19
detectors/cds/tools/chlorodb/subdb/lib/db.selcc.awk Normal file
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@ -0,0 +1,19 @@
#
{
N[$NF]++
E[$NF, N[$NF]] = $1
}
END {
cmax = 1
nmax = N[1]
for (i in N) {
if (N[i] > nmax) {
nmax = N[i]
cmax = i
}
}
for (i = 1 ; i <= nmax ; i++)
print E[cmax, i]
}

17
detectors/cds/tools/chlorodb/subdb/lib/db.subdb.awk Normal file
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@ -0,0 +1,17 @@
#
BEGIN {
if (FILE == "") FILE = "db.sel.txt"
while (getline < FILE)
INC[$1] = $1
close(FILE)
}
/^>/ {
name = substr($1, 2)
ok = name in INC
}
ok {
print $0
}

21
detectors/cds/tools/chlorodb/subdb/lib/db.todl.awk Normal file
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@ -0,0 +1,21 @@
#
{
node[$1]++
node[$2]++
link[++M] = $1 " " $2
}
END {
for (n in node)
N++
print "DL n=" N
print "format = edgelist1"
print "labels embedded:"
print "data:"
for (i = 1 ; i <= M ; i++)
print link[i]
}

4
detectors/cds/tools/compare/go_compare.sh
View File

@ -47,8 +47,8 @@ $AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/$PrdType.cds_short.awk > P_$$
Notify "compare bank to predictions"
$AwkCmd -f $LIB_DIR/libnws.awk \
-f $LIB_DIR/compareCds.awk \
$AwkCmd -f $LIB_DIR/libnws.awk \
-f $LIB_DIR/compare.cds.awk \
R_$$ P_$$ > S_$$
# base statistics

2
detectors/cds/tools/compare/go_summarize.sh
View File

@ -15,6 +15,8 @@ NeedArg 1
egrep '^#|^MATCH' $* | awk -f $LIB_DIR/summary.cmp.awk > compare.txt
Notify "text file: compare.txt"
$LIB_DIR/summarize_cmp.r

19
detectors/cds/tools/lib/cds2fasta.awk Normal file
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@ -0,0 +1,19 @@
#
# get fasta sequence from cds list
#
# [-v FIELD=13] CDS sequence
# [-v FIELD=14] Prot Sequence
#
BEGIN {
if (CHARPERLINE == "") CHARPERLINE = 50
if (FIELD == "") FIELD = 14
}
/^#/ { next }
{
name = $1 "@" $2 "@" $3 "@" $5 "@" $6 "@" $7 "@" $8 "@" int($9/3)
comment = $NF
PrintFasta($FIELD, name " " comment)
}

0
detectors/cds/tools/lib/compareCds.awk → detectors/cds/tools/lib/compare.cds.awk
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97
detectors/cds/tools/lib/embl.cds_long.awk Normal file
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@ -0,0 +1,97 @@
#
# get cds features from embl (long version)
#
# -v FASTA
# @include lib.embl.awk
BEGIN {
print "#locus locustag genefam gene from to strand nexon length status start stop dnaseq protseq product"
if (HEADONLY != "") exit(0)
if (MAXSPAN == "") MAXSPAN = 10000
if (FASTA == "") Error("No FASTA file specified", 1)
if (! TestPath(FASTA)) Error("Fasta file: '" FASTA "' not found", 1)
Seq = tolower(ReadFasta(FASTA))
}
/^ID / {
locus = $2
gsub(";", "", locus)
incds = 0
next
}
/^FT CDS/ {
revstrand = match($3, "^complement")
s = substr($0, 22)
gsub("^complement", "", s)
ok = ! match(s, "complement|order")
nexon = Nexons(s)
SpanLocation(s, sloc)
spanlen = sloc[2] - sloc[1] + 1
len = LenLocation(s)
ok = ok && (len < MAXSPAN)
cdsseq = ok ? SeqLocation(Seq, s, revstrand) : "XXX"
cstart = substr(cdsseq, 1,3)
cstop = substr(cdsseq, length(cdsseq)-2)
gene = "none"
locustag = "none"
product = "none"
translation = "X"
incds = 1
next
}
(incds && /^FT [^ ]/) {
print locus, locustag, GeneFamily(gene), gene, sloc[1], sloc[2], (revstrand ? "R" : "D"),
nexon, len, (ok ? "Ok" : "Error"), cstart, cstop, cdsseq, translation, product
incds = 0
next
}
/^FT \/gene=/ {
split($0, a, "=")
gene = a[2]
gsub("^[^a-z,A-Z]+", "", gene)
gsub("\"", "", gene)
gsub(" ", "_", gene)
next
}
/^FT \/locus_tag=/ {
split($0, a, "=")
locustag = a[2]
gsub("\"", "", locustag)
gsub(" ", "_", locustag)
next
}
/^FT \/product=/ {
split($0, a, "=")
product = a[2]
gsub("\"", "", product)
gsub(" ", "_", product)
next
}
/^FT \/translation=/ {
split($0, a, "=")
translation = a[2]
gsub("\"", "", translation)
gsub(" ", "", translation)
next
}
END {
if (incds) {
print locus, locustag, GeneFamily(gene), gene, sloc[1], sloc[2], (revstrand ? "R" : "D"),
nexon, len, (ok ? "Ok" : "Error"), cstart, cstop, cdsseq, translation, product
}
}

97
detectors/cds/tools/lib/embl.info.awk Normal file
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@ -0,0 +1,97 @@
#
# get feature info from embl
#
# @include libgbk.awk
function GC(s, _local_, i, len) {
s = toupper(s)
len = length(s)
gsub("G|C", "", s)
return ((len - length(s)) * 100 / (len ? len : 1))
}
#
# rules
#
BEGIN {
print "#locus orga len oklen gc nbCds nbCds_int0 nbCds_int1 nbCds_intsup1 perCds_noex meanCdsSize nbtRNA nbrRNA nboRNA"
}
/^ID/ {
locus = $2
gsub(";", "", locus)
next
}
/^OS/ {
orga = substr($0, 6)
gsub(" ", "_", orga)
next
}
/^FT source/ {
GetLoc($3, loc);
len = loc[2];
next
}
/^FT CDS/ {
meanCds = meanCds * nbCds + LenLocation($3)
nbCds++
meanCds /= nbCds
n = Nexons($3)
if (n > 3) n = 3
nbCdx[n]++
next
}
/^FT tRNA/ {
nbTrna++
next
}
/^FT rRNA/ {
nbRrna++
next
}
/^FT mRNA/ {
next
}
/^FT .*RNA/ {
nbOrna++
next
}
/^SQ / {
inseq = 1
seq = ""
next
}
inseq && /^ / {
s = $0
gsub("[0-9]+", "", s)
gsub(" ", "", s)
seq = seq "" s
next
}
/^\/\// {
oklen = (len == length(seq) ? "ok" : "wrong")
gc = GC(seq)
print locus, orga, len, oklen, gc, nbCds+0, nbCdx[1]+0, \
nbCdx[2]+0, nbCdx[3]+0, (nbCdx[1]+0)*100/Max(1, nbCds+0), \
meanCds+0, nbTrna+0, nbRrna+0, nbOrna+0
nbCds = nbTrna = nbRrna = nbOrna = len = inseq = meanCds = 0
delete nbCdx
orga = locus = "?"
}

97
detectors/cds/tools/lib/embl.intron.awk Normal file
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@ -0,0 +1,97 @@
#
# get intron features from embl
#
# @include libembl.awk
BEGIN {
print "#locus locustag genefam gene from to strand intron_num intron_nb acceptor-donor status"
if (HEADONLY != "") exit(0)
if (FASTA == "") Error("No FASTA file specified", 1)
if (! TestPath(FASTA)) Error("Fasta file: '" FASTA "' not found", 1)
Seq = tolower(ReadFasta(FASTA))
}
/^ID / {
locus = $2
gsub(";", "", locus)
next
}
/^FT CDS/ {
revstrand = match($3, "^complement")
s = substr($0, 22)
gsub("^complement", "", s)
ok = ! match(s, "complement|order")
if (! ok) next
na = ParseLocation(s, locs)
if (na < 2) next
delete SINfo
Ninfo = 0
val = locs[1][1]
for (i = 2 ; i <= na ; i++) {
if (locs[i][1] < val) ok = 0
val = locs[i][1]
}
if (! ok) next
val = locs[1][2]
for (i = 2 ; i <= na ; i++) {
if (locs[i][2] < val) ok = 0
val = locs[i][2]
}
if (! ok) next
from = locs[1][2] + 1
for (i = 2 ; i <= na ; i++) {
to = locs[i][1] - 1
inseq = SeqLocation(Seq, (from - 4) ".." (to + 4), revstrand)
SINfo[++Ninfo] = from " " to " " (revstrand ? "R" : "D") " "\
(revstrand ? na-i+1 : i-1) " " na-1 " "\
substr(inseq, 1,4) "."\
substr(inseq, 5,6) "-"\
substr(inseq, length(inseq)-9, 6) "."\
substr(inseq, length(inseq)-3, 4) " "\
"ok"
from = locs[i][2] + 1
}
gene = "none"
locustag = "none"
next
}
/^FT \/gene=/ {
split($0, a, "=")
gene = a[2]
gsub("^[^a-z,A-Z]+", "", gene)
gsub("\"", "", gene)
gsub(" ", "_", gene)
next
}
/^FT \/locus_tag=/ {
split($0, a, "=")
locustag = a[2]
gsub("\"", "", locustag)
gsub(" ", "_", locustag)
next
}
/^FT \/translation=/ {
for (i = 1 ; i <= Ninfo ; i++)
print locus, locustag, GeneFamily(gene), gene, SINfo[i]
Ninfo = 0
next
}
/^\/\// {
locus = "?"
}

36
detectors/cds/tools/lib/embl.tofasta.awk Normal file
View File

@ -0,0 +1,36 @@
#
# get fasta sequence from embl
#
/^ID / {
locus = $2
gsub(";", "", locus)
next
}
/^SQ / {
inseq = 1
nln = 0
delete seq
next
}
/^\/\// {
inseq = 0
print ">" locus
for (i = 1 ; i <= nln ; i++)
print seq[i]
next
}
inseq {
s = $0
gsub(" ", "", s)
gsub("[0-9]+", "", s)
seq[++nln] = s
next
}

99
detectors/cds/tools/lib/gbk.cds_long.awk Normal file
View File

@ -0,0 +1,99 @@
#
# get cds features from genbank (long version)
#
# -v FASTA
# @include libgbk.awk
BEGIN {
print "#locus locustag genefam gene from to strand nexon length status start stop dnaseq protseq product"
if (HEADONLY != "") exit(0)
if (MAXSPAN == "") MAXSPAN = 10000
if (FASTA == "") Error("No FASTA file specified", 1)
if (! TestPath(FASTA)) Error("Fasta file: '" FASTA "' not found", 1)
Seq = tolower(ReadFasta(FASTA))
}
/^LOCUS/ {
locus = $2
incds = 0
next
}
/^ CDS/ {
revstrand = match($2, "^complement")
s = substr($0, 22)
gsub("^complement", "", s)
ok = ! match(s, "complement|order")
nexon = Nexons(s)
SpanLocation(s, sloc)
spanlen = sloc[2] - sloc[1] + 1
len = LenLocation(s)
ok = ok && (len < MAXSPAN)
cdsseq = ok ? SeqLocation(Seq, s, revstrand) : "XXX"
cstart = substr(cdsseq, 1,3)
cstop = substr(cdsseq, length(cdsseq)-2)
gene = "none"
locustag = "none"
product = "none"
translation = "X"
incds = 1
next
}
(incds && /^ [^ ]/) {
print locus, locustag, GeneFamily(gene), gene, sloc[1], sloc[2], (revstrand ? "R" : "D"),
nexon, len, (ok ? "Ok" : "Error"), cstart, cstop, cdsseq, translation, product
incds = 0
next
}
/^ \/gene=/ {
split($0, a, "=")
gene = a[2]
gsub("^[^a-z,A-Z]+", "", gene)
gsub("\"", "", gene)
gsub(" ", "_", gene)
next
}
/^ \/locus_tag=/ {
split($0, a, "=")
locustag = a[2]
gsub("\"", "", locustag)
gsub(" ", "_", locustag)
next
}
/^ \/product=/ {
split($0, a, "=")
product = a[2]
gsub("\"", "", product)
gsub(" ", "_", product)
next
}
/^ \/translation=/ {
split($0, a, "=")
translation = a[2]
gsub("\"", "", translation)
gsub(" ", "", translation)
next
}
/^\/\// {
locus = "?"
}
END {
if (incds) {
print locus, locustag, GeneFamily(gene), gene, sloc[1], sloc[2], (revstrand ? "R" : "D"),
nexon, len, (ok ? "Ok" : "Error"), cstart, cstop, cdsseq, translation, product
}
}

97
detectors/cds/tools/lib/gbk.info.awk Normal file
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#
# get feature info from genbank
#
# @include libgbk.awk
function GC(s, _local_, i, len) {
s = toupper(s)
len = length(s)
gsub("G|C", "", s)
return ((len - length(s)) * 100 / len)
}
#
# rules
#
BEGIN {
print "#locus orga len oklen gc nbCds nbCds_int0 nbCds_int1 nbCds_intsup1 perCds_noex meanCdsSize nbtRNA nbrRNA nboRNA"
}
/^LOCUS/ {
locus = $2
next
}
/^ ORGANISM/ {
orga = substr($0, 13)
split(orga, a, ";")
orga = a[1]
gsub(" ", "_", orga)
next
}
/^ source/ {
GetLoc($2, loc);
len = loc[2];
next
}
/^ CDS/ {
meanCds = meanCds * nbCds + LenLocation($2)
nbCds++
meanCds /= nbCds
n = Nexons($2)
if (n > 3) n = 3
nbCdx[n]++
next
}
/^ tRNA/ {
nbTrna++
next
}
/^ rRNA/ {
nbRrna++
next
}
/^ mRNA/ {
next
}
/^ .*RNA/ {
nbOrna++
next
}
/^ORIGIN/ {
inseq = 1
seq = ""
next
}
inseq && /^ +[1-9][0-9]*/ {
s = substr($0, 11)
gsub(" ", "", s)
seq = seq "" s
next
}
/^\/\// {
oklen = (len == length(seq) ? "ok" : "wrong")
gc = GC(seq)
print locus, orga, len, oklen, gc, nbCds+0, nbCdx[1]+0, \
nbCdx[2]+0, nbCdx[3]+0, (nbCdx[1]+0)*100/Max(1, nbCds+0), \
meanCds+0, nbTrna+0, nbRrna+0, nbOrna+0
nbCds = nbTrna = nbRrna = nbOrna = len = inseq = meanCds = 0
delete nbCdx
orga = locus = "?"
}

96
detectors/cds/tools/lib/gbk.intron.awk Normal file
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#
# get intron features from genbank
#
# @include libgbk.awk
BEGIN {
print "#locus locustag genefam gene from to strand intron_num intron_nb acceptor-donor status"
if (HEADONLY != "") exit(0)
if (FASTA == "") Error("No FASTA file specified", 1)
if (! TestPath(FASTA)) Error("Fasta file: '" FASTA "' not found", 1)
Seq = tolower(ReadFasta(FASTA))
}
/^LOCUS/ {
locus = $2
next
}
/^ CDS/ {
revstrand = match($2, "^complement")
s = substr($0, 22)
gsub("^complement", "", s)
ok = ! match(s, "complement|order")
if (! ok) next
na = ParseLocation(s, locs)
if (na < 2) next
delete SINfo
Ninfo = 0
val = locs[1][1]
for (i = 2 ; i <= na ; i++) {
if (locs[i][1] < val) ok = 0
val = locs[i][1]
}
if (! ok) next
val = locs[1][2]
for (i = 2 ; i <= na ; i++) {
if (locs[i][2] < val) ok = 0
val = locs[i][2]
}
if (! ok) next
from = locs[1][2] + 1
for (i = 2 ; i <= na ; i++) {
to = locs[i][1] - 1
inseq = SeqLocation(Seq, (from - 4) ".." (to + 4), revstrand)
SINfo[++Ninfo] = from " " to " " (revstrand ? "R" : "D") " "\
(revstrand ? na-i+1 : i-1) " " na-1 " "\
substr(inseq, 1,4) "."\
substr(inseq, 5,6) "-"\
substr(inseq, length(inseq)-9, 6) "."\
substr(inseq, length(inseq)-3, 4) " "\
"ok"
from = locs[i][2] + 1
}
gene = "none"
locustag = "none"
next
}
/^ \/gene=/ {
split($0, a, "=")
gene = a[2]
gsub("^[^a-z,A-Z]+", "", gene)
gsub("\"", "", gene)
gsub(" ", "_", gene)
next
}
/^ \/locus_tag=/ {
split($0, a, "=")
locustag = a[2]
gsub("\"", "", locustag)
gsub(" ", "_", locustag)
next
}
/^ \/translation=/ {
for (i = 1 ; i <= Ninfo ; i++)
print locus, locustag, GeneFamily(gene), gene, SINfo[i]
Ninfo = 0
next
}
/^\/\// {
locus = "?"
}

32
detectors/cds/tools/lib/gbk.tofasta.awk Normal file
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#
# get fasta sequence from genbank
#
/^LOCUS/ {
locus = $2
next
}
/^ORIGIN/ {
inseq = 1
nln = 0
delete seq
}
inseq && /^ +[1-9][0-9]*/ {
s = substr($0, 11)
gsub(" ", "", s)
seq[++nln] = s
next
}
/^\/\// {
print ">" locus
for (i = 1 ; i <= nln ; i++)
print seq[i]
}

31
detectors/cds/tools/lib/install.rpackages.r Executable file
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#!/usr/bin/env Rscript
#
# check and install required packages
#
out <- function(...) {
cat(paste0('+ ', ..., '\n'), file=stderr())
}
installed <- function(package) {
package %in% rownames(installed.packages())
}
check <- function(package, repos="http://cran.univ-lyon1.fr") {
if (installed(package)) {
out("R package ", package, " installed")
} else {
out("Installing R package ", package, " from ", repos)
install.packages(package, repos=repos)
}
invisible(installed(package))
}
check("grid")
check("gridExtra")
check("vcd")
check("plotrix")
check("igraph")
quit(save='no', status=0)

224
detectors/cds/tools/lib/make.models.r Executable file
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#!/usr/bin/env Rscript
#
# compute start, stop, splice-junctions models for core DB
#
# source("make.models.r")
#
LIB_DIR <- Sys.getenv("LIB_DIR")
if (LIB_DIR == "") LIB_DIR = "."
source(paste0(LIB_DIR, "/util.base.r"))
source(paste0(LIB_DIR, "/util.cons.r"))
source(paste0(LIB_DIR, "/util.modelio.r"))
# -------------------------------
# parameters
# -------------------------------
# core cutoffs
source("db.models.params.txt")
# -------------------------------
# genome infos
# -------------------------------
notify("loading info table")
chromo <- read.table("db.info.txt", com="", head=T, stringsAsFactors=F)
# -------------------------------
# CDS
# -------------------------------
notify("loading cds table")
cds <- read.table("db.cds.txt", com="", header=T, stringsAsFactors=F)
cds$start <- as.factor(cds$start)
cds$stop <- as.factor(cds$stop)
cds <- cds[cds$status=="Ok",]
cds <- cds[cds$genefam!="none",]
cds$categ <- "dust"
x <- sort(table(cds$genefam), dec=T)
ok <- names(x[x >= CORE_NCDS_CUTOFF])
cds$categ[cds$genefam %in% ok] <- "core"
x <- x[! names(x) %in% ok]
ok <- names(x[x >= SHEL_NCDS_CUTOFF])
cds$categ[cds$genefam %in% ok] <- "shell"
#
cds.ori <- cds
cds.lst <- split(cds.ori, cds.ori$categ)
#
# write out families
#
# patterns & names
invisible(lapply(cds.lst, function(cds) {
x <- sort(table(cds$genefam), decreasing=T)
tab <- paste0("^", names(x), "$")
names(tab) <- names(x)
y <- sapply(split(cds$gene, cds$genefam), function(g) {
head(names(sort(table(g), decreasing=T)), 1)
})
tab <- cbind(tab, y[names(x)])
categ <- unique(cds$categ)
f <- paste0("db.", categ, ".pat.txt")
notify("writing patterns for", categ, ":", f)
write.table(tab, file=f, quote=F, col.names=F, row.names=T)
}))
# -------------------------------
# Start models (core only)
# -------------------------------
if (! "core" %in% names(cds.lst)) {
notify("*** no gene found in core")
notify("*** please change parameters")
quit(save='no', status=1)
}
cds <- cds.lst[["core"]]
#
# start by genes
#
tab <- split(cds$start, cds$genefam)
fatg <- sapply(tab, function(x) table(x)["atg"]/length(x)*100)
names(fatg) <- names(tab)
start.dft <- names(which(fatg >= CORE_START_ATG_CUTOFF))
start.spc <- names(which(fatg < CORE_START_ATG_CUTOFF))
tab <- cds[cds$genefam %in% start.dft,]
tab <- table(tab$start)
# default model
x <- sort(tab[tab>=CORE_START_DFT_CUTOFF], decreasing=T)
write.model.start(x, "default")
# gene specific models
invisible(sapply(start.spc, function(g) {
x <- cds[cds$genefam == g,]
tx <- table(x$start)
tx <- sort(tx[tx>=CORE_START_OTH_CUTOFF], decreasing=T)
write.model.start(tx, g)
}))
# -------------------------------
# Stop models (core only)
# -------------------------------
# write default stop model
tab <- table(cds$stop)
x <- sort(tab[tab>=CORE_STOP_CUTOFF], decreasing=T)
write.model.stop(x, "default")
# -------------------------------
# splice junctions
# -------------------------------
notify("loading intron table")
intron <- read.table("db.intron.txt", com="", header=T, stringsAsFactors=F)
# remove invalid sequences
intron$seq <- gsub("\\.|-", "", intron$acceptor.donor)
lseq <- nchar(gsub("[^acgt]", "", intron$seq))
intron <- intron[lseq == 20,]
# remove genes out of core
intron <- intron[intron$genefam %in% cds$genefam,]
# acceptors / donors
intron$acc <- substr(intron$seq, 5, 6)
intron$don <- substr(intron$seq, 15, 16)
# consensus
cons.px <- cons.build(intron$acceptor.donor)
cons.px <- cons.px[,! is.nan(colSums(cons.px))]
seq.px <- sapply(intron$acceptor.donor, function(s) gsub("[^acgt]", "", s))
conf.px <- cons.confusion(cons.px, seq.px)
sfam <- split(conf.px$l2scor, intron$genefam)
sfam <- sfam[order(sapply(sfam, median))]
# extract splice exceptions
name.bad <- names(which(sapply(sfam, median) < 0))
name.spc <- names(which(sapply(sfam[name.bad], length) >= CORE_SPLICE_CUTOFF))
name.ok <- setdiff(unique(intron$genefam), name.bad)
name.bad <- setdiff(name.bad, name.spc)
name.list <- c(sapply(name.spc, function(x) x), list(default=name.ok))
cons <- lapply(name.list, function(x) cons.build(intron[intron$genefam %in% x, "acceptor.donor"]))
# write junction models
invisible(sapply(names(cons), function(n) write.model.splice3(cons[[n]], n)))
invisible(sapply(names(cons), function(n) write.model.splice5(cons[[n]], n)))
# use uniform model for bad guys
invisible(sapply(name.bad, function(n) write.unif.splice(3, n)))
invisible(sapply(name.bad, function(n) write.unif.splice(5, n)))
invisible(write.unif.splice('', "none"))
# -------------------------------
# keep data for plotting
# -------------------------------
DB <- list()
params <- list()
params$CORE_NCDS_CUTOFF <- CORE_NCDS_CUTOFF
params$CORE_START_ATG_CUTOFF <- CORE_START_ATG_CUTOFF
params$CORE_START_DFT_CUTOFF <- CORE_START_DFT_CUTOFF
params$CORE_START_OTH_CUTOFF <- CORE_START_OTH_CUTOFF
params$CORE_STOP_CUTOFF <- CORE_STOP_CUTOFF
params$CORE_SPLICE_CUTOFF <- CORE_SPLICE_CUTOFF
params$SHEL_NCDS_CUTOFF <- SHEL_NCDS_CUTOFF
DB$params <- params
DB$chromo <- chromo
DB$cds.lst <- cds.lst
DB$intron <- intron
DB$cons <- cons
notify("saving db.data.Rdata")
save(DB, file="db.data.Rdata")
# -------------------------------
# end
# -------------------------------
quit(save='no')

424
detectors/cds/tools/lib/plot.models.r Executable file
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#!/usr/bin/env Rscript
#
# plots models previously computed by make.models.r
#
# source("plot.models.r")
#
require(vcd)
require(plotrix)
LIBDIR <- Sys.getenv("LIB_DIR")
if (LIBDIR == "") LIBDIR = "."
source(paste0(LIBDIR, "/util.base.r"))
source(paste0(LIBDIR, "/util.plot.r"))
source(paste0(LIBDIR, "/util.cons.r"))
source(paste0(LIBDIR, "/util.grid.r"))
# -------------------------------
# setup
# -------------------------------
OUT.DEV <- TRUE
OUT.TYPE <- "pdf"
OUT.FILE <- "models"
if (OUT.DEV) uplot.init.dev(OUT.FILE, OUT.TYPE)
# -------------------------------
# Load data
# -------------------------------
notify("loading DB data")
load("db.data.Rdata")
params <- DB$params
chromo <- DB$chromo
cds.lst <- DB$cds.lst
intron <- DB$intron
cons <- DB$cons
# -------------------------------
# Genomes infos
# -------------------------------
grd.titlepage("Species")
grd.textpage(lineno=1, "# org: ", nrow(chromo))
#
# general stats
#
grd.hist(chromo, "len", main="Histogram of chromosome length")
grd.hist(chromo, "gc", pos.quant=c(0.75, 0.6), main="Histogram of chromosome GC")
grd.hist(chromo, "nbCds")
grd.fplot(chromo, "len", "nbCds")
#
# nb cds no introns
#
chromo$nbCds_Mono <- chromo$nbCds_int0
chromo$nbCds_Poly <- chromo$nbCds_int1 + chromo$nbCds_intsup1
chromo$percentPoly <- round(chromo$nbCds_Poly * 100 / (chromo$nbCds_Poly + chromo$nbCds_Mono))
grd.hist(chromo, "nbCds_Mono", main="Histogram of monoexonic Cds")
grd.hist(chromo, "nbCds_Poly", main="Histogram of polyexonic Cds")
grd.hist(chromo, "percentPoly", pos.sum=c(0.23,0.6), main="Histogram of % polyexonic")
grd.fplot(chromo, "nbCds", "nbCds_Mono", TRUE, ablin=list(a=0, b=1, col=3))
grd.fplot(chromo, "nbCds", "nbCds_Poly")
#
# cds size
#
grd.hist(chromo, "meanCdsSize", pos.quant=NULL, main="Histogram of Cds size")
# -------------------------------
# CDS
# -------------------------------
cds.all <- do.call(rbind, cds.lst)
grd.titlepage("CDS")
grd.textpage(lineno=1, "# core cds core cutoff: ", params$CORE_NCDS_CUTOFF)
grd.textpage(lineno=2, "# core cds shell cutoff: ", params$SHEL_NCDS_CUTOFF)
grd.textpage(lineno=4, "# total cds: ", nrow(cds.all))
grd.textpage(lineno=5, "# core cds: ", nrow(cds.lst[["core"]]))
grd.textpage(lineno=6, "# shell cds: ", nrow(cds.lst[["shell"]]))
grd.textpage(lineno=7, "# dust cds: ", nrow(cds.lst[["dust"]]))
grd.textpage(lineno=9, "# total org: ", length(unique(cds.all$X.locus)))
grd.textpage(lineno=10, "# core org: ", length(unique(cds.lst[["core"]]$X.locus)))
grd.textpage(lineno=11, "# shell org: ", length(unique(cds.lst[["shell"]]$X.locus)))
grd.textpage(lineno=12, "# dust org: ", length(unique(cds.lst[["dust"]]$X.locus)))
grd.textpage(lineno=14, "# total families: ", length(unique(cds.all$genefam)))
grd.textpage(lineno=15, "# core families: ", length(unique(cds.lst[["core"]]$genefam)))
grd.textpage(lineno=16, "# shell families: ", length(unique(cds.lst[["shell"]]$genefam)))
grd.textpage(lineno=17, "# dust families: ", length(unique(cds.lst[["dust"]]$genefam)))
uplot.setup(mfrow=c(2,2), xpd=NA)
x <- sapply(cds.lst, nrow)
uplot.pie(x, main="CDS", text.r=1.1, col=c(3,2,4))
x <- sapply(cds.lst, function(cds) length(unique(cds$X.locus)))
uplot.pie(x, main="ORG", text.r=1.1, col=c(3,2,4))
x <- sapply(cds.lst, function(cds) length(unique(cds$genefam)))
uplot.pie(x, main="FAM", text.r=1.1, col=c(3,2,4))
uplot.setup(xpd=F)
#
# plot genes cutoff
#
cds.all <- do.call(rbind, cds.lst)
cds.byfam <- split(cds.all, cds.all$genefam)
tab <- sort(sapply(cds.byfam, nrow), decreasing=T)
cols <- rep("red", length(tab))
cols[tab >= params$SHEL_NCDS_CUTOFF] <- "blue"
cols[tab >= params$CORE_NCDS_CUTOFF] <- "green"
barplot(tab, col=cols, border=NA, main="# genes")
cols <- cols[tab >= 50]
tab <- tab[tab >= 50]
barplot(tab, col=cols, border=NA, las=2, cex.names=0.5, main="# genes in core")
abline(h=params$CORE_NCDS_CUTOFF, col=1)
text(50, 200, "CORE_NCDS_CUTOFF", pos=3)
#
# cds length for core
#
invisible(sapply(c("core", "shell", "dust"), function(what) {
cds <- cds.lst[[what]]
x <- split(cds$length, cds$genefam)
x <- x[order(sapply(x, mean))]
uplot.setup(mfrow=c(2,1))
boxplot(x, pars = list(boxwex = 0.8, staplewex = 0.5, outwex = 0.5, outcex = 0.1),
las=2, cex.axis=0.5, main=paste0(what, " genes - length distribution"))
boxplot(x, pars = list(boxwex = 0.8, staplewex = 0.5, outwex = 0.5, outcex = 0.1), ylim=c(0,2000),
las=2, cex.axis=0.5, main=paste0(what, " genes - length distribution zoom"))
uplot.setup()
}))
# -------------------------------
# starts & stops
# -------------------------------
cds <- cds.lst[["core"]]
grd.titlepage("Starts and Stops")
tab <- sort(table(cds$start), dec=T)
tab <- tab[tab >= 100]
tab <- tab / sum(tab) * 100
barplot(tab, log="y", las=1, ylim=c(0.1, 100), main="start frequencies (%)")
text(0.7, 50, round(tab[1], 2))
text(1.9, 2.3, round(tab[2], 2))
text(3.1, 2.3, round(tab[3], 2))
#
# start by org and gc
#
x <- split(cds$start, cds$X.locus)
fatg <- sapply(x, function(x) table(x)["atg"]/length(x)*100)
names(fatg) <- names(x)
chromo$fatg <- round(fatg[chromo$X.locus], 2)
fgtg <- sapply(x, function(x) table(x)["gtg"]/length(x)*100)
names(fgtg) <- names(x)
chromo$fgtg <- round(fgtg[chromo$X.locus], 2)
facg <- sapply(x, function(x) table(x)["acg"]/length(x)*100)
names(facg) <- names(x)
chromo$facg <- round(facg[chromo$X.locus], 2)
grd.hist(chromo, "fatg", pos.quant=c(0.5, 0.6), main="Histogram of atg freq. by org")
grd.hist(chromo, "fgtg", main="Histogram of gtg freq. by org")
grd.hist(chromo, "facg", pos.sum=c(0.3, 0.6), main="Histogram of acg freq. by org")
grd.fplot(chromo, "gc", "fatg", main="atg freq. by org GC", pos=c(0.2, 0.3))
grd.fplot(chromo, "gc", "fgtg", main="gtg freq. by org GC")
grd.fplot(chromo, "gc", "facg", main="acg freq. by org GC")
ter <- cbind(fatg, fgtg, facg)
colnames(ter) <- c("ATG", "GTG", "ACG")
igc <- cut(chromo$gc, breaks=quantile(chromo$gc, seq(0, 1, 0.1)), include.lowest=T, labels=1:10)
cols <- rainbow(10)[igc]
ternaryplot(ter, col=cols, cex=0.2, main="Start by org", labels="outside")
#
# start by common genes
#
x <- split(cds$start, cds$genefam)
fatg <- sapply(x, function(x) table(x)["atg"]/length(x)*100)
names(fatg) <- names(x)
fgtg <- sapply(x, function(x) table(x)["gtg"]/length(x)*100)
names(fgtg) <- names(x)
facg <- sapply(x, function(x) table(x)["acg"]/length(x)*100)
names(facg) <- names(x)
barplot(sort(fatg)[1:10], las=2, main="atg freq. by gene")
barplot(sort(fgtg, dec=T)[1:10], las=2, main="gtg freq. by gene")
barplot(sort(facg, dec=T)[1:10], las=2, main="acg freq. by gene")
ter <- cbind(fatg, fgtg, facg)
colnames(ter) <- c("ATG", "GTG", "ACG")
ternaryplot(ter, col=1, cex=0.5, id=rownames(ter), main="Starts by genes", labels="outside")
# -------------------------------
# stops
# -------------------------------
#
# stop by org and gc
#
tab <- sort(table(cds$stop), dec=T)
tab <- tab[tab >= 100]
tab <- tab / sum(tab) * 100
barplot(tab, log="y", las=1, ylim=c(0.1, 100), main="stop frequencies (%)")
text(0.7, 80, round(tab[1], 2))
text(1.9, 30, round(tab[2], 2))
text(3.1, 25, round(tab[3], 2))
x <- split(cds$stop, cds$X.locus)
ftaa <- sapply(x, function(x) table(x)["taa"]/length(x)*100)
names(ftaa) <- names(x)
chromo$ftaa <- round(ftaa[chromo$X.locus], 2)
ftag <- sapply(x, function(x) table(x)["tag"]/length(x)*100)
names(ftag) <- names(x)
chromo$ftag <- round(ftag[chromo$X.locus], 2)
ftga <- sapply(x, function(x) table(x)["tga"]/length(x)*100)
names(ftga) <- names(x)
chromo$ftga <- round(ftga[chromo$X.locus], 2)
grd.hist(chromo, "ftaa", pos.quant=c(0.7, 0.6), main="Histogram of taa freq. by org")
grd.hist(chromo, "ftag", pos.quant=c(0.8, 0.6), main="Histogram of tag freq. by org")
grd.hist(chromo, "ftga", pos.quant=c(0.8, 0.6), main="Histogram of tga freq. by org")
grd.fplot(chromo, "gc", "ftaa", main="taa freq. by org GC", pos=c(0.2, 0.3))
grd.fplot(chromo, "gc", "ftag", main="tag freq. by org GC")
grd.fplot(chromo, "gc", "ftga", main="tga freq. by org GC")
ter <- cbind(ftaa, ftag, ftga)
colnames(ter) <- c("TAA", "TAG", "TGA")
igc <- cut(chromo$gc, breaks=quantile(chromo$gc, seq(0, 1, 0.1)), include.lowest=T, labels=1:10)
cols <- rainbow(10)[igc]
ternaryplot(ter, col=cols, cex=0.2, main="Stops by org", labels="outside")
#
# stop by common genes
#
x <- split(cds$stop, cds$genefam)
ftaa <- sapply(x, function(x) table(x)["taa"]/length(x)*100)
names(ftaa) <- names(x)
ftag <- sapply(x, function(x) table(x)["tag"]/length(x)*100)
names(ftag) <- names(x)
ftga <- sapply(x, function(x) table(x)["tga"]/length(x)*100)
names(ftga) <- names(x)
barplot(sort(ftaa), las=2, cex.names=0.5, ylim=c(0,100), main="taa freq. by gene")
barplot(sort(ftag), las=2, cex.names=0.5, ylim=c(0,100), main="tag freq. by gene")
barplot(sort(ftga), las=2, cex.names=0.5, ylim=c(0,100), main="tga freq. by gene")
ter <- cbind(ftaa, ftag, ftga)
colnames(ter) <- c("TAA", "TAG", "TGA")
ternaryplot(ter, col=1, cex=0.3, id=rownames(ter), main="Stops by genes", labels="outside")
# -------------------------------
# splice junctions
# -------------------------------
grd.titlepage("Splice Junctions")
grd.textpage(lineno=1, "# intron in core: ", nrow(intron))
#
# intron size
#
intron$size <- intron$to - intron$from + 1
grd.hist(intron, "size", pos.quant=NULL, main="Histogram of intron size", br=1000, xlim=c(0,2000))
#
# nb intron / gene
#
x <- split(intron, intron$genefam)
x <- x[order(sapply(x, function(x) mean(x$intron_nb)), decreasing=T)]
nmax <- max(intron$intron_nb)
lintron <- lapply(x, function(x) x$intron_nb)
mintron <- sapply(lintron, function(x) table(factor(x, levels=1:nmax)))
lintron0 <- table(cds[cds$nexon == 1,"genefam"])[names(lintron)]
mintron <- rbind("0"=lintron0, mintron)
mintron <- t(t(mintron)/colSums(mintron))
mintron[mintron==0] <- NA
nn <- nrow(mintron)
xx <- mintron[nn:1,]
ll <- lapply(1:nn, function(i) xx[i,])
mintron <- mintron[,do.call(order, c(ll, decreasing=T))]
battleship.plot(mintron, maxxspan=0.3, maxyspan=0.3,
cex.labels=0.7,
main="% intron per polyexonic gene")
#
# acceptors / donors
#
tab <- sort(table(intron$acc), dec=T)
tab <- tab[tab >= 100]
tab <- tab / sum(tab) * 100
barplot(tab, log="y", las=1, ylim=c(0.1, 100), main="acceptor frequencies (%)")
text(0.7, 50, round(tab[1], 2))
text(1.9, 3, round(tab[2], 2))
text(3.1, 2.3, round(tab[3], 2))
tab <- sort(table(intron$don), dec=T)
tab <- tab[tab >= 100]
tab <- tab / sum(tab) * 100
barplot(tab, log="y", las=1, ylim=c(0.1, 100), main="donor frequencies (%)")
text(0.7, 50, round(tab[1], 1))
text(1.9, 40, round(tab[2], 1))
text(3.1, 15, round(tab[3], 1))
text(4.3, 12, round(tab[4], 1))
#
# consensus all
#
cons$all <- cons.build(intron$acceptor.donor)
invisible(sapply(rev(names(cons)), function(what) {
cons.plot(cons[[what]], paste0("consensus ", what))
}))
#
# default consensus score by consensus length
#
cons.def <- cons[["default"]]
cons.def <- cons.def[,! is.nan(colSums(cons.def))]
seq.def <- sapply(intron$acceptor.donor, function(s) gsub("[^acgt]", "", s))
epx <- apply(cons.def, 2, function(col) -sum(col * log(col, base=4)))
opx <- order(epx)
conf.def <- lapply(seq(2, length(opx), by=2), function(n) {
pos <- head(opx, n)
notify(n, "/", length(opx))
cons.confusion(cons.def, seq.def, thresh=0, pos=pos)
})
acc <- sapply(conf.def, function(x) x$acc)
sen <- sapply(conf.def, function(x) x$sen)
sel <- sapply(conf.def, function(x) x$sel)
plot(sel, ylim=c(0.7, 1), pch=1, type="b", main="accuracy by nb consensus positions", ylab="")
lines(sen, type="b", pch=2)
lines(acc, type="b", pch=3)
legend(1, 0.95, c("sensit.", "select.", "accur."), pch=1:3, horiz=T, bty="n")
#
# default consensus score by genes
#
conf.def <- cons.confusion(cons.def, seq.def, thresh=0)
cons.histconf(conf.def)
sfam <- split(conf.def$l2scor, intron$genefam)
sfam <- sfam[order(sapply(sfam, median))]
boxplot(sfam, pars = list(boxwex = 0.8, staplewex = 0.5, outwex = 0.5, outcex = 0.1),
las=2, cex.axis=0.7, main="default junction logr score by genes")
abline(h=0)
#
# end
#
if (OUT.DEV) {
cat("+ plot file:", paste0(OUT.FILE, ".", OUT.TYPE), "\n")
invisible(dev.off())
}
quit(save='no')

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detectors/cds/tools/lib/summarize_cmp.r Executable file
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#!/usr/bin/env Rscript
#
# plot summary graphics of comparisons
#
#
LIBDIR <- Sys.getenv("LIB_DIR")
if (LIBDIR == "") LIBDIR = "."
source(paste0(LIBDIR, "/util.plot.r"))
COLORS <- 2:10
#
OUT.DEV <- TRUE
OUT.TYPE <- "pdf"
OUT.FILE <- "compare"
if (OUT.DEV) uplot.init.dev(OUT.FILE, OUT.TYPE)
#
tab <- read.table("compare.txt", header=T, comment.char="", stringsAsFactors=F)
#
par(xpd=NA)
#
sel <- c("cor", "alcor", "acc", "wrong", "over", "misstot")
tab$ptot <- rowSums(tab[,sel])
for (s in sel)
tab[,paste0("p", s)] <- tab[,s] * 100 / tab$ptot
colors <- head(COLORS, length(sel))
cols <- paste0("p", sel)
ord <- order(tab$pcor+tab$palcor+tab$pacc, decreasing=T)
barplot(t(tab[ord,cols]), names.arg=tab$X.org[ord],
ylim=c(0,100), col=colors, las=2, cex.names=0.5)
legend(0, 110, sel, fill=colors, cex=0.7, horiz=T)
#
sel <- c("cor", "alcor", "acc", "wrong", "over", "misschlo")
tab$rtot <- rowSums(tab[,sel])
for (s in sel)
tab[,paste0("r", s)] <- tab[,s] * 100 / tab$rtot
colors <- head(COLORS, length(sel))
cols <- paste0("r", sel)
ord <- order(tab$rcor+tab$ralcor+tab$racc, decreasing=T)
barplot(t(tab[ord,cols]), names.arg=tab$X.org[ord],
ylim=c(0,100), col=colors, las=2, cex.names=0.5)
legend(0, 110, sel, fill=colors, cex=0.7, horiz=T)
#
if (OUT.DEV) {
cat("# plot file:", paste0(OUT.FILE, ".", OUT.TYPE), "\n")
invisible(dev.off())
}
quit(save='no')

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detectors/cds/tools/lib/summary.cmp.awk Normal file
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#
#
function getOrg(s, _local_, a, na, org) {
na = split(s, a, "/")
na = split(a[na], a, "\\.")
return a[1]
}
BEGIN {
PROCINFO["sorted_in"] = "@ind_num_asc"
print "#org tot cor alcor acc wrong over misstot misschlo missoth"
}
/MISSED in ChloroDB/ {
org = getOrg($1)
Org[org]++
Cnt[org]["MISSCHLORO"] = $2
next
}
/MISSED not in ChloroDB/ {
org = getOrg($1)
Org[org]++
Cnt[org]["MISSNOTCHLORO"] = $2
next
}
/^#/ { next }
/^.*:MATCH/ {
org = getOrg($1)
Org[org]++
split($NF, a, "\\.")
Cnt[org][a[1]]++
}
END {
for (org in Org) {
Cnt[org]["TOTAL"] = Cnt[org]["CORRECT"] + Cnt[org]["ALMOST_CORRECT"] \
+ Cnt[org]["ACCEPTABLE"] + Cnt[org]["WRONG"] \
+ Cnt[org]["MISSED"]
}
for (org in Org) {
print org, Cnt[org]["TOTAL"]+0, Cnt[org]["CORRECT"]+0, \
Cnt[org]["ALMOST_CORRECT"]+0, Cnt[org]["ACCEPTABLE"]+0, \
Cnt[org]["WRONG"]+0, Cnt[org]["OVERPRED"]+0, \
Cnt[org]["MISSED"]+0, \
Cnt[org]["MISSCHLORO"]+0, Cnt[org]["MISSNOTCHLORO"]+0
}
}

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detectors/cds/tools/lib/util.base.r Normal file
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#
# R basic utilities
#
#
# notify on stderr
#
notify <- function(...) cat("+", ..., "\n")

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detectors/cds/tools/lib/util.cons.r Normal file
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#
# R consensus utilities
#
#
# compute consensus
#
cons.build <- function(seqs, backcount=1) {
xx <- do.call(rbind, sapply(seqs, strsplit, "", USE.NAMES=F))
lv <- c("a", "c", "g", "t", ".", "-")
mx <- apply(xx, 2, function(x) table(factor(x, levels=lv)))[1:4,]
cx <- colSums(mx)
mx <- mx + backcount
mx[,cx==0] <- 0
apply(mx, 2, function(x) x / sum(x))
}
#
# score consensus
#
cons.score <- function(cons, seq, pos=1:ncol(cons)) {
seq <- strsplit(seq, "")[[1]]
if (length(seq) != ncol(cons)) {
warning("incompatible seq and cons size")
return(NA)
}
ppx <- sapply(pos, function(i) cons[seq[i],i])
sum(log10(ppx+1e-6))
}
#
# logratio to uniform model score
#
cons.logratio <- function(cons, seq, m0=NULL, pos=1:ncol(cons)) {
if (is.null(m0)) {
m0 <- matrix(rep(0.25, 4), nrow=4, ncol=ncol(cons))
rownames(m0) <- c('a', 'c', 'g', 't')
}
sc <- cons.score(cons, seq, pos=pos)
sc0 <- cons.score(m0, seq, pos=pos)
2 * (log(10^sc, base=2) - log(10^sc0, base=2))
}
#
# shuffle sequence
#
seq.shuf <- function(seq) {
paste0(sample(strsplit(seq, "")[[1]], nchar(seq), replace=F), collapse="")
}
#
# compute confusion matrix between actual and shuffled sequences
#
cons.confusion <- function(cons, seq, m0=NULL, pos=1:ncol(cons), thresh=0) {
som <- function(x) sum(x, na.rm=T)
res <- list()
res$l2scor <- l2scor <- sapply(seq, function(s) cons.logratio(cons, s, m0=m0, pos=pos))
seq <- sapply(seq, seq.shuf)
res$r2scor <- r2scor <- sapply(seq, function(s) cons.logratio(cons, s, m0=m0, pos=pos))
res$conf <- conf <- matrix(c(som(l2scor >= thresh), som(l2scor < thresh),
som(r2scor >= thresh), som(r2scor < thresh)),
nrow=2, byrow=T)
res$acc <- sum(diag(conf)) / sum(conf)
res$sen <- conf[1,1] / sum(conf[1,])
res$sel <- conf[1,1] / sum(conf[,1])
res
}
#
# plot consensus
#
cons.plot <- function(cons, main="consensus") {
cols <- c("blue", "orange", "red", "green")
bp <- barplot(cons, col=cols, ylim=c(0,1), main=main)
plx <- apply(cons, 2, function(col) -sum(col * log(col+1e-6, base=4)))
lines(bp, plx, type="b", pch=19)
legend(0, 1.1, c("a","c","g","t"), fill=cols, horiz=T, xpd=NA, bty="n")
legend(20, 1.1, "entropy", pch=19, horiz=T, xpd=NA, bty="n")
invisible()
}
#
# plot confusion scores histograms
#
cons.histconf <- function(conf, main="junction logr score") {
lrh <- hist(c(conf$l2scor, conf$r2scor), br=50, plot=F)
lh <- hist(conf$l2scor, br=lrh$breaks, plot=F)
rh <- hist(conf$r2scor, br=lrh$breaks, plot=F)
xx <- rbind(lh$counts, rh$counts) / sum(lh$counts)
colnames(xx) <- lrh$mids
barplot(xx, col=c(3,2), beside=T, main=main)
legend(0, 0.1, c("true", "shuffled"), fill=c(3,2), horiz=F, xpd=NA)
invisible()
}

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detectors/cds/tools/lib/util.grid.r Normal file
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#
# R misc grid plotting
#
require(grid)
require(gridExtra)
#
# get line height
#
grd.lineheight <- function(s="X") {
convertHeight(unit(1,"strheight", s), "native", valueOnly=T)
}
#
# quantile table
#
grd.qtab <- function(df, what, cols, n=5) {
df <- df[order(df[,what], decreasing=T),cols]
sep <- head(df,1)
sep[] <- "-"
rbind(head(df, n), sep, tail(df, n))
}
#
# histogram with tables
#
grd.hist <- function(df, what, cols = c(1,2, which(colnames(df) == what)),
breaks=50, pos.sum=c(0.2,0.6), pos.quant=c(0.7,0.6), cex=0.7,
main=paste0("Histogram of ", what), ...) {
hist(df[,what], breaks=breaks, xlab=what, main=main, ...)
if (! is.null(pos.sum)) {
pushViewport(viewport(pos.sum[1], pos.sum[2], gp=gpar(cex=cex)))
grid.table(x<-summary(df[,what]), rows=names(x))
popViewport()
}
if (! is.null(pos.quant)) {
pushViewport(viewport(pos.quant[1], pos.quant[2], gp=gpar(cex=cex)))
grid.table(grd.qtab(df, what, cols), rows=NULL)
popViewport()
}
invisible()
}
#
# plot with fit
#
grd.fplot <- function(df, what.x, what.y, linfit=T, pos=c(0.2, 0.8), ablin=NULL, ...) {
plot(df[,what.x], df[,what.y], xlab=what.x, ylab=what.y, ...)
if (linfit) {
fit <- lm(df[,what.y] ~ df[,what.x])
abline(fit, col=2)
pushViewport(viewport(gp=gpar(col=2)))
a <- sprintf("%.2e", coef(fit)[2])
b <- sprintf("%.2e", coef(fit)[1])
grid.text(paste0(what.y, " = ", a, " * ", what.x, " + ", b),
pos[1], pos[2], just="left")
pos[2] = pos[2] - 2 * grd.lineheight()
grid.text(paste0("R2=", round(summary(fit)$r.squared, 3)),
pos[1], pos[2], just="left")
popViewport()
}
if (! is.null(ablin))
do.call(abline, ablin)
invisible()
}
#
# write text
#
grd.textpage <- function(..., lineno=0, left=0.1, top=0.9, cex=1, fact=1.4) {
txt <- do.call(paste0, list(...))
pushViewport(viewport(gp=gpar(cex=cex)))
grid.text(txt, left, top-lineno*grd.lineheight()*fact, just="left")
popViewport()
invisible(txt)
}
#
# title page
#
grd.titlepage <- function(title, x=0.5, y=0.7, cex=3, ...) {
notify("processing", title)
grid.newpage()
grid.text(title, x, y, gp=gpar(cex=cex), ...)
invisible()
}

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detectors/cds/tools/lib/util.modelio.r Normal file
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#
# R models I/O utilities
#
#
# write start model
#
write.model.start <- function(frq, what) {
dir.create("models", showWarnings=F)
fil <- paste0("models/start.", what, ".frq")
notify("writing start model:", fil)
cat("# start model :", what, "\n", file=fil)
for (x in names(frq))
cat(x, frq[x]/sum(frq), frq[x], "\n", file=fil, append=T)
invisible(fil)
}
#
# write stop model
#
write.model.stop <- function(frq, what) {
dir.create("models", showWarnings=F)
fil <- paste0("models/stop.", what, ".frq")
notify("writing stop model:", fil)
cat("# stop model :", what, "(freq. ignored)\n", file=fil)
for (x in names(frq))
cat(x, frq[x]/sum(frq), frq[x], "\n", file=fil, append=T)
invisible(fil)
}
#
# write splice3 model
# [FIXME] positions are hard-coded
#
write.model.splice3 <- function(cons, what) {
dir.create("models", showWarnings=F)
fil <- paste0("models/splice3.", what, ".frq")
notify("writing splice3 model:", fil)
.catcons <- function(i) {
cat(round(cons[c("a","c","g","t"), i]*100, 0), "\n",
file=fil, append=T)
}
cat("# 3' splice model :", what, "\n", file=fil)
cat("# A C G T\n", file=fil, append=T)
sapply(seq.int(1, 4), .catcons)
cat("splice\n", file=fil, append=T)
sapply(seq.int(6, 11), .catcons)
invisible(fil)
}
#
# write splice5 model
# [FIXME] positions are hard-coded
#
write.model.splice5 <- function(cons, what) {
dir.create("models", showWarnings=F)
fil <- paste0("models/splice5.", what, ".frq")
notify("writing splice5 model:", fil)
.catcons <- function(i) {
cat(round(cons[c("a","c","g","t"), i]*100, 0), "\n",
file=fil, append=T)
}
cat("# 5' splice model :", what, "\n", file=fil)
cat("# A C G T\n", file=fil, append=T)
sapply(seq.int(13, 18), .catcons)
cat("splice\n", file=fil, append=T)
sapply(seq.int(20, 23), .catcons)
invisible(fil)
}
#
# write splice3/5 uniform model
#
write.unif.splice <- function(pos, what) {
dir.create("models", showWarnings=F)
fil <- paste0("models/splice", pos, ".", what, ".frq")
notify("writing uniform splice", pos, "model:", fil)
cat("# 3'/5' splice null model", file=fil)
cat("# A C G T\n", file=fil, append=T)
cat("25 25 25 25\n", file=fil, append=T)
cat("splice\n", file=fil, append=T)
cat("25 25 25 25\n", file=fil, append=T)
invisible(fil)
}

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#
# R plot utilities
#
#
# setup graphic device
# tiff: high resolution 600 dpi
# pdf
#
uplot.init.dev <- function(fname, type="pdf", width=7, height=7, resol=600, ...) {
fname <- paste0(fname, ".", type)
res <- NULL
if (type == "tiff") {
res <- tiff(fname, width=width, height=height, units="in", res=resol, ...)
}
if (type == "pdf") {
res <- pdf(fname, width=width, height=height, ...)
}
invisible(res)
}
#
# convert pdf to tiff using ghostscript
#
uplot.convert2tiff <- function(fname, resol=600) {
infile <- paste0(fname, ".pdf")
oufile <- paste0(fname, ".tif")
cmd <- paste0("echo quit | gs -r", resol, "-dBATCH -dNOPAUSE -sDEVICE=tiff12nc -sCompression=lzw -sOutputFile=", oufile, " ", infile)
system(cmd)
}
#
# default plot setup
#
uplot.setup <- function(mfrow=c(1,1),
las=1,
mgp=c(2, 0.7, 0),
oma=c(0, 0, 0, 0),
mar=c(4, 3, 3, 2),
cex.main=1,
font.main=1,
family='Helvetica', ...) {
par(mfrow=mfrow, las=las, mgp=mgp, oma=oma, mar=mar, cex.main=cex.main, font.main=font.main, family=family, ...)
}
#
# pie plot
#
uplot.pie <- function(tab, main="", labels=c("name", "val", "per"), text.r=0.5, text.col="black", text.cex=1, main.pos=c(0,0), main.col="black", ...) {
pie(tab, edges=2000, main="", labels="", ...)
text(main.pos[1], main.pos[2], main, cex=1.5, col=main.col)
prop <- tab/sum(tab)
theta <- 2*pi * (cumsum(prop) - prop/2)
lab <- list(name=names(tab), val=tab, per=sprintf("%d%%", round(prop*100)))
lab <- apply(data.frame(lab[labels]), 1, paste, collapse="\n")
if (length(lab) > 0)
text(text.r*cos(theta), text.r*sin(theta), lab, cex=text.cex, col=text.col)
invisible(NULL)
}
#
# plot utility : color representation of a table
#
uplot.table <- function(tab, col=heat.colors(100), with.lines=TRUE) {
image(as.matrix(tab), xaxt="n", yaxt="n", col=col)
nli <- nrow(tab)
nco <- ncol(tab)
dx <- 0.5 / (nli-1)
dy <- 0.5 / (nco-1)
xf <- (seq_len(nli)-1)/(nli-1) - dx
yf <- (seq_len(nco)-1)/(nco-1) - dy
if (with.lines) {
segments(xf, -dy, xf, 1+dy)
segments(-dx, yf, 1+dx, yf)
}
Axis(c(0,1), at=xf+dx, side=1, labels=rownames(tab), las=2, cex.axis=0.5, padj=0)
Axis(c(0,1), at=yf+dy, side=2, labels=colnames(tab), las=2, cex.axis=0.5, padj=0)
invisible(NULL)
}
#
# plot utility : identify points within user's rectangle
#
rect.identify <- function(data) {
if (is.null(dim(data))) data <- cbind(seq_along(data), data)
xy <- locator(n=2, type='n')
r <- matrix(c(range(xy$x), range(xy$y)), ncol=2, byrow=TRUE)
rect(r[1,1], r[2,1], r[1,2], r[2,2], border='red')
.in.range <- function(p, r) {
.in.int <- function(i) {
(p[i] >= r[i,1]) && (p[i] <= r[i,2])
}
.in.int(1) && .in.int(2)
}
isel <- which(apply(data, 1, .in.range, r))
points(data[isel,], col='red', pch=19)
isel
}