Params: ./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc,104,r-ACGU-_,103,l-ACGU-_,160,l-ACGU-_,159,l-ACGU-_,199,r-ACGU-_,198,l-ACGU-_,239,r-ACGU-_,238,l-ACGU-_,284,l-ACGU-_,283,r-ACGU-_,302,l-ACGU-_,299,r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub,189,100/sub,227,100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub,189,100/sub,227,100/sub,270,100 Build: release Host: bicycle.cs.washington.edu pid: 15327 ----hmm-from-cmFileName: Rfam/cm/RF00023.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Saureus_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00023.cm 1 1 100000 0 cfsqp 0 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Saureus_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00023.cm 1 1 100000 0 cfsqp 0 1 Build: release Host: gattaca.cs.washington.edu ----hmm-from-cmFileName: Rfam/cm/RF00023.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Saureus_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00023.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Saureus_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00023.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu Exploded HMM has 2506 states ----hmm-from-cmFileName: Rfam/cm/RF00023.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Saureus_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00023.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Saureus_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00023.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,104,r-ACGU-_/remember-nuc,103,l-ACGU-_/remember-nuc,160,l-ACGU-_/remember-nuc,159,l-ACGU-_/remember-nuc,199,r-ACGU-_/remember-nuc,198,l-ACGU-_/remember-nuc,239,r-ACGU-_/remember-nuc,238,l-ACGU-_/remember-nuc,284,l-ACGU-_/remember-nuc,283,r-ACGU-_/remember-nuc,302,l-ACGU-_/remember-nuc,299,r-AU-CG-_ ----hmm-from-cmFileName: Rfam/cm/RF00023.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Saureus_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00023.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Saureus_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00023.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/sub,189,100/sub,227,100 ----hmm-from-cmFileName: Rfam/cm/RF00023.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Saureus_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00023.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Saureus_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00023.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/sub,189,100/sub,227,100/sub,270,100 ----cmFile: Rfam/cm/RF00023.cm (global) ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/org.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/org.dat.fasta.gz ----sequence: #18951,sp|AF022186.2|AF022186 Cyanidium caldarium strain RK1 chloroplast, complete genome. ----isReversed: 1 ----hitSequence: GGGGCUGAAAGGAUAUUCGACAUAUUAAUUUCGUGCGCUAUGAUGCAAGCCGAGAAUGCUUAUCUCGUAAAAAAGCAGACAAAGAAAUAAAUGCAAACAAUAUUAUUGAAAUUAGCAAUAUUAGAAAACCAGCUCUAGUAGUCUAGCCUGAUUCAGUUAUUUCUAAAUUAUUUAUGUUAUGUUAUUUAAGCUUGUAGUAACUAUCUAGUGUACAAUUUCUAUGGACGUGGGUUCAAUUCCCACCAGCUCCACAA hit 0 : 109751 109498 (rev) 43.06 bits [[[[[[[,,,,,,,,,.,,,,,((((((((--..-(((-((-(((((((((((,,,,,., 1 GGGGgUGaUuaUGGUu.UUCGACagGaauagu..gaaggcuUaaggugCAuGuCGAGG.u 56 GGGG:UG +A+GG+U UUCGACA:: +:A+U + U: +:U:CA:G:CGAG U 55171 GGGGCUG--AAAGGAUaUUCGACAUAUUAAUUuc-GUGCGCUAUGAUGCAAGCCGAGAaU 55227 <<<<<<_____________>>>>>>,.,,,,,,,,,,,,,,,,,,,,,,,,,,....... 57 gcggcuggCCUCGUAAAAAagccgcA.aAAAAAUAAcUGCAAAcAAcAAaAAc....... 108 :C:::U CUCGUAAAAAA:::G: AA AAAUAA+UGCAAACAA+A +A + 55228 GCUUAU---CUCGUAAAAAAGCAGACaAAGAAAUAAAUGCAAACAAUAUUAUUgaaauua 55284 ..............,,,<<<<<<<<<<_________>>>>->>>>>><<<<<<<<<<<-- 109 ..............UACgcuuuagcugCUUAAccAgcugccguuuggcguucuccaugga 154 GCU+U::: G +UA C :: :U C +U+++::::+A 55285 gcaauauuagaaaaCCAGCUCUAGUAGUCUAG----CCUGAUU----CAGUUAUUUCUAA 55336 <<<________>>>-->>>>------>>>>>>>,,,,,,,,,,,,,,,,,<<<<<-<<<< 155 auucugcCcuuuguuuuauggaaggcgucaacgcaaacuaguAagggAUcguuuagaaau 214 AUU +U+UGUU ::::+ 55337 AUU---AUUUAUGUUAUGUUA--------------------------------------- 55354 <<________>>>>>>->>>>>,,,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<____ 215 cccgucuggggguaguuuagaaaaAAAuuuaAAucaGgcaUagucuauuacuagcuUGuu 274 U 55355 ----------------------------------------U------------------- 55355 ____>>>->>>>>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,)))))---))))))))- 275 cuuuggccgauaauagaugAAAauUaAAAaAaaAauagACUAAaCaUGUAGaacguuugu 334 UAA:C:UGUAG:A:+ : U 55356 ---------------------------------------UUAAGCUUGUAGUAACUAUCU 55376 )))...---)))))))),,,<<<<<_______>>>>>]]]]]]]:::: 335 ugg...cAauauuUuuGGACggGGGUUCGAuUCCCccCAcCUCCACCA 379 CAAU:+ ::UGGACG:GGGUUC AUUCCC:CCA:CUCCAC A 55377 AGUguaCAAUUUCUAUGGACGUGGGUUCAAUUCCCACCAGCUCCACAA 55424 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/org.dat.fasta.gz ----sequence: #21972,sp|AF041468.1|AF041468 Guillardia theta complete plastid genome. ----isReversed: 1 ----hitSequence: GGGGCUGAUUUGGAUUCGACAUAUAAAUUUGCGUGUUUCAUUAUGAAGCAAGUCAAGUUUAAUGAUCUUGUAAAAAACAUUAAAGUACAAAUAAAUGCAAGCAAUAUAGUUUCAUUUAGUUCAAAACGUUUAGUCUCUUUUGCAUAAGCAAAAUGUGUUAAUAACUUUCUUAGUAGAAAUUGGAGAAGUUUACUAAGAUUUAUAUUUACUCCAUAAUUAUUUUAAAGAUGGUAAAAAGGUGAUUCAUCAUUUGUAUGUUUCUAAACUUUGUGAAAGAAUAGUGGGCUCCAUUUAUAAUGAACGUGGGUUCAAAUCCCACCAGCUCCA hit 1 : 50514 50188 (rev) 59.40 bits [[[[[[[,,,,,,,,,,,,,,((((((((--.....-(((-((-(((((((((((,,,,, 1 GGGGgUGaUuaUGGUuUUCGACagGaauagu.....gaaggcuUaaggugCAuGuCGAGG 55 GGGG:UG U+UGG+ UUCGACA: :A+U G: :+ :UA:+::GCA:GUC AG 71011 GGGGCUG-AUUUGGA-UUCGACAUAUAAAUUugcguGUUUCAUUAUGAAGCAAGUCAAG- 71067 ,<<<<<<____________._>>>>>>,.,,,,,,,,,,,,,,,,,,,,,,,,,,..... 56 ugcggcuggCCUCGUAAAA.AagccgcA.aAAAAAUAAcUGCAAAcAAcAAaAAc..... 108 U:::::: +CU GUAAAA A::::::A +A AAAUAA+UGCAA CAA+A A + 71068 UUUAAUGA-UCUUGUAAAAaACAUUAAAgUACAAAUAAAUGCAAGCAAUAUAGUUucauu 71126 .............,,,<<<<<<<<<<_____....____>>>>->>>>>><<<<<<<<<< 109 .............UACgcuuuagcugCUUAA....ccAgcugccguuuggcguucuccau 151 U+ + :+::::+:C UAA + G:+:: ::+: +:::U:: :A 71127 uaguucaaaacguUUAGUCUCUUUUGCAUAAgcaaAAUGUGUUAAUAACUUUCUUAGUAG 71186 <--<<<________>>>-->>>>------>>>>>>>,,,,,,,,,,,,,,,,,<<<<<-< 152 ggaauucugcCcuuuguuuuauggaaggcgucaacgcaaacuaguAagggAUcguuuaga 211 :+A:U + ++ G:UU: U:+ A ::A::: 71187 AAAUU----GGAGAAGUUUACUAAGAUU-UAUAUUU------------------------ 71217 <<<<<________>>>>>>->>>>>,,,,,,,,,,,,,,,,,,,,.<<<<<<<<<<-<<< 212 aaucccgucuggggguaguuuagaaaaAAAuuuaAAucaGgcaUa.gucuauuacuagcu 270 +++ + AA AUUU+AA++A G UA : : +U +:: 71218 ------ACUCCAU------------AAUUAUUUUAAAGAUGG-UAaAAAGGU-----GAU 71253 ________>>>->>>>>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,))).))---)))) 271 UGuucuuuggccgauaauagaugAAAauUaAAAaAaaAauagACUAAaCa.UGUAGaacg 329 U UC UU::+ A+ : : CUAAAC: UGU A::+ 71254 UCAUCAUUUGU-----AUGUUU---------------------CUAAACUuUGUGAAAGA 71287 ))))-)))...---)))))))),,,<<<<<_______>>>>>]]]]]]]:::: 330 uuuguugg...cAauauuUuuGGACggGGGUUCGAuUCCCccCAcCUCCACCA 379 :U: U: : CA U: :UG ACG:GGGUUC A UCCC:CCA:CUCCA 71288 AUAGUGGGcucCAUUUAUAAUGAACGUGGGUUCAAAUCCCACCAGCUCCA--- 71337 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/org.dat.fasta.gz ----sequence: #22742,sp|AF049491.1|AF049491 Thalassiosira weissflogii cytochrome c-550 (psbV) gene, partial cds; tRNA-Arg, tmRNA and tRNA-Met genes, complete sequence; and ribosomal protein L19 (rpL19) and 2 Fe-2 S ferredoxin (petF) genes, complete cds, chloroplast genes for chloroplast products. ----isReversed: 0 ----hitSequence: GGGGCUGAUUUGGUUUCGACAUUUAAAACUUCUUUCUAUGUGUCAGGUCAAAGUUUGUAUUCUUUGUAAAAAAAUACUAAAAUACUAAUAAAUGCUAAUAAUAUAAUACCGUUUAUUUUUAAAGCAGUAAAAACAAAAAAAGAAGCAAUGGCUUUAAAUUUUGCUGUAUAGUUCAUUAACUUAGGUUAUUAAAUAUUUUUUCAUUAUAACUGGACUUUUCUCUAGUUUAUAGUUUAGAAUAAAUUUAAAUUUUGCAAAACUCGUUCGAAAAUUUUCGGGCUAAACCUGUAAACGCAAAUACUAAGAAAUUUUAGAUGGACAUGGGUUCAAUUCCCAUCAGUUCCA hit 2 : 488 832 (fwd) 66.91 bits [[[[[[[,,,,,,,,,,,,,,((((((((--.-(((-((-(((((((((((,,,,,.,<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagu.gaaggcuUaaggugCAuGuCGAGG.ugc 58 GGG :UG U+UGGU UUCGACA: :A:A++ : ::U::+: :CA:GUC A G U:+ 488 GGGGCUG-AUUUGGU-UUCGACAUUUAAAACu-UCUUUCUAUGUGUCAGGUCAAAGuUUG 544 <<<<____________._>>>>>>,..,,,,,,,,,,,,,,,,,,,,,,,,,,......, 59 ggcuggCCUCGUAAAA.AagccgcA..aAAAAAUAAcUGCAAAcAAcAAaAAc......U 109 ::U C U GUAAAA AA:: +:A +A +AAUAA+UGC AA AA+A AA 545 UAUU--CUUUGUAAAAaAAUACUAAaaUACUAAUAAAUGCUAAUAAUAUAAUAccguuuA 602 ,,<<<<<<<<<<_____.................____>>>>->>>>>><<<<<<<<<<< 110 ACgcuuuagcugCUUAA.................ccAgcugccguuuggcguucuccaug 152 + ::U::++::G UAA + GC::+ +::U::+:U::::: :: 603 UUUUUAAAGCAG--UAAaaacaaaaaaagaagcaAUGGCUUUAAAUUUUGCUGUAUAGUU 660 --<<<________>>>-->>>>------>>>>>>>,,,,,,,,,,,,,,,,,<<<<<-<< 153 gaauucugcCcuuuguuuuauggaaggcgucaacgcaaacuaguAagggAUcguuuagaa 212 A:U: C+U+:G:U :: :+ A +::::A:+ +UAA G G :U:++: 661 CAUUA---ACUUAGGUUAUUAAAUAUUUUUUCAUU-------AUAACUG---GACUUUUC 707 <<<<________>>>>>>->>>>>,,,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<__ 213 aucccgucuggggguaguuuagaaaaAAAuuuaAAucaGgcaUagucuauuacuagcuUG 272 : +: GU+ :+ ::+U:A: A+AAAUUUAAA 708 UCUA-GUU----UAUAGUUUAGA-AUAAAUUUAAA------------------------- 736 ______>>>->>>>>>>>>>.,,,,,,,,,,,,,,,,,,,,,,,,,)))))---)))))) 273 uucuuuggccgauaauagau.gAAAauUaAAAaAaaAauagACUAAaCaUGUAGaacguu 331 UU+U + A A U+G+U GAAAAUU+ +G CUAAAC:UGUA : :+:: 737 UUUUGC----AAAACUCGUUcGAAAAUUU--------UCGGGCUAAACCUGUAAACGCAA 784 ))-)))...---)))))))),,,<<<<<_______>>>>>]]]]]]]:::: 332 uguugg...cAauauuUuuGGACggGGGUUCGAuUCCCccCAcCUCCACCA 379 ::+ : A U:U: :UGGAC::GGGUUC AUUCCC::CA: UCCA 785 AUACUAagaAAUUUUAGAUGGACAUGGGUUCAAUUCCCAUCAGUUCCA--- 832 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/org.dat.fasta.gz ----sequence: #43523,sp|AF166114.1|AF166114 Mesostigma viride chloroplast DNA, complete genome. ----isReversed: 0 ----hitSequence: GGGGUUGAAAUGGUUUCGACGUUUUAGUAUAUAUCUUCUUACAAGCAAGUCGAGAAUGAACCAAUCUCGUAAACUUGAGUUCAAUUGCAAAUAAAUGCUAACAAUAUUUUACCUUUUAAUCGUAAGACAGCCGUAGCUGUUUAAAAGUUUUUUGAUAACUUCGAGCAUUUUUGAUUUGUUAAAUACAAUUGUUAUAAAACAAAUUAAAUAAUAGUUUUUGUUUCUUUACAAAUAAUGUAGAAAUAAUUUUUUUUAGCUUUUCAAGCUCCAGCUUUGUGGAUUAGCAAAGCUAAACUUGUGAAUACAAAGAAGAGAUCAAACUAAAGCGGACGCGGGUUCAAAACCCGCCAGCUCCA hit 3 : 20729 21084 (fwd) 81.00 bits [[[[[[[,,,,,,,,,,,,,,((((((((--...-(((-((-(((((((((((,,,,,., 1 GGGGgUGaUuaUGGUuUUCGACagGaauagu...gaaggcuUaaggugCAuGuCGAGG.u 56 GGGG:UG +AUGGU UUCGAC:+ ::::+ A : ::U+: :GCA:GUCGAG U 20729 GGGGUUG-AAAUGGU-UUCGACGUUUUAGUAuau-AUCUUCUUACAAGCAAGUCGAGAaU 20785 <<<<<<____________..._>>>>>>,.,,,,,,,,,,,,,,,,,,,,,,,,,,.... 57 gcggcuggCCUCGUAAAA...AagccgcA.aAAAAAUAAcUGCAAAcAAcAAaAAc.... 108 ::::C+ +CUCGUAAA +G::::A + AAAUAA+UGC AACAA+A + 20786 GAACCAA-UCUCGUAAACuug-AGUUCAAuUGCAAAUAAAUGCUAACAAUAUUUUAccuu 20843 ...........,,,<<<<<<<<<<_________>>>>->>>>>><<<<<<<<<<<--<<< 109 ...........UACgcuuuagcugCUUAAccAgcugccguuuggcguucuccauggaauu 157 GC: U:+C+: UUAA :+G++:U : : U :::::::G A U 20844 uuaaucguaagACAGCCGUAGCUGUUUAA----AAGUUUUUU--GAUAACUUCGAGCAUU 20897 ________>>>-->>>>------>>>>>>>,,,,,,,,,,,,,,,,,<<<<<-<<<<<<_ 158 cugcCcuuuguuuuauggaaggcgucaacgcaaacuaguAagggAUcguuuagaaauccc 217 + +++U U U:::: A + +::: A :+AA++ A UAA AU+GU:::+:+:: + 20898 ---UUUGAUUUGUUAAAUACAAUUGUUAUAAAACAAAUUAAAUAAUAGUUUUUGUUUCU- 20953 _______>>>>>>->>>>>,,,,,,,,,,,,,,,,,,,,.<<<<<<<<<<-<<<______ 218 gucuggggguaguuuagaaaaAAAuuuaAAucaGgcaUa.gucuauuacuagcuUGuucu 276 U+ + + ::+:U:::A A+AA+UUU+ UA :U:U+:: A+:U+ CU 20954 -UUACAAAUAAUGUAGAA-AUAAUUUUUUU-------UAgCUUUUCA---AGCUCCAGCU 21001 __>>>->>>>>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,)))))---))))))))-)) 277 uuggccgauaauagaugAAAauUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguug 336 UUG:++ U::+A:A: CUAAAC:UGU : :+:: : 21002 UUGUGGAUUAGCAAAG---------------------CUAAACUUGUGA-AUACAAAGAA 21039 ).....---)))))))),,,<<<<<_______>>>>>]]]]]]]:::: 337 g.....cAauauuUuuGGACggGGGUUCGAuUCCCccCAcCUCCACCA 379 G AA:::: +:GGACG:GGGUUC A CCC:CCA:CUCCA 21040 GagaucAAACUAAAGCGGACGCGGGUUCAAAACCCGCCAGCUCCA--- 21084 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/org.dat.fasta.gz ----sequence: #175040,sp|U30821.1|CC30821 Cyanophora paradoxa cyanelle, complete genome. ----isReversed: 1 ----hitSequence: GGGGCUGUUUAGGUUUCGACGUUUUUUUCUAAUUAUGUUUGUUAAGCAAGUCGAGGAUUUGUUCUAUCUCGAAAAUCAAGAACUCUCAAAAUUUAAACGCAACUAAUAUUGUACGUUUUAACCGUAAAGCAGCUUUCGCUGUUUAAUAAUUACUUUUAAUUUAAAAACCUAAUUUUUUUAGGAAUUUAUUUAUUUAUUGUUUAUCCUGCUUAAUGAAUUAAAAAAAGCUAUACUUGUGAAUAAACGCAUAAUUUAAAAAAACGGACGUGGGUUCAAAUCCCACCAGCUCCA hit 4 : 84810 84520 (rev) 71.05 bits [[[[[[[,,,,,,,,,,,,,,((((((((--....-(((-((-(((((((((((,,,,,. 1 GGGGgUGaUuaUGGUuUUCGACagGaauagu....gaaggcuUaaggugCAuGuCGAGG. 55 GGGG:UG UU++GGU UUCGAC:: ::U+++ : G +U::: :GCA:GUCGAGG 50790 GGGGCUG-UUUAGGU-UUCGACGUUUUUUUCuaau-UAUGUUUGUUAAGCAAGUCGAGGa 50846 ,<<<<<<____________.._>>>>>>,..,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 56 ugcggcuggCCUCGUAAAA..AagccgcA..aAAAAAUAAcUGCAAAcAAcAAaAAcUAC 111 U::G::: ++CUCG AAA+ A:::C:: AAAA+ UAA++GCAA AA+A + UAC 50847 UUUGUUCUAUCUCGAAAAUcaAGAACUC-ucAAAAUUUAAACGCAACUAAUAUUG--UAC 50903 <<<<<<<<<<_________>>>>->>>>>><<<<<<<<<<<--<<<________>>>--> 112 gcuuuagcugCUUAAccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuu 171 G UUU::+:: UAA ::+: :UUU CG+U U+:A+++A : C+UUU: UU 50904 GUUUUAACCG--UAA----AGCAGCUUU--CGCUGUUUAAUAAUU----ACUUUUAAUU- 50950 >>>------>>>>>>>,,,,,,,,,,,,,,,,,<<<<<-<<<<<<________>>>>>>- 172 auggaaggcgucaacgcaaacuaguAagggAUcguuuagaaaucccgucuggggguaguu 231 U:+AA++C 50951 -UAAAAACC--------------------------------------------------- 50958 >>>>>,,,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<________>>>->>>>>>>>> 232 uagaaaaAAAuuuaAAucaGgcaUagucuauuacuagcuUGuucuuuggccgauaauaga 291 +AA+UUU+ U AGG :U:+AUU+: +:::U +U+U U:::+ :+AAU+:A 50959 ------UAAUUUUU--UUAGGA---AUUUAUUUAUUUAUU-GUUUAUCCUGCUUAAUGAA 51006 >,,,,,,,,,,,,,,,,,,,,,,,,,)))))---))))))))-)))..---)))))))), 292 ugAAAauUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguugg..cAauauuUuuGG 349 : UAAAAA A+ CUA AC:UGU : :::+ : A+A:: ::GG 51007 U------UAAAAA------AAGCUAUACUUGUGA-AUAAACGCAUAauUUAAAAAAACGG 51053 ,,<<<<<_______>>>>>]]]]]]]:::: 350 ACggGGGUUCGAuUCCCccCAcCUCCACCA 379 ACG:GGGUUC A UCCC:CCA:CUCCA 51054 ACGUGGGUUCAAAUCCCACCAGCUCCA--- 51080 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/org.dat.fasta.gz ----sequence: #207907,sp|Z67753.1|OSCHLPLXX Odontella sinensis complete chloroplast genome ----isReversed: 0 ----hitSequence: GGGGCUGACUUGGUUUCGACAUUUAAAAAUUGUUACAGUAUGAUGCAGGUCGAAGUUUCUAAUCUUCGUAAAAAAAGAGAAAUUUAUAAUAAAUGCUAAUAAUUUAAUUUCUUCUGUGUUUAAAAGUUUAUCAACUAAGCAAAAUAGUUUAAAUUUAAGUUUUGCUGUUUAAGUUUUAUGCACAUUUAAUGAUCUAGUAAAUAACUUUGUUCGCUAUAAUUUAUAUUUAUAACUAGACUUUUGUCUUUUUUAUAGUUUAGAAUAACUUUAUCAUUUCAAACCUCGUUCCAUCUAGUUGAACUAAACCUGUGAACGAAUACUAUAAUAAAAUUUUUAGAUGGACGUGGGUUCGACUCCCAUCAGCUCCA hit 5 : 95843 96210 (fwd) 83.00 bits [[[[[[[,,,,,,,,,,,,,,((((((((--..-(((-((-(((((((((((,,,,,,<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagu..gaaggcuUaaggugCAuGuCGAGGugc 58 GGGG:UG ++UGGU UUCGACA: :A:A+ G ::+ :UA:+: GCA:GUCGA GU:: 95843 GGGGCUG-ACUUGGU-UUCGACAUUUAAAAAuuGUUACAGUAUGAUGCAGGUCGAAGUUU 95900 <<<<____________._>>>>>>,.,,,,,,,,,,,,,,,,,,,,,,,,,,....,,,< 59 ggcuggCCUCGUAAAA.AagccgcA.aAAAAAUAAcUGCAAAcAAcAAaAAc....UACg 112 :::+ C UCGUAAAA A+:::::A + A+AAUAA+UGC AA AA+ AA + + : 95901 CUAAU-CUUCGUAAAAaAAGAGAAAuUUAUAAUAAAUGCUAAUAAUUUAAUUucuuCUGU 95959 <<<<<<<<<_________>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->> 113 cuuuagcugCUUAAccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuua 172 :+++:: :G UUA +CA C: : :+++::: +U :::+U +A+U + ++ UG+UU A 95960 GUUUAAAAGUUUA-UCAACUAAGCAAAAUAGUUUAAAUUUAAGU----UUUGCUGUUUAA 96014 >>------>>>>>>>,,,,,,,,,,,,,,,,,<<<<<-<<<<<<________>>>>>>-> 173 uggaaggcgucaacgcaaacuaguAagggAUcguuuagaaaucccgucuggggguaguuu 232 +: ++ :: A+ : +A G++ U+GU::A+A::U++ GU++G +U::UUU 96015 GUUUUAUGCACAUUU--------AAUGAUCUAGUAAAUAACUUU-GUUCGCU-AUAAUUU 96064 >>>>,,,,,,,,,,,,,,,,,,,,...<<<<<<<<<<-<<<________>>>->>>>>>> 233 agaaaaAAAuuuaAAucaGgcaUa...gucuauuacuagcuUGuucuuuggccgauaaua 289 ::A + AU++ AG+C+U :U:+ :: : ::: G + +::: : :: + 96065 AUA--UUUAUAA---CUAGACUUUuguCUUUUUUAUAGUUUAGAAUAACUUUAUCAUUUC 96119 >>>..,,,,,,,,,,,,,,,,,,,,,,,,,)))))---))))))))-))).....---)) 290 gau..gAAAauUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguugg.....cAaua 342 :A: + + A + A U++ACUAAAC:UGU A :+:U: U:: U: 96120 AAAccUCGUUCCAUCU---AGUUGAACUAAACCUGUGAACGAAUACUAUAauaaaAUUUU 96176 )))))),,,<<<<<_______>>>>>]]]]]]]:::: 343 uuUuuGGACggGGGUUCGAuUCCCccCAcCUCCACCA 379 U: :UGGAC :GGGUUCGA+UCCC: CA:CUCCA 96177 UAGAUGGACGUGGGUUCGACUCCCAUCAGCUCCA--- 96210 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/phg.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #355,sp|AB003477.1|AB003477 Synechococcus sp. gene for hypothetical protein, partial cds. ----isReversed: 0 ----hitSequence: GGGGCUGUAAUGGUUUCGACGUGUUGGUGAAUCCUUCACCGUGAUUCAGGCCGAGAGGGAGUCCACUCUCGUAAAUCCAGGCUCAACCAAAAGUAACUGCGAACAACAUCGUUCCUUUCGCUCGUAAGGCUGCUCCUGUAGCUGCUUAAACGCCACAAACUUUCUGGCUCGAGCGUCUAGUCGUAGACUCCGUUAAUACGCCUAGACUUAAACCCCCAACGGAUGCUCGAGUGGCGGCCUCAGGUCCGUCCUCUCGCUAAGCAAAAACCUGAGCAUCCCGCCAACGGGGAUAAUCGUUGGCUCCCGCACAGUGGGUCAACCGUGCUAAGCCUGUGAACGAGCGGAAAGUUACUAGUCAAUGCGGACAGCGGUUCGAUUCCGCUCAGCUCCA hit 6 : 1390 1780 (fwd) 91.95 bits [[[[[[[,,,,,,,,,,,,,,((((((((--....-(((-((-(((((((((((,,,,,. 1 GGGGgUGaUuaUGGUuUUCGACagGaauagu....gaaggcuUaaggugCAuGuCGAGG. 55 GGGG:UG U+AUGGU UUCGAC:+G::::+ : + : ::+: :CA:G:CGAG 1390 GGGGCUG-UAAUGGU-UUCGACGUGUUGGUGaauc-CUUCACCGUGAUUCAGGCCGAGAg 1446 ,<<<<<<____________.._>>>>>>,.,,,,,,,,,,,,,,,,,,,,,,,,,,.... 56 ugcggcuggCCUCGUAAAA..AagccgcA.aAAAAAUAAcUGCAAAcAAcAAaAAc.... 108 +::::C: +CUCGUAAA+ A:G::::A AAAA UAACUGC AACAACA + + 1447 GGAGUCCACUCUCGUAAAUccAGGCUCAAcCAAAAGUAACUGCGAACAACAUCGUUccuu 1506 ..............,,,<<<<<<<<<<_________>>>>->>>>>><<<<<<<<<<<-- 109 ..............UACgcuuuagcugCUUAAccAgcugccguuuggcguucuccaugga 154 :++:+:G++GCUUAA C++C :+:++: ::U: :::: G 1507 ucgcucguaaggcuGCUCCUGUAGCUGCUUAA---ACGCCACAAACUUUCUGGCUCGAGC 1563 <<<________>>>-->>>>------>>>>>>>.,,,,,,,,,,,,,,,,,.<<<<<-<< 155 auucugcCcuuuguuuuauggaaggcgucaacg.caaacuaguAagggAUc.guuuagaa 212 ::+ G+C U+:: U+ :::+A+++ : :A:: +AAAC++ +AA GGAU+ :: ++:: 1564 GUCUAGUCGUAGACUCCGUUAAUACGCCUAGACuUAAACCCCCAACGGAUGcUCGAGUGG 1623 <<<<_..._______>>>>>>->>>>>,,,,,,,,,,,,,,,,,,,,..<<<<<<<<<<- 213 auccc...gucuggggguaguuuagaaaaAAAuuuaAAucaGgcaUa..gucuauuacua 267 :::CC G ++ G:::::U+ :: A A+++A U+AG U+ :C:::: : A 1624 CGGCCucaGGUCC--GUCCUCUCGCUA-AGCAAAAACCUGAGCA-UCccGCCAACGGGGA 1679 <<<________>>>->>>>>>>>>>..,,,,,,,,,,,,,,,,,,,,,,,,,)))))--- 268 gcuUGuucuuuggccgauaauagau..gAAAauUaAAAaAaaAauagACUAAaCaUGUAG 325 :::U +U+ +:::C : ::::G: AA + CUAA:C:UGU 1680 UAAUCGUUGGCUCCCGCACAGUGGGuc--------------AACCGUGCUAAGCCUGUGA 1725 ))))))))-)))....---)))))))),,,<<<<<_______>>>>>]]]]]]]:::: 326 aacguuuguugg....cAauauuUuuGGACggGGGUUCGAuUCCCccCAcCUCCACCA 379 : :+::: + : A+::::U+:GGAC:G+GGUUCGAUUCC+C:CA:CUCCA 1726 ACGAGCGGAAAGuuacUAGUCAAUGCGGACAGCGGUUCGAUUCCGCUCAGCUCCA--- 1780 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #9272,sp|AB063521.2|AB063521 Wigglesworthia brevipalpis DNA, complete genome, section 1/2. ----isReversed: 0 ----hitSequence: GGGGCUGAUUAUGGAUUCGACGAAAUAAACAAAACUAAAGAUGCAUGUCGAGCAGAGGUGGACUCGUAAAACCUCAAAUUGAUAAUUGCAAAACAUAAGUACAACGAGCCUGCUCUAUUAGCAGCUUAAUUAGAAUAAAAUCUUAGGCUCCUUCUUAGAUAUAUUAUCUCUAGAUGUAUCAAUAGAAGUCAAAAUUAGAGAUCGCGAUAUGAACGGGCUUGUACGUUCCUACGCUAAAAUAAUACAAGAUAAUUUUUAGUUCACACUUCUUUCUGUAGAACUAAAAAUAUUUAAGAAAGAAUAAACAUGUAGUAUCAAUAGAAUUGAAGUUUCGGACGCGGGUUCAAAUCCCGCCAGCUCCA hit 7 : 122211 122572 (fwd) 110.79 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,,<<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGGugcgg 60 GGGG:UGAUUAUGG+ UUCGAC:::A +++:::+:: : + U:CAUGUCGAG G:GG 122211 GGGGCUGAUUAUGGA-UUCGACGAAAUAAACAAAACUA-AAGAUGCAUGUCGAGCAGAGG 122268 <<_____________>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,.........,,, 61 cuggCCUCGUAAAAAagccgcAaAAAAAUAAcUGCAAAcAAcAAaAAc.........UAC 111 UGG CUCGUAAAA CC:CAAA + AUAA UGCAAA+ A+AA AC 122269 -UGGACUCGUAAAA---CCUCAAAUUGAUAAUUGCAAAACAUAAGUACaacgagccuGCU 122324 <<<<<<<<<<_____......____>>>>->>>>>><<<<<<<<<<<--<<<________ 112 gcuuuagcugCUUAA......ccAgcugccguuuggcguucuccauggaauucugcCcuu 165 :: +++++::CUUAA ++A ::++++++ :: :U::+: AU: A U +C+ U 122325 CUAUUAGCAGCUUAAuuagaaUAAAAUCUUAGGCUCCUUCUUAGAUAUAUU---AUCUCU 122381 >>>-->>>>------>>>>>>>,,,,,,,,,,,,,,,,,<<<<<-<<<<<<________> 166 uguuuuauggaaggcgucaacgcaaacuaguAagggAUcguuuagaaaucccgucugggg 225 G U :AU +A++G :+::A: +U AG+GAUCG:: : :::C G++UG 122382 AGAUGUAUCAAUAGAAGUCAAA-------AUUAGAGAUCGCGAUAUGAACGGGCUUGUAC 122434 >>>>>->>>>>,,,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<________>>>->>> 226 guaguuuagaaaaAAAuuuaAAucaGgcaUagucuauuacuagcuUGuucuuuggccgau 285 G::: U: :: AA++UAA +CA+G UA U:U: + :U :C:++U++UU+:G: G: 122435 GUUCCUACGC---UAAAAUAAUACAAGA-UAAUUUUUAGUUCACACUUCUUUCUGUAGAA 122490 >>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,)))))---))))))))-)))---))))) 286 aauagaugAAAauUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguuggcAauauuU 345 + :A:A A+UUAA AA AGA UAAACAUGUAG:A + ::: ::: + U: 122491 CUAAAAA--UAUUUAAGAA------AGAAUAAACAUGUAGUAUCAAUAGAAU-UGAAGUU 122541 ))),,,<<<<<_______>>>>>]]]]]]]:::: 346 uuGGACggGGGUUCGAuUCCCccCAcCUCCACCA 379 ::GGACG:GGGUUC A UCCC:CCA:CUCCA 122542 UCGGACGCGGGUUCAAAUCCCGCCAGCUCCA--- 122572 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #16410,sp|AC074317.5|AC074317 Staphylococcus aureus clone sabac-103, complete sequence. ----isReversed: 1 ----hitSequence: GGGGACGUUCAUGGAUUCGACAGGGGUCCCCCGAGCUCAUUAAGCGUGUCGGAGGGUUGUCUUCGUCAUCAACACACACAGUUUAUAAUAACUGGCAAAUCAAACAAUAAUUUCGCAGUAGCUGCCUAAUCGCACUCUGCAUCGCCUAACAGCAUUUCCUAUGUGCUGUUAACGCGAUUCAACCUUAAUAGGAUAUGCUAAACACUGCCGUUUGAAGUCUGUUUAGAAGAAACUUAAUCAAACUAGCAUCAUGUUGGUUGUUUAUCACUUUUCAUGAUGCGAAACCUAUCGAUAAACUACACACGUAGAAAGAUGUGUAUCAGGACCUUUGGACGCGGGUUCAAAUCCCGCCGUCUCCA hit 8 : 11254 10896 (rev) 146.69 bits [[[[[[[,,,,,,,,,,,,,,((((((((--.-(((-((-(((((((((((,,,,,.,<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagu.gaaggcuUaaggugCAuGuCGAGG.ugc 58 GGGG::G+U+AUGG+ UUCGACAGG::U: + ::+GCU :::::GC:UGUCG G +:: 26416 GGGGACGUUCAUGGA-UUCGACAGGGGUCCCc-CGAGCUCAUUAAGCGUGUCGGAGgGUU 26473 <<<<_____________>>>>>>,....,,,,,,,,,,,,,,,,,,,,,,,,,,...,,, 59 ggcuggCCUCGUAAAAAagccgcA....aAAAAAUAAcUGCAAAcAAcAAaAAc...UAC 111 G: C UCGU A AA+:C::A + A+AAUAACUG +AA+ AA+AA+ U+C 26474 GU----CUUCGUCAUCAACACACAcaguUUAUAAUAACUGGCAAAUCAAACAAUaauUUC 26529 <<<<<<<<<<_________>>>>->>>>>><<<<<<<<<<<--<<<________>>>--> 112 gcuuuagcugCUUAAccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuu 171 :C+ U:GC+:C+UAA :+GC :U +G:::::+:::A::G AUU +CCU+UGU +: 26530 GCAGUAGCUGCCUAA----UCGCACUCUGCAUCGCCUAACAGCAUU---UCCUAUGUGCU 26582 >>>------>>>>>>>,,,,,,,,,,,,,,,,,<<<<<-<<<<<<________>>>>>>- 172 auggaaggcgucaacgcaaacuaguAagggAUcguuuagaaaucccgucuggggguaguu 231 :U:+A G+ ::+:::: + UA+UA G++AU G+U:A :A:+:CCGU+UG+ G:+:G:U 26583 GUUAACGCGAUUCAAC---CUUAAUAGGAUAU-GCUAAACACUGCCGUUUGAAGUCUGUU 26638 >>>>>,,,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<________>>>->>>>>>>>> 232 uagaaaaAAAuuuaAAucaGgcaUagucuauuacuagcuUGuucuuuggccgauaauaga 291 U:G AA AA+ U+AAUCA++C UA:::U::U:: ++ UGUU+ U+ + ::A::A:: 26639 UAG--AAGAAACUUAAUCAAAC-UAGCAUCAUGU-UGGUUGUUUAUCACUUUUCAUGAUG 26694 >,,,,,,,,,,,,,,,,,,,,,,,,,)))))---))))))))-))).---)))))))),, 292 ugAAAauUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguugg.cAauauuUuuGGA 350 : +AA+ A+ + AUA+ACUA ACA:GUAG :::::UGU+:: CA+:A::UUUGGA 26695 C--GAAACCUAU---CGAUAAACUACACACGUAG-AAAGAUGUGUAuCAGGACCUUUGGA 26748 ,<<<<<_______>>>>>]]]]]]]:::: 351 CggGGGUUCGAuUCCCccCAcCUCCACCA 379 CG:GGGUUC A UCCC:CC::CUCCA 26749 CGCGGGUUCAAAUCCCGCCGUCUCCA--- 26774 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #16821,sp|AE000590.1|AE000590 Helicobacter pylori 26695 section 68 of 134 of the complete genome. ----isReversed: 1 ----hitSequence: GGGGCUGACUUGGAUUUCGACAGAUUUCUUGUCGCACAGAUAGCAUGCCAAGCGCUGCUUGUAAAACAGCAACAAAAAUAACUGUAAACAACACAGAUUACGCUCCAGCUUACGCUAAAGCUGCGUGAGUUAAUCUCCUUUUGGAGCUGGACUGAUUAGAAUUUCUAGCGUUUUAAUCGCUCCAUAACCUUAAGCUAGACGCUUUUAAAAGGUGGUUCGCCUUUUAAACUAAGAAACAAGAACUCUUGAAACUAUCUCAAGGUUUUAGAAAGUUGGACCAGAGCUAGUUUUAAGGCUAAAAAACCAACCAAUUUUCUAAGCAUUGUAGAAGUUUGUGUUUAGGGCAAGAUUUUUGGACUGGGGUUCGAUUCCCCACAGCUCCACCA hit 9 : 7784 7399 (rev) 98.32 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,,<<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGGugcgg 60 GGGG:UG ++UGG+UUUCGACAG: +U:+U ::G:: A::::GCAUG:C AG GC:G 4756 GGGGCUG-ACUUGGAUUUCGACAGAUUUCUU-GUCGCACAGAUAGCAUGCCAAG-CGCUG 4812 <<_____________>>>>>>,.,,,,,,,,,,,,,,,,,,,,,,,,,,........... 61 cuggCCUCGUAAAAAagccgcA.aAAAAAUAAcUGCAAAcAAcAAaAAc........... 108 CU GUAAAA C:GCA AAAAAUAACUG AAACAACA A A+ 4813 -----CUUGUAAAA---CAGCAaCAAAAAUAACUGUAAACAACACAGAUuacgcuccagc 4864 .,,,<<<<<<<<<<_________>>>>->>>>>><<<<<<<<<<<--<<<________>> 109 .UACgcuuuagcugCUUAAccAgcugccguuuggcguucuccauggaauucugcCcuuug 167 UACGCU: :+:U:C U A G:U:++: : C +U: ::::G : + UU : 4865 uUACGCUAAAGCUGCGUGA---GUUAAUCUC---CUUUUGGAGCUGGAC----UGAUUAG 4914 >-->>>>------>>>>>>>.....,,,,,,,,,,,,,,,,,<<<<<-<<<<<<______ 168 uuuuauggaaggcgucaacg.....caaacuaguAagggAUcguuuagaaaucccgucug 222 U::::+ G + :A+ G +AA+CU++++ +GA+ G:+::++:::: +G +U 4915 AAUUUCUAGCGUUUUAAUCGcuccaUAACCUUAAGCUAGAC-GCUUUUAAAAGGUGGUUC 4973 __>>>>>>->>>>>,,,,,,,,,,,,,,,,,,,,.<<<<<<<<<<-<<<________>>> 223 gggguaguuuagaaaaAAAuuuaAAucaGgcaUa.gucuauuacuagcuUGuucuuuggc 281 G ::::++::+:A+AAA ++ AA UC G A + ::+:: : +::U G UUG:: 4974 GCCUUUUAAACUAAGAAACAAGAACUCUUGA-AAcUAUCUCAAGGUUUUAGAAAGUUGGA 5032 ->>>>>>>>>>.........,,,,,,,,,,,,,,,,,,,,,,,,,))).))---)))))) 282 cgauaauagau.........gAAAauUaAAAaAaaAauagACUAAaCa.UGUAGaacguu 331 C : ::+:: + AAAA+ AA +AAU CUAA:CA UGUAGA::::U 5033 CCAGAGCUAGUuuuaaggcuAAAAAACCAAC---CAAUUUUCUAAGCAuUGUAGAAGUUU 5089 ))-)))....---)))))))),,,<<<<<_______>>>>>]]]]]]]:::: 332 uguugg....cAauauuUuuGGACggGGGUUCGAuUCCCccCAcCUCCACCA 379 :: :: CAA:A+ :UUGGAC:GGGGUUCGAUUCCCC:CA:CUCCACCA 5090 GUGUUUagggCAAGAUUUUUGGACUGGGGUUCGAUUCCCCACAGCUCCACCA 5141 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #16969,sp|AE000749.1|AE000749 Aquifex aeolicus VF5 section 81 of 109 of the complete genome. ----isReversed: 1 ----hitSequence: GGGGGCGGAAAGGAUUCGACGGGGACAGGCGGUCCCCGAGGAGCAGGCCGGGUGGCUCCCGUAACAGCCGCUAAAACAGCUCCCGAAGCUGAACUCGCUCUCGCUGCCUAAUUAAACGGCAGCGCGUCCCCGGUAGGUUUGCGGGUGGCCUACCGGAGGGCGUCAGAGACACCCGCUCGGGCUACUCGGUCGCACGGGGCUGAGUAGCUGACACCUAACCCGUGCUACCCUCGGGGAGCUUGCCCGUGGGCGACCCGAGGGGAAAUCCUGAACACGGGCUAAGCCUGUAGAGCCUCGGAUGUGGCCGCCGUCCUCGGACGCGGGUUCGAUUCCCGCCGCCUCCACCA hit 10 : 2436 2090 (rev) 111.21 bits [[[[[[[,,,,,,,,,,,,,,((((((((--.-(((-((-(((((((((((,,,,,,<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagu.gaaggcuUaaggugCAuGuCGAGGugcg 59 GGGGG:G +A+GG+ UUCGAC:G::A: G G :+C: :A+G GCA:G:CG G U: : 13598 GGGGGCG-GAAAGGA-UUCGACGGGGACAGGcGGUCCCC-GAGGAGCAGGCCGGG-UGGC 13653 <<<_____________>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<< 60 gcuggCCUCGUAAAAAagccgcAaAAAAAUAAcUGCAAAcAAcAAaAAcUACgcuuuagc 119 : C CGUAA A ++:: : AAAA A CU C+ A++ ++AA C GC+:+ :C 13654 U-----CCCGUAACA-GCCGCU---AAAACAGCUCCCGAAGCUGAACUC---GCUCUCGC 13701 <<_________>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->>>>----- 120 ugCUUAAccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuuauggaagg 179 +:C+UAA++A :+G:C +:+ U:+:: :U:G :UU +C + UG:++:A: G AGG 13702 UGCCUAAUUAAACGGCAGCG--CGUCCCCGGUAGGUUU---GCGGGUGGCCUACCGGAGG 13756 ->>>>>>>.,,,,,,,,,,,,,,,,,.<<<<<-<<<<<<________>>>>>>->>>>>, 180 cgucaacg.caaacuaguAagggAUc.guuuagaaaucccgucuggggguaguuuagaaa 237 ::+:A ++A G UC +::UA +::::C G+ +GGG ::::+ UA::+ 13757 GCGUCAGAg-------ACACCCGCUCgGGCUACUCGGUC-GCACGGG-GCUGAGUAGCU- 13806 ,,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<________>>>->>>>>>>>>>,,,,, 238 aAAAuuuaAAucaGgcaUagucuauuacuagcuUGuucuuuggccgauaauagaugAAAa 297 A A UAA C+ GC UA :C:::::::AGCUUG +C U GGC+:::::::G: AAA 13807 GACACCUAACCCGUGC-UA-CCCUCGGGGAGCUUGCCCGUGGGCGACCCGAGGGG--AAA 13862 ,,,,,,,,,,,,,,,,,,,,)))))---))))))))-)))...---)))))))),,,<<< 298 uUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguugg...cAauauuUuuGGACggG 354 U A A A +G CUAA:C:UGUAGA C+U::G+: C :U::U:GGACG:G 13863 UCCUGA---ACACGGGCUAAGCCUGUAGAGCCUCGGAUGUggcCGCCGUCCUCGGACGCG 13919 <<_______>>>>>]]]]]]]:::: 355 GGUUCGAuUCCCccCAcCUCCACCA 379 GGUUCGAUUCCC:CC:CCUCCACCA 13920 GGUUCGAUUCCCGCCGCCUCCACCA 13944 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #17332,sp|AE001118.1|AE001118 Borrelia burgdorferi B31 (section 4 of 70) of the complete genome. ----isReversed: 1 ----hitSequence: GGGGAUGUUUUGGAUUUGACUGAAAAUGUUAAUAUUGUAAGUUGCAGGCAGAGGGAAUCUCUUAAAACUUCUAAAAUAAAUGCAAAAAAUAAUAACUUUACAAGCUCAAAUCUUGUAAUGGCUGCUUAAGUUAGCAGAGGGUUUUGUUGAAUUUGGCUUUGAGGUUCACUUAUACUCUUUUCGACAUCAAAGCUUGCUUAAAAAUGUUUUCAAGUUGAUUUUUAGGGACUUUUAUACUUGAGAGCAAUUUGGUGGUUUGCUAGUAUUUCCAAACCAUAUUGCUUAAUAAAAUACUAGAUAAGCUUGUAGAAGCUUAUAGUAUUAUUUUUAGGACGCGGGUUCAAUUCCCGCCAUCUCCA hit 11 : 7347 6989 (rev) 113.52 bits [[[[[[[,,,,,,,,,,,,,,((((((((--.-(((-((-(((((((((((,,,,,,<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagu.gaaggcuUaaggugCAuGuCGAGGugcg 59 GGGG:UG UU+UGG+ UU GAC:G:AA:+GU ++:+ ::UAA+:UGCA:G: GAG : : 3042 GGGGAUG-UUUUGGA-UUUGACUGAAAAUGUuAAUAUUGUAAGUUGCAGGCAGAG--GGA 3097 <<<_____________>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,........... 60 gcuggCCUCGUAAAAAagccgcAaAAAAAUAAcUGCAAAcAAcAAaAAc........... 108 : +CUC UAAAA +:: : AAAAUAA+UGCAAA+AA+AA+AAC 3098 A----UCUCUUAAAA--CUUCU---AAAAUAAAUGCAAAAAAUAAUAACuuuacaagcuc 3148 ....,,,<<<<<<<<<<_________>>>>->>>>>><<<<<<<<<<<--<<<_______ 109 ....UACgcuuuagcugCUUAAccAgcugccguuuggcguucuccauggaauucugcCcu 164 + G + + ::U:CUUAA G:U::C + G:::U:::U GA:U++ GC +U 3149 aaauCUUGUAAUGGCUGCUUAA---GUUAGCAG----AGGGUUUUGUUGAAUUUGGCUUU 3201 _>>>-->>>>------>>>>>>>..,,,,,,,,,,,,,,,,,<<<<<-<<<<<<______ 165 uuguuuuauggaaggcgucaacg..caaacuaguAagggAUcguuuagaaaucccgucug 222 +G:UU A:: A++++:U:::C +U A +G U G:UUA A::: :+ UC 3202 GAGGUUCACUUAUACUCUUUUCGac-------AUCAAAGCUUGCUUAAAAAUGUUUUCAA 3254 __>>>>>>->>>>>,,,,,,,,,,,,,,,,,,,,.<<<<<<<<<<-<<<________>>> 223 gggguaguuuagaaaaAAAuuuaAAucaGgcaUa.gucuauuacuagcuUGuucuuuggc 281 G : :::UUUAG: +A +UU++A U ++G + :U+U :U +::UG U U ::+ 3255 GUUGAUUUUUAGG-GACUUUUAUACUUGAGA-GCaAUUUGGU---GGUUUGCUAGUAUUU 3309 ->>>>>>>>>>.,,,,,,,,,,,,,,,,,,,,,,,,,)))))---))))))))-)))--- 282 cgauaauagau.gAAAauUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguuggcAa 340 C A A: A+A: G A+UAAA A A + UAA:C:UGUAGAA:+UU::++:+ 3310 CCAAACCAUAUuGCUUAAUAAA----AUACUAGAUAAGCUUGUAGAAGCUUAUAGUA-UU 3364 )))))))),,,<<<<<_______>>>>>]]]]]]]:::: 341 uauuUuuGGACggGGGUUCGAuUCCCccCAcCUCCACCA 379 +:UU:U:GGACG:GGGUUC AUUCCC:CCA:CUCCA 3365 AUUUUUAGGACGCGGGUUCAAUUCCCGCCAUCUCCA--- 3400 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #17488,sp|AE001276.1|AE001276 Chlamydia trachomatis section 3 of 87 of the complete genome. ----isReversed: 1 ----hitSequence: GGGGGUGUAAAGGUUUCGACUUAGAAAUGAAGCGUUAAUUGCAUGCGGAGGGCGUUGGCUGGCCUCCUAAAAAGCCGACAAAACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUCAGCUUCGCUGAUCUCGAAGAUCUAAGAGUAGCUGCUUAAUUAGCAAAGUUGUUACCUAAAUACGGGUGACCCGGUGUUCGCGAGCUCCACCAGAGGUUUUCGAAACACCGUCAUGUAUCUGGUUAGAACUUAGGUCCUUUAAUUCUCGAGGAAAUGAGUUUGAAAUUUAAUGAGAGUCGUUAGUCUCUAUAGGGGUUUCUAGCUGAGGAGACAUAACGUAUAGUACCUAGGAACUAAGCAUGUAGAGGUUAGCGGGGAGUUUACUAAGGACGAGAGUUCGACUCUCUCCACCUCCA hit 12 : 9890 9474 (rev) 118.97 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,..,<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGG..ugc 58 GGGGGUG U+A+GGU UUCGAC:::: :A+ AA GC:U+A::UGCAUG: GAGG +: 204 GGGGGUG-UAAAGGU-UUCGACUUAGAAAUG-AA-GCGUUAAUUGCAUGCGGAGGgcGUU 259 <<<<_____________>>>>>>,.,,,,,,,,,,,,,,,,,,,,,,,,,,......... 59 ggcuggCCUCGUAAAAAagccgcA.aAAAAAUAAcUGCAAAcAAcAAaAAc......... 108 GGCUGGCCUC UAAAA AGCC : AAA AAUAA+UGC+ A+ +AA + 260 GGCUGGCCUCCUAAAA-AGCCGACaAAACAAUAAAUGCCGAACCUAAGGCUgaaugcgaa 318 ...........................,,,<<<<<<<<<<_____........____>>> 109 ...........................UACgcuuuagcugCUUAA........ccAgcug 133 + : ::+:G:U:CUUAA + G:U: 319 auuaucagcuucgcugaucucgaagauCUAAGAGUAGCUGCUUAAuuagcaaaGUUGUUA 378 >->>>>>><<<<<<<<<<<--<<<__.......______>>>-->>>>------>>>>>> 134 ccguuuggcguucuccauggaauucu.......gcCcuuuguuuuauggaaggcgucaac 186 CC:+:: :C :::::C :GG+:U+C CC +G:UUU: G+AA C::::: 379 CCUAAAUACGGGUGACCCGGUGUUCGcgagcucCACCAGAGGUUUUCGAAACACCGUCAU 438 >,,,,,,,,,,,,,,,,,<<<<<-<<<<<<_...._______>>>>>>->>>>>,,,,,, 187 gcaaacuaguAagggAUcguuuagaaauccc....gucuggggguaguuuagaaaaAAAu 242 G + GG U+G::::+A :CC+ UCU G GG: U :::: + AA+ 439 G-------UAUCUGGUUAGAACUUAGGUCCUuuaaUUCUCGAGGAAAUGAGUU--UGAAA 489 ,,,,,,,,,,,,,,<<<<<<<<<<-<<<________>>>->>>>>>>>>>,,,,,,,,,, 243 uuaAAucaGgcaUagucuauuacuagcuUGuucuuuggccgauaauagaugAAAauUaAA 302 UU+AAU+AG+ U+GU :U: CUA:: G+U+U U :: GA :A: AU AA UA A 490 UUUAAUGAGAG-UCGUUAGUCUCUAUAGGGGUUUCUAGCUGAGGAGACAU--AACGUAUA 546 ,,,,,,,,,,,,,,,)))))---))))))))-))).---)))))))),,,<<<<<_____ 303 AaAaaAauagACUAAaCaUGUAGaacguuuguugg.cAauauuUuuGGACggGGGUUCGA 361 +A + A ++ACUAA:CAUGUAG A::U+:G +GG U: ::::GGACG:G:GUUCGA 547 GUACCUAGGAACUAAGCAUGUAG-AGGUUAGCGGGgAGUUUACUAAGGACGAGAGUUCGA 605 __>>>>>]]]]]]]:::: 362 uUCCCccCAcCUCCACCA 379 +UC:C:CCACCUCCA 606 CUCUCUCCACCUCCA--- 620 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #17638,sp|AE001503.1|AE001503 Helicobacter pylori, strain J99 section 64 of 132 of the complete genome. ----isReversed: 1 ----hitSequence: GGGGCUGACUUGGAUUUCGACAGAUUUCUUGUCGCACAGAUAGCAUGCCAAGCGCUGCUUGUAAAACAGCAACAAAAAUAACUGUAAACAACGCAGAUUACGCUCCAGCUUACGCUAAAGCUGCGUGAGUUAAUCUCCUUUUGGAGCUGGACUGAUUAGAAUUUCUAGCGUUUUAAUCGCUCCAUAACCUUAAGCUAGACGCUUUUAAAAGGUGGUUCGCCUUUUAAACUAAGAAACAAGAACUCUUGAAACUAUCUCAAGGUUUUAGAAAGUUGGACCAGAACUAGUUUUAAGGCUAAAAAGCUAAUCAAUUUUCUAAGCAUUGUAGAAGUUUGUGUUUAGGACAAGAUUUUUGGACUGGGGUUCGAUUCCCCACAGCUCCACCA hit 13 : 7009 6624 (rev) 98.10 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,,<<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGGugcgg 60 GGGG:UG ++UGG+UUUCGACAG: +U:+U ::G:: A::::GCAUG:C AG GC:G 4746 GGGGCUG-ACUUGGAUUUCGACAGAUUUCUU-GUCGCACAGAUAGCAUGCCAAG-CGCUG 4802 <<_____________>>>>>>,.,,,,,,,,,,,,,,,,,,,,,,,,,,........... 61 cuggCCUCGUAAAAAagccgcA.aAAAAAUAAcUGCAAAcAAcAAaAAc........... 108 CU GUAAAA C:GCA AAAAAUAACUG AAACAAC+ A A+ 4803 -----CUUGUAAAA---CAGCAaCAAAAAUAACUGUAAACAACGCAGAUuacgcuccagc 4854 .,,,<<<<<<<<<<_________>>>>->>>>>><<<<<<<<<<<--<<<________>> 109 .UACgcuuuagcugCUUAAccAgcugccguuuggcguucuccauggaauucugcCcuuug 167 UACGCU: :+:U:C U A G:U:++: : C +U: ::::G : + UU : 4855 uUACGCUAAAGCUGCGUGA---GUUAAUCUC---CUUUUGGAGCUGGAC----UGAUUAG 4904 >-->>>>------>>>>>>>.....,,,,,,,,,,,,,,,,,<<<<<-<<<<<<______ 168 uuuuauggaaggcgucaacg.....caaacuaguAagggAUcguuuagaaaucccgucug 222 U::::+ G + :A+ G +AA+CU++++ +GA+ G:+::++:::: +G +U 4905 AAUUUCUAGCGUUUUAAUCGcuccaUAACCUUAAGCUAGAC-GCUUUUAAAAGGUGGUUC 4963 __>>>>>>->>>>>,,,,,,,,,,,,,,,,,,,,.<<<<<<<<<<-<<<________>>> 223 gggguaguuuagaaaaAAAuuuaAAucaGgcaUa.gucuauuacuagcuUGuucuuuggc 281 G ::::++::+:A+AAA ++ AA UC G A + ::+:: : +::U G UUG:: 4964 GCCUUUUAAACUAAGAAACAAGAACUCUUGA-AAcUAUCUCAAGGUUUUAGAAAGUUGGA 5022 ->>>>>>>>>>........,,,,,,,,,,,,,,,,,,,,,,,,,))).))---))))))) 282 cgauaauagau........gAAAauUaAAAaAaaAauagACUAAaCa.UGUAGaacguuu 332 C : ::+:: + AAAA+ AA+ +AAU CUAA:CA UGUAGA::::U: 5023 CCAGAACUAGUuuuaaggcUAAAAAGCUAAU--CAAUUUUCUAAGCAuUGUAGAAGUUUG 5080 )-)))....---)))))))),,,<<<<<_______>>>>>]]]]]]]:::: 333 guugg....cAauauuUuuGGACggGGGUUCGAuUCCCccCAcCUCCACCA 379 : :: CAA:A+ :UUGGAC:GGGGUUCGAUUCCCC:CA:CUCCACCA 5081 UGUUUaggaCAAGAUUUUUGGACUGGGGUUCGAUUCCCCACAGCUCCACCA 5131 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #17729,sp|AE001597.1|AE001597 Chlamydia pneumoniae section 13 of 103 of the complete genome. ----isReversed: 1 ----hitSequence: GGGGGUGUAUAGGUUUCGACUUGAAAAUGAAGUGUUAAUUGCAUGCGGAGGGCGUUGGCUGGCCUCCUAAAAAGCCAACAAAACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUUAGCUUGUUUGACUCAGUAGAGGAAAGACUAGCUGCUUAAUUAGCAAAAGUUGUUAGCUAGAUAAUCUCUAGGUAACCCGGUAUCUGCGAGCUCCACCAGAGGCUUGCAAAAUACCGUCAUUUAUCUGGUUGGAACUUACUUUCUCUAAUUCUCAAGGAAGUUCGUUCGAGAUUUUUGAGAGUCAUUGGCUGCUAUAGAGGCUUCUAGCUAAGGGAGUCCAAUGUAAACAAUUCUAGAAGAUAAGCAUGUAGAGGUUAGCAGGGAGUUUGUCAAGGACGAGAGUUCGAGUCUCUCCACCUCCA hit 14 : 3555 3133 (rev) 98.79 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,..,<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGG..ugc 58 GGGGGUG U+++GGU UUCGAC:::A :A+ +A:G :U+A::UGCAUG: GAGG +:: 6753 GGGGGUG-UAUAGGU-UUCGACUUGAAAAU--GAAGUGUUAAUUGCAUGCGGAGGgcGUU 6808 <<<<_____________>>>>>>,.,,,,,,,,,,,,,,,,,,,,,,,,,,......... 59 ggcuggCCUCGUAAAAAagccgcA.aAAAAAUAAcUGCAAAcAAcAAaAAc......... 108 GGCUGGCCUC UAAAA AGCC:: AAA AAUAA+UGC+ A+ +AA + 6809 GGCUGGCCUCCUAAAA-AGCCAACaAAACAAUAAAUGCCGAACCUAAGGCUgaaugcgaa 6867 ...........................,,,<<<<<<<<<<_____.........____>> 109 ...........................UACgcuuuagcugCUUAA.........ccAgcu 132 A : ::+:::U:CUUAA + G:U 6868 auuauuagcuuguuugacucaguagagGAAAGACUAGCUGCUUAAuuagcaaaaGUUGUU 6927 >>->>>>>>..............<<<<<<<<<<<--<<<________>>>-->>>>---- 133 gccguuugg..............cguucuccauggaauucugcCcuuuguuuuauggaag 178 ::C:+:: : CG+U +::::G+ :U: CC :G:+UU:::+AA 6928 AGCUAGAUAaucucuagguaaccCGGUAUCUGCGAGCUC--CACCAGAGGCUUGCAAAAU 6985 -->>>>>>>,,,,,,,,,,,,,,,,,<<<<<-<<<<<<_...._______>>>>>>->>> 179 gcgucaacgcaaacuaguAagggAUcguuuagaaauccc....gucuggggguaguuuag 234 C:+ A U++U GG+ ::: +A::::C+ UCU + G::::UU :: 6986 ACCG------UCAUUUAUCUGGUUG-GAACUUACUUUCUcuaaUUCUCAAGGAAGUUCGU 7038 >>,,,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<________>>>->>>>>>>>>>,, 235 aaaaAAAuuuaAAucaGgcaUagucuauuacuagcuUGuucuuuggccgauaauagaugA 294 : +A A+UUU U+AG+ U+ + :+:C:A:: G+++U U :: :A:+: + 7039 UCGAGAUUUU---UGAGAG-UCAUUGGCUGCUAUAGAGGCUUCUAGCUAAGGGAGUCC-- 7092 ,,,,,,,,,,,,.,,,,,,,,,,,)))))---))))))))-))).---)))))))),,,< 295 AAauUaAAAaAa.aAauagACUAAaCaUGUAGaacguuuguugg.cAauauuUuuGGACg 352 AA+ UAAA AA+ + A A+ UAA:CAUGUAG A::U+: :G+ U: U:::GGACG 7093 AAUGUAAACAAUuCUAGAAGAUAAGCAUGUAG-AGGUUAGCAGGgAGUUUGUCAAGGACG 7151 <<<<_______>>>>>]]]]]]]:::: 353 gGGGUUCGAuUCCCccCAcCUCCACCA 379 :G:GUUCGA UC:C:CCACCUCCA 7152 AGAGUUCGAGUCUCUCCACCUCCA--- 7175 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #17858,sp|AE001727.1|AE001727 Thermotoga maritima section 39 of 136 of the complete genome. ----isReversed: 0 ----hitSequence: GGAUGGAGUCCCCUGGGAAGCGAGCCGAGGUCCCCACCUCCUCGUAAAAAAGGUGGGACAAAGAAUAAGUGCCAACGAACCUGUUGCUGUUGCCGCUUAAUAGAUAAGCGGCCGUCCUCUCCGAAGUUGGCUGGGCUUCGGAAGAGGGCGUGAGAGAUCCAGCCUACCGAUUCAGCUUCGCCUUCCGGCCUGAAUCGGGAAAACUCAGGAAGGCUGUGGGAGAGGACACCCUGCCCGUGGGAGGUCCCUCCCGAGAGCGAAAACACGGGCUGCGCUCGGAGAAGCCCAGGGGCCUCCAUCUUCGGACGGGGGUUCGAAUCCCCCCGCCUCCACCA hit 15 : 1 335 (fwd) 64.69 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,,<<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGGugcgg 60 G :AU:G + :+::U::G::GC::G:CGAGGU C:: 1 G------------------------GAUGGA-GUCCCCUGGGAAGCGAGCCGAGGUCCCC 35 <<_.___________._>>>>>>,.,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<< 61 cug.gCCUCGUAAAA.AagccgcA.aAAAAAUAAcUGCAAAcAAcAAaAAcUACgcuuua 117 :: CCUCGUAAAA A::::G A AAA AAUAA UGC+AAC+A + + GCU U 36 ACCu-CCUCGUAAAAaAGGUGGGAcAAAGAAUAAGUGCCAACGAACCUGUU---GCUGUU 91 <<<<_____....____>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->>> 118 gcugCUUAA....ccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuuau 173 GC:GCUUAA ++AGC:GC CGU+CUC:::++A+:+ G+C++ +:+U++:: 92 GCCGCUUAAuagaUAAGCGGC-------CGUCCUCUCCGAAGUU--GGCUGGGCUUCGGA 142 >------>>>>>>>,,,,,,,,,,,,,,,,,<<<<<-<<<<<<_......_______>>> 174 ggaaggcgucaacgcaaacuaguAagggAUcguuuagaaauccc......gucugggggu 227 :GA GGCGU G++AG++ ++G+::A : :+:C +++U GG:+ 143 AGAGGGCGU------------GAGAGAUCCAGCCUACCGAUUCAgcuucgCCUUCCGGCC 190 >>>->>>>>,,,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<________>>>->>>>> 228 aguuuagaaaaAAAuuuaAAucaGgcaUagucuauuacuagcuUGuucuuuggccgauaa 287 : :+U:: + AAA+ U A AGGC U ++: :+:+: :C:++++C U:G: :+:+: 191 UGAAUCG--GGAAAACUCAGGAAGGC-UGUGGGAGAGGACACCCUGCCCGUGGGAGGUCC 247 >>>>>.,,,,,,,,,,,,,,,,,,,,,,,,,)))))---))))))))-))).---))))) 288 uagau.gAAAauUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguugg.cAauauuU 345 :+ GA+A AAAA +A +G CU :C::G AG ::G:::: : + C :AU:U 248 CUCC-cGAGAGCGAAAA---CAC-GGGCUGCGCUCGGAG-AAGCCCAGGGGcCUCCAUCU 301 ))),,,<<<<<_______>>>>>]]]]]]]:::: 346 uuGGACggGGGUUCGAuUCCCccCAcCUCCACCA 379 U GGACGGGGGUUCGA UCCCCCC+CCUCCACCA 302 UCGGACGGGGGUUCGAAUCCCCCCGCCUCCACCA 335 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #18035,sp|AE001939.1|AE001939 Deinococcus radiodurans R1 section 76 of 229 of the complete chromosome 1. ----isReversed: 0 ----hitSequence: GGGGGUGACCCGGUUUCGACAGGGGAACUGAAGGUGAUGUUGCGUGUCGAGGUGCCGUUGGCCUCGUAAACAAACGGCAAAGCCAUUUAACUGGCAACCAGAACUACGCUCUCGCUGCUUAAGUGAGAUGACGACCGUGCAGCCCGGCCUUUGGCGUCGCGGAAGUCACUAAAAAAGAAGGCUAGCCCAGGCGAUUCUCCAUAGCCGACGGCGAAACUUUAUGGAGCUACGGCCUGCGAGAACCUGCCCACUGGUGAGCGCCGGCCCGACAAUCAAACAGUGGGAUACACACGUAGACGCACGCUGGACGGACCUUUGGACGGCGGUUCGACUCCGCCCACCUCCACCA hit 16 : 5041 5389 (fwd) 135.42 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,,<<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGGugcgg 60 GGGGGUG + GGU UUCGACAGG:: UG+A+G : :+: GC:UGUCGAGGUGC:G 5041 GGGGGUG-ACCCGGU-UUCGACAGGGGAACUGAAGGUG-AUGUUGCGUGUCGAGGUGCCG 5097 <<_____________>>>>>>,..,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<< 61 cuggCCUCGUAAAAAagccgcA..aAAAAAUAAcUGCAAAcAAcAAaAAcUACgcuuuag 118 :UGGCCUCGUAAA AA:C:GCA A+ UAACUG +AAC A AA+ UACGCU+++: 5098 UUGGCCUCGUAAACAAACGGCAaaGCCAUUUAACUGGCAACCAGAAC---UACGCUCUCG 5154 <<<_________>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->>>>---- 119 cugCUUAAccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuuauggaag 178 :+:CUUAA G:+:: ++ ++ C ::G :: G+CCUUU::+ :: G A+ 5155 CUGCUUAA---GUGAGAUG----ACGACCGUGCAGCCC---GGCCUUUGGCGUCGCGGAA 5204 -->>>>>>>,,,,,,,,,,,,,,,,,<<<<<-<<<<<<________>>>>>>->>>>>,, 179 gcgucaacgcaaacuaguAagggAUcguuuagaaaucccgucuggggguaguuuagaaaa 238 G+ ++ A+ A+++A GG U+G+:::G::: :+ +UC+ : ::: ::: +A 5205 GUC------ACUAAAAAAGAAGGCUAGCCCAGGCGAUU-CUCCAUA-GCCGACGGC--GA 5254 ,,,,,,,,,,,,,,,,,,.<<<<<<<<<<-<<<________>>>->>>>>>>>>>.,,,, 239 AAAuuuaAAucaGgcaUa.gucuauuacuagcuUGuucuuuggccgauaauagau.gAAA 296 AA UUUA U+++GC UA :+C:+:::+:A:C:UG +C U:G:+:+:::+:G+: GA A 5255 AACUUUA--UGGAGC-UAcGGCCUGCGAGAACCUGCCCACUGGUGAGCGCCGGCCcGACA 5311 ,,,,,,,,,,,,,,,,,,,,,)))))---))))))))-)))---)))))))),,,<<<<< 297 auUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguuggcAauauuUuuGGACggGGG 356 AU AAA +A U+G UA ACA:GUAGA :+: : U+G+ + ::UUUGGACGG+GG 5312 AUCAAA----CAGUGGGAUACACACGUAGACGCACGCUGGA-CGGACCUUUGGACGGCGG 5366 _______>>>>>]]]]]]]:::: 357 UUCGAuUCCCccCAcCUCCACCA 379 UUCGA+UCC+CCCACCUCCACCA 5367 UUCGACUCCGCCCACCUCCACCA 5389 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #18243,sp|AE002154.1|AE002154 Ureaplasma urealyticum section 55 of 59 of the complete genome. ----isReversed: 1 ----hitSequence: GGGGAUGUCACGGUUUCGACGUGACACAUUAAUUUUUAAUUGCAGUGGGGUUAGCCCCUUAUCGCUUUCGAGGCAUUUUAAAUGCAGAAAAUAAAAAAUCUUCUGAAGUAGAAUUAAACCCAGCGUUUAUGGCUUCAGCUACUAAUGCAAACUACGCUUUUGCGUACUAAUUAGUUAUUAGUAGAAACGUUCAUUAACAUAAUUACUAUUGGUUGGUUUUUGGGCUUAUUUUACAAUAGUUUUAAAUUUAAAAUUCUUAUUUGUUGUUUAAAUUUAAAUAGAUUUAACAAAUAGUUAGUUAAUUUUAAAUUUGUUUUAUUAGUUAUUAACUACACUAUUUUUAAUAAAACUAAACUGUAGAUAUUAUUAAUUAUGUGUUGCGGAAAGGGGUUCGACUCCCCUCAUCUCCACCA hit 17 : 2543 2131 (rev) 115.98 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,,<<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGGugcgg 60 GGGG:UG U+A GGU UUCGAC:+GA:::+U ::: :UU+A:::GCA GU G G U:::: 16955 GGGGAUG-UCACGGU-UUCGACGUGACACAU-UAAUUUUUAAUUGCA-GUGGGG-UUAGC 17009 <<_____________>>>>>>,..,,,,,,,,,,,,,,,,,,,,,,,,,,.......... 61 cuggCCUCGUAAAAAagccgcA..aAAAAAUAAcUGCAAAcAAcAAaAAc.......... 108 C U+A ++:::: A++ UAA+UGCA A+AA+AAAAA 17010 ------CCCUUAUC-GCUUUCGagGCAUUUUAAAUGCAGAAAAUAAAAAAucuucugaag 17062 ............................................,,,<<<<<<<<<<___ 109 ............................................UACgcuuuagcugCUU 124 UAC+C+U+:+:: +U 17063 uagaauuaaacccagcguuuauggcuucagcuacuaaugcaaacUACGCUUUUGCGUACU 17122 ______>>>>->>>>>>...<<<<<<<<<<<--<<<________>>>-->>>>------> 125 AAccAgcugccguuugg...cguucuccauggaauucugcCcuuuguuuuauggaaggcg 181 AA++AG ::++:+U+G+ +:+::U::A:: A:UU C+ UUG:UU::U: +GG : 17123 AAUUAGUUAUUAGUAGAaacGUUCAUUAACAUAAUU---ACUAUUGGUUGGUUUUUGGGC 17179 >>>>>>,,,,,,,,,,,,,,,,,<<<<<-<<<<<<________>>>>>>->>>>>,,,,, 182 ucaacgcaaacuaguAagggAUcguuuagaaaucccgucuggggguaguuuagaaaaAAA 241 U::+:++A A+UAGU + AU :U: A + :U+: U+UG :+U: ++U :A:A+A A 17180 UUAUUUUACAAUAGUUUUAAAU-UUAAAAUUCUUA--UUUGUUGUUUAAAUUUAAAUAGA 17236 ,,,,,,,,,,,,,,,<<<<<<<<<<-<<<________>>>->>>>>>>>>>.,,,,,,,, 242 uuuaAAucaGgcaUagucuauuacuagcuUGuucuuuggccgauaauagau.gAAAauUa 300 UUUAA + A + +UA:U+: U:+::A:::UGUU+U U::: ::+:A :+A: A +UU+ 17237 UUUAACAAAUAGUUAGUUAAUUUUAAAUUUGUUUUAUUAGUUAUUAACUACaCUAUUUUU 17296 ,,,,,,,,,,,,,,,,,)))))---))))))))-)))---)))))))),,,<<<<<____ 301 AAAaAaaAauagACUAAaCaUGUAGaacguuuguuggcAauauuUuuGGACggGGGUUCG 360 AA+A A+ACUAAAC UGUAGA:::U+U:+::: A :::UU+:GGA :GGGGUUCG 17297 AAUA------AAACUAAAC-UGUAGAUAUUAUUAAUU-AUGUGUUGCGGAAAGGGGUUCG 17348 ___>>>>>]]]]]]]:::: 361 AuUCCCccCAcCUCCACCA 379 A+UCCCC:CA:CUCCACCA 17349 ACUCCCCUCAUCUCCACCA 17367 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #18300,sp|AE002224.2|AE002224 Chlamydophila pneumoniae AR39, section 52 of 94 of the complete genome. ----isReversed: 0 ----hitSequence: GGGGGUGUAUAGGUUUCGACUUGAAAAUGAAGUGUUAAUUGCAUGCGGAGGGCGUUGGCUGGCCUCCUAAAAAGCCAACAAAACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUUAGCUUGUUUGACUCAGUAGAGGAAAGACUAGCUGCUUAAUUAGCAAAAGUUGUUAGCUAGAUAAUCUCUAGGUAACCCGGUAUCUGCGAGCUCCACCAGAGGCUUGCAAAAUACCGUCAUUUAUCUGGUUGGAACUUACUUUCUCUAAUUCUCAAGGAAGUUCGUUCGAGAUUUUUGAGAGUCAUUGGCUGCUAUAGAGGCUUCUAGCUAAGGGAGUCCAAUGUAAACAAUUCUAGAAGAUAAGCAUGUAGAGGUUAGCAGGGAGUUUGUCAAGGACGAGAGUUCGAGUCUCUCCACCUCCA hit 18 : 6757 7179 (fwd) 98.79 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,..,<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGG..ugc 58 GGGGGUG U+++GGU UUCGAC:::A :A+ +A:G :U+A::UGCAUG: GAGG +:: 6757 GGGGGUG-UAUAGGU-UUCGACUUGAAAAU--GAAGUGUUAAUUGCAUGCGGAGGgcGUU 6812 <<<<_____________>>>>>>,.,,,,,,,,,,,,,,,,,,,,,,,,,,......... 59 ggcuggCCUCGUAAAAAagccgcA.aAAAAAUAAcUGCAAAcAAcAAaAAc......... 108 GGCUGGCCUC UAAAA AGCC:: AAA AAUAA+UGC+ A+ +AA + 6813 GGCUGGCCUCCUAAAA-AGCCAACaAAACAAUAAAUGCCGAACCUAAGGCUgaaugcgaa 6871 ...........................,,,<<<<<<<<<<_____.........____>> 109 ...........................UACgcuuuagcugCUUAA.........ccAgcu 132 A : ::+:::U:CUUAA + G:U 6872 auuauuagcuuguuugacucaguagagGAAAGACUAGCUGCUUAAuuagcaaaaGUUGUU 6931 >>->>>>>>..............<<<<<<<<<<<--<<<________>>>-->>>>---- 133 gccguuugg..............cguucuccauggaauucugcCcuuuguuuuauggaag 178 ::C:+:: : CG+U +::::G+ :U: CC :G:+UU:::+AA 6932 AGCUAGAUAaucucuagguaaccCGGUAUCUGCGAGCUC--CACCAGAGGCUUGCAAAAU 6989 -->>>>>>>,,,,,,,,,,,,,,,,,<<<<<-<<<<<<_...._______>>>>>>->>> 179 gcgucaacgcaaacuaguAagggAUcguuuagaaauccc....gucuggggguaguuuag 234 C:+ A U++U GG+ ::: +A::::C+ UCU + G::::UU :: 6990 ACCG------UCAUUUAUCUGGUUG-GAACUUACUUUCUcuaaUUCUCAAGGAAGUUCGU 7042 >>,,,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<________>>>->>>>>>>>>>,, 235 aaaaAAAuuuaAAucaGgcaUagucuauuacuagcuUGuucuuuggccgauaauagaugA 294 : +A A+UUU U+AG+ U+ + :+:C:A:: G+++U U :: :A:+: + 7043 UCGAGAUUUU---UGAGAG-UCAUUGGCUGCUAUAGAGGCUUCUAGCUAAGGGAGUCC-- 7096 ,,,,,,,,,,,,.,,,,,,,,,,,)))))---))))))))-))).---)))))))),,,< 295 AAauUaAAAaAa.aAauagACUAAaCaUGUAGaacguuuguugg.cAauauuUuuGGACg 352 AA+ UAAA AA+ + A A+ UAA:CAUGUAG A::U+: :G+ U: U:::GGACG 7097 AAUGUAAACAAUuCUAGAAGAUAAGCAUGUAG-AGGUUAGCAGGgAGUUUGUCAAGGACG 7155 <<<<_______>>>>>]]]]]]]:::: 353 gGGGUUCGAuUCCCccCAcCUCCACCA 379 :G:GUUCGA UC:C:CCACCUCCA 7156 AGAGUUCGAGUCUCUCCACCUCCA--- 7179 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #18370,sp|AE002296.1|AE002296 Chlamydia muridarum section 28 of 85 of the complete genome. ----isReversed: 1 ----hitSequence: GGGGGUGUAAAGGUUUCGACUUAGAAAUGAAGCGUUAAUUGCAUGCGGAGGGCGUUGGCUGGCCUCCUAAAAAGCCGACAAAACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUCAGCUUCGCUGAUCUUAAUGAUCUAAGAGUUGCUGCUUAAUUAGCAAAGUUGUUACCUAAGUACUGGUAACCCGGUGUUCGCGAGCUCCACCAGAGGUUUUCGAAACGCCGUCAUUUAUCUGGUUAGAAUUAGGGCCUUUUAACUCUCAAGGGAACUAAUUUGAAUUUUAAUGAGAGUCGUUGGUCUCUAUAGAGGUUUCUAGCUGAGGAGAUAUAACGUAAAAUAUUCUAGAAACUAAGCAUGUAGAGGUUAGCGGGGAGUUUACUAAGGACGAGAGUUCGAAUCUCUCCACCUCCA hit 19 : 3595 3178 (rev) 125.34 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,..,<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGG..ugc 58 GGGGGUG U+A+GGU UUCGAC:::: :A+ AA GC:U+A::UGCAUG: GAGG +: 6843 GGGGGUG-UAAAGGU-UUCGACUUAGAAAUG-AA-GCGUUAAUUGCAUGCGGAGGgcGUU 6898 <<<<_____________>>>>>>,.,,,,,,,,,,,,,,,,,,,,,,,,,,......... 59 ggcuggCCUCGUAAAAAagccgcA.aAAAAAUAAcUGCAAAcAAcAAaAAc......... 108 GGCUGGCCUC UAAAA AGCC : AAA AAUAA+UGC+ A+ +AA + 6899 GGCUGGCCUCCUAAAA-AGCCGACaAAACAAUAAAUGCCGAACCUAAGGCUgaaugcgaa 6957 ...........................,,,<<<<<<<<<<_________>>>>->>>>>> 109 ...........................UACgcuuuagcugCUUAAccAgcugccguuugg 141 + : :+:::U:CUUAA :U::C:+: : 6958 auuaucagcuucgcugaucuuaaugauCUAAGAGUUGCUGCUUAA----UUAGCAAAGUU 7013 .....................<<<<<<<<<<<--<<<________>>>-->>>>------ 142 .....................cguucuccauggaauucugcCcuuuguuuuauggaaggc 180 CG+U +:C::G+ :U: CC :G:UUU::G+AA GC 7014 guuaccuaaguacugguaaccCGGUGUUCGCGAGCUC--CACCAGAGGUUUUCGAAACGC 7071 >>>>>>>,,,,,,,,,,,,,,,,,<<<<<-<<<<<<_...._______>>>>>>->>>>> 181 gucaacgcaaacuaguAagggAUcguuuagaaauccc....gucuggggguaguuuagaa 236 :+ ++U+ + GG U+G::U: : :C:+ +UCU + :G: :U:A:: 7072 CG-------UCAUUUAUCUGGUUAGAAUUAGGGCCUUuuaaCUCUCAAGGGAACUAAUU- 7123 ,,,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<________>>>->>>>>>>>>>,,,, 237 aaAAAuuuaAAucaGgcaUagucuauuacuagcuUGuucuuuggccgauaauagaugAAA 296 + AAUUU+AAU+AG+ U+GU+::U: CUA:: G+U+U U :: GA :A::+AU AA 7124 -UGAAUUUUAAUGAGAG-UCGUUGGUCUCUAUAGAGGUUUCUAGCUGAGGAGAUAU--AA 7179 ,,,,,,,,,,.,,,,,,,,,,,)))))---))))))))-))).---)))))))),,,<<< 297 auUaAAAaAa.aAauagACUAAaCaUGUAGaacguuuguugg.cAauauuUuuGGACggG 354 UAAAA+A+ + A A+ACUAA:CAUGUAG A::U+:G +GG U: ::::GGACG:G 7180 CGUAAAAUAUuCUAGAAACUAAGCAUGUAG-AGGUUAGCGGGgAGUUUACUAAGGACGAG 7238 <<_______>>>>>]]]]]]]:::: 355 GGUUCGAuUCCCccCAcCUCCACCA 379 :GUUCGA UC:C:CCACCUCCA 7239 AGUUCGAAUCUCUCCACCUCCA--- 7260 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #18521,sp|AE002452.1|AE002452 Neisseria meningitidis serogroup B strain MC58 section 94 of 206 of the complete genome. ----isReversed: 1 ----hitSequence: GGGGGCGACCUUGGUUUCGACGAGGGUUGCGAAGCAGAUGCGGGCAUACCGGGGUCUCAGAUUCCCGUAAAACACUGAAUUCAAAUAGUCGCAAACGACGAAACUUACGCUUUAGCCGCUUAAGGCUAGCCGUUGCAGCAGUCGGUCAAUGGGCUGUGUGGCGAAAGCCACCGCAACGUCAUCUUACAUUGACUGGUUUCCUACCGGGUUACUUGGCAGGAAAUAAGACUUAAGGUAACUGGUUUCCAAAAGGCCUGUUGGUCGGCAUGAUGGAAAUAAGAUUUUCAAAUAGACACAACUAAGUAUGUAGAACGCUUUGUAGAGGACUUUCGGACGGGGGUUCGAUUCCCCCCGCCUCCACCA hit 20 : 5751 5389 (rev) 155.68 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,.,<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGG.ugcg 59 GGGGG:GA ++UGGU UUCGAC::G::U:G+GA:G+: +::G:GCAU::CG GG :C: 6323 GGGGGCGACCUUGGU-UUCGACGAGGGUUGCGAAGCAGAUGCGGGCAUACCGGGGuCUCA 6381 <<<_____________>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<< 60 gcuggCCUCGUAAAAAagccgcAaAAAAAUAAcUGCAAAcAAcAAaAAcUACgcuuuagc 119 G : +C CGUAAAA : C:G:A+ AAAUA +GCAAAC+AC+AAA +UACGCUU+::: 6382 GAU--UCCCGUAAAA-CACUGAAUUCAAAUAGUCGCAAACGACGAAACUUACGCUUUAGC 6438 <<_________>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->>>>----- 120 ugCUUAAccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuuauggaagg 179 GCUUAA GC ::C:+UUG :::: :C::: AA + + UGU U:::G+AAG+ 6439 CGCUUAA--GGCUAGCCGUUG-CAGCAGUCGGUCAA-----UGGGCUGUGUGGCGAAAGC 6490 ->>>>>>>..,,,,,,,,,,,,,,,,,<<<<<-<<<<<<________>>>>>>->>>>>, 180 cgucaacg..caaacuaguAagggAUcguuuagaaaucccgucuggggguaguuuagaaa 237 C: :::: ++A CU+++A G U+GU::: A: : G +U : :G +:::A A 6491 CACCGCAAcgUCAUCUUACAUUGACUGGUUUCCUACCG--GGUUAC--UUGGCAGGAA-A 6545 ,,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<________>>>->>>>>>>>>>.,,,, 238 aAAAuuuaAAucaGgcaUagucuauuacuagcuUGuucuuuggccgauaauagau.gAAA 296 +AA + U+AA + ++C U GU:U::+:+: GC:UGUU U+:GC :+:+::A:AU A 6546 UAAGACUUAAGGUAAC-UGGUUUCCAAAAGGCCUGUUGGUCGGCAUGAUGGAAAUaAGAU 6604 ,,,,,,,,,,,,,,,,,,,,,)))))---))))))))-)))---)))))))),,,<<<<< 297 auUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguuggcAauauuUuuGGACggGGG 356 +UU AAA+A +A + +ACUAA::AUGUAGA:C::+ : U:G A+:A::U::GGACGGGGG 6605 UUUCAAAUA-GACACAACUAAGUAUGUAGAACGCUUUGUAG-AGGACUUUCGGACGGGGG 6662 _______>>>>>]]]]]]]:::: 357 UUCGAuUCCCccCAcCUCCACCA 379 UUCGAUUCCCCCC:CCUCCACCA 6663 UUCGAUUCCCCCCGCCUCCACCA 6685 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #18860,sp|AE004078.1|AE004078 Xylella fastidiosa 9a5c, section 224 of 229 of the complete genome. ----isReversed: 0 ----hitSequence: GGGGGUGCACUGGCUUCGACGGGGGUCACAAAAUCACUUGGUGCAUGCCGAGGGGGCCGCUUUCCUCGUAAAUCCAGCAGCAAACUUAUAGUUGCCAACGAAGACAACUUCGCUGUAGCCGCUUAAGGCUUAAGCCUCGAAACUGCUUGUGUCCGUGCUCGCAGCGUAGAGUCAUCAUCACGGAACCGCUGAGACGUGGCCGUCUGCCCAUCCUCGGUUAAAUCUAGCAGACUGGUUUCCGGGUGCGCUUUGCCUGUCGUGCUGCCCGGCGACGAGACCUAACGGCGAGGAUAAGCAUGUAGGGCCGGGGAUGGAGUACUUUCGGACGGCGGUUCGAUUCCGCCCACCUCCACCA hit 21 : 5137 5491 (fwd) 152.44 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,.,<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGG.ugcg 59 GGGGGUG + UGG UUCGAC:GG::U:+++AA: C: :+G: CAUG:CGAGG +GC 5137 GGGGGUG-CACUGGC-UUCGACGGGGGUCACAAAAUCACUUGGUGCAUGCCGAGGgGGCC 5194 <<<_.___________._>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<< 60 gcug.gCCUCGUAAAA.AagccgcAaAAAAAUAAcUGCAAAcAAcAAaAAcUACgcuuua 117 GCU CCUCGUAAA+ AGC GCAAA ++AUA UGC+AAC+A +A+AACU+CGCU +A 5195 GCUUu-CCUCGUAAAUcCAGCAGCAAACUUAUAGUUGCCAACGAAGACAACUUCGCUGUA 5253 <<<<_________>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->>>>--- 118 gcugCUUAAccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuuauggaa 177 GC GCUUAA G+ C: :::::+:++AA:U +C+U U:U+++:+: 5254 GCCGCUUAA---------GG----CUUAAGCCUCGAAACU---GCUUGUGUCCGUGCUCG 5297 --->>>>>>>,,,,,,,,,,,,,,,,,<<<<<-<<<<<<_._______>>>>>>->>>>> 178 ggcgucaacgcaaacuaguAagggAUcguuuagaaauccc.gucuggggguaguuuagaa 236 :::: :G A +A +A GG A+CG++::GA :U C GUCUG U: U ::+ 5298 CAGCGUAGAG-UCAUCAUCACGGAACCGCUGAGACGUGGCcGUCUGCCCAUCCUCGGU-- 5354 ,,,,,,,,,,,,,,,,,,,,.<<<<<<<<<<-<<<________>>>->>>>>>>>>>.., 237 aaAAAuuuaAAucaGgcaUa.gucuauuacuagcuUGuucuuuggccgauaauagau..g 293 +AAAU UA CAG+C U + +:::::: +C:U+++CU U:G++ ::::::+ + G 5355 -UAAAUCUA--GCAGAC-UGgUUUCCGGGUGCGCUUUGCCUGUCGUGCUGCCCGGCGacG 5410 ,,,,,,,,,,,,,,,,,,,,,,,,)))))---))))))))-)))---)))))))),,,<< 294 AAAauUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguuggcAauauuUuuGGACgg 353 A+A UAA + AG UAA:CAUGUAG :C+: :G+:GG A+:A::UU:GGACGG 5411 AGACCUAAC----GGCGAGGAUAAGCAUGUAGGGCCGGGGAUGG-AGUACUUUCGGACGG 5465 <<<_______>>>>>]]]]]]]:::: 354 GGGUUCGAuUCCCccCAcCUCCACCA 379 +GGUUCGAUUCC+CCCACCUCCACCA 5466 CGGUUCGAUUCCGCCCACCUCCACCA 5491 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #18943,sp|AE004170.1|AE004170 Vibrio cholerae chromosome I, section 78 of 251 of the complete chromosome. ----isReversed: 1 ----hitSequence: GGGGCUGAUUCAGGAUUCGACGGGAAUUUUGCAGUCUGAGGUGCAUGCCGAGGUGCGGUAGGCCUCGUUAACAAACCGCAAAAAAAUAGUCGCAAACGACGAAAACUACGCACUAGCAGCUUAAUACCCUGCUCAGAGCCCUUCCUCCCUAGCUUCCGCUUGUAAGACGGGGAAAUCAGGAAGGUCAAACCAAAUCAAGCUGGCGUGGAUUCCCCCACCUGAGGGAUGAAGCGCGAGAUCUAAUUCAGGUUAGCCAUUCGUUAGCGUGUCGGUUCGCAGGCGGUGGUGAAAUUAAAGAUCGACUAAGCAUGUAGUACCAAAGAUGAAUGGUUUUCGGACGGGGGUUCAACUCCCCCCAGCUCCACCA hit 22 : 3459 3093 (rev) 210.38 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,,<<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGGugcgg 60 GGGG:UGAUU +GG+ UUCGAC:GGAA::+UG:AG C: : +GU:CAUG:CGAGGUGCGG 7804 GGGGCUGAUUCAGGA-UUCGACGGGAAUUUUGCAGUCU-GAGGUGCAUGCCGAGGUGCGG 7861 <<_____________>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<<< 61 cuggCCUCGUAAAAAagccgcAaAAAAAUAAcUGCAAAcAAcAAaAAcUACgcuuuagcu 120 :+GGCCUCGU+AA A+:CCGCAAAAAAAUA +GCAAAC+AC+AAAACUAC:C::+:GC: 7862 UAGGCCUCGUUAACAAACCGCAAAAAAAUAGUCGCAAACGACGAAAACUACGCACUAGCA 7921 <_________>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->>>>------ 121 gCUUAAccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuuauggaaggc 180 GCUUAA++ +C:GC+:+::G:C:UU:::C:: + ::UC+ +C+U U:: ::GGAA+ C 7922 GCUUAAUACCCUGCUCAGAGCCCUUCCUCCCUAGCUUCC-GCUUGUAAGACGGGGAAAUC 7980 >>>>>>>.,,,,,,,,,,,,,,,,,<<<<<-<<<<<<_._______>>>>>>->>>>>,, 181 gucaacg.caaacuaguAagggAUcguuuagaaauccc.gucuggggguaguuuagaaaa 238 :::AA:G CAAAC+A++ +G U+G:::+G+:+:CCC +CUG+GGG:+:+++::: 7981 AGGAAGGuCAAACCAAAUCAAGCUGGCGUGGAUUCCCCcACCUGAGGGAUGAAGCGC--G 8038 ,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<________>>>->>>>>>>>>>,,,,,, 239 AAAuuuaAAucaGgcaUagucuauuacuagcuUGuucuuuggccgauaauagaugAAAau 298 A AU UAA UCAGG UAG:C::U:::UAGC:UGU+ UU:GC G::: ::G:U +AA+ 8039 AGAUCUAAUUCAGGU-UAGCCAUUCGUUAGCGUGUCGGUUCGCAGGCG-GUGGU--GAAA 8094 ,,,,,,,,,,,,,,,,,,,)))))---))))))))-)))---)))))))),,,<<<<<__ 299 UaAAAaAaaAauagACUAAaCaUGUAGaacguuuguuggcAauauuUuuGGACggGGGUU 358 U+AA A AU GACUAA:CAUGUAG:AC+ ::G+UG: A ::UUUU:GGACGGGGGUU 8095 UUAA----AGAUCGACUAAGCAUGUAGUACCAAAGAUGA-AUGGUUUUCGGACGGGGGUU 8149 _____>>>>>]]]]]]]:::: 359 CGAuUCCCccCAcCUCCACCA 379 C A+UCCCCCCA:CUCCACCA 8150 CAACUCCCCCCAGCUCCACCA 8170 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #19287,sp|AE004517.1|AE004517 Pseudomonas aeruginosa PAO1, section 78 of 529 of the complete genome. ----isReversed: 1 ----hitSequence: GGGGCCGAUUAGGAUUCGACGCCGGUAACAAAACUUGAGGGGCAUGCCGAGCUGGUAGCAGAACUCGUAAAUUCGCUGCUGCAAACUUAUAGUUGCCAACGACGACAACUACGCUCUAGCUGCUUAAUGCGGCUAGCAGUCGCUAGGGGAUGCCUGUAAACCCGAAACGACUGUCAGAUAGAACAGGAUCGCCGCCAAGUUCGCUGUAGACGUAACGGCUAAAACUCAUACAGCUCGCUCCAAGCACCCUGCCACUCGGGCGGCGCGGAGUUAACUCAGUAGAGCUGGCUAAGCAUGUAGAACCGAUAGCGGAGAGCUGGCGGACGGGGGUUCAAAUCCCCCCGGCUCCACCA hit 23 : 7001 6649 (rev) 155.32 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,.,<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGG.ugcg 59 GGGG::G U++GG+ UUCGAC:::::: ++ AA :UU::+G:GCAUG:CGAG +G : 3822 GGGGCCG-AUUAGGA-UUCGACGCCGGUAAC-AAAACUUGAGGGGCAUGCCGAGCuGGUA 3878 <<<____________..._>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<< 60 gcuggCCUCGUAAAA...AagccgcAaAAAAAUAAcUGCAAAcAAcAAaAAcUACgcuuu 116 GC+G+ CUCGUAAA+ +GC: CAAA ++AUA UGC+AAC+AC+A+AACUACGCU++ 3879 GCAGAACUCGUAAAUucgCUGCUGCAAACUUAUAGUUGCCAACGACGACAACUACGCUCU 3938 <<<<<_________>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->>>>-- 117 agcugCUUAAccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuuaugga 176 +GC+GCUUAA GC+GC+++ ::UC C: : G : GCC++U : ++ : :+ 3939 AGCUGCUUAA--UGCGGCUAG----CAGUCGCUAGGGGAU---GCCUGUAAACCCGAAAC 3989 ---->>>>>>>.,,,,,,,,,,,,,,,,,<<<<<-<<<<<<________>>>>>>->>>> 177 aggcgucaacg.caaacuaguAagggAUcguuuagaaaucccgucuggggguaguuuaga 235 +++G CA:: G+A GGAUCG:::: AA::: + CUG :::GU+:::: 3990 GACUGUCAGAUa-------GAACAGGAUCGCCGCCAAGUU--CGCUGUA-GACGUAACGG 4039 >,,,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<________>>>->>>>>>>>>>,,, 236 aaaAAAuuuaAAucaGgcaUagucuauuacuagcuUGuucuuuggccgauaauagaugAA 295 +AAA+ U A U +GC U+G:::: : A:C:UG + U+:G:CG : ::::U 4040 -CUAAAACUCA-UACAGC-UCGCUCCAAGC-ACCCUGCCACUCGGGCGGCGCGGAGU--U 4093 ,,,,,,,,,,,,,,,,,,,,,,)))))---))))))))-)))---)))))))),,,<<<< 296 AauUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguuggcAauauuUuuGGACggGG 355 AA U A +A +A G CUAA:CAUGUAGA:C+::U: GG A+ ::::::GGACGGGG 4094 AACUCAGUA--GAGCUGGCUAAGCAUGUAGAACCGAUAGCGG-AGAGCUGGCGGACGGGG 4150 <_______>>>>>]]]]]]]:::: 356 GUUCGAuUCCCccCAcCUCCACCA 379 GUUC A UCCCCCC::CUCCACCA 4151 GUUCAAAUCCCCCCGGCUCCACCA 4174 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #20255,sp|AE005491.1|AE005491 Escherichia coli O157:H7 EDL933 genome, contig 3 of 3, section 110 of 290. ----isReversed: 0 ----hitSequence: GGGGCUGAUUCUGGAUUCGACGGGAUUUGCGAAACCCAAGGUGCAUGCCGAGGGGCGGUUGGCCUCGUAAAAAGCCGCAAAAAAUAGUCGCAAACGACGAAAACUACGCUUUAGCAGCUUAAUAACCUGCUUAGAGCCCUCUCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCCAAAAGAGAUCGCGUGGAAGCCCUGCCUGGGGUUGAAGCGUUAAAACUUAAUCAGGCUAGUUUGUUAGUGGCGUGUCCGUCCGCAGCUGGCAAGCGAAUGUAAAGACUGACUAAGCAUGUAGUACCGAGGACGUAGGAAUUUCGGACGCGGGUUCAACUCCCGCCAGCUCCACCA hit 24 : 9259 9621 (fwd) 224.09 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,,<<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGGugcgg 60 GGGG:UGAUU UGG+ UUCGAC:GGA:U:G+G:A +C: ::+GU:CAUG:CGAGG+GCGG 9259 GGGGCUGAUUCUGGA-UUCGACGGGAUUUGCGAAACCC-AAGGUGCAUGCCGAGGGGCGG 9316 <<_____________>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<<< 61 cuggCCUCGUAAAAAagccgcAaAAAAAUAAcUGCAAAcAAcAAaAAcUACgcuuuagcu 120 :UGGCCUCGUAAAA A:CCGC AAAAAAUA +GCAAAC+AC+AAAACUAC:C+++:GC: 9317 UUGGCCUCGUAAAA-AGCCGC-AAAAAAUAGUCGCAAACGACGAAAACUACGCUUUAGCA 9374 <_________>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->>>>------ 121 gCUUAAccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuuauggaaggc 180 GCUUAA++A+C:GC+:+++G:C:U:::+C:::+ ::+C+GC CUU+:: +:::G+ + 9375 GCUUAAUAACCUGCUUAGAGCCCUCUCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAA- 9433 >>>>>>>.,,,,,,,,,,,,,,,,,<<<<<-<<<<<<________>>>>>>->>>>>,,, 181 gucaacg.caaacuaguAagggAUcguuuagaaaucccgucuggggguaguuuagaaaaA 239 :::A:G CAAAC++++AAG+GAUCG:::+G+A: CC+G+CUGG GG :G+++::: +A 9434 -GAGAGGuCAAACCCAAAAGAGAUCGCGUGGAAGCCCUGCCUGG-GGUUGAAGCGU--UA 9489 ,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<________>>>->>>>>>>>>>,,,,,,, 240 AAuuuaAAucaGgcaUagucuauuacuagcuUGuucuuuggccgauaauagaugAAAauU 299 AA+ U+AAUCAGGC UA:::U :+A:U GC:UGU+C U+:GC G:U+: A::: +AAU 9490 AAACUUAAUCAGGC-UAGUUUGUUAGUGGCGUGUCCGUCCGCAGCUGGCAAGC--GAAUG 9546 ,,,,,,,,,,,,,,,,,,)))))---))))))))-)))---)))))))),,,<<<<<___ 300 aAAAaAaaAauagACUAAaCaUGUAGaacguuuguuggcAauauuUuuGGACggGGGUUC 359 +AAA +A GACUAA:CAUGUAG:AC+:::G+ G: A+:A:UUU:GGACG:GGGUUC 9547 UAAA---GAC-UGACUAAGCAUGUAGUACCGAGGACGU-AGGAAUUUCGGACGCGGGUUC 9601 ____>>>>>]]]]]]]:::: 360 GAuUCCCccCAcCUCCACCA 379 A+UCCC:CCA:CUCCACCA 9602 AACUCCCGCCAGCUCCACCA 9621 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #20876,sp|AE006115.1|AE006115 Pasteurella multocida PM70 section 82 of 204 of the complete genome. ----isReversed: 1 ----hitSequence: GGGGCUGAUUCUGGAUUCGACGGGAUUAGCGAAGCCCAAGGUGCACGUCGAGGUGCGGUAGGCCUCGUAAAUAAACCGCAAAAAAAUAGUCGCAAACGACGAACAAUACGCUUUAGCAGCUUAAUAACCUGCUCAUAGCCUUCUCUCCCCAGCUUCCGCUCGUAAGACGGGGAUCAAGAGGAGUCAAAUUCAAACGAGAUCGCGUGGACGCCUCCGCUUGAGGAUCGAAGCGUUAAAUUGAAUCAAGCUAGUUUAUCUAUCGCGUGUCUGUCCGCAGUGGGUAAAUGAAAUUAAAGACGAGACUAAACGUGUAGUACUGAAGGUAGAGUAAUUUCGGACGCGGGUUCAACUCCCGCCAGCUCCACCA hit 25 : 421 55 (rev) 218.50 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,,<<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGGugcgg 60 GGGG:UGAUU UGG+ UUCGAC:GGA:UAG+ +::GC: ::+GU:CA:GUCGAGGUGCGG 8471 GGGGCUGAUUCUGGA-UUCGACGGGAUUAGC-GAAGCCCAAGGUGCACGUCGAGGUGCGG 8528 <<_____________>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<<< 61 cuggCCUCGUAAAAAagccgcAaAAAAAUAAcUGCAAAcAAcAAaAAcUACgcuuuagcu 120 :+GGCCUCGUAAA+A+:CCGCAAAAAAAUA +GCAAAC+AC+AA A UAC:C+U+:GC: 8529 UAGGCCUCGUAAAUAAACCGCAAAAAAAUAGUCGCAAACGACGAACAAUACGCUUUAGCA 8588 <_________>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->>>>------ 121 gCUUAAccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuuauggaaggc 180 GCUUAA++A+C:GC+:+U+G:C: :::+C:::+ ::+C+GC C+U+:: +:::G+ + 8589 GCUUAAUAACCUGCUCAUAGCCUUCUCUCCCCAGCUUCCGCUCGUAAGACGGGGAUCAA- 8647 >>>>>>>.,,,,,,,,,,,,,,,,,<<<<<-<<<<<<_._______>>>>>>->>>>>,, 181 gucaacg.caaacuaguAagggAUcguuuagaaauccc.gucuggggguaguuuagaaaa 238 ::: :G CAAA U+++A G+GAUCG+::+G+:: ::C G++UG+G:: ::+++:: + 8648 -GAGGAGuCAAAUUCAAACGAGAUCGCGUGGACGCCUCcGCUUGAGGAUCGAAGCG---U 8703 ,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<________>>>->>>>>>>>>>,,,,,, 239 AAAuuuaAAucaGgcaUagucuauuacuagcuUGuucuuuggccgauaauagaugAAAau 298 AA+UU AAUCA+GC UAGU:UA:: :U GC:UGU++ U+:GC G: ::UA:AU +AA+ 8704 UAAAUUGAAUCAAGC-UAGUUUAUCUAUCGCGUGUCUGUCCGCAGUGGGUAAAU--GAAA 8760 ,,,,,,,,,,,,,,,,,,,)))))---))))))))-)))---)))))))),,,<<<<<__ 299 UaAAAaAaaAauagACUAAaCaUGUAGaacguuuguuggcAauauuUuuGGACggGGGUU 358 U+AAA +A AGACUAAAC:UGUAG:AC+:::G ::+ A+UA:UUU:GGACG:GGGUU 8761 UUAAA---GACGAGACUAAACGUGUAGUACUGAAGGUAG-AGUAAUUUCGGACGCGGGUU 8816 _____>>>>>]]]]]]]:::: 359 CGAuUCCCccCAcCUCCACCA 379 C A+UCCC:CCA:CUCCACCA 8817 CAACUCCCGCCAGCUCCACCA 8837 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #21133,sp|AE006373.1|AE006373 Lactococcus lactis subsp. lactis IL1403 section 135 of 218 of the complete genome. ----isReversed: 1 ----hitSequence: GGGGGCGUUACGGAUUCGACAGGCAUUGUCGCGCAUGAACUGCAACUGCUGAGGGAUCAGGAUAAUCAUCCGCAGAUAAAUAUAACUGCUAAAAAUAAUACACAAACUUACGCAAUGGCAGCCUAAACAGCACCAUGCGUGCCUGAUUUUUGCUCUCUGAUGGCAAUUUGACGGCCUAAACUUUUAGUCAGAUACGUUGUUGUGGAGGCUUGACGCAGCAAAAGAGAUUUAAAGCCCCGCAAAAUGUCGCUGUUUGAGACUGGCUUUGGCAUUUUGUUAAAUUUGAGAAAGUCCUAUGGUUGUAGACGUUGAUGUAGCAAGGUGUUUGGACAGGGGUUCGACUCCCCUCGCCUCCA hit 26 : 6190 5835 (rev) 112.26 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,,<<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGGugcgg 60 GGGGG:G UUA GG+ UUCGACAGG:A::GU :::G::U:A::UGCA: : G G G 4351 GGGGGCG-UUACGGA-UUCGACAGGCAUUGU-CGCGCAUGAACUGCAACUGCUG-AGGGA 4406 <<____________._>>>>>>,..,,,,,,,,,,,,,,,,,,,,,,,,,,......,,, 61 cuggCCUCGUAAAA.AagccgcA..aAAAAAUAAcUGCAAAcAAcAAaAAc......UAC 111 +C G +AA+ A C CA +AAA+AUAACUGC AA+AA+AA+A UAC 4407 ----UCAGGAUAAUcA-UCCGCAgaUAAAUAUAACUGCUAAAAAUAAUACAcaaacuUAC 4461 <<<<<<<<<<_____...____>>>>->>>>>><<<<<<<<<<<--<<<________>>> 112 gcuuuagcugCUUAA...ccAgcugccguuuggcguucuccauggaauucugcCcuuugu 168 GC+ U::::GC+UAA CA+C:::C:U + :U:::::: G :: +C+++U:: 4462 GCAAUGGCAGCCUAAacaGCACCAUGCGU----GCCUGAUUUUUGCUC----UCUGAUGG 4513 -->>>>------>>>>>>>,,,,,,,,,,,,,,,,,..<<<<<-<<<<<<________>> 169 uuuauggaaggcgucaacgcaaacuaguAagggAUc..guuuagaaaucccgucuggggg 226 + :::GA GGC:::A: + UAGU AG++A++ GU:: G:A: C: :G 4514 CAAUUUGACGGCCUAAACU---UUUAGUCAGAUACGuuGUUGUGGAGGCU--------UG 4562 >>>>->>>>>,,,,,,,,,,,,,,,,,,,,.<<<<<<<<<<-<<<________>>>->>> 227 uaguuuagaaaaAAAuuuaAAucaGgcaUa.gucuauuacuagcuUGuucuuuggccgau 285 :G:+ ::AA A A +UU+AA++ C + : ::+U:: ++ UUG U G + : 4563 ACGCAGCAAA-AGAGAUUUAAAGCCCC-GCaAAAUGUCGC-UGUUUGAGACUGGCUUUGG 4619 >>>>>>>.,,,,,,,,,,,,,,,,,,,,,,,,,)))))---))))))))-))).---))) 286 aauagau.gAAAauUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguugg.cAauau 343 :A+:: : AAA+UU A +AA++ CUA : :UGUAG A::U:::U::: CAA::U 4620 CAUUUUGuUAAAUUUGA-----GAAAGUCCUAUGGUUGUAG-ACGUUGAUGUAgCAAGGU 4673 ))))),,,<<<<<_______>>>>>]]]]]]]:::: 344 uUuuGGACggGGGUUCGAuUCCCccCAcCUCCACCA 379 :UUUGGAC:GGGGUUCGA+UCCCC:C:CCUCCA 4674 GUUUGGACAGGGGUUCGACUCCCCUCGCCUCCA--- 4706 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #21319,sp|AE006568.1|AE006568 Streptococcus pyogenes M1 GAS strain SF370, section 97 of 167 of the complete genome. ----isReversed: 0 ----hitSequence: GGGGUUGUUACGGAUUCGACAGGCAUUAUGAGGCAUGUUUUGCGUCCCAUCGGCAGAUGUAAAUUGCCAGUUAAAUAUAACUGCAAAAAAUACAAACUCUUACGCUUUAGCUGCCUAAAAACCAGCUAGCGUGACUUCUACAAGAUUGCUUGUGUCCUGUUAGAAGUCUCAAAAUAGCAAGCUACGGUUACGAAAUUGUCUAGUUUCGUGACAAGAGAUUGAUAGACUCGCAAACUAAUGGCUUGAGUUAUGUGUCUUUAGUUUGUUAAAUGAAGACAUAACCUAUGGACGUAGACAAAUAUGUUGGCAGGUGUUUGGACGUGGGUUCGACUCCCACCAGCUCCAUCA hit 27 : 801 1148 (fwd) 139.25 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,,<<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGGugcgg 60 GGGG:UG UUA GG+ UUCGACAGG:A::+U :+G::U::: UGC:U :C +:C G 801 GGGGUUG-UUACGGA-UUCGACAGGCAUUAU-GAGGCAUGUUUUGCGUCCCAUC-GGCAG 856 <<____________._>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,...,,,<<<<< 61 cuggCCUCGUAAAA.AagccgcAaAAAAAUAAcUGCAAAcAAcAAaAAc...UACgcuuu 116 GUAAA+ ++C G: +AAA+AUAACUGCAAA+AA+A AAAC UACGCUUU 857 ------AUGUAAAUu-GCCAGU-UAAAUAUAACUGCAAAAAAUACAAACucuUACGCUUU 908 <<<<<_____...____>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->>> 117 agcugCUUAA...ccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuuau 173 A::UGC+UAA CCAGCU::CGU :::U ::::::GA:U +C+U UG:++::: 909 AGCUGCCUAAaaaCCAGCUAGCGU----GACUUCUACAAGAUU----GCUUGUGUCCUGU 960 >------>>>>>>>..,,,,,,,,,,,,,,,,,<<<<<-<<<<<<________>>>>>>- 174 ggaaggcgucaacg..caaacuaguAagggAUcguuuagaaaucccgucuggggguaguu 231 :+ A+G+:: A::: G+AAG +A++GU ::G :U+ GUCU G +U: U 961 UAGAAGUCUCAAAAua-------GCAAGCUACGGUUACGAAAUU--GUCUAG--UUUCGU 1009 >>>>>,,,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<__.______>>>->>>>>>>> 232 uagaaaaAAAuuuaAAucaGgcaUagucuauuacuagcuUG.uucuuuggccgauaauag 290 :: A A A AUU + AG+C U+G:::A:UA: +C:UG +U+ U :G+C :UA:U:: 1010 GACA-AGAGAUUG---AUAGAC-UCGCAAACUAAUGGCUUGaGUUAUGUGUCUUUAGUUU 1064 >>,,,,,,,,,,,,,,,,,,,,,,,,,)))))---))))))))-))).---)))))))), 291 augAAAauUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguugg.cAauauuUuuGG 349 :U AA+U AA A AUA+ CUA : A:GUAG A :::::U+: A::U:UUUGG 1065 GU--UAAAUGAAG---ACAUAACCUAUGGACGUAG-ACAAAUAUGUUgGCAGGUGUUUGG 1118 ,,<<<<<_______>>>>>]]]]]]]:::: 350 ACggGGGUUCGAuUCCCccCAcCUCCACCA 379 ACG:GGGUUCGA+UCCC:CCA:CUCCA CA 1119 ACGUGGGUUCGACUCCCACCAGCUCCAUCA 1148 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #21882,sp|AE007135.1|AE007135 Mycobacterium tuberculosis CDC1551, section 221 of 280 of the complete genome. ----isReversed: 1 ----hitSequence: GGGGCUGAACGGUUUCGACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCAAGAGACCACCGUAAGCGUCGUUGCGACCAAAUAAGCGCCGAUUCACAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACGGCUAGUCUGUCAGACCGGGAACGCCCUCGGCCCGGACCCUGGCAUCAGCUAGAGGGAUCCACCGAUGAGUCCGGUCGCGGGACUCCUCGGGACAACCACAGCGACUGGGAUCGUCAUCUCGGCUAGUUCGCGUGACCGGGAGAUCCGAGCAGAGGCAUAGCGAACUGCGCACGGAGAAGCCUUGAGGGAAUGCCGUAGGACCCGGGUUCGAUUCCCGGCAGCUCCACCG hit 28 : 3867 3500 (rev) 65.17 bits [[[[[[[,,,,,,,,,,,,,,((((((((--.-(((-((-(((((((((((,,,,,..,< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagu.gaaggcuUaaggugCAuGuCGAGG..ug 57 GGGG:UG +A GGU UUCGAC: ::: :+U +A+ C: ::+::GC:UG:CG G +G 11710 GGGGCUG--AACGGU-UUCGACUUCGCGCAUc-GAAUCAAGGGAAGCGUGCCGGUGcaGG 11765 <<<<<_.___________.._>>>>>>,,,,,,,,,,,,,,,,,,.,,,,,,,,,..... 58 cggcug.gCCUCGUAAAA..AagccgcAaAAAAAUAAcUGCAAAc.AAcAAaAAc..... 108 C::+ G C CGUAA +::GC A AAAUAA +GC+ A ACA +A C 11766 CAAGAGaCCACCGUAAGCgu-CGUUGCGACCAAAUAAGCGCCGAUuCACAUCAGCgcgac 11824 ,,,<<<<<<<<<<_____...____>>>>->>>>>><<<<<<<<<<<--<<<________ 109 UACgcuuuagcugCUUAA...ccAgcugccguuuggcguucuccauggaauucugcCcuu 165 UACGCU+U:::UGC+UAA C GCU::+: :G :: ::::+GA : GCCCU 11825 UACGCUCUCGCUGCCUAAgcgACGGCUAGUC-----UGUCAGACCGGGAAC---GCCCUC 11876 >>>-->>>>------>>>>>>>,,,,,,,,,,,,,,,,,.<<<<<-<<<<<<________ 166 uguuuuauggaaggcgucaacgcaaacuaguAagggAUc.guuuagaaaucccgucuggg 224 : +++::: +GGC: :: C: ++AGGGAUC ::::A+::::CC G ++G G 11877 GGCCCGGACCCUGGCAUCAGCU--------AGAGGGAUCcACCGAUGAGUCC-GGUCGCG 11927 >>>>>>->>>>>,,,,,,,,,,,,,,,,,,,,.<<<<<<<<<<-<<<________>>>-> 225 gguaguuuagaaaaAAAuuuaAAucaGgcaUa.gucuauuacuagcuUGuucuuuggccg 283 GG:::: U::::A AA + ++ G+C U G + ::: :+ ::++ +U :: +: 11928 GGACUCCUCGGGACAACCAC---AGCGAC-UGgGAUCGUCAUCUCGGCUAGUUCGCGUGA 11983 >>>>>>>>>.,,,,,,,,,,,,,,,,,,,,,,,,,)))))---))))))))-)))---)) 284 auaauagau.gAAAauUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguuggcAaua 342 ::: + U A + A A+ A ++ACU :CA:G AGA::+:::G++G+ AA: 11984 CCGGGAGAUcCGAGCAGAGGCAU--AGCGAACUGCGCACGGAGAAGCCUUGAGGG-AAUG 12040 )))))),,,<<<<<_______>>>>>]]]]]]]:::: 343 uuUuuGGACggGGGUUCGAuUCCCccCAcCUCCACCA 379 ::: :GGAC::GGGUUCGAUUCCC::CA:CUCCACC 12041 CCGUAGGACCCGGGUUCGAUUCCCGGCAGCUCCACCG 12077 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #22138,sp|AE007393.1|AE007393 Streptococcus pneumoniae TIGR4 section 76 of 194 of the complete genome. ----isReversed: 0 ----hitSequence: GGGGUCGUUACGGAUUCGACAGGCAUUAUGAGGCAUAUUUUGCGACUCGUGUGGCGACGUAAACGCUCAGUUAAAUAUAACUGCAAAAAAUAACACUUCUUACGCUCUAGCUGCCUAAAAACCAGCAGGCGUGACCCGAUUUGGAUUGCUCGUGUUCAAUGACAGGUCUUAUUAUUAGCGAGAUACGAUUAAGCCUUGUCUAGCGGUUUGAUAAGAGAUUGAUAGACUCGCAGUUUCUAGACUUGAGUUAUGUGUCGAGGGGCUGUUAAAAUAAUACAUAACCUAUGGUUGUAGACAAAUAUGUUGGCAGGUGUUUGGACGUGGGUUCGACUCCCACCGGCUCCA hit 29 : 1725 2069 (fwd) 133.81 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,,<<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGGugcgg 60 GGGG::G UUA GG+ UUCGACAGG:A::+U :+G::U::: UGC:: :CG G UG++: 1725 GGGGUCG-UUACGGA-UUCGACAGGCAUUAU-GAGGCAUAUUUUGCGACUCGUG-UGGCG 1780 <<_____________>>>>>>,..,,,,,,,,,,,,,,,,,,,,,,,,,,...,,,<<<< 61 cuggCCUCGUAAAAAagccgcA..aAAAAAUAAcUGCAAAcAAcAAaAAc...UACgcuu 115 CGUAAA +:++CA +AAA+AUAACUGCAAA+AA+AA+A + UACGCU+ 1781 ------ACGUAAA---CGCUCAguUAAAUAUAACUGCAAAAAAUAACACUucuUACGCUC 1831 <<<<<<_____...____>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->> 116 uagcugCUUAA...ccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuua 172 UA:C+GC+UAA CCAGC+G:CGU : ::+ : :U+GA:U +C+ UG:U++A 1832 UAGCUGCCUAAaaaCCAGCAGGCGU----GACCCGAUUUGGAUU----GCUCGUGUUCAA 1883 >>------>>>>>>>.,,,,,,,,,,,,,,,,,<<<<<-<<<<<<________>>>>>>- 173 uggaaggcgucaacg.caaacuaguAagggAUcguuuagaaaucccgucuggggguaguu 231 : + AGG+: +:: : ++ G+GAU+ ::U A::::+ GUCU G ::::UU 1884 UGACAGGUCUUAUUAu-------UAGCGAGAUACGAUUAAGCCUU-GUCUAG--CGGUUU 1933 >>>>>,,,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<__.______>>>->>>>>>>> 232 uagaaaaAAAuuuaAAucaGgcaUagucuauuacuagcuUG.uucuuuggccgauaauag 290 A:: A A AUU + AG+C U+G:::::+::: :C:UG +U+ U :G:C:::+:::: 1934 GAUA-AGAGAUUG---AUAGAC-UCGCAGUUUCUAGACUUGaGUUAUGUGUCGAGGGGCU 1988 >>,,,,,,,,,,,,,,.,,,,,,,,,,,)))))---))))))))-))).---)))))))) 291 augAAAauUaAAAaAa.aAauagACUAAaCaUGUAGaacguuuguugg.cAauauuUuuG 348 :U UAAAA+AA A AUA+ CUA : ::GUAG A :::::U+: A::U:UUUG 1989 GU------UAAAAUAAuACAUAACCUAUGGUUGUAG-ACAAAUAUGUUgGCAGGUGUUUG 2041 ,,,<<<<<_______>>>>>]]]]]]]:::: 349 GACggGGGUUCGAuUCCCccCAcCUCCACCA 379 GACG:GGGUUCGA+UCCC:CC::CUCCA 2042 GACGUGGGUUCGACUCCCACCGGCUCCA--- 2069 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #22331,sp|AE007587.1|AE007587 Clostridium acetobutylicum ATCC824 section 75 of 356 of the complete genome. ----isReversed: 0 ----hitSequence: GGGGGCGCUUUUGGUUUCGACGGGGAUGAUGUUACGUUUGAGAAGCGAGUCGAGGGAACCUGUGGACCCGCGUUAAAAAACUAUAGGCCUUAAAAAUAAAGGAUAACGAAAAUAAUUUAGCUUUAGCUGCGUAGUCAGCUAACGUCAGCCUGAGAGUCCCGCGACUCAGAGUCUGGCGUCGACAGCGGGGAACCGAGCCUUACAAAGCUUUGAGUAAGGAACGGAAUUUAUGAAGCUACUGAAGUGAAAAGCUUGUUUGUAGGCGUUUCAUGGAGGGAAUGUUAAAAUACAAACUGCACUCGGAGAUGCUUAAAUGAAACCAUUUUCGGACAGGGGUUCGAUUCCCCUCGCCUCCACUA hit 30 : 2639 2997 (fwd) 137.34 bits [[[[[[[,,,,,,,,,,,,,,((((((((--..-(((-((-(((((((((((,,,,,.., 1 GGGGgUGaUuaUGGUuUUCGACagGaauagu..gaaggcuUaaggugCAuGuCGAGG..u 56 GGGGG:G UU+UGGU UUCGAC:GG:AU:+U :::G:UU::G :GC::GUCGAGG 2639 GGGGGCGCUUUUGGU-UUCGACGGGGAUGAUgu-UACGUUUGAGAAGCGAGUCGAGGgaA 2696 <<<<<<_.____________>>>>>>,.....,,,,,,,,,,,,,,,,,,,,,,,,,,,, 57 gcggcug.gCCUCGUAAAAAagccgcA.....aAAAAAUAAcUGCAAAcAAcAAaAAcUA 110 G::G CC CGU+AAAA::C A +AAAAAUAA+ G AAC+A AA+AA+U+ 2697 CCUGUGGaCCCGCGUUAAAAAACUAUAggccuUAAAAAUAAAGGAUAACGAAAAUAAUUU 2756 ,<<<<<<<<<<_________>>>>->>>>>><<<<<<<<<<<--<<<________>>>-- 111 CgcuuuagcugCUUAAccAgcugccguuuggcguucuccauggaauucugcCcuuuguuu 170 GCUU++GC+GC UA C+GC+++ GU:: CC ::GA : CCC+ : U+ 2757 AGCUUUAGCUGCGUAG---UCAGCUAA----CGUCAGCCUGAGAGU----CCCGCGACUC 2805 >>>>------>>>>>>>,,,,,,,,,,,,,,,,,..<<<<<-<<<<<<________>>>> 171 uauggaaggcgucaacgcaaacuaguAagggAUc..guuuagaaaucccgucugggggua 228 :: G +GGCG ::AC G++ GG A+C G:::: :AA ::+ :: A 2806 AGAGUCUGGCGUCGACA-------GCGGGGAACCgaGCCUUACAAAGCU-------UUGA 2851 >>->>>>>,,,,,,,,,,,,,,,,,,,,.<<<<<<<<<<-<<<________>>>->>>>> 229 guuuagaaaaAAAuuuaAAucaGgcaUa.gucuauuacuagcuUGuucuuuggccgauaa 287 G:+::::A AAUUUA U+A+GC UA + +U:A::AGCUUGUU+ U GGC+::U:A 2852 GUAAGGAACGGAAUUUA--UGAAGC-UAcUGAAGUGAAAAGCUUGUUUGUAGGCGUUUCA 2908 >>>>>.,,,,,,,,,,,,,,,,,,,,,,,,,)))))---))))))))-))).---))))) 288 uagau.gAAAauUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguugg.cAauauuU 345 + + GAA UUAAA A A A+ACU AC::G AG : G::U:+::: A :AU:U 2909 UGGAGgGAAUGUUAAA----AUACAAACUGCACUCGGAG-AUGCUUAAAUGaAACCAUUU 2963 ))),,,<<<<<_______>>>>>]]]]]]]:::: 346 uuGGACggGGGUUCGAuUCCCccCAcCUCCACCA 379 U:GGAC:GGGGUUCGAUUCCCC:C:CCUCCAC A 2964 UCGGACAGGGGUUCGAUUCCCCUCGCCUCCACUA 2997 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #23192,sp|AE008453.1|AE008453 Streptococcus pneumoniae R6 section 69 of 184 of the complete genome. ----isReversed: 0 ----hitSequence: GGGGUCGUUACGGAUUCGACAGGCAUUAUGAGGCAUAUUUUGCGACUCGUGUGGCGACGUAAACGCUCAGUUAAAUAUAACUGCAAAAAAUAACACUUCUUACGCUCUAGCUGCCUAAAAACCAGCAGGCGUGACCCGAUUUGGAUUGCUCGUGUUCAAUGACAGGUCUUAUUAUUAGCGAGAUACGAUUAAGCCUUGUCUAGCGGCUUGAUAAGAGAUUGAUAGACUCGCAGUUUCUAGACUUGAGUUAUGUGUCGAGGGGCUGUUAAAAUAAUACAUAACCUAUGGUUGUAGACAAAUAUGUUGGCAGGUGUUUGGACGUGGGUUCGACUCCCACCGGCUCCA hit 31 : 8604 8948 (fwd) 134.03 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,,<<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGGugcgg 60 GGGG::G UUA GG+ UUCGACAGG:A::+U :+G::U::: UGC:: :CG G UG++: 8604 GGGGUCG-UUACGGA-UUCGACAGGCAUUAU-GAGGCAUAUUUUGCGACUCGUG-UGGCG 8659 <<_____________>>>>>>,..,,,,,,,,,,,,,,,,,,,,,,,,,,...,,,<<<< 61 cuggCCUCGUAAAAAagccgcA..aAAAAAUAAcUGCAAAcAAcAAaAAc...UACgcuu 115 CGUAAA +:++CA +AAA+AUAACUGCAAA+AA+AA+A + UACGCU+ 8660 ------ACGUAAA---CGCUCAguUAAAUAUAACUGCAAAAAAUAACACUucuUACGCUC 8710 <<<<<<_____...____>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->> 116 uagcugCUUAA...ccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuua 172 UA:C+GC+UAA CCAGC+G:CGU +:::C + :U+GA:U +C+ UG:U++A 8711 UAGCUGCCUAAaaaCCAGCAGGCGU----GACCCGAUUUGGAUU----GCUCGUGUUCAA 8762 >>------>>>>>>>,,,,,,,,,,,,,,,,,<<<<<-<<<<<<________>>>>>>-> 173 uggaaggcgucaacgcaaacuaguAagggAUcguuuagaaaucccgucuggggguaguuu 232 : + AGG C:::+ A UAG++AG++A+ G:::A :::+: GUCU :+:::UU 8763 UGACAGG--UCUUAU--UAUUAGCGAGAUAC-GAUUAAGCCUU--GUCUA---GCGGCUU 8812 >>>>,,,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<__.______>>>->>>>>>>>> 233 agaaaaAAAuuuaAAucaGgcaUagucuauuacuagcuUG.uucuuuggccgauaauaga 291 :::AA A AUU + AG+C U+G:::::+::: :C:UG +U+ U :G:C:::+::::: 8813 GAUAAGAGAUUG---AUAGAC-UCGCAGUUUCUAGACUUGaGUUAUGUGUCGAGGGGCUG 8868 >,,,,,,,,,,,,,,.,,,,,,,,,,,)))))---))))))))-))).---)))))))), 292 ugAAAauUaAAAaAa.aAauagACUAAaCaUGUAGaacguuuguugg.cAauauuUuuGG 349 U UAAAA+AA A AUA+ CUA : ::GUAG A :::::U+: A::U:UUUGG 8869 U------UAAAAUAAuACAUAACCUAUGGUUGUAG-ACAAAUAUGUUgGCAGGUGUUUGG 8921 ,,<<<<<_______>>>>>]]]]]]]:::: 350 ACggGGGUUCGAuUCCCccCAcCUCCACCA 379 ACG:GGGUUCGA+UCCC:CC::CUCCA 8922 ACGUGGGUUCGACUCCCACCGGCUCCA--- 8948 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #23548,sp|AE008823.1|AE008823 Salmonella typhimurium LT2, section 127 of 220 of the complete genome. ----isReversed: 0 ----hitSequence: UAAAAAGCCGCAAAAAAAUAGUCGCAAACGACGAAACCUACGCUUUAGCAGCUUAAUAACCUGCUUAGAGCCCUCUCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCCAAAAGAGAUCGCGCGGAUGCCCUGCCUGGGGUUGAAGCGUUAAAACGAAUCAGGCUAGUCUGGUAGUGGCGUGUCCGUCCGCAGGUGCCAGGCGAAUGUAAAGACUGACUAAGCAUGUAGUACCGAGGAUGUAGGAAUUUCGGACGCGGGUUCAACUCCCGC hit 32 : 1 285 (fwd) 38.37 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,,<<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGGugcgg 60 : ::+:::CA 1 -----------------------------------UAAAAAGCCGCA--------A---- 13 <<_____________>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<<< 61 cuggCCUCGUAAAAAagccgcAaAAAAAUAAcUGCAAAcAAcAAaAAcUACgcuuuagcu 120 AAAAAUA +GCAAAC+AC+AAA CUAC:C+++:GC: 14 -----------------------AAAAAUAGUCGCAAACGACGAAACCUACGCUUUAGCA 50 <_________>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->>>>------ 121 gCUUAAccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuuauggaaggc 180 GCUUAA++A+C:GC+:+++G:C:U:::+C:::+ ::+C+GC CUU+:: +:::G+ + 51 GCUUAAUAACCUGCUUAGAGCCCUCUCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAA- 109 >>>>>>>.,,,,,,,,,,,,,,,,,<<<<<-<<<<<<________>>>>>>->>>>>,,, 181 gucaacg.caaacuaguAagggAUcguuuagaaaucccgucuggggguaguuuagaaaaA 239 :::A:G CAAAC++++AAG+GAUCG:: +G+:: CC+G+CUGG GG ::+++ :: +A 110 -GAGAGGuCAAACCCAAAAGAGAUCGCGCGGAUGCCCUGCCUGG-GGUUGAAGCGU--UA 165 ,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<________>>>->>>>>>>>>>,,,,,,, 240 AAuuuaAAucaGgcaUagucuauuacuagcuUGuucuuuggccgauaauagaugAAAauU 299 AA+ AAUCAGGC UA::CU :+A+U GC:UGU+C U+:GC G+U+: AG:: +AAU 166 AAACG-AAUCAGGC-UAGUCUGGUAGUGGCGUGUCCGUCCGCAGGUGCCAGGC--GAAUG 221 ,,,,,,,,,,,,,,,,,,.)))))---))))))))-)))---)))))))),,,<<<<<__ 300 aAAAaAaaAauagACUAA.aCaUGUAGaacguuuguuggcAauauuUuuGGACggGGGUU 358 +AAA +A GACUAA UGUAG:::+::: +UG+ A++A UUU GGACG:GGGUU 222 UAAA---GAC-UGACUAAgCA-UGUAGUACCGAGGAUGU-AGGAAUUUCGGACGCGGGUU 275 _____>>>>>]]]]]]]:::: 359 CGAuUCCCccCAcCUCCACCA 379 C A+UCCC:C 276 CAACUCCCGC----------- 285 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #24759,sp|AE010048.1|AE010048 Streptococcus pyogenes strain MGAS8232, section 96 of 173 of the complete genome. ----isReversed: 0 ----hitSequence: GGGGUUGUUACGGAUUCGACAGGCAUUAUGAGGCAUGUUUUGCGUCCCAUCGGCAGAUGUAAAUUGCCAGUUAAAUAUAACUGCAAAAAAUACAAACUCUUACGCUUUAGCUGCCUAAAAACCAGCUAGCGUGACUUCUACAAGAUUGCUUGUGUCCUGUUAGAAGUCUCAAAAUAGCAAGCUACGGUUACGAAAUUGUCUAGUUUCGUGACAAGAGAUUGAUAGACUCGCAAACUAAUGGCUUGAGUUAUGUGUCUUUAGUUUGUUAAAUGAAGACAUAACCUAUGGACGUAGACAAAUAUGUUGGCAGGUGUUUGGACGUGGGUUCGACUCCCACCGGCUCCAUCA hit 33 : 800 1147 (fwd) 134.14 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,,<<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGGugcgg 60 GGGG: G UUA GG+ UUCGACAGG:A::+U :+G::U::: UGC:U :C +:C G 800 GGGGUUG-UUACGGA-UUCGACAGGCAUUAU-GAGGCAUGUUUUGCGUCCCAUC-GGCAG 855 <<____________._>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,...,,,<<<<< 61 cuggCCUCGUAAAA.AagccgcAaAAAAAUAAcUGCAAAcAAcAAaAAc...UACgcuuu 116 GUAAA+ ++C G: +AAA+AUAACUGCAAA+AA+A AAAC UACGCUUU 856 ------AUGUAAAUu-GCCAGU-UAAAUAUAACUGCAAAAAAUACAAACucuUACGCUUU 907 <<<<<_____...____>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->>> 117 agcugCUUAA...ccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuuau 173 A::UGC+UAA CCAGCU::CGU :::U ::::::GA:U +C+U UG:++::: 908 AGCUGCCUAAaaaCCAGCUAGCGU----GACUUCUACAAGAUU----GCUUGUGUCCUGU 959 >------>>>>>>>..,,,,,,,,,,,,,,,,,<<<<<-<<<<<<________>>>>>>- 174 ggaaggcgucaacg..caaacuaguAagggAUcguuuagaaaucccgucuggggguaguu 231 :+ A+G+:: A::: G+AAG +A++GU ::G :U+ GUCU G +U: U 960 UAGAAGUCUCAAAAua-------GCAAGCUACGGUUACGAAAUU--GUCUAG--UUUCGU 1008 >>>>>,,,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<__.______>>>->>>>>>>> 232 uagaaaaAAAuuuaAAucaGgcaUagucuauuacuagcuUG.uucuuuggccgauaauag 290 :: A A A AUU + AG+C U+G:::A:UA: +C:UG +U+ U :G+C :UA:U:: 1009 GACA-AGAGAUUG---AUAGAC-UCGCAAACUAAUGGCUUGaGUUAUGUGUCUUUAGUUU 1063 >>,,,,,,,,,,,,,,,,,,,,,,,,,)))))---))))))))-))).---)))))))), 291 augAAAauUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguugg.cAauauuUuuGG 349 :U AA+U AA A AUA+ CUA : A:GUAG A :::::U+: A::U:UUUGG 1064 GU--UAAAUGAAG---ACAUAACCUAUGGACGUAG-ACAAAUAUGUUgGCAGGUGUUUGG 1117 ,,<<<<<_______>>>>>]]]]]]]:::: 350 ACggGGGUUCGAuUCCCccCAcCUCCACCA 379 ACG:GGGUUCGA+UCCC:CC :CUCCA CA 1118 ACGUGGGUUCGACUCCCACCGGCUCCAUCA 1147 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #25275,sp|AE010567.1|AE010567 Fusobacterium nucleatum subsp. nucleatum ATCC 25586, section 109 of 197 of the complete genome. ----isReversed: 1 ----hitSequence: GGGGAUGCAAAGGUUUCGACGGGGUUGUGAGGUUAUAGGUAGCAAGUCAGGCUUGUCGCUGUGAGAGACUAAACACAUCUUUUAGAUGGAAACAAAGAUUACGCUUUAGCUGCUUAGUUCAGCUACACCUUGGAUAACUUAUUCUAUACGGGUUUUUCAAAGGUGUUGACUAGUAUAGAUCACCAUAAAUGAUUUCUCUAAGUUUAUGGGACAUUUUAGAGGAUAGUUUUAGUUAGCCCUGUUUACGGGAGUAAUUAUUACGAAAUUUAAUAGUAAACUAAACUUGUAGAAGCUUAUGGUCAUUAUGAUUUCGGACACGAGUUCGACUCUCGUCAUCUCCACCA hit 34 : 1932 1589 (rev) 119.43 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,,<<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGGugcgg 60 GGGG:UG +A+GGU UUCGAC:GG::::+ : + ::UA:G::GCA:GUC G :: G 9244 GGGGAUG-CAAAGGU-UUCGACGGGGUUGUG-AGGUUAUAGGUAGCAAGUCAGG--CUUG 9298 <<_____________>>>>>>,...,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<< 61 cuggCCUCGUAAAAAagccgcA...aAAAAAUAAcUGCAAAcAAcAAaAAcUACgcuuua 117 : C GU A A +:C ::A A ++ UA +UG AAACAA +A+ UACGCUU+: 9299 U---CGCUGUGAGA-GACUAAAcacAUCUUUUAGAUGGAAACAAAGAU---UACGCUUUA 9351 <<<<_________>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->>>>--- 118 gcugCUUAAccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuuauggaa 177 ::+:CUUA :+::C:+ :::U: A::+ :U:+U + + :G:UU::U +AA 9352 GCUGCUUAG---UUCAGCUA----CACCUUGGAUAACUUAUUCUAUACGGGUUUUUCAAA 9404 --->>>>>>>.,,,,,,,,,,,,,,,,,<<<<<-<<<<<<________>>>>>>->>>>> 178 ggcgucaacg.caaacuaguAagggAUcguuuagaaaucccgucuggggguaguuuagaa 236 GG+:U::: GUA G ++:::UA A: :++ UCU +: :UUUA::: 9405 GGUGUUGACUa-------GUAUAGAUCACCAUAAAUGAUU--UCUC---UAAGUUUAUGG 9452 ,,,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<________>>>->>>>>>>>>>,,,, 237 aaAAAuuuaAAucaGgcaUagucuauuacuagcuUGuucuuuggccgauaauagaugAAA 296 A AUUU+ ++AGG UA:U+::::+:: C:UGUU+ :G +::+::::+A: AA 9453 -GACAUUUU--AGAGGA-UAGUUUUAGUUAGCCCUGUUUACGGGAGUAAUUAUUAC-GAA 9507 ,,,,,,,,,,,,,,,,,,,,,)))))---))))))))-)))..---)))))))),,,<<< 297 auUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguugg..cAauauuUuuGGACggG 354 AUU+AA+ A UA+ACUAAAC:UGUAG ::G:U::U+ : A::::UU:GGAC::G 9508 AUUUAAU----AGUAAACUAAACUUGUAG-AAGCUUAUGGUcaUUAUGAUUUCGGACACG 9562 <<_______>>>>>]]]]]]]:::: 355 GGUUCGAuUCCCccCAcCUCCACCA 379 :GUUCGA+UC:C::CA:CUCCACCA 9563 AGUUCGACUCUCGUCAUCUCCACCA 9587 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #25915,sp|AE011207.1|AE011207 Leptospira interrogans serovar lai str. 56601 chromosome I, section 16 of 397 of the complete sequence. ----isReversed: 0 ----hitSequence: GGGGACGAAAUUGGUUUCGACUGUUGUUGCCAGGGGUUAUGUGGCGUGUAGAGGUUGUAGGCUCCUCUAAAAACCUUCAAACAAUAACCGCUAAUAACGAAUUAGCUUUAGCAGCUUAAUCUCUGCUACGGAACUUUAGUUUUUUCUCUCGAAUUCUAAAUGUUCUGACAAUGAUCGGGAGGCGAUUCUUUUGGUUUUUGGUUCCUAAAAGAGUUUGUAUUUGAGCCGAAUAGGAAAGAGAGUCCUGUCUGAGGGUGAACCUCUUUCCGAAAUUUUAUACACAGACUACACACGUAGAGGCUGAUCUGGGGCGCAAUAGGACGCGGGUUCGAACCCCGCCGUCUCCA hit 35 : 9134 9480 (fwd) 102.71 bits [[[[[[[,,,,,,,,,,,,,,((((((((--.-(((-((-(((((((((((,,,,,.,<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagu.gaaggcuUaaggugCAuGuCGAGG.ugc 58 GGGG::GA ++UGGU UUCGAC:G ::: G+ A: G UA G::GC:UGU GAGG UG: 9134 GGGGACGAAAUUGGU-UUCGACUGUUGUUGCc-AGGGGUUAUGUGGCGUGUAGAGGuUGU 9191 <<<<_____________>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<< 59 ggcuggCCUCGUAAAAAagccgcAaAAAAAUAAcUGCAAAcAAcAAaAAcUACgcuuuag 118 :G G +C UAAAAA +C::C AAA AAUAAC+GC AA AAC+AA U+ +C+UU:+ 9192 AG--GCUCCUCUAAAAA-CCUUC-AAACAAUAACCGCUAAUAACGAA---UUAGCUUUAG 9244 <<<_____......____>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->> 119 cugCUUAA......ccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuua 172 ::+CUUAA C+A++::+C:UU+G+ UU+::: :G+A:U C +UG:U+U: 9245 CAGCUUAAucucugCUACGGAACUUUAGUUUUUUCUCUCGAAUU----CUAAAUGUUCUG 9300 >>------>>>>>>>,,,,,,,,,,,,,,,,,<<<<<-<<<<<<________>>>>>>-> 173 uggaaggcgucaacgcaaacuaguAagggAUcguuuagaaaucccgucuggggguaguuu 232 :+A+G +:: G A G GAU :::U:+::+::: :::+:: : 9301 ACAAUGAUCG------------GGAGGCGAU-UCUUUUGGUUUU--------UGGUUCCU 9339 >>>>,,,,,,,,,,,,,,,,,,,,...<<<<<<<<<<-<<<________>>>->>>>>>> 233 agaaaaAAAuuuaAAucaGgcaUa...gucuauuacuagcuUGuucuuuggccgauaaua 289 A:::+A +U UA U+AG C A G+::A:+ A+::+++UCU ::+ GA +:U: 9340 AAAAGAGUUUGUAUUUGAGCC-GAauaGGAAAGAG--AGUCCUGUCUGAGGGUGAACCUC 9396 >>>.,,,,,,,,,,,,,,,,,,,,,,,,,)))))---))))))))-))).---))))))) 290 gau.gAAAauUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguugg.cAauauuUuu 347 :+U AAAUU+ A+ A A AGACUA ACA:GUAG ::G U U :G + ::: U: 9397 UUUcCGAAAUUUUAU---ACACAGACUACACACGUAG-AGGCUGAUCUGg-GGCGCAAUA 9451 ),,,<<<<<_______>>>>>]]]]]]]:::: 348 GGACggGGGUUCGAuUCCCccCAcCUCCACCA 379 GGACG:GGGUUCGA CCC:CC::CUCCA 9452 GGACGCGGGUUCGAACCCCGCCGUCUCCA--- 9480 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #26491,sp|AE011783.1|AE011783 Xanthomonas axonopodis pv. citri str. 306, section 161 of 469 of the complete genome. ----isReversed: 1 ----hitSequence: GGGGGUGCACUGGUUUCGACGGGGGUCGCGAAGUCGCUUGGCGCAUGCCGAGGGGGCAGCUUUCCUCGUUAAUCCAGCAGCAAACUUUUAGUUGCCAACGAUGACAACUACGGUUCGGACUUCGCUAUCGCCGCUUAAUUGGCUUUAGUUGUAGUUCUACAGCCGCCUAAGGCGAACCCCCGAACCUACUUGUGCCCGUGCUCGUAGGUGUAGGGUCAUUAUCACGGAACCAUCGGUAGUGGCUGCCUGUCAGCUACCGGUCAGAUAAAGCAGGCUGGUUUCCAGGUGCGCUUUGCCAACCGUGCUGCCUGGGAACGAGAUCUAACGGAGGGCUAAGCAUGUAGUGCUGGGGAUGGAGUGCUUCCGGACGGCGGUUCGAUUCCGCCCACCUCCACCA hit 36 : 5129 4733 (rev) 144.70 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,.,<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGG.ugcg 59 GGGGGUG + UGGU UUCGAC::G::::G+GAAG C: :+G::CAUG:CGAGG +GC 7337 GGGGGUG-CACUGGU-UUCGACGGGGGUCGCGAAGUCGCUUGGCGCAUGCCGAGGgGGCA 7394 <<<_.___________._>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,......... 60 gcug.gCCUCGUAAAA.AagccgcAaAAAAAUAAcUGCAAAcAAcAAaAAc......... 108 GCU CCUCGU+AA+ AGC GCAAA ++ UA UGC+AAC+A++A+AAC 7395 GCUUu-CCUCGUUAAUcCAGCAGCAAACUUUUAGUUGCCAACGAUGACAACuacgguucg 7453 ...,,,<<<<<<<<<<_________>>>>->>>>>>........................ 109 ...UACgcuuuagcugCUUAAccAgcugccguuugg........................ 141 U+C+C+:U+:C :CUUAA : G:C+U:+G+ 7454 gacUUCGCUAUCGCCGCUUAA----UUGGCUUUAGUuguaguucuacagccgccuaaggc 7509 ....<<<<<<<<<<<--<<<________>>>-->>>>------>>>>>>>,,,,,,,,,, 142 ....cguucuccauggaauucugcCcuuuguuuuauggaaggcgucaacgcaaacuaguA 197 ::::::C:U: +: + GCCC+U+ :+ :A:G ++G :::::: +A 7510 gaacCCCCGAACCUACUUGU--GCCCGUGCUCGUAGGUGUAGGGUCAUUA-------UCA 7560 ,,,,,,,.<<<<<-<<<<<<________>>>>>>->>>>>,,,,,,,,,,,,,,,,,,,, 198 agggAUc.guuuagaaaucccgucuggggguaguuuagaaaaAAAuuuaAAucaGgcaUa 256 GG A+C :: : : ::C+ G+CUG +G:: : : ::+A AA+ CAGGC U 7561 CGGAACCaUCGGUAGUGGCU-GCCUGUCAGCUACCGGUCAGAUAAA-----GCAGGC-UG 7613 ..<<<<<<<<<<-<<<________>>>->>>>>>>>>>..,,,,,,,,,,,,,,,,,,,, 257 ..gucuauuacuagcuUGuucuuuggccgauaauagau..gAAAauUaAAAaAaaAauag 312 :C:A:: +C:U+++C +:G++ ::U:G: GA+A+ UAA + ++G 7614 guUUCCAGGUG-CGCUUUGCCAACCGUGCUGCCUGGGAacGAGAUCUAA-----CGGAGG 7667 ,,,,,)))))---))))))))-)))---)))))))),,,<<<<<_______>>>>>]]]] 313 ACUAAaCaUGUAGaacguuuguuggcAauauuUuuGGACggGGGUUCGAuUCCCccCAcC 372 CUAA:CAUGUAG::C+: :G+UGG A+::::U::GGACGG+GGUUCGAUUCC+CCCACC 7668 GCUAAGCAUGUAGUGCUGGGGAUGG-AGUGCUUCCGGACGGCGGUUCGAUUCCGCCCACC 7726 ]]]:::: 373 UCCACCA 379 UCCACCA 7727 UCCACCA 7733 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #26954,sp|AE012247.1|AE012247 Xanthomonas campestris pv. campestris str. ATCC 33913, section 155 of 460 of the complete genome. ----isReversed: 1 ----hitSequence: GGGGGUGCACUGGUUUCGACGGGGGUCGCGAAGUCGCUUGGCGCAUGCCGAGGGGGCAGCUUUCCUCGUUAAUCCAGCAGCAAACUUUUAGUUGCCAACGACGACAACUACGGUUCGGACUUCGCUAUCGCCGCUUAAUUGGCUUUAGUUGUAGUUCUACAGCCGCCUAAGGCGAACCCCCGAAACUACUUGUGCCCGUGCUCGUAGAUGUAGGGUCAUUAUCACGGAACCGCCGGUAGUGGCUGCCUGUCAGCUAUCGGUUAGAUCAAGCAGGCUGGUUUUCAGGUGCGCUUUGCCCGCCGUGCUGCCUGGGAACGAGAUCUAACGGAGGGAUAAGCAUGUAGUGCUGGGGAUGGAGUGCUUCCGGACGGCGGUUCGAUUCCGCCCACCUCCACCA hit 37 : 3390 2994 (rev) 143.03 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,.,<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGG.ugcg 59 GGGGGUG + UGGU UUCGAC::G::::G+GAAG C: :+G::CAUG:CGAGG +GC 9451 GGGGGUG-CACUGGU-UUCGACGGGGGUCGCGAAGUCGCUUGGCGCAUGCCGAGGgGGCA 9508 <<<_.___________._>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,......... 60 gcug.gCCUCGUAAAA.AagccgcAaAAAAAUAAcUGCAAAcAAcAAaAAc......... 108 GCU CCUCGU+AA+ AGC GCAAA ++ UA UGC+AAC+AC+A+AAC 9509 GCUUu-CCUCGUUAAUcCAGCAGCAAACUUUUAGUUGCCAACGACGACAACuacgguucg 9567 ...,,,<<<<<<<<<<_________>>>>->>>>>>........................ 109 ...UACgcuuuagcugCUUAAccAgcugccguuugg........................ 141 U+C+C+:U+:C :CUUAA : G:C+U:+G+ 9568 gacUUCGCUAUCGCCGCUUAA----UUGGCUUUAGUuguaguucuacagccgccuaaggc 9623 ....<<<<<<<<<<<--<<<________>>>-->>>>------>>>>>>>,,,,,,,,,, 142 ....cguucuccauggaauucugcCcuuuguuuuauggaaggcgucaacgcaaacuaguA 197 ::::::::U: +: + GCCC+U+ :+ :A:: ++G :::::: +A 9624 gaacCCCCGAAACUACUUGU--GCCCGUGCUCGUAGAUGUAGGGUCAUUA-------UCA 9674 ,,,,,,,<<<<<-<<<<<<________>>>>>>->>>>>,,,,,,,,,,,,,,,,,,,,. 198 agggAUcguuuagaaaucccgucuggggguaguuuagaaaaAAAuuuaAAucaGgcaUa. 256 GG A+CG+:: +A:+ :+G+CUG : +:U+ :: A +U AA CAGGC U 9675 CGGAACCGCCGGUAGUGGCUGCCUG--UCAGCUAUCG---GUUAGAUCAAGCAGGC-UGg 9728 .<<<<<<<<<<-<<<________>>>->>>>>>>>>>.,,,,,,,,,,,,,,,,,,,,,, 257 .gucuauuacuagcuUGuucuuuggccgauaauagau.gAAAauUaAAAaAaaAauagAC 314 U+:: : +: ::UUG +C +G::C:+ : ::+A GA+A+ UAA + ++G 9729 uUUUCAGGUGCGCUUUGCCCGCCGUGCUGCCUGGGAAcGAGAUCUAA-----CGGAGGGA 9783 ,,,)))))---))))))))-)))---)))))))),,,<<<<<_______>>>>>]]]]]] 315 UAAaCaUGUAGaacguuuguuggcAauauuUuuGGACggGGGUUCGAuUCCCccCAcCUC 374 UAA:CAUGUAG::C+: :G+UGG A+::::U::GGACGG+GGUUCGAUUCC+CCCACCUC 9784 UAAGCAUGUAGUGCUGGGGAUGG-AGUGCUUCCGGACGGCGGUUCGAUUCCGCCCACCUC 9842 ]:::: 375 CACCA 379 CACCA 9843 CACCA 9847 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #27268,sp|AE012561.1|AE012561 Xylella fastidiosa Temecula1, section 9 of 9 of the complete genome. ----isReversed: 0 ----hitSequence: GGGGGUGCACUGGCUUCGACGGGGGUCACAAAAUCACUUGGUGCAUGCCGAGGGGGCCGCUUUCCUCGUAAAUCCAGCAGCACACUUAUAGUUGCCAACGAAGACAACUUCGCUCUAGCCGCUUAAGGCUUAAGCCUCGAAACUGCUUGUGUCCGUGCUCGCAGCGUAGAGUCAUCAUCACGGAACCGCUGAGACGUGGCCGUCUGCCCACCCUUGGUUAAAUCUAGCAGACUGGUUUCCGGGUGCGCUUUGCCUGUCGUGCUGCCCGGCGACGAGACCUAACGGCCAGGAUAAGCAUGUAGGGCCGGGGACGGAGUACUUUCGGACGGCGGUUCGAUUCCGCCCACCUCCACCA hit 38 : 39892 40246 (fwd) 151.19 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,.,<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGG.ugcg 59 GGGGGUG + UGG UUCGAC:GG::U:+++AA C: :+G: CAUG:CGAGG +GC 39892 GGGGGUG-CACUGGC-UUCGACGGGGGUCACAAAAUCACUUGGUGCAUGCCGAGGgGGCC 39949 <<<_.___________._>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<< 60 gcug.gCCUCGUAAAA.AagccgcAaAAAAAUAAcUGCAAAcAAcAAaAAcUACgcuuua 117 GCU CCUCGUAAA+ AGC GCA A ++AUA UGC+AAC+A +A+AACU+CGCU++A 39950 GCUUu-CCUCGUAAAUcCAGCAGCACACUUAUAGUUGCCAACGAAGACAACUUCGCUCUA 40008 <<<<_________>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->>>>--- 118 gcugCUUAAccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuuauggaa 177 GC GCUUAA G+ C: :::::+:++AA:U +C+U U:U+++:+: 40009 GCCGCUUAA---------GG----CUUAAGCCUCGAAACU---GCUUGUGUCCGUGCUCG 40052 --->>>>>>>,,,,,,,,,,,,,,,,,<<<<<-<<<<<<_._______>>>>>>->>>>> 178 ggcgucaacgcaaacuaguAagggAUcguuuagaaauccc.gucuggggguaguuuagaa 236 :::: :G A +A +A GG A+CG++::GA :+ C GUCUG +: UU::+ 40053 CAGCGUAGAG-UCAUCAUCACGGAACCGCUGAGACGUGGCcGUCUGCCCACCCUUGGU-- 40109 ,,,,,,,,,,,,,,,,,,,,.<<<<<<<<<<-<<<________>>>->>>>>>>>>>.., 237 aaAAAuuuaAAucaGgcaUa.gucuauuacuagcuUGuucuuuggccgauaauagau..g 293 +AAAU UA CAG+C U + +:::::: +C:U+++CU U:G++ ::::::+ + G 40110 -UAAAUCUA--GCAGAC-UGgUUUCCGGGUGCGCUUUGCCUGUCGUGCUGCCCGGCGacG 40165 ,,,,,,,,,,,,,,,,,,,,,,,,)))))---))))))))-)))---)))))))),,,<< 294 AAAauUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguuggcAauauuUuuGGACgg 353 A+A UAA + AG UAA:CAUGUAG :C+: :G+ GG A+:A::UU:GGACGG 40166 AGACCUAAC----GGCCAGGAUAAGCAUGUAGGGCCGGGGACGG-AGUACUUUCGGACGG 40220 <<<_______>>>>>]]]]]]]:::: 354 GGGUUCGAuUCCCccCAcCUCCACCA 379 +GGUUCGAUUCC+CCCACCUCCACCA 40221 CGGUUCGAUUCCGCCCACCUCCACCA 40246 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #27328,sp|AE012839.1|AE012839 Chlorobium tepidum TLS section 60 of 194 of the complete genome. ----isReversed: 0 ----hitSequence: GGGGAUGACAGGCUAUCGACAGGAUAGGUGUGAGAUGUCGUUGCACUCCGAGUUUCAGCAUGGACGGACUCGUUAAACAAGUCUAUGUACCAAUAGAUGCAGACGAUUAUUCGUAUGCAAUGGCUGCCUGAUUAGCACAAGUUAAUUCAGAAGCCAUCGUCCUGCGGUGAAUGCGCUUACUCUGAAGCCGCCGGAUGGCAUAACCCGCGCUUGAGCCUACGGGUUCGCGCAAGUAAGCUCCGUACAUUCAUGCCCGAGGGGGUGUGCGGGUAACCAAUCGGGAUAAGGGGACGAACGCUGCUGGCGGUGUAAUCGGACCACGAAAAACCAACCACCAGAGAUGAGUGUGGUAACUGCAUCGAGCAGUGUCCUGGACGCGGGUUCAAGUCCCGCCAUCUCCACCA hit 39 : 3209 3612 (fwd) 42.50 bits [[[[[[[,,,,,,,,,,.,,,,((((((((--.-(((-((-(((((((((((,,,,,.,< 1 GGGGgUGaUuaUGGUuU.UCGACagGaauagu.gaaggcuUaaggugCAuGuCGAGG.ug 57 GGGG:UG + +GG U UCGACA: :A:AG G G + +:U:CA:::CGAG U: 3209 GGGGAUG--ACAGGC-UaUCGACAG-GAUAGGuGUGAGAUGUCGUUGCACUCCGAGUuUC 3264 <<<<<__....__________._>>>>>>,..,,,,,,,,,,,,,,,,,,,,,,,,,,,, 58 cggcugg....CCUCGUAAAA.AagccgcA..aAAAAAUAAcUGCAAAcAAcAAaAAcUA 110 :G::UGG CUCGU+AAA AA::C:: +A AAUA +UGCA AC+A+ A+ UA 3265 AGCAUGGacggACUCGUUAAAcAAGUCUA-ugUACCAAUAGAUGCAGACGAUUAUUCGUA 3323 ,<<<<<<<<<<_____............................................ 111 CgcuuuagcugCUUAA............................................ 126 :C :+ ::+:C+U A 3324 UGCAAUGGCUGCCUGAuuagcacaaguuaauucagaagccaucguccugcggugaaugcg 3383 .____>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->>>>------>>>>> 127 .ccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuuauggaaggcgucaa 185 ++A+:+:: +: G:CG+ + C U:+ :: GC CUU ::++:A GG + + 3384 cUUACUCUGAAGCCGCCGGAUGGCAUAACCC---GCGCUUGAGCCUACGGGUUCGC---- 3436 >>,,,,,,,,,,,,,,,,,<<<<<-<<<<<<_.._______>>>>>>->>>>>,,,,,,, 186 cgcaaacuaguAagggAUcguuuagaaauccc..gucuggggguaguuuagaaaaAAAuu 243 G+AAG A G:U :G :: ::C G+C+G+G:: :: U: G: ++AA + 3437 ---------GCAAGUAA--GCUCCGUACAUUCauGCCCGAGGGGGUGUGCGG-GUAACCA 3484 ,,,,,,,,,,,,,..<<<<<<<<<<-<<<________>>>->>>>>>>>>>..,,,,,,, 244 uaAAucaGgcaUa..gucuauuacuagcuUGuucuuuggccgauaauagau..gAAAauU 299 + UC+GG UA :+ ::+: +CU +++ +GG++ A:+:: +: GAAAA+ 3485 A---UCGGGA-UAagGGGACGAA--CGCU--GCUGGCGGUGUAAUCGGACCacGAAAAAC 3536 ,,,,,,,,,,,,,,,,,,)))))---))))))))-))).---)))))))),,,<<<<<__ 300 aAAAaAaaAauagACUAAaCaUGUAGaacguuuguugg.cAauauuUuuGGACggGGGUU 358 AA + A + A :::UGU G:A:+ + U CA+U:U: :UGGACG:GGGUU 3537 CAA----CCACCAGAGAUGAGUGUGGUAACUGCAUCGAgCAGUGUC-CUGGACGCGGGUU 3591 _____>>>>>]]]]]]]:::: 359 CGAuUCCCccCAcCUCCACCA 379 C A UCCC:CCA:CUCCACCA 3592 CAAGUCCCGCCAUCUCCACCA 3612 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #27552,sp|AE013063.1|AE013063 Thermoanaerobacter tengcongensis strain MB4T, section 90 of 244 of the complete genome. ----isReversed: 0 ----hitSequence: GGGGGUGUGUUGGUUUCGACGGGGGCGGUCGAGGUAAAAGUAGCGAGCCGAGUUCUCCACCAGCUCGUAAAAAAGGUGGAAAAAAAUAAACGCAGACAGAGAACUCGCUUACGCUGCCUAAUUAAAGGCGGCCGUCCAGCCUGAAAUGCCCACGUUUCAGGACUGGGCGUCAAAAGAGUGGGGAACUGGUUUUGCCUGCGCCUCGGGGCAAAACCGGAAUAAUGAGGCUACCGAAGCGGUUAUCCUGUCGCUGGGAGAACCGCUGAGGGAAAGCUAAAACAGCGACUGCGCUCGGAGAAGCUUUUACCGGGACGCCUUCGGACCGGGGUUCGAAUCCCCGCACCUCCACCA hit 40 : 8484 8834 (fwd) 136.95 bits [[[[[[[,,,,,,,,,,,,,,((((((((--.-(((-((-(((((((((((,,,,,..,< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagu.gaaggcuUaaggugCAuGuCGAGG..ug 57 GGGGGUG U +UGGU UUCGAC:GG::::GU + G:: A:G::GC::G:CGAG U 8484 GGGGGUG-UGUUGGU-UUCGACGGGGGCGGUc-GAGGUAAAAGUAGCGAGCCGAGUucUC 8540 <<<<<_____________>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<< 58 cggcuggCCUCGUAAAAAagccgcAaAAAAAUAAcUGCAAAcAAcAAaAAcUACgcuuua 117 C: C+G CUCGUAAAAA+G :G AAAAAAAUAA++GCA ACA +AA C GCUU 8541 CACCAG--CUCGUAAAAAAGGUGGAAAAAAAUAAACGCAGACAGAGAACUC---GCUUAC 8595 <<<<_________>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->>>>--- 118 gcugCUUAAccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuuauggaa 177 GC+:C+UAA++A :+GC CGU+C+ C:U +AAU +CC + GUUU A:G+ + 8596 GCUGCCUAAUUAAAGGCGGC----CGUCCAGCCUGAAAU----GCCCACGUUUCAGGACU 8647 --->>>>>>>..,,,,,,,,,,,,,,,,,<<<<<-<<<<<<_.._______>>>>>>->> 178 ggcgucaacg..caaacuaguAagggAUcguuuagaaauccc..gucuggggguaguuua 233 GG CAAA+ AGU+ GG A +U:+++ ::CC+ G+CU GGGG:: +++: 8648 GGGC------guCAAAAGAGUGGGGAA---CUGGUUUUGCCUgcGCCUCGGGGCAAAACC 8698 >>>,,,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<________>>>->>>>>>>>>>. 234 gaaaaAAAuuuaAAucaGgcaUagucuauuacuagcuUGuucuuuggccgauaauagau. 292 G +AA A+ U+AGGC UA:: :::: :U+:::+++UC U::: G: :::: :: 8699 G--GAAUAA-----UGAGGC-UACCGAAGCGGUUAUCCUGUCGCUGGGAGAACCGCUGAg 8750 .,,,,,,,,,,,,,,,,,,,,,,,,,)))))---))))))))-))).---)))))))),, 293 .gAAAauUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguugg.cAauauuUuuGGA 350 GAAA UAAAA +A GACU :C::G AG ::G:U::U + A::::UU:GGA 8751 gGAAAGCUAAAA---CAG-CGACUGCGCUCGGAG-AAGCUUUUACCgGGACGCCUUCGGA 8805 ,<<<<<_______>>>>>]]]]]]]:::: 351 CggGGGUUCGAuUCCCccCAcCUCCACCA 379 C:GGGGUUCGA UCCCC:CACCUCCACCA 8806 CCGGGGUUCGAAUCCCCGCACCUCCACCA 8834 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #28393,sp|AE013908.1|AE013908 Yersinia pestis KIM section 308 of 415 of the complete genome. ----isReversed: 0 ----hitSequence: GGGGCUGAUUCUGGAUUCGACGGGAUUCGCGAAACCCAAGGUGCAUGCCGAGGUGCGGUGGCCUCGUAAAAAACCGCAAAAAAAAUAGUUGCAAACGACGAAAACUACGCACUAGCAGCUUAAUAACCUGCUUAGAGCCCUCUCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCUAAAAGAGCUCGUGUGGAAACCUUGCCUGGGGUGGAAGCAUUAAAACUAAUCAGGAUAGUUUGUCAGUAGCGUGUCCAUCCGCAGCUGGCCGGCGAAUGUAAUGAUUGGACUAAGCAUGUAGUGCCGACGGUGUAGUAAUUUCGGACGGGGGUUCAAAUCCCCCCAGCUCCACCA hit 41 : 10909 11272 (fwd) 212.10 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,,<<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGGugcgg 60 GGGG:UGAUU UGG+ UUCGAC:GGA:U:G+G:A:+C: ::+G::CAUG:CGAGGUGCGG 10909 GGGGCUGAUUCUGGA-UUCGACGGGAUUCGCGAAACCC-AAGGUGCAUGCCGAGGUGCGG 10966 <<_____________>>>>>>,.,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<< 61 cuggCCUCGUAAAAAagccgcA.aAAAAAUAAcUGCAAAcAAcAAaAAcUACgcuuuagc 119 ::G CCUCGUAAAA ::CCGCA AAAAAAUA UGCAAAC+AC+AAAACUAC:C::+:GC 10967 UGG-CCUCGUAAAA-AACCGCAaAAAAAAUAGUUGCAAACGACGAAAACUACGCACUAGC 11024 <<_________>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->>>>----- 120 ugCUUAAccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuuauggaagg 179 :GCUUAA++A+C:GC+:+::G:C:U:::+C:::+ ::+C+GC CUU+:: +:::G+ + 11025 AGCUUAAUAACCUGCUUAGAGCCCUCUCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAA 11084 ->>>>>>>.,,,,,,,,,,,,,,,,,<<<<<-<<<<<<________>>>>>>->>>>>,, 180 cgucaacg.caaacuaguAagggAUcguuuagaaaucccgucuggggguaguuuagaaaa 238 :::A:G CAAAC++++AAG+G UCGU : G A::C:+G+CUG :G::G + : A + 11085 --GAGAGGuCAAACCUAAAAGAGCUCGUGUGGAAACCUUGCCUG--GGGUGGAAGCA--U 11138 ,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<________>>>->>>>>>>>>>,,,,,, 239 AAAuuuaAAucaGgcaUagucuauuacuagcuUGuucuuuggccgauaauagaugAAAau 298 AA++ +AAUCAGG UA::++ ::A:UAGC:UGU+C U+:GC G:U:: ++:: +AAU 11139 UAAAACUAAUCAGGA-UAGUUUGUCAGUAGCGUGUCCAUCCGCAGCUGGCCGGC--GAAU 11195 ,,,,,,,,,,,,,,,,,,,)))))---))))))))-)))---)))))))),,,<<<<<__ 299 UaAAAaAaaAauagACUAAaCaUGUAGaacguuuguuggcAauauuUuuGGACggGGGUU 358 +AA+ +A U+GACUAA:CAUGUAG::C+:::G :G: A+:A:UUU:GGACGGGGGUU 11196 GUAAU---GAUUGGACUAAGCAUGUAGUGCCGACGGUGU-AGUAAUUUCGGACGGGGGUU 11251 _____>>>>>]]]]]]]:::: 359 CGAuUCCCccCAcCUCCACCA 379 C A UCCCCCCA:CUCCACCA 11252 CAAAUCCCCCCAGCUCCACCA 11272 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #28501,sp|AE014016.1|AE014016 Buchnera aphidicola str. Bp (Baizongia pistaciae), section 1 of 2 of the complete genome. ----isReversed: 1 ----hitSequence: GGGGCUGAUAUUGGAUUUGACAAAAUUAUUGAAAACUGAUGUGCAUGCCGAGGAUGGUUUGCCUCGUUAAAAAACCAUAAAAAAUAGUAGCAAAACAAAAUCAAUACGCUUUAGCAGCUUAAUAAUCUGAAUAAAGCCCUUCUUUUAAACAUAUUCUCUUAAUGUUUAAUUUAUAUAGAAGGUUAAUCUAAAGAGAUCGCAACUCAAAUCUAUUUUGAAAGAUUUUUUGUUGCUAAAUAAAAACUUCAAAAUAUAUAUCUAUAAUGAGUCUAUACAUCGAUAGAUAAGAAAAGAUAAUAGACUAAGCAUGUAGUAUCUGAAGUCGUAAAAAUUUUGGACGCGGGUUCGAAUCCCGCCAGCUCCA hit 42 : 200304 199941 (rev) 135.33 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,,<<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGGugcgg 60 GGGG:UGAU++UGG+ UU GACA::A:U +UG:A: CU :A: UGCAUG:CGAGG +GG 109700 GGGGCUGAUAUUGGA-UUUGACAAAAUUAUUGAAAACU-GAUGUGCAUGCCGAGGA-UGG 109756 <<_____________>>>>>>,.,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<< 61 cuggCCUCGUAAAAAagccgcA.aAAAAAUAAcUGCAAAcAAcAAaAAcUACgcuuuagc 119 :U GCCUCGU+AAAAA:CC A AAAAAAUA GCAAA+ A AA+ A UAC:C+++:+C 109757 UUUGCCUCGUUAAAAAACC--AuAAAAAAUAGUAGCAAAACAAAAUCAAUACGCUUUAGC 109814 <<_________>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->>>>----- 120 ugCUUAAccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuuauggaagg 179 :GCUUAA++A C:G+ :+++G:C:UU:+:: ::+ A: +U C CUU :U U:: : ++ 109815 AGCUUAAUAAUCUGAAUAAAGCCCUUCUUUUAAACAUAUU-CUCUUAAUGUUUAAUUUAU 109873 ->>>>>>>,,,,,,,,,,,,,,,,,<<<<<-<<<<<<_._______>>>>>>->>>>>,, 180 cgucaacgcaaacuaguAagggAUcguuuagaaauccc.gucuggggguaguuuagaaaa 238 :+:AA:G A+U+ +AAG+GAUC+:: +::::::+ U+UG+ ::::::U ::++ 109874 AUAGAAGG-UUAAUCUAAAGAGAUCGCAACUCAAAUCUaUUUUGAAAGAUUUUUUGUUGC 109932 ,,,,,,,,,,,,,,,,,,.<<<<<<<<<<-<<<________>>>->>>>>>>>>>,,,,, 239 AAAuuuaAAucaGgcaUa.gucuauuacuagcuUGuucuuuggccgauaauagaugAAAa 297 AA+U+AAA+C A A :U : ::+ UA::: GU++ U :::CG +:: : A: AAA 109933 UAAAUAAAAACUUCAAAAuAUAUAUCUAUAAUGAGUCUAUACAUCGAUAGAUAAG--AAA 109990 ,,,,,,,,,,,,,,,,,,,,)))))---))))))))-)))..---)))))))),,,<<<< 298 uUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguugg..cAauauuUuuGGACggGG 355 + A AA+ AGACUAA:CAUGUAG :U:UG+:G: AA A:U::UGGACG:GG 109991 AGAUAAU------AGACUAAGCAUGUAG--UAUCUGAAGUcgUAAAAAUUUUGGACGCGG 110042 <_______>>>>>]]]]]]]:::: 356 GUUCGAuUCCCccCAcCUCCACCA 379 GUUCGA UCCC:CCA:CUCCA 110043 GUUCGAAUCCCGCCAGCUCCA--- 110063 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #28521,sp|AE014094.1|AE014094 Buchnera aphidicola str. Sg (Schizaphis graminum) section 19 of 57 of the complete genome. ----isReversed: 1 ----hitSequence: GGGGCUGUUUUUGGAUUCGACAAAGUUAUCAAAAAAGUAAAGUGCAUGCCGAGGAACGGUUUGCCUCGAUAAAAAACCGUAAAAAAAUAGCUGCAAAUAAUAAACAAAACUACGCUUUAGCAGCUUAAAAAACUGUAUAAAGCCCUUUCAUCUCUGACUUCUCUCUUGAGAACGAGAAAUUUUUAAGAAAGGCCGACAUUUAAAGAGAAAAAUGUGAGCACUAUGCUUGAUAGUGACACAAAAUUAAUUUUUCAAGCUAUAAGCUUAAAAUGAGUUUUUCCAAAUUAAGCAAUGAAAAAAUAAAGAAAAACUAAGCAUGUAGUAUCUUUAUUUAUAGAAAUUUUGGACGCGGGUUCAAAUCCCGCCAGCUCCA hit 43 : 4741 4369 (rev) 159.48 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,,<<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGGugcgg 60 GGGG:UG+UU+UGG+ UUCGACA::::U +++::: : UA:: :GCAUG:CGAGG CGG 9166 GGGGCUGUUUUUGGA-UUCGACAAAGUUAUCAAAAAAGUAAAGUGCAUGCCGAGGAACGG 9224 <<_____________>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,...,,,<<<<<< 61 cuggCCUCGUAAAAAagccgcAaAAAAAUAAcUGCAAAcAAcAAaAAc...UACgcuuua 117 :U GCCUCG +AAAAA:CCG AAAAAAAUA CUGCAAA AA+AAA A UAC:C+++: 9225 UUUGCCUCGAUAAAAAACCGUAAAAAAAUAGCUGCAAAUAAUAAACAAaacUACGCUUUA 9284 <<<<_________>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->>>>--- 118 gcugCUUAAccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuuauggaa 177 +C:GCUUAA +A C:G+ :+++G: :UU:::::+: :U++ +C+ UU: :+::GAA 9285 GCAGCUUAAAAAACUGUAUAAAGCCCUUUCAUCUCUGACUUC-UCUCUUGAGAACGAGAA 9343 --->>>>>>>.......,,,,,,,,,,,,,,,,,<<<<<-<<<<<<________>>>>>> 178 ggcgucaacg.......caaacuaguAagggAUcguuuagaaaucccgucuggggguagu 230 + +:::AA: ++A UA+++AG+ A +:::: G:A:::+ G++UG+ :::G: 9344 AUUUUUAAGAaaggccgACAUUUAAAGAGAAAAAUGUGAGCACUAU-GCUUGAU-AGUGA 9401 ->>>>>,,,,,,,,,,,,,,,,,,,,...<<<<<<<<<<-<<<________>>>->>>>> 231 uuagaaaaAAAuuuaAAucaGgcaUa...gucuauuacuagcuUGuucuuuggccgauaa 287 ::::A+ AAUUU+ UCA+GC UA :::UA:::: A +U+UUU C :::: 9402 CACAAAAUUAAUUUU--UCAAGC-UAuaaGCUUAAAAUGA-----GUUUUU---CCAAAU 9450 >>>>>,,,,,,,,,,,,,,.,,,,,,,,,,,)))))---))))))))-))).---))))) 288 uagaugAAAauUaAAAaAa.aAauagACUAAaCaUGUAGaacguuuguugg.cAauauuU 345 UA::: AA+ AAAAA+A A A+A+ACUAA:CAUGUAG : ::U :+::: A+ A::: 9451 UAAGC--AAUGAAAAAAUAaAGAAAAACUAAGCAUGUAG-UAUCUUUAUUUaUAGAAAUU 9507 ))),,,<<<<<_______>>>>>]]]]]]]:::: 346 uuGGACggGGGUUCGAuUCCCccCAcCUCCACCA 379 :UGGACG:GGGUUC A UCCC:CCA:CUCCA 9508 UUGGACGCGGGUUCAAAUCCCGCCAGCUCCA--- 9538 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #28579,sp|AE014155.1|AE014155 Streptococcus pyogenes MGAS315, section 20 of 37 of the complete genome. ----isReversed: 0 ----hitSequence: GGGGUUGUUACGGAUUCGACAGGCAUUAUGAGGCAUGUUUUGCGUCCCAUCGGCAGAUGUAAAUUGCCAGUUAAAUAUAACUGCAAAAAAUACAAACUCUUACGCUUUAGCUGCCUAAAAACCAGCUAGCGUGACUUCUACAAGAUUGCUUGUGUCCUGUUAGAAGUCUCAAAAUAGCAAGCUACGGUUACGAAAUUGUCUAGUUUCGUGACAAGAGAUUGAUAGACUCGCAAACUAAUGGCUUGAGUUAUGUGUCUUUAGUUUGUUAAAUGAAGACAUAACCUAUGGACGUAGACAAAUAUGUUGGCAGGUGUUUGGACGUGGGUUCGACUCCCACCGGCUCCAUCA hit 44 : 8794 9141 (fwd) 134.14 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,,<<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGGugcgg 60 GGGG: G UUA GG+ UUCGACAGG:A::+U :+G::U::: UGC:U :C +:C G 8794 GGGGUUG-UUACGGA-UUCGACAGGCAUUAU-GAGGCAUGUUUUGCGUCCCAUC-GGCAG 8849 <<____________._>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,...,,,<<<<< 61 cuggCCUCGUAAAA.AagccgcAaAAAAAUAAcUGCAAAcAAcAAaAAc...UACgcuuu 116 GUAAA+ ++C G: +AAA+AUAACUGCAAA+AA+A AAAC UACGCUUU 8850 ------AUGUAAAUu-GCCAGU-UAAAUAUAACUGCAAAAAAUACAAACucuUACGCUUU 8901 <<<<<_____...____>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->>> 117 agcugCUUAA...ccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuuau 173 A::UGC+UAA CCAGCU::CGU :::U ::::::GA:U +C+U UG:++::: 8902 AGCUGCCUAAaaaCCAGCUAGCGU----GACUUCUACAAGAUU----GCUUGUGUCCUGU 8953 >------>>>>>>>..,,,,,,,,,,,,,,,,,<<<<<-<<<<<<________>>>>>>- 174 ggaaggcgucaacg..caaacuaguAagggAUcguuuagaaaucccgucuggggguaguu 231 :+ A+G+:: A::: G+AAG +A++GU ::G :U+ GUCU G +U: U 8954 UAGAAGUCUCAAAAua-------GCAAGCUACGGUUACGAAAUU--GUCUAG--UUUCGU 9002 >>>>>,,,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<__.______>>>->>>>>>>> 232 uagaaaaAAAuuuaAAucaGgcaUagucuauuacuagcuUG.uucuuuggccgauaauag 290 :: A A A AUU + AG+C U+G:::A:UA: +C:UG +U+ U :G+C :UA:U:: 9003 GACA-AGAGAUUG---AUAGAC-UCGCAAACUAAUGGCUUGaGUUAUGUGUCUUUAGUUU 9057 >>,,,,,,,,,,,,,,,,,,,,,,,,,)))))---))))))))-))).---)))))))), 291 augAAAauUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguugg.cAauauuUuuGG 349 :U AA+U AA A AUA+ CUA : A:GUAG A :::::U+: A::U:UUUGG 9058 GU--UAAAUGAAG---ACAUAACCUAUGGACGUAG-ACAAAUAUGUUgGCAGGUGUUUGG 9111 ,,<<<<<_______>>>>>]]]]]]]:::: 350 ACggGGGUUCGAuUCCCccCAcCUCCACCA 379 ACG:GGGUUCGA+UCCC:CC :CUCCA CA 9112 ACGUGGGUUCGACUCCCACCGGCUCCAUCA 9141 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #28639,sp|AE014233.1|AE014233 Streptococcus agalactiae 2603V/R section 43 of 100 of the complete genome. ----isReversed: 1 ----hitSequence: GGGGUCGUUACGGAUUCGACAGGCAUUAUGAGGUAUAUUUCGCGACUCAUCGGCAGAUGUAAAAUGCCAGUUAAAUAUAACUGCAAAAAAUACAAAUUCUUACGCAUUAGCUGCCUAAAAAACAGCCUGCGUGAUCUUCACAAGAUUGUUUGCGUUUUGCUAGAAGGUCUUAUUUAUCAGCAAACUACGUUUGGCUACUGUCUAGUUAGUUAAAAAGAGAUUUAUAGACUCGCUAUGUGAGGGCUUGAGUUAUGUGUCAUCACCUAGUUAAAUCAAUACAUAACCUAUAGUUGUAGACAAAUAUAUUAGCAGAUGUUUGGACGUGGGUUCGACUCCCACCGGCUCCA hit 45 : 14673 14327 (rev) 125.82 bits [[[[[[[,,,,,,,,,,,,,,((((((((---(((-((-(((((((((((,,,,,,<<<< 1 GGGGgUGaUuaUGGUuUUCGACagGaauagugaaggcuUaaggugCAuGuCGAGGugcgg 60 GGGG::G UUA GG+ UUCGACAGG:AU:+U : G::U::: :GC:: UC +:C G 6883 GGGGUCG-UUACGGA-UUCGACAGGCAUUAU-GAGGUAUAUUUCGCGACUCAUC-GGCAG 6938 <<____________._>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,...,,,<<<<< 61 cuggCCUCGUAAAA.AagccgcAaAAAAAUAAcUGCAAAcAAcAAaAAc...UACgcuuu 116 GUAAAA ++C G: +AAA+AUAACUGCAAA+AA+A AAA+ UACGC+UU 6939 ------AUGUAAAAu-GCCAGU-UAAAUAUAACUGCAAAAAAUACAAAUucuUACGCAUU 6990 <<<<<_____...____>>>>->>>>>><<<<<<<<<<<--<<<________>>>-->>> 117 agcugCUUAA...ccAgcugccguuuggcguucuccauggaauucugcCcuuuguuuuau 173 A::+GC+UAA CAGC+::CGU + U::+ : ::GA:U + +U G:UU:: 6991 AGCUGCCUAAaaaACAGCCUGCGU----GAUCUUCACAAGAUU----GUUUGCGUUUUGC 7042 >------>>>>>>>,,,,,,,,,,,,,,,,,<<<<<-<<<<<<________>>>>>>->> 174 ggaaggcgucaacgcaaacuaguAagggAUcguuuagaaaucccgucuggggguaguuua 233 :+ A+G +::A + A +AG+AA +A+ GU:U G::A + GUCU G + A::U A 7043 UAGAAGGUCUUAUU--UAUCAGCAAACUAC-GUUUGGCUACU--GUCUAG--UUAGUUAA 7095 >>>,,,,,,,,,,,,,,,,,,,,<<<<<<<<<<-<<<__.______>>>->>>>>>>>>> 234 gaaaaAAAuuuaAAucaGgcaUagucuauuacuagcuUG.uucuuuggccgauaauagau 292 :AA+A A+UU+ AG+C U+G:::+:U::: +C:UG +U+ U :G+C:::A:+:::U 7096 AAAGAGAUUUA----UAGAC-UCGCUAUGUGAGGGCUUGaGUUAUGUGUCAUCACCUAGU 7150 ,,,,,,,,,,,,,,,,,,,,,,,,,)))))---))))))))-))).---)))))))),,, 293 gAAAauUaAAAaAaaAauagACUAAaCaUGUAGaacguuuguugg.cAauauuUuuGGAC 351 AA+U AA+ A AUA+ CUA A ::GUAG : :::::U : A:AU:UUUGGAC 7151 --UAAAUCAAU---ACAUAACCUAUAGUUGUAG-ACAAAUAUAUUaGCAGAUGUUUGGAC 7204 <<<<<_______>>>>>]]]]]]]:::: 352 ggGGGUUCGAuUCCCccCAcCUCCACCA 379 G:GGGUUCGA+UCCC:CC::CUCCA 7205 GUGGGUUCGACUCCCACCGGCUCCA--- 7229 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #29142,sp|AE014761.1|AE014761 Bifidobacterium longum NCC2705 section 148 of 202 of the complete genome. ----isReversed: 0 ----hitSequence: GGGGGCGAUCGGUUUCGACGGUGACCUGUUCGCUGCAGGGAAGCGUGCCGAGAACGCCGGGUCCGCUCGUGGAUGACCCCGGCAAAAGAAUAAGUGCUAAAUCUAACCGCACUGAGUUCGCUCUCGCUGCCUGAUUUUUAGUCAGGAUUAACCAGUGAGCAGCCGCUCCGUUCACUCCUCCUCGUCUUUGGGAGGAUGCUGAGCGUCGUUUAGAAGACUUGCUGAUGCAGUUGAGCCUCAGGGCUGCAUCGGGACUUUAACUGCGGAUAUGCUCGCCAUCAGUUGUCUGCGACAUCGAUGGGGGCAGAAAAAUCGCCAACUUGGCCAGCAGACUACGCACGUAGAAGACUGUGGGCUCGGUCAUCGGACCGGGGUUCAAUUCCCCGCGCCUCCACCA hit 46 : 658 1054 (fwd) 83.08 bits [[[[[[[,,,,,,,,,,,,,,((((((((--...-(((-((-(((((((((((,,,,,., 1 GGGGgUGaUuaUGGUuUUCGACagGaauagu...gaaggcuUaaggugCAuGuCGAGG.u 56 GGGGG:G ++ GGU UUCGAC:G :A::+ ::G:: ::+::GC:UG:CGAG 658 GGGGGCG--AUCGGU-UUCGACGGUGACCUGuuc-GCUGCA-GGGAAGCGUGCCGAGAaC 712 <<<<<<_.___________.._>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,..... 57 gcggcug.gCCUCGUAAAA..AagccgcAaAAAAAUAAcUGCAAAcAAcAAaAAc..... 108 GC:G : CUCGU A+ : C:GCAAAA AAUAA UGC AA+ +AA+ C 713 GCCGGGUcCGCUCGUGGAUgaCCCCGGCAAAAGAAUAAGUGCUAAAUCUAACCGCacuga 772 .,,,<<<<<<