Params: ./cmzasha --no-stderr --filter 150 43.5 Rfam/cm/RF00169.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00169_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00169_fwdinf_hmmtype1_advance_copy.bin Build: release Host: xmen.cs.washington.edu pid: 2314 ----hmm-from-cmFileName: Rfam/cm/RF00169.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-greedy-node 150 43.50 Rfam/cm/RF00169.cm forward-alg-inf 100000 cycling-node cfsqp-elim-gauss 0 1 Build: release Host: recycle.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-greedy-node 150 43.50 Rfam/cm/RF00169.cm forward-alg-inf 100000 cycling-node cfsqp-elim-gauss 0 1 Build: release Host: recycle.cs.washington.edu ----hmm-from-cmFileName: ../zasha-infernal/Rfam/cm/RF00169.cm ----hmm-build-info: ;(default construction of HMM) Params: --set-input-mm-file Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf ../zasha-infernal/Rfam/cm/RF00169.cm 1 1 100000 1 Build: release Host: SERENA ;Params: --set-input-mm-file Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf ../zasha-infernal/Rfam/cm/RF00169.cm 1 1 100000 1 Build: release Host: SERENA ----cmFile: Rfam/cm/RF00169.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/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: #16401,sp|AC025951.19|AC025951 Staphylococcus aureus clone sabac-32, complete sequence. ----isReversed: 0 ----hitSequence: GAUUUCGGUCCUAUGCAAUAUGAACCCAUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCAUCAUAUGUGCCGUAGGGUAGCCGAGAUUUAGC hit 0 : 16427 16529 (fwd) 77.96 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G::U G: CC:::GCAA:::GA ACCC:UGAACC::GUCAGGUCC GA GGAAGCAGC: 16427 GAUUUCGGuCCUAUGCAAUAUGA-ACCCAUGAACCAUGUCAGGUCCUGACGGAAGCAGCA 16485 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:GG+U+ UC:::UGUGCC:::G+GU :C G:: +A+C 16486 UUAAGUGGAUCAUCAUAUGUGCCGUAGGGUagCCGAGAUUUAGC 16529 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #16755,sp|AE000524.1|AE000524 Helicobacter pylori 26695 section 2 of 134 of the complete genome. ----isReversed: 1 ----hitSequence: UAUUUAGACCUAUGCAAUAGGAUUUUAGGGUAACGCUUCAGGGUAGGAAUACAGCAGAGUCCCCUAAUUUCUUGUGUGCCUUAGCCAUCUGAAUAGGAG hit 1 : 4105 4007 (rev) 57.26 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 +:::U GACC:: GCAA:::GA+++::G G A C ::UCAGG:::GGAA:::AGCAG:: 6430 UAUUUAGACCUAUGCAAUAGGAUUUUAGGGUAACGCUUCAGGGUAGGAAUACAGCAGAGU 6489 --->>>>---->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 C::+U UUC:::UGUGCC ::G +UCUG:::+G+ 6490 C-CCCUAAU-UUCUUGUGUGCCUUAGCCAUCUGAAUAGGAG 6528 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #16979,sp|AE000759.1|AE000759 Aquifex aeolicus VF5 section 91 of 109 of the complete genome. ----isReversed: 0 ----hitSequence: UAUUAAUUAGCCCUGCGGCGGGACAGGGUGAACUCCCCCAGGCCCGAAAGGGAGCAAGGGUAAGCCCGCCGUCCCGUGCGCAGGGUCCUAAAACAAAUACCCU hit 2 : 8326 8428 (fwd) 51.13 bits :<<<<-<<.-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->> 1 ggcuuGGa.Cccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGC 58 +:::: :+ + C:C GC:+CG:GA :GUGAAC C:+ :AGG:CCG AAGG:AGCA:+ 8326 UAUUAAUUaG-CCCuGCGGCGGGA-CAGGGUGAACUCCCCCAGGCCCGAAAGGGAGCAAG 8383 >>--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 59 cgUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :GUAAGC: + + UC:CGUG:GC G:G+ U +:+::::+ C 8384 GGUAAGCCCGCCGUCCCGUGCGCAGGGUCCUaaAACAAAUACCCU 8428 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #17365,sp|AE001151.1|AE001151 Borrelia burgdorferi B31 (section 37 of 70) of the complete genome. ----isReversed: 0 ----hitSequence: UCCUAGGACCCGUACUAUCAAGUAUUGCUGAAUCCCGUCAGGACUGGAAGGUAGCAGCGGUAAGCGAUUUUUUUGAUGAGUACGUAAGUCUUAGGUUUAA hit 3 : 4235 4334 (fwd) 57.74 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +:C::GGA : :: :C A:::::+A+:::+GAA CC:GUCAGG:C:GGAA:G:AGCAGC: 4235 UCCUAGGA-CCCGuACUAUCAAGUAUUGCUGAAUCCCGUCAGGACUGGAAGGUAGCAGCG 4293 >--->>>>--.-->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguu.uuucgcgUGuGcCgcgguguuCugggccgacC 101 GU A+:::+U UU:::::UG G: :: : G UCU::G: + 4294 GU-AAGCGAUuUUUUUGAUGAGUACGUAAG-UCUUAGGUUUAA 4334 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #17401,sp|AE001187.1|AE001187 Treponema pallidum section 3 of 87 of the complete genome. ----isReversed: 1 ----hitSequence: UCCGGGGCCGCCCACGAAAUAUCCCCCAAACCCCGCUAGGUCCGGAAGGAAGCAACGGUAGGGGGACGCUUCGGUGCGCGAUCCGCCCCGGUUUUC hit 4 : 2892 2797 (rev) 57.60 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 +:C::GG: CGC CA ::: :A+CCC:: AACCC:G :AGGUCCGGAAGGAAGCA:C:G 9786 UCCGGGGC--CGCCCACGAAAUAUCCCCCAAACCCCGCUAGGUCCGGAAGGAAGCAACGG 9843 --->>>>---->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 U A::GG++ : ::: GUG CGCG U :C+::G: + C 9844 U-AGGGGGA-CGCUUCGGUG-CGCGAUCCGCCCCGGUUUUC 9881 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #17510,sp|AE001298.1|AE001298 Chlamydia trachomatis section 25 of 87 of the complete genome. ----isReversed: 1 ----hitSequence: GCUGGGGACCUCUUAAGAUGAGAGACUUCUGAACCGGGUCAGGAUCGGAAGGUAGCAGCCCUAAGGAUAGGCCUUUUGUGCUAGGAGUUUUCUCUGGCUUAC hit 5 : 7270 7169 (rev) 66.38 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G:: :GGACC::: +::A::::A AC:::UGAACC:GGUCAGG::CGGAAG::AGCAGCC 5153 GCUGGGGACCUCUuAAGAUGAGAGACUUCUGAACCGGGUCAGGAUCGGAAGGUAGCAGCC 5212 >--->>>>--.-->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguu.uuucgcgUGuGcCgcgguguuCugggccgacC 101 :UAAG:::+ + U::::UG:: :::GU+UUCU: ::C+ C 5213 CUAAGGAUAGgCCUUUUGUGCU-AGGAGUUUUCUCUGGCUUAC 5254 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #17576,sp|AE001441.1|AE001441 Helicobacter pylori, strain J99 section 2 of 132 of the complete genome. ----isReversed: 1 ----hitSequence: UAUUUGGACCUAUGCAAUAGGACUUUAGGGUAACGCUUCAGGGUAGGAAUACAGCAGAGUCCCCUAAUUUCUUGUGUGCCUUAGCCAUCUGAAUAGGAG hit 6 : 7008 6910 (rev) 59.32 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 +:::UGGACC:: GCAA:::GA ++::G G A C ::UCAGG:::GGAA:::AGCAG:: 6360 UAUUUGGACCUAUGCAAUAGGACUUUAGGGUAACGCUUCAGGGUAGGAAUACAGCAGAGU 6419 --->>>>---->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 C::+U UUC:::UGUGCC ::G +UCUG:::+G+ 6420 C-CCCUAAU-UUCUUGUGUGCCUUAGCCAUCUGAAUAGGAG 6458 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #17756,sp|AE001624.1|AE001624 Chlamydia pneumoniae section 40 of 103 of the complete genome. ----isReversed: 1 ----hitSequence: GUUGGGGGCCUUUUAAGAGAAGGAACCUGCGAAUCGGGUCAGGACUGGAAGGUAGCAGCCCUAAGGAGAGUUUUCUUUUGCUAAAAGAAUGUUCUCCAACUUAC hit 7 : 2125 2022 (rev) 63.46 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G::::GG:CC::: +::A ::G:AACC: :GAA C:GGUCAGG:C:GGAA:G:AGCAGCC 12793 GUUGGGGGCCUUUuAAGAGAAGGAACCUGCGAAUCGGGUCAGGACUGGAAGGUAGCAGCC 12852 >--->>>>--.-->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguu.uuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAA: :G+ UU:C:: UG:: :::G U :CU::::C+ C 12853 CUAAGGAGAGuUUUCUUUUGCU-AAAAGAAUguUCUCCAACUUAC 12896 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #17900,sp|AE001769.1|AE001769 Thermotoga maritima section 81 of 136 of the complete genome. ----isReversed: 1 ----hitSequence: GACCGGGUCCCACGCAACGGAACCCUGUGAACCUGGUCAGGCCCGGGAGGGAGCAGCCAUAAGCAGGUGUUUCCGUGUGCCGUGGGGGAGCCCGGUUGGAG hit 8 : 12519 12419 (rev) 87.36 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 G:C::GG:CCC:CGCAACG::A CC:GUGAACC:GGUCAGG:CCGG AGG:AGCAGCC: 519 GACCGGGUCCCACGCAACGGAA-CCCUGUGAACCUGGUCAGGCCCGGGAGGGAGCAGCCA 577 --->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 UAAGC:G+U UU::CGUGUGCCG:GG+G :C+::G: G+ 578 UAAGCAGGUGUUUCCGUGUGCCGUGGGGGaGCCCGGUUGGAG 619 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #18152,sp|AE002056.1|AE002056 Deinococcus radiodurans R1 section 193 of 229 of the complete chromosome 1. ----isReversed: 0 ----hitSequence: UUGCUGGUGCAGCGCAGCGCGGACGCCCGAACCUGGUCAGAGCCGGAAGGCAGCAGCCAUAAGGGAUGCUUUGCGGGUGCCGUUGCCUUCCGGCAAUGCU hit 9 : 2937 3036 (fwd) 85.73 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 +:::UGG +C::CGCA+CGC:: AC:C::GAACC:GGUCAG :CCGGAAGG:AGCAGCC: 2937 UUGCUGGUGCAGCGCAGCGCGG-ACGCCCGAACCUGGUCAGAGCCGGAAGGCAGCAGCCA 2995 --->>>>---->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 UAA::G:U +U::GCG GUGCCG::G U C+G:::+++C 2996 UAAGGGAUGCUUUGCGGGUGCCGUUGCCUUCCGGCAAUGCU 3036 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #18201,sp|AE002112.1|AE002112 Ureaplasma urealyticum section 13 of 59 of the complete genome. ----isReversed: 1 ----hitSequence: AAUAUAUAUGUCAUUACAAUAUUAAGUAGCGAACCUUGUCAGGCCAGAGAUGGAGCAGCAAUAGCAAUAUCUUUUUAUGUGUGAUGACAUAUAUUAAUGUAAU hit 10 : 7386 7284 (rev) 55.51 bits :<<<<-<<.-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->> 1 ggcuuGGa.Cccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGC 58 :: :A +:C:: :CAA:: +A A : G:GAACC::GUCAGG:C:G A:G:AGCAGC 6917 AAUAUAUAuGUCAUuACAAUAUUA-AGUAGCGAACCUUGUCAGGCCAGAGAUGGAGCAGC 6975 >>--->>>>--.-->>>>>-->>>->>>>---.>>->>>>::::: 59 cgUAAgcgguu.uuucgcgUGuGcCgcggugu.uCugggccgacC 101 ::U A:C :U+ +UU+ ::UGUG: ::G: U U:U :: +A 6976 AAU-AGCAAUAuCUUUUUAUGUGUGAUGACAUaUAUUAAUGUAAU 7019 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #18277,sp|AE002198.2|AE002198 Chlamydophila pneumoniae AR39, section 29 of 94 of the complete genome. ----isReversed: 0 ----hitSequence: GUUGGGGGCCUUUUAAGAGAAGGAACCUGCGAAUCGGGUCAGGACUGGAAGGUAGCAGCCCUAAGGAGAGUUUUCUUUUGCUAAAAGAAUGUUCUCCAACUUAC hit 11 : 1639 1742 (fwd) 63.46 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G::::GG:CC::: +::A ::G:AACC: :GAA C:GGUCAGG:C:GGAA:G:AGCAGCC 1639 GUUGGGGGCCUUUuAAGAGAAGGAACCUGCGAAUCGGGUCAGGACUGGAAGGUAGCAGCC 1698 >--->>>>--.-->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguu.uuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAA: :G+ UU:C:: UG:: :::G U :CU::::C+ C 1699 CUAAGGAGAGuUUUCUUUUGCU-AAAAGAAUguUCUCCAACUUAC 1742 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #18394,sp|AE002321.1|AE002321 Chlamydia muridarum section 52 of 85 of the complete genome. ----isReversed: 1 ----hitSequence: GUCGGGGACCUCUUAAGAUGAGAGACUUCUGAACCGGGUCAGGAUCGGAAGAUAGCAGCCCUAAGGAAAGGCCUUUUGUGCUAAGAGUCUUCUCUGACUUAC hit 12 : 7246 7145 (rev) 70.60 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G:C :GGACC::: +::A::::A AC:::UGAACC:GGUCAGG::CGGAAG::AGCAGCC 5152 GUCGGGGACCUCUuAAGAUGAGAGACUUCUGAACCGGGUCAGGAUCGGAAGAUAGCAGCC 5211 >--->>>>--.-->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguu.uuucgcgUGuGcCgcgguguuCugggccgacC 101 :UAAG:::+ + U::::UG:: :::GU UUCU: G:C+ C 5212 CUAAGGAAAGgCCUUUUGUGCU-AAGAGUCUUCUCUGACUUAC 5253 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #18519,sp|AE002450.1|AE002450 Neisseria meningitidis serogroup B strain MC58 section 92 of 206 of the complete genome. ----isReversed: 1 ----hitSequence: GGCGGGUCUCCCCGCAUGGCAAAUCGGAACACCGGGUCAGGGGCGGAAGCCAGCAGCCCACUCCAAUGCGCCAGUGCCGGGGGUUUGGCCCGCCGCCC hit 13 : 10937 10840 (rev) 60.29 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 GGC::G:: CC:CGCA :GC A+ :G: ACC:GGUCAGG: CGGAAG :AGCAGCC: 29 GGCGGGUCUCCCCGCAUGGCAA-AUCGGAACACCGGGUCAGGGGCGGAAGCCAGCAGCCC 87 --->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 :C: +U GC: GUGCCG:GG++U ::+::GCCG CC 88 A-CUCCAAU--GCGCCAGUGCCGGGGGUUuGGCCCGCCGCCC 126 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #18722,sp|AE003940.1|AE003940 Xylella fastidiosa 9a5c, section 86 of 229 of the complete genome. ----isReversed: 0 ----hitSequence: CUGCCGGUCCCUCGCAACGCUAGAUCGAAAACCCCGCCAGGGCCGGAAGGCAGCAACGGUAUUGAUUGAUGCGGGUGCCGAGAUCAACCGGUGGGGCC hit 14 : 637 734 (fwd) 75.06 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 +: ::GG+C:C:CGCAACGC+: :C+: AACCC:G :AGG:CCGGAAGG:AGCA:C:G 637 CUGCCGGUCCCUCGCAACGCUA-GAUCGAAAACCCCGCCAGGGCCGGAAGGCAGCAACGG 695 --->>>>---->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 U A:+G:UU :+GCG GUGCCG:G:U ++C+:: : G+CC 696 U-AUUGAUU-GAUGCGGGUGCCGAGAUCAACCGGUGGGGCC 734 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #18961,sp|AE004188.1|AE004188 Vibrio cholerae chromosome I, section 96 of 251 of the complete chromosome. ----isReversed: 0 ----hitSequence: GCCCUGGUCCUCCCGCAACACUAGUUCGUGAACCUGGUCAGAUCCGGAAGGAAGCAGCCACAGCGGAUGAUGUGUGUGCCGGGAUGUGGCUGGGGUCUCC hit 15 : 3985 4084 (fwd) 87.37 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G:C:UGG: C:C:CGCAAC:C+: +:CGUGAACC:GGUCAG UCCGGAAGGAAGCAGCC 3985 GCCCUGGUcCUCCCGCAACACUA-GUUCGUGAACCUGGUCAGAUCCGGAAGGAAGCAGCC 4043 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 : AGCG:+U :+G:GUGUGCCG:G:UGU :CUG:G: CC 4044 AC-AGCGGAU-GAUGUGUGUGCCGGGAUGUgGCUGGGGUCUCC 4084 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #19351,sp|AE004581.1|AE004581 Pseudomonas aeruginosa PAO1, section 142 of 529 of the complete genome. ----isReversed: 0 ----hitSequence: CUGUCGGUCCCCCCGCAACGAUUACCCGUCAACCUGGUCAGGUCCGGAAGGAAGCAGCCACAGCGGGAACAUCGUGUGCCGGGGUGUGGCUGGCGGGGCC hit 16 : 9670 9769 (fwd) 94.16 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +::U:GG: CCC:CGCAACG:+ ACCCGU AACC:GGUCAGGUCCGGAAGGAAGCAGCC 9670 CUGUCGGUcCCCCCGCAACGAUU-ACCCGUCAACCUGGUCAGGUCCGGAAGGAAGCAGCC 9728 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 : AGCGG++ +:CGUGUGCCG:GGUGU :CU:G:: G+CC 9729 AC-AGCGGGA-ACAUCGUGUGCCGGGGUGUgGCUGGCGGGGCC 9769 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #19988,sp|AE005224.1|AE005224 Escherichia coli O157:H7 EDL933 genome, contig 1 of 3, section 48 of 155. ----isReversed: 0 ----hitSequence: CUGUUGGUUCUCCCGCAACGCUACUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCCAAGGCAGAUGACGCGUGUGCCGGGAUGUAGCUGGCAGGGCC hit 17 : 9131 9230 (fwd) 83.14 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +::UUGG: C:C:CGCAACGC : +C:GU ACC GGUCAGGUCCGGAAGGAAGCAGCC 9131 CUGUUGGUuCUCCCGCAACGCUA-CUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCC 9189 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 GC:G+U : GCGUGUGCCG:G:UGU :CUGG:: G+CC 9190 AA-GGCAGAU-GACGCGUGUGCCGGGAUGUaGCUGGCAGGGCC 9230 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #20461,sp|AE005700.1|AE005700 Caulobacter crescentus CB15 section 26 of 359 of the complete genome. ----isReversed: 0 ----hitSequence: CGGAGAUCGGCGCGGACGGAGUCCUCGCCAACCUGGUCAGGGCCGAGAGGCAGCAGCCACAACGAGAUCACCUCUGGGUCGUCUGCCGGUCUCCACCUC hit 18 : 4149 4247 (fwd) 53.36 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G::: ::+ :C :::+::: C:CG: AACC:GGUCAGG:CCG AGG:AGCAGCC 4149 CGGAGAUCGGCGCgGACGGAGU--CCUCGCCAACCUGGUCAGGGCCGAGAGGCAGCAGCC 4206 >--->>>>---->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 : A:CG:++U + :::UG:::CG: + ::U:::C+ C 4207 AC-AACGAGAUCACCUCUGGGUCGUCUGCCGGUCUCCACCUC 4247 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #20853,sp|AE006092.1|AE006092 Pasteurella multocida PM70 section 59 of 204 of the complete genome. ----isReversed: 0 ----hitSequence: UUCUCGGUUCCUCGCAAUGGUGUCUGGUUUACCCGGUCAGGUUCGGAAGAAAGCAGCCAAAGUCAGAAUUUCUGUGUGCCGAGAUCAAGCUGGGAAGGUU hit 19 : 9479 9578 (fwd) 73.39 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 +:CU:GG: :C:CGCAA:::+: +C::+U ACC GGUCAGGU:CGGAAG:AAGCAGCC 9479 UUCUCGGUUCCUCGCAAUGGUG-UCUGGUUUACCCGGUCAGGUUCGGAAGAAAGCAGCCA 9537 --->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 AG+::++ U:+:::UGUGCCG:G:U + :CU:GG:+G+ 9538 A-AGUCAGAAUUUCUGUGUGCCGAGAUCAaGCUGGGAAGGUU 9578 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #21065,sp|AE006305.1|AE006305 Lactococcus lactis subsp. lactis IL1403 section 67 of 218 of the complete genome. ----isReversed: 0 ----hitSequence: UUCGGAGCAAUAAGUUUCUUACGAAGCGUGUCAGGACCUGACGGUAGCAGCACUAAGUAUGGAGCUUAUGUGCUCUUUUUUUGU hit 20 : 11173 11256 (fwd) 49.99 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 : C :: GCAA:::G:++C::::GAA C::GUCAGG:CC GA GG:AGCAGC:: 11173 ------UUC-GGAGCAAUAAGUUUCUUACGAAGCGUGUCAGGACCUGACGGUAGCAGCAC 11225 --->>>>---->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 UAA::::+ :C:::UGUGC ::+U+U :U 11226 UAAGUAUGG-AGCUUAUGUGCUCUUUUUUUGU--------- 11256 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #21240,sp|AE006489.1|AE006489 Streptococcus pyogenes M1 GAS strain SF370, section 18 of 167 of the complete genome. ----isReversed: 0 ----hitSequence: UAAUAAUAGGCGGAGCAACACUUGUGCGUGAAGUGGGUCAGGGGAGGAAUCCAGCAGCCCUAAGCGAUUUUCGGGUGUGUGCUCUUUUUUUGUUGACUUUAC hit 21 : 4472 4573 (fwd) 61.25 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 + U: :A+ :: GCAAC:C+: +:CGUGAA :GGUCAGG: :GGAA: :AGCAGCC 4472 UAAUAAUAGGCGGaGCAACACUU-GUGCGUGAAGUGGGUCAGGGGAGGAAUCCAGCAGCC 4530 >--->>>>--.-->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguu.uuucgcgUGuGcCgcgguguuCugggccgacC 101 :UAAGCG:UU U :+G:GUGUGC :: U+UU:U:G + C 4531 CUAAGCGAUUuUCGGGUGUGUGCUCUUUUUUUGUUGACUUUAC 4573 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #21926,sp|AE007179.1|AE007179 Mycobacterium tuberculosis CDC1551, section 265 of 280 of the complete genome. ----isReversed: 1 ----hitSequence: CACGGUGGACCCCGCGCGGCGUCUAUCCUGUGAACUCCCCCAGGGCUGGAAGGCAGCAAGGGUCAACGGGCUCUGUCGGGUGCGCGGGGUCCCCUUCAGCC hit 22 : 1542 1442 (rev) 48.93 bits :<<<<-<<.-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->> 1 ggcuuGGa.Cccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGC 58 +: :: G: CCC:: GC:+CG : A+CC:G+GAAC C:+ :AGG:C:GGAA:G:AGCA:+ 14626 CACGGUGGaCCCCGcGCGGCGUCUAUCCUGUGAACUCCCCCAGGGCUGGAAGGCAGCAAG 14685 >>--->>>>---->>>>>-->>>->>>>--->>->>>>::::: 59 cgUAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 :GU A+C:G+ U : CG G:GC ::GG+ :C+:: :C +CC 14686 GGUCAACGGGCUCUGUCGGGUGCGCGGGG--UCCCCUUCAGCC 14726 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #22064,sp|AE007319.1|AE007319 Streptococcus pneumoniae TIGR4 section 2 of 194 of the complete genome. ----isReversed: 0 ----hitSequence: GUGGAGCAACAGUUCUGCGUGAAGCGGGUCAGGGGAGGAAUCCAGCAGCCCUAAGCGAUUUGAAUUGUGUGCUCUUUUUU hit 23 : 10469 10548 (fwd) 54.84 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 :: GCAAC::+ +:CGUGAA C:GGUCAGG: :GGAA: :AGCAGCC 10469 ---------GUGGaGCAACAGUU-CUGCGUGAAGCGGGUCAGGGGAGGAAUCCAGCAGCC 10518 >--->>>>---->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 :UAAGCG:UUU +::GUGUGC :: U+U 10519 CUAAGCGAUUUGAAUUGUGUGCUCUUUUUU------------ 10548 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #22269,sp|AE007525.1|AE007525 Clostridium acetobutylicum ATCC824 section 13 of 356 of the complete genome. ----isReversed: 0 ----hitSequence: GAAUUGGGUCCCACGCAACGGAAAUUCAUGAACUCCGUCAGGUCCGGAAGGAAGCAGCGGUAAGUGAAAUCUUCCGUGUGCCGUGGAUAAAUCUGAUUUGAGU hit 24 : 2612 2714 (fwd) 93.41 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G:::UGG: CCC:CGCAACG::A A+:C:UGAAC C:GUCAGGUCCGGAAGGAAGCAGC: 2612 GAAUUGGGuCCCACGCAACGGAA-AUUCAUGAACUCCGUCAGGUCCGGAAGGAAGCAGCG 2670 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 GUAAG:G:++U U::CGUGUGCCG:GG ++ :CUG::: GA+ 2671 GUAAGUGAAAUCUUCCGUGUGCCGUGGAUAaaUCUGAUUUGAGU 2714 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #22691,sp|AE007951.1|AE007951 Agrobacterium tumefaciens str. C58 circular chromosome, section 9 of 254 of the complete sequence. ----isReversed: 1 ----hitSequence: GGAGGUUGGUGGUGGACGAGCCACUCGCCAACCGGGUCAGGUCCGGAAGGAAGCAGCCCUAACGAGCCAGGCACGGGUCGCCGUGCCAGCCUCCCACC hit 25 : 6862 6765 (rev) 56.64 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 GG::: ::+:+G: :::+ GC: AC:CG: AACC:GGUCAGGUCCGGAAGGAAGCAGCC 3208 GGAGGUUGGUGGUgGACGAGCC--ACUCGCCAACCGGGUCAGGUCCGGAAGGAAGCAGCC 3265 >--->>>>---->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 :U A:CG:+ +:GC G:::C:C+:UG :: :::CC ACC 3266 CU-AACGAGC-CAGGCACGGGUCGCCGUGCCAGCCUCCCACC 3305 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #23125,sp|AE008386.1|AE008386 Streptococcus pneumoniae R6 section 2 of 184 of the complete genome. ----isReversed: 0 ----hitSequence: AAAUAGUGGAGCAACAGUUCUGCGUGAAGCGGGUCAGGGGAGGAAUCCAGCAGCCCUAAGCGAUUUGAAUUGUGUGCUCUUUUUUUCGUGC hit 26 : 10463 10553 (fwd) 55.55 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 :: :G :: GCAAC::+ +:CGUGAA C:GGUCAGG: :GGAA: :AGCAGCC 10463 AAAUAG----UGGaGCAACAGUU-CUGCGUGAAGCGGGUCAGGGGAGGAAUCCAGCAGCC 10517 >--->>>>---->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 :UAAGCG:UUU +::GUGUGC :: + : ::CG +C 10518 CUAAGCGAUUUGAAUUGUGUGCUCUUU------UUUUCGUGC 10553 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #23446,sp|AE008717.1|AE008717 Salmonella typhimurium LT2, section 25 of 220 of the complete genome. ----isReversed: 0 ----hitSequence: CUGUUGGUUCUCCCGCAACGCUACUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCCAAGGCAGAUGACGCGUGUGCCGGGAUGUAGCUGGCAGGGCC hit 27 : 10281 10380 (fwd) 83.14 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +::UUGG: C:C:CGCAACGC : +C:GU ACC GGUCAGGUCCGGAAGGAAGCAGCC 10281 CUGUUGGUuCUCCCGCAACGCUA-CUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCC 10339 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 GC:G+U : GCGUGUGCCG:G:UGU :CUGG:: G+CC 10340 AA-GGCAGAU-GACGCGUGUGCCGGGAUGUaGCUGGCAGGGCC 10380 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #23705,sp|AE008984.1|AE008984 Agrobacterium tumefaciens strain C58 circular chromosome, section 10 of 256 of the complete sequence. ----isReversed: 1 ----hitSequence: GGAGGUUGGUGGUGGACGAGCCACUCGCCAACCGGGUCAGGUCCGGAAGGAAGCAGCCCUAACGAGCCAGGCACGGGUCGCCGUGCCAGCCUCCCACC hit 28 : 134 37 (rev) 56.64 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 GG::: ::+:+G: :::+ GC: AC:CG: AACC:GGUCAGGUCCGGAAGGAAGCAGCC 10404 GGAGGUUGGUGGUgGACGAGCC--ACUCGCCAACCGGGUCAGGUCCGGAAGGAAGCAGCC 10461 >--->>>>---->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 :U A:CG:+ +:GC G:::C:C+:UG :: :::CC ACC 10462 CU-AACGAGC-CAGGCACGGGUCGCCGUGCCAGCCUCCCACC 10501 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #24341,sp|AE009624.1|AE009624 Brucella melitensis 16M chromosome I, section 181 of 195 of the complete sequence. ----isReversed: 0 ----hitSequence: GGGAGGUUGGUGGUGGACGAGCCACUCGCCAACCGGGUCAGGUCCGGAAGGAAGCAGCCCUAACGAGCCACGGCACGGGUCAUCGUGCCAGCCUCCCACCC hit 29 : 3418 3518 (fwd) 57.42 bits :<<<<-<<.-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->> 1 ggcuuGGa.Cccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGC 58 GG:::G:+ +:+:: :::+ GC: AC:CG: AACC:GGUCAGGUCCGGAAGGAAGCAGC 3418 GGGAGGUUgGUGGUgGACGAGCC--ACUCGCCAACCGGGUCAGGUCCGGAAGGAAGCAGC 3475 >>--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 59 cgUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 C:U A:CG:+ + :GC G:::C::+:UG +:+:::CC CC 3476 CCU-AACGAGCCACGGCACGGGUCAUCGUGCcAGCCUCCCACCC 3518 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #24680,sp|AE009969.1|AE009969 Streptococcus pyogenes strain MGAS8232, section 17 of 173 of the complete genome. ----isReversed: 0 ----hitSequence: UAAUAAUAGGCGGAGCAACACUUGUGCGUGAAGUGGGUCAGGGGAGGAAUCCAGCAGCCCUAAGCGAUUUUCGGGUGUGUGCUCUUUUUUUGUUGACUUUAC hit 30 : 3440 3541 (fwd) 61.25 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 + U: :A+ :: GCAAC:C+: +:CGUGAA :GGUCAGG: :GGAA: :AGCAGCC 3440 UAAUAAUAGGCGGaGCAACACUU-GUGCGUGAAGUGGGUCAGGGGAGGAAUCCAGCAGCC 3498 >--->>>>--.-->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguu.uuucgcgUGuGcCgcgguguuCugggccgacC 101 :UAAGCG:UU U :+G:GUGUGC :: U+UU:U:G + C 3499 CUAAGCGAUUuUCGGGUGUGUGCUCUUUUUUUGUUGACUUUAC 3541 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #25238,sp|AE010530.1|AE010530 Fusobacterium nucleatum subsp. nucleatum ATCC 25586, section 72 of 197 of the complete genome. ----isReversed: 0 ----hitSequence: GGGGAUAUGAUAUAUUAUUGUCGAACCGUGUCAGAUCUGGAAGGAAGCAGCACUAAGAUUUAUAGUAUAUGCAUGUCUUCCU hit 31 : 10609 10690 (fwd) 49.15 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G: :G: :::A:::::+A+: ::GAACC::GUCAG UC:GGAA:GAAGCAGC: 10609 ------GG--GGAuAUGAUAUAUUAUUGUCGAACCGUGUCAGAUCUGGAAGGAAGCAGCA 10660 >--->>>>---->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 :UAA:: :U+U :::::UG::: :C:+ :CU 10661 CUAAGAUUUAUAGUAUAUGCAUGUCUU---CCU--------- 10690 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #26447,sp|AE011739.1|AE011739 Xanthomonas axonopodis pv. citri str. 306, section 117 of 469 of the complete genome. ----isReversed: 1 ----hitSequence: CCGUCGGUCCCUCGCGACGCUAGAUCGAAAAUCCCGCCAGGGCCGGAAGGCAGCAACGGUAUCGAUUGAUGCGGGCGCCGAGGUCAACCGGCGGGGAC hit 32 : 1899 1802 (rev) 78.20 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 +::U:GG+CCC:CGC:ACGC+: :CG: AA CC:G :AGG:CCGGAAGG:AGCA:C:G 9408 CCGUCGGUCCCUCGCGACGCUA-GAUCGAAAAUCCCGCCAGGGCCGGAAGGCAGCAACGG 9466 --->>>>---->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 U A:CG:UU :+GCG G:GCCG:GGU ++C+:G:: G+ C 9467 U-AUCGAUU-GAUGCGGGCGCCGAGGUCAACCGGCGGGGAC 9505 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #26904,sp|AE012197.1|AE012197 Xanthomonas campestris pv. campestris str. ATCC 33913, section 105 of 460 of the complete genome. ----isReversed: 0 ----hitSequence: CCGUCGGUCCCUCGCGACGCUAGAUCGAAAAUCCCGCCAGGGCCGGAAGGCAGCAACGGUAUCGAUUGAUGCGGGCGCCGAGGUCAACCGGCGGGGAC hit 33 : 305 402 (fwd) 78.20 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 +::U:GG+CCC:CGC:ACGC+: :CG: AA CC:G :AGG:CCGGAAGG:AGCA:C:G 305 CCGUCGGUCCCUCGCGACGCUA-GAUCGAAAAUCCCGCCAGGGCCGGAAGGCAGCAACGG 363 --->>>>---->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 U A:CG:UU :+GCG G:GCCG:GGU ++C+:G:: G+ C 364 U-AUCGAUU-GAUGCGGGCGCCGAGGUCAACCGGCGGGGAC 402 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #27261,sp|AE012554.1|AE012554 Xylella fastidiosa Temecula1, section 2 of 9 of the complete genome. ----isReversed: 0 ----hitSequence: CUGCCGGUCCCUCGCAACGCUAGAUCGAAAACCCCGCCAGGGCCGGAAGGCAGCAACGGUAUUGAUUGAUGCGGGUGCCGAGAUCAACCGGUGGGGCC hit 34 : 97705 97802 (fwd) 75.06 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 +: ::GG+C:C:CGCAACGC+: :C+: AACCC:G :AGG:CCGGAAGG:AGCA:C:G 97705 CUGCCGGUCCCUCGCAACGCUA-GAUCGAAAACCCCGCCAGGGCCGGAAGGCAGCAACGG 97763 --->>>>---->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 U A:+G:UU :+GCG GUGCCG:G:U ++C+:: : G+CC 97764 U-AUUGAUU-GAUGCGGGUGCCGAGAUCAACCGGUGGGGCC 97802 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #27270,sp|AE012781.1|AE012781 Chlorobium tepidum TLS section 2 of 194 of the complete genome. ----isReversed: 1 ----hitSequence: GAGUAAGUCCUAUACAGCAUUCUCUUGCCCAACCAUGUCAGGUCCGGAAGGAAGCAGCAUCCGGUAAUGUGAGUGCGUGAUAUAGUCAGCUUGCUCUCCU hit 35 : 271 172 (rev) 63.26 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 G::U: G:CC::: CA+C::+:+ +: :: AACC::GUCAGGUCCGGAAGGAAGCAGC:: 10211 GAGUAAGUCCUAUACAGCAUUCUCUUGCCCAACCAUGUCAGGUCCGGAAGGAAGCAGCAU 10270 --->>>>---->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 :: :+U U:+::G GUG :::GU +:CU:G::C+ C 10271 C-CGGUAAUGUGAGUGCGUGAUAUAGUCAGCUUGCUCUCCU 10310 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #27467,sp|AE012978.1|AE012978 Thermoanaerobacter tengcongensis strain MB4T, section 5 of 244 of the complete genome. ----isReversed: 0 ----hitSequence: UACUUGAGUCCUGCGCAACGGAGAUUUGCGAACCCCGUCAGGUCCGGAAGGAAGCAGCGGUAAGCAAACACCUCCGUGUGCCGCAGGGGUGCUUGAGUGGAGC hit 36 : 9827 9929 (fwd) 87.77 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +:C:UG:: CC:GCGCAACG::: A+::G:GAACCC:GUCAGGUCCGGAAGGAAGCAGC: 9827 UACUUGAGuCCUGCGCAACGGAG-AUUUGCGAACCCCGUCAGGUCCGGAAGGAAGCAGCG 9885 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 GUAA:C::+ :::CGUGUGCCGC:G+G ::UG:G: GA+C 9886 GUAAGCAAACACCUCCGUGUGCCGCAGGGGugCUUGAGUGGAGC 9929 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #28193,sp|AE013708.1|AE013708 Yersinia pestis KIM section 108 of 415 of the complete genome. ----isReversed: 0 ----hitSequence: CUGUUGGUUCUCCCGCAACACUAACUUGUGAACUCGGUCAGGUCCGGAAGGAAGCAGCCGCAGCAGGCGAGGUGUGUGCCGGGAUGUAGCUGGCAGGGCC hit 37 : 4576 4675 (fwd) 93.18 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +::UUGG: C:C:CGCAAC:C+: AC::GUGAAC CGGUCAGGUCCGGAAGGAAGCAGCC 4576 CUGUUGGUuCUCCCGCAACACUA-ACUUGUGAACUCGGUCAGGUCCGGAAGGAAGCAGCC 4634 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 G AGC::+ :+G:GUGUGCCG:G:UGU :CUGG:: G+CC 4635 GC-AGCAGGC-GAGGUGUGUGCCGGGAUGUaGCUGGCAGGGCC 4675 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #28502,sp|AE014017.1|AE014017 Buchnera aphidicola str. Bp (Baizongia pistaciae), section 2 of 2 of the complete genome. ----isReversed: 1 ----hitSequence: UGUUAGUACUCUAUAAUACUGUAAUUCUUAAGAAUUUGGUCAGGAUUGGAAAAUAGCAGCCAUAUUAAGACAGUACAGGUAUUACGAAUAUUACUAACAGAGA hit 38 : 189606 189504 (rev) 49.03 bits :<<<<-<<.-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->> 1 ggcuuGGa.Cccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGC 58 +G:::G:A :: : ::A :G:: ++C::::GAA :GGUCAGG:::GGAA:::AGCAGC 116432 UGUUAGUAcUCUAUaAUACUGUAAUUCUUAAGAAUUUGGUCAGGAUUGGAAAAUAGCAGC 116491 >>--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 59 cgUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 C:U A::::+++ ::C: GU:: : :: ++ U:+:::C+GA+ 116492 CAU-AUUAAGACAGUACAGGUAUUACGAAUAuUACUAACAGAGA 116534 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #28549,sp|AE014122.1|AE014122 Buchnera aphidicola str. Sg (Schizaphis graminum) section 47 of 57 of the complete genome. ----isReversed: 1 ----hitSequence: CUGUUAGUCCUAAACACUGUUAAAUUGAAUAAUUGGUCAGAUCUGGAAAGAAGCAGCCAAAUCAAUCGAUACAGGUGUUUUGAUAUAGCUAACAGAAUC hit 39 : 13297 13199 (rev) 51.15 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 +::: G:C:::::CA :G:+: A ::G: A :GGUCAG UC:GGAA:GAAGCAGCC: 73 CUGUUAGUCCUAAACACUGUUA-AAUUGAAUAAUUGGUCAGAUCUGGAAAGAAGCAGCCA 131 --->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 A:C::U :+:C: GUG: ::::U U :CU ::: A C 132 A-AUCAAUC-GAUACAGGUGUUUUGAUAUaGCUAACAGAAUC 171 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #28563,sp|AE014139.1|AE014139 Streptococcus pyogenes MGAS315, section 4 of 37 of the complete genome. ----isReversed: 0 ----hitSequence: UAAUAAUAGGCGGAGCAACACUUGUGCGUGAAGUGGGUCAGGGGAGGAAUCCAGCAGCCCUAAGCGAUUUUCGGGUGUGUGCUCUUUUUUUUGUUGACUUUAC hit 40 : 28322 28424 (fwd) 59.87 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 + U: :A+ :: GCAAC:C+: +:CGUGAA :GGUCAGG: :GGAA: :AGCAGCC 28322 UAAUAAUAGGCGGaGCAACACUU-GUGCGUGAAGUGGGUCAGGGGAGGAAUCCAGCAGCC 28380 >--->>>>--.-->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguu.uuucgcgUGuGcCgcggugu.uCugggccgacC 101 :UAAGCG:UU U :+G:GUGUGC :: U+U U:U:G + C 28381 CUAAGCGAUUuUCGGGUGUGUGCUCUUUUUUuUGUUGACUUUAC 28424 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #28615,sp|AE014209.1|AE014209 Streptococcus agalactiae 2603V/R section 19 of 100 of the complete genome. ----isReversed: 0 ----hitSequence: UGGAGCAACAUUUACUCGUGAAGUGGGUCAGGGGAGGAAUCCAGCAGCCCUAAGCGAUGCUAAAUGUGUGCUCUUUUU hit 41 : 18006 18083 (fwd) 54.59 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 :: GCAAC::+ AC:CGUGAA :GGUCAGG: :GGAA: :AGCAGCC: 18006 ---------UGGAGCAACAUUU-ACUCGUGAAGUGGGUCAGGGGAGGAAUCCAGCAGCCC 18055 --->>>>---->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 UAAGCG:U +U +::GUGUGC :: U+ 18056 UAAGCGAUGCUAAAUGUGUGCUCUUUUU------------- 18083 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #28700,sp|AE014318.1|AE014318 Brucella suis 1330 chromosome I section 4 of 190 of the complete genome. ----isReversed: 1 ----hitSequence: GGGAGGUUGGUGGUGGACGAGCCACUCGCCAACCGGGUCAGGUCCGGAAGGAAGCAGCCCUAACGAGCCACGGCACGGGUCAUCGUGCCAGCCUCCCACCC hit 42 : 5996 5896 (rev) 57.42 bits :<<<<-<<.-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->> 1 ggcuuGGa.Cccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGC 58 GG:::G:+ +:+:: :::+ GC: AC:CG: AACC:GGUCAGGUCCGGAAGGAAGCAGC 5629 GGGAGGUUgGUGGUgGACGAGCC--ACUCGCCAACCGGGUCAGGUCCGGAAGGAAGCAGC 5686 >>--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 59 cgUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 C:U A:CG:+ + :GC G:::C::+:UG +:+:::CC CC 5687 CCU-AACGAGCCACGGCACGGGUCAUCGUGCcAGCCUCCCACCC 5729 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #29223,sp|AE014879.1|AE014879 Streptococcus mutans UA159 section 27 of 185 of the complete genome. ----isReversed: 0 ----hitSequence: UAAUAGAUAUCGGAGCAACAGCUUUGCGUGAAGCGGGUCAGGGGAGGAAUCCAGCAGCCCUAAGCGAUGUAAGCUGUGUGCUCUAUUUUUUGUGUAAUAGU hit 43 : 5292 5392 (fwd) 61.36 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 + :U:G: ::G:GCAAC::: ++:CGUGAA C:GGUCAGG: :GGAA: :AGCAGCC 5292 UAAUAGAUaUCGGAGCAACAGCU-UUGCGUGAAGCGGGUCAGGGGAGGAAUCCAGCAGCC 5350 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 :UAAGCG:U U :::GUGUGC :C::U+U : :G: ++A+ 5351 CUAAGCGAUGUAAGCUGUGUGC-UCUAUUUuUUGUGUAAUAGU 5392 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #29416,sp|AE015072.1|AE015072 Shigella flexneri 2a str. 301 section 35 of 412 of the complete genome. ----isReversed: 0 ----hitSequence: CUGUUGGUUCUCCCGCAAUGCUACUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCCAAGGCAGAUGACGCGUGUGCCGGGAUGUAGCUGGCAGGGCC hit 44 : 2645 2744 (fwd) 81.54 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +::UUGG: C:C:CGCAA:GC : +C:GU ACC GGUCAGGUCCGGAAGGAAGCAGCC 2645 CUGUUGGUuCUCCCGCAAUGCUA-CUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCC 2703 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 GC:G+U : GC:UGUGCCG:G:UGU :CUGG:: G+CC 2704 AA-GGCAGAU-GACGCGUGUGCCGGGAUGUaGCUGGCAGGGCC 2744 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #29967,sp|AE015625.1|AE015625 Shewanella oneidensis MR-1 section 174 of 457 of the complete genome. ----isReversed: 0 ----hitSequence: CCUAGGGUCCCCCCGCAAUGAUAACUUGUGAACUCGGCCAGGCCCGGAAGGGAGCAACCGCAGCAAGCGACUCGUGUGCCGGGGUGUCGGCUCUAGGGGAA hit 45 : 7728 7828 (fwd) 76.91 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +::::GG: CCC:CGCAA:G: : AC::GUGAAC CGG :AGG:CCGGAAGG:AGCA:CC 7728 CCUAGGGUcCCCCCGCAAUGAUA-ACUUGUGAACUCGGCCAGGCCCGGAAGGGAGCAACC 7786 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 G AGC::+ : :C:UGUGCCG:GGUGU :CU:::: G+ 7787 GC-AGCAAGC-GACUCGUGUGCCGGGGUGUcgGCUCUAGGGGAA 7828 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30273,sp|AE015936.1|AE015936 Clostridium tetani E88, section 1 of 10 of the complete genome. ----isReversed: 1 ----hitSequence: GAAUUGGGUCCCACGCAACGGAAACUCAUGAAACCCGUCAGGUCCGGAAGGAAGCAGCGGUAAGUGAUAAUUUUCGUGUGCCGUGGAUAAACCUGGUUUGAGU hit 46 : 24077 23975 (rev) 92.04 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G::UUGG: CCC:CGCAACG::A AC:C:UGAA CC:GUCAGGUCCGGAAGGAAGCAGC: 275953 GAAUUGGGuCCCACGCAACGGAA-ACUCAUGAAACCCGUCAGGUCCGGAAGGAAGCAGCG 276011 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 GUAAG:G:U+ UU::CGUGUGCCG:GG ++ :CUGG:: GA+ 276012 GUAAGUGAUAAUUUUCGUGUGCCGUGGAUAaaCCUGGUUUGAGU 276055 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30290,sp|AE016751.1|AE016751 Staphylococcus epidermidis ATCC 12228, section 8 of 9 of the complete genome. ----isReversed: 1 ----hitSequence: GAUUUCGGUCCUAUGCAAUAUGAACCCAUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCCUCAUAUGUGCCGUAGGGUAGCCGAGAUUUAGC hit 47 : 278474 278372 (rev) 78.49 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G::U G: CC:::GCAA:::GA ACCC:UGAACC::GUCAGGUCC GA GGAAGCAGC: 21802 GAUUUCGGuCCUAUGCAAUAUGA-ACCCAUGAACCAUGUCAGGUCCUGACGGAAGCAGCA 21860 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:GG+U+ UC:::UGUGCC:::G+GU :C G:: +A+C 21861 UUAAGUGGAUCCUCAUAUGUGCCGUAGGGUagCCGAGAUUUAGC 21904 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30293,sp|AE016756.1|AE016756 Escherichia coli CFT073 section 2 of 18 of the complete genome. ----isReversed: 0 ----hitSequence: CUGUUGGUUCUCCCGCAACGCUACUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCCAAGGCAGAUGACGCGUGUGCCGGGAUGUAGCUGGCAGGGCC hit 48 : 250756 250855 (fwd) 83.14 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +::UUGG: C:C:CGCAACGC : +C:GU ACC GGUCAGGUCCGGAAGGAAGCAGCC 250756 CUGUUGGUuCUCCCGCAACGCUA-CUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCC 250814 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 GC:G+U : GCGUGUGCCG:G:UGU :CUGG:: G+CC 250815 AA-GGCAGAU-GACGCGUGUGCCGGGAUGUaGCUGGCAGGGCC 250855 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30326,sp|AE016790.1|AE016790 Pseudomonas putida KT2440 section 17 of 21 of the complete genome. ----isReversed: 1 ----hitSequence: CCAUCGGUCCCCCCGCAUUGAUUACCCGUUAACCUGGUCAGGCCCGGAAGGGAGCAGCCAUAGCGGGAACAUCGAGUGCCGGGGUGUGGCUGGUGGGGCC hit 49 : 27184 27085 (rev) 88.03 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +::U:GG: CCC:CGCA :G:+ ACCCGU AACC:GGUCAGG:CCGGAAGG:AGCAGCC 273059 CCAUCGGUcCCCCCGCAUUGAUU-ACCCGUUAACCUGGUCAGGCCCGGAAGGGAGCAGCC 273117 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 :U AGCGG++ +:C: GUGCCG:GGUGU :CU:G:: G+CC 273118 AU-AGCGGGA-ACAUCGAGUGCCGGGGUGUgGCUGGUGGGGCC 273158 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30341,sp|AE016807.1|AE016807 Vibrio vulnificus CMCP6 chromosome I section 11 of 11 of the complete sequence. ----isReversed: 1 ----hitSequence: CUCUGGUCCUCUCGCAACAAUAGUUCGUGAACUCGGUCAGGUCCGGAAGGAAGCAGCCGCAGCGAAUGACUUGUGUGCCGGGAUGUGGCUGGGGUCCC hit 50 : 204906 204809 (rev) 84.42 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 +:CU+G::C:C CGCAAC:: : +:CGUGAAC CGGUCAGGUCCGGAAGGAAGCAGCCG 62033 CUCUGGUCCUCUCGCAACAAUA-GUUCGUGAACUCGGUCAGGUCCGGAAGGAAGCAGCCG 62091 --->>>>---->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 AGCG:+U : ::GUGUGCCG G:UGU::++GG: + CC 62092 C-AGCGAAU-GACUUGUGUGCCGGGAUGUGGCUGGGGUCCC 62130 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30360,sp|AE016842.1|AE016842 Salmonella enterica subsp. enterica serovar Typhi Ty2, section 9 of 16 of the complete genome. ----isReversed: 1 ----hitSequence: CUGUUGGUUCUCCCGCAACGCUACUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCCAAGGCAGAUGACGCGUGUGCCGGGAUGUAGCUGGCAGGGCC hit 51 : 59881 59782 (rev) 83.14 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +::UUGG: C:C:CGCAACGC : +C:GU ACC GGUCAGGUCCGGAAGGAAGCAGCC 240149 CUGUUGGUuCUCCCGCAACGCUA-CUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCC 240207 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 GC:G+U : GCGUGUGCCG:G:UGU :CUGG:: G+CC 240208 AA-GGCAGAU-GACGCGUGUGCCGGGAUGUaGCUGGCAGGGCC 240248 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30370,sp|AE016852.1|AE016852 Tropheryma whipplei str. Twist, section 3 of 3 of the complete genome. ----isReversed: 1 ----hitSequence: UAGUUUGCCUCCGCGCGGCGUUACCCGGGUGAACUCCCCCAGGUUAGGAAUAAAGCAAGGGUAGCUCGGCUCUGGCGGGUGUGCGGGGGUCUUGCGGGCUCCGUU hit 52 : 219821 219717 (rev) 49.01 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +::UU G:C:C:: :C:+CG:+A C GUGAAC C:+ :AGGU::GGAA::AAGCA:+: 104407 UAGUUUGCCUCCGcGCGGCGUUACCCGGGUGAACUCCCCCAGGUUAGGAAUAAAGCAAGG 104466 >--->>>>--.-->>>>>-->>>->>>>---...>>->>>>::::: 60 gUAAgcgguu.uuucgcgUGuGcCgcggugu...uCugggccgacC 101 GU AGC + U U+:CG G:G: ::G:+GU :C GG::C + 104467 GU-AGCUCGGcUCUGGCGGGUGUGCGGGGGUcuuGCGGGCUCCGUU 104511 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30386,sp|AE016869.1|AE016869 Pseudomonas syringae pv. tomato str. DC3000 section 14 of 21 of the complete genome. ----isReversed: 1 ----hitSequence: CCAUCGGUCCCCCCGCAACGAUUACCCGUGAACCUGGUCAGAUCCGGAAGGAAGCAGCCACAGCGGGAACAUUGUGUGCCGGGGUGUGGCUGGUGGGGGC hit 53 : 50218 50119 (rev) 91.71 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +::U:GG: CCC:CGCAAC::+ ACCCGUGAACC:GGUCAG UCCGGAAGGAAGCAGCC 260750 CCAUCGGUcCCCCCGCAACGAUU-ACCCGUGAACCUGGUCAGAUCCGGAAGGAAGCAGCC 260808 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 : AGCGG++ +::GUGUGCCG:GGUGU :CU:G:: G++C 260809 AC-AGCGGGA-ACAUUGUGUGCCGGGGUGUgGCUGGUGGGGGC 260849 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30422,sp|AE016953.1|AE016953 Enterococcus faecalis V583, section 7 of 11 of the complete genome. ----isReversed: 1 ----hitSequence: UUGCCGAAAGGCUAGGACAAUGGCGGGCUAGUGAAUUGUGUCAGAUCCGGAAGGAAGCAGCACUAAGCAAGUGCCGCCAUGUGUCUGAUUGAAUAAGGAACGUAU hit 54 : 287032 286928 (rev) 48.19 bits :<<<<-<<.-<<<<..<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->-> 1 ggcuuGGa.Cccgc..gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAG 57 +: ::G:A + : :CAA:G::: C: GUGAA ::GUCAG UCCGGAAGGAAGCAG 15210 UUGCCGAAaGGCUAggACAAUGGCGGGCUAGUGAAUUGUGUCAGAUCCGGAAGGAAGCAG 15269 >>>--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 58 CcgUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 C::UAAGC :+U :::C:UGUG:C: UG+ U: :: :CG 15270 CACUAAGCAAGUGCCGCCAUGUGUCUGAUUGAaUAAGGAACGUAU 15314 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30429,sp|AE016962.1|AE016962 Coxiella burnetii strain RSA 493, section 3 of 7 of the complete genome. ----isReversed: 1 ----hitSequence: GCAGGGGUCCCCUCGCGACGAAUUGCCGUGAACCCCGCCAGGCCCGGAAGGGAGCAACGGUAGCGGUGGAUUUGGGUGCCGAGGUGCGGCUUUUGUGGCU hit 55 : 1746 1647 (rev) 75.22 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G:: +GG: CCC:CGC:AC::: + CCGUGAACCC:G :AGG:CCGGAAGG:AGCA:C: 298720 GCAGGGGUcCCCUCGCGACGAAU-UGCCGUGAACCCCGCCAGGCCCGGAAGGGAGCAACG 298778 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 GU AGCGGU :::G G:GCCG:GGUG :CU+ :: G+C 298779 GU-AGCGGUG-GAUUUGGGUGCCGAGGUGCgGCUUUUGUGGCU 298819 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30435,sp|AE016968.1|AE016968 Mycoplasma gallisepticum strain R section 2 of 4 of the complete genome. ----isReversed: 0 ----hitSequence: UAGCCAUUACAACAAUUAACACGAACCAUGUCAGGUCAGAAAUGAAGCAGCAUUAAGUAUCUUAAUUGUGUGUAAUGGCUUUUU hit 56 : 153147 153230 (fwd) 51.54 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 A+CC:: :CAAC::+ AAC ::GAACC::GUCAGGUC:G AA:GAAGCAGC: 153147 ------UAGCCAUuACAACAAUUAAC--ACGAACCAUGUCAGGUCAGAAAUGAAGCAGCA 153198 >--->>>>---->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 :UAA:: +U UU +::GUGUG: ::GG +UU U 153199 UUAAGU-AUCUUAAUUGUGUGUAAUGGCUUUUU--------- 153230 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30439,sp|AE016979.1|AE016979 Shigella flexneri 2a str. 2457T section 2 of 16 of the complete genome. ----isReversed: 0 ----hitSequence: CUGUUGGUUCUCCCGCAAUGCUACUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCCAAGGCAGAUGACGCGUGUGCCGGGAUGUAGCUGGCAGGGCC hit 57 : 122818 122917 (fwd) 81.54 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +::UUGG: C:C:CGCAA:GC : +C:GU ACC GGUCAGGUCCGGAAGGAAGCAGCC 122818 CUGUUGGUuCUCCCGCAAUGCUA-CUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCC 122876 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 GC:G+U : GC:UGUGCCG:G:UGU :CUGG:: G+CC 122877 AA-GGCAGAU-GACGCGUGUGCCGGGAUGUaGCUGGCAGGGCC 122917 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30455,sp|AE016995.1|AE016995 Chlamydophila caviae GPIC section 2 of 4 of the complete genome. ----isReversed: 0 ----hitSequence: GUUGGGGACCUUUUAAGAGAAGAGACCUACGAAUCGGGUCAGGACUGGAAGGUAGCAGCCCUAAGAAGUGUUUUCUUUUGCUAGAAGUGUUCUCCAACUUAC hit 58 : 141474 141575 (fwd) 68.28 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G::::GGACC::: +::A ::GA ACC: :GAA C:GGUCAGG:C:GGAA:G:AGCAGCC 141474 GUUGGGGACCUUUuAAGAGAAGAGACCUACGAAUCGGGUCAGGACUGGAAGGUAGCAGCC 141533 >--->>>>--.-->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguu.uuucgcgUGuGcCgcgguguuCugggccgacC 101 :UAA: :GU UUUC:: UG:: :::GUGUUCU::::C+ C 141534 CUAAGAAGUGuUUUCUUUUGCU-AGAAGUGUUCUCCAACUUAC 141575 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30458,sp|AE016998.1|AE016998 Bacillus cereus ATCC 14579 section 1 of 18 of the complete genome. ----isReversed: 0 ----hitSequence: CGUUUGGGUCCUGCGCAACGGGACCCCGUGAACCUUGUCAGGUCCGGAAGGAAGCAGCAAUAAGCGGGUCUUCUCGUGUGCCGCAGGAGUGCCUGAACCGAGC hit 59 : 25108 25210 (fwd) 97.57 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G::UGG: CC:GCGCAACG:GA CCCGUGAACC::GUCAGGUCCGGAAGGAAGCAGC: 25108 CGUUUGGGuCCUGCGCAACGGGA-CCCCGUGAACCUUGUCAGGUCCGGAAGGAAGCAGCA 25166 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAGCGG+U+UUC:CGUGUGCCGC:G+ :CUG::CCGA+C 25167 AUAAGCGGGUCUUCUCGUGUGCCGCAGGAGugCCUGAACCGAGC 25210 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30476,sp|AE017024.1|AE017024 Bacillus anthracis str. Ames section 1 of 18 of the complete genome. ----isReversed: 0 ----hitSequence: CGUUUGGGUCCUGCGCAACGGGACCCCGUGAACCUUGUCAGGUCCGGAAGGAAGCAGCAAUAAGCGGGUCUUCUCGUGUGCCGCAGGAGUGCCUGAACCGAGC hit 60 : 25228 25330 (fwd) 97.57 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G::UGG: CC:GCGCAACG:GA CCCGUGAACC::GUCAGGUCCGGAAGGAAGCAGC: 25228 CGUUUGGGuCCUGCGCAACGGGA-CCCCGUGAACCUUGUCAGGUCCGGAAGGAAGCAGCA 25286 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAGCGG+U+UUC:CGUGUGCCGC:G+ :CUG::CCGA+C 25287 AUAAGCGGGUCUUCUCGUGUGCCGCAGGAGugCCUGAACCGAGC 25330 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30503,sp|AE017154.1|AE017154 Haemophilus ducreyi strain 35000HP section 4 of 6 of the complete genome. ----isReversed: 1 ----hitSequence: UUAUUGGUUUCUCGCAGCAGAAUUCAGCUUACUUAGUCAGGGCCGGAAGGAAGCAGCUUGGGUUGAAUUUCUGGGUGCCGGGAGUCGCUGGUAAUACC hit 61 : 180281 180184 (rev) 68.26 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 +::UUGG: :C CGCA+C:::A ++C:+: AC :GUCAGG CCGGAAGG AGCAGC: 120260 UUAUUGGUUUCUCGCAGCAGAA-UUCAGCUUACUUAGUCAGGGCCGGAAGGAAGCAGCUU 120318 --->>>>---->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 :+:G++ UU:::G GUGCCG G:++ :CUGG::++ACC 120319 G-GGUUGAA-UUUCUGGGUGCCGGGAGUCGCUGGUAAUACC 120357 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30507,sp|AE017158.1|AE017158 Chlamydophila pneumoniae TW-183, section 2 of 4 of the complete genome. ----isReversed: 1 ----hitSequence: GUUGGGGGCCUUUUAAGAGAAGGAACCUGCGAAUCGGGUCAGGACUGGAAGGUAGCAGCCCUAAGGAGAGUUUUCUUUUGCUAAAAGAAUGUUCUCCAACUUAC hit 62 : 144055 143952 (rev) 63.46 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G::::GG:CC::: +::A ::G:AACC: :GAA C:GGUCAGG:C:GGAA:G:AGCAGCC 156326 GUUGGGGGCCUUUuAAGAGAAGGAACCUGCGAAUCGGGUCAGGACUGGAAGGUAGCAGCC 156385 >--->>>>--.-->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguu.uuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAA: :G+ UU:C:: UG:: :::G U :CU::::C+ C 156386 CUAAGGAGAGuUUUCUUUUGCU-AAAAGAAUguUCUCCAACUUAC 156429 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30514,sp|AE017165.1|AE017165 Prochlorococcus marinus subsp. marinus str. CCMP1375 section 5 of 6 of the complete genome. ----isReversed: 1 ----hitSequence: GACUCGGGCCCAUGCGGCUUCGACGCCUAAAUCUGGUCAGGACCGGAAGGUAGCAGCCACAAGGGAUGCUUGAAUCUGGCGUGGAUUCCGGGUCACCU hit 63 : 76327 76230 (rev) 60.88 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G:CU:GG: :C :+:+: :+: AC:C:U AA C:GGUCAGG:CCGGAAGG:AGCAGCC 223817 GACUCGGG--CCCaUGCGGCUUCGACGCCUAAAUCUGGUCAGGACCGGAAGGUAGCAGCC 223874 >--->>>>--.-->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguu.uuucgcgUGuGcCgcgguguuCugggccgacC 101 : AAG:G:U UU:+: :UG:+: G: + :C+:GG:C C 223875 ACAAGGGAUGcUUGAAUCUGGCGUGGAU---UCCGGGUCACCU 223914 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #44185,sp|AF132127.1|AF132127 Streptococcus mutans sorbitol phosphoenolpyruvate:sugar phosphotransferase operon, complete sequence and unknown gene. ----isReversed: 0 ----hitSequence: UAAUAGAUAUCGGAGCAACAGCUUUGCGUGAAGCGGGUCAGGGGAGGAAUCCAGCAGCCCUAAGCGAUGUAAGCUGUGUGCUCUAUUUUUUGUGUAAUAGU hit 64 : 652 752 (fwd) 61.36 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 + :U:G: ::G:GCAAC::: ++:CGUGAA C:GGUCAGG: :GGAA: :AGCAGCC 652 UAAUAGAUaUCGGAGCAACAGCU-UUGCGUGAAGCGGGUCAGGGGAGGAAUCCAGCAGCC 710 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 :UAAGCG:U U :::GUGUGC :C::U+U : :G: ++A+ 711 CUAAGCGAUGUAAGCUGUGUGC-UCUAUUUuUUGUGUAAUAGU 752 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz ----sequence: #1572,sp|AF203881.1|AF203881 Zymomonas mobilis strain ZM4 clone 43F4, complete sequence. ----isReversed: 1 ----hitSequence: GUGGAAGUCGGGCGGACGGUGCUGUCGCCAACCCGGUCAGGUCCGGAAGGAAGCAGCCGUAACGAAUUUUUAUCGGGUCGUUCCGGCUUCCAUCGUC hit 65 : 14961 14865 (rev) 59.81 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 G:::: G: C+G +:ACG:+: + :CG: AACCCGGUCAGGUCCGGAAGGAAGCAGCCG 5605 GUGGAAGU-CGGGCGGACGGUGCUGUCGCCAACCCGGUCAGGUCCGGAAGGAAGCAGCCG 5663 --->>>>--.-->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguu.uuucgcgUGuGcCgcgguguuCugggccgacC 101 U A:CG:+U UU:+:CG G:+ C+G :CU:::: + C 5664 U-AACGAAUuUUUAUCGGGUCGUUCCG---GCUUCCAUCGUC 5701 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz ----sequence: #10103,sp|AF269814.1|AF269814 Staphylococcus epidermidis strain SR1 clone step.1023h12 genomic sequence. ----isReversed: 0 ----hitSequence: GAUUUCGGUCCUAUGCAAUAUGAACCCAUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCCUCAUAUGUGCCGUAGGGUAGCCGAGAUUUAGC hit 66 : 2628 2730 (fwd) 78.49 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G::U G: CC:::GCAA:::GA ACCC:UGAACC::GUCAGGUCC GA GGAAGCAGC: 2628 GAUUUCGGuCCUAUGCAAUAUGA-ACCCAUGAACCAUGUCAGGUCCUGACGGAAGCAGCA 2686 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:GG+U+ UC:::UGUGCC:::G+GU :C G:: +A+C 2687 UUAAGUGGAUCCUCAUAUGUGCCGUAGGGUagCCGAGAUUUAGC 2730 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz ----sequence: #10120,sp|AF269831.1|AF269831 Staphylococcus epidermidis strain SR1 clone step.1025d12 genomic sequence. ----isReversed: 0 ----hitSequence: GAUUUCGGUCCUAUGCAAUAUGAACCCAUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCCUCAUAUGUGCCGUAGGGUAGCCGAGAUUUAGC hit 67 : 1332 1434 (fwd) 78.49 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G::U G: CC:::GCAA:::GA ACCC:UGAACC::GUCAGGUCC GA GGAAGCAGC: 1332 GAUUUCGGuCCUAUGCAAUAUGA-ACCCAUGAACCAUGUCAGGUCCUGACGGAAGCAGCA 1390 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:GG+U+ UC:::UGUGCC:::G+GU :C G:: +A+C 1391 UUAAGUGGAUCCUCAUAUGUGCCGUAGGGUagCCGAGAUUUAGC 1434 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz ----sequence: #23744,sp|AF368293.1|AF368293 Staphylococcus aureus small cytoplasmic RNA gene, complete sequence. ----isReversed: 0 ----hitSequence: GAUUUCGGUCCUAUGCAAUAUGAACCCAUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCAUCAUAUGUGCCGUAGGGUAGCCGAGAUUUAGC hit 68 : 122 224 (fwd) 77.96 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G::U G: CC:::GCAA:::GA ACCC:UGAACC::GUCAGGUCC GA GGAAGCAGC: 122 GAUUUCGGuCCUAUGCAAUAUGA-ACCCAUGAACCAUGUCAGGUCCUGACGGAAGCAGCA 180 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:GG+U+ UC:::UGUGCC:::G+GU :C G:: +A+C 181 UUAAGUGGAUCAUCAUAUGUGCCGUAGGGUagCCGAGAUUUAGC 224 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz ----sequence: #40191,sp|AF482014.1|AF482014 Neisseria gonorrhoeae SRP 4.5S RNA (ffs) gene, complete sequence. ----isReversed: 0 ----hitSequence: UGCGGGUCUCCCCGCAUGGCAAAUCGGAACACCGGGUCAGGGGCGGAAGCCAGCAGCCCACUCCGAUGCGCCAGUGCCGGGGGUUUGGUCCGCCGCCC hit 69 : 11 108 (fwd) 64.28 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 +GC::G:: CC:CGCA :GC A+C:G: ACC:GGUCAGG: CGGAAG :AGCAGCC: 11 UGCGGGUCUCCCCGCAUGGCAA-AUCGGAACACCGGGUCAGGGGCGGAAGCCAGCAGCCC 69 --->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 :C:G+U GC: GUGCCG:GG++U ::U::GCCG CC 70 A-CUCCGAU--GCGCCAGUGCCGGGGGUUuGGUCCGCCGCCC 108 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #343,sp|AJ414155.1|AJ414155 Yersinia pestis strain CO92 complete genome; segment 15/20 ----isReversed: 1 ----hitSequence: CUGUUGGUUCUCCCGCAACACUAACUUGUGAACUCGGUCAGGUCCGGAAGGAAGCAGCCGCAGCAGGCGAGGUGUGUGCCGGGAUGUAGCUGGCAGGGCC hit 70 : 123559 123460 (rev) 93.18 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +::UUGG: C:C:CGCAAC:C+: AC::GUGAAC CGGUCAGGUCCGGAAGGAAGCAGCC 81492 CUGUUGGUuCUCCCGCAACACUA-ACUUGUGAACUCGGUCAGGUCCGGAAGGAAGCAGCC 81550 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 G AGC::+ :+G:GUGUGCCG:G:UGU :CUGG:: G+CC 81551 GC-AGCAGGC-GAGGUGUGUGCCGGGAUGUaGCUGGCAGGGCC 81591 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #418,sp|AL591984.1|AL591984 Listeria monocytogenes strain EGD, complete genome, segment 12/12 ----isReversed: 1 ----hitSequence: AGGUUGGGUCUUGCGCAAUGGGAACCUGUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGCAGUGCUUCUCAUGUGCCGCGAGGUCGCCUGGCCCGAGC hit 71 : 65413 65311 (rev) 97.49 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G:UUGG: C::GCGCAA:G:GA ACC:GUGAACC::GUCAGGUCCGGAAGGAAGCAGC: 160116 AGGUUGGGuCUUGCGCAAUGGGA-ACCUGUGAACCAUGUCAGGUCCGGAAGGAAGCAGCA 160174 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAGC:GU +UUC:C:UGUGCCGC::+GU :CUGG:CCGA+C 160175 UUAAGCAGUGCUUCUCAUGUGCCGCGAGGUcgCCUGGCCCGAGC 160218 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #429,sp|AL596173.1|AL596173 Listeria innocua Clip11262 complete genome, segment 11/12 ----isReversed: 1 ----hitSequence: AGGUUGGGUCUUGCGCAAUGGGAACCUGUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAUCAGUGCUUCUCAUGUGCCGCGAGGUUGCCUGGCCCGAGC hit 72 : 263872 263770 (rev) 93.09 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G:UUGG: C::GCGCAA:G:GA ACC:G GAACC::GUCAGGUCCGGAAGGAAGCAGC: 41179 AGGUUGGGuCUUGCGCAAUGGGA-ACCUGUGAACCAUGUCAGGUCCGGAAGGAAGCAGCA 41237 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAA C:GU +UUC:C:UGUGCCGC::+GU :CUGG:CCGA+C 41238 UUAAUCAGUGCUUCUCAUGUGCCGCGAGGUugCCUGGCCCGAGC 41281 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #432,sp|AL627266.1|AL627266 Salmonella enterica serovar Typhi (Salmonella typhi) strain CT18, complete chromosome; segment 2/20 ----isReversed: 0 ----hitSequence: CUGUUGGUUCUCCCGCAACGCUACUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCCAAGGCAGAUGACGCGUGUGCCGGGAUGUAGCUGGCAGGGCC hit 73 : 266291 266390 (fwd) 83.14 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +::UUGG: C:C:CGCAACGC : +C:GU ACC GGUCAGGUCCGGAAGGAAGCAGCC 266291 CUGUUGGUuCUCCCGCAACGCUA-CUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCC 266349 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 GC:G+U : GCGUGUGCCG:G:UGU :CUGG:: G+CC 266350 AA-GGCAGAU-GACGCGUGUGCCGGGAUGUaGCUGGCAGGGCC 266390 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #457,sp|AL646063.1|AL646063 Ralstonia solanacearum GMI1000 chromosome, complete sequence; segment 7/19 ----isReversed: 1 ----hitSequence: GGACGGGCCUCCUCGCAUGGUGGCGCGGUCAACCUGGUCAGGUCGGGAACGAAGCAGCCACAGCCGUUUUCCGCCAGUGCCGAGGGUCAGGCUCGUCCCCCU hit 74 : 55640 55539 (rev) 74.15 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 GG:::GG: CC:CGCA :G:G: C:GU AACC:GGUCAGGUC GGAA GAAGCAGCC 151411 GGACGGGCcUCCUCGCAUGGUGG-CGCGGUCAACCUGGUCAGGUCGGGAACGAAGCAGCC 151469 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 : AGC:GUUUU:C:C: GUGCCG:GG++ :CU:::CC C 151470 AC-AGCCGUUUUCCGCCAGUGCCGAGGGUCagGCUCGUCCCCCU 151512 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #482,sp|AL935253.1|AL935253 Lactobacillus plantarum strain WCFS1 complete genome; segment 2/11 ----isReversed: 0 ----hitSequence: CGCAAGGCCAAAAGGCAAGGGUGGAUUUACGAAUCGUGUCAGGUCCGGAAGGAAGCAGCACUAAGUUUGCUUCAUCUUGUGCCUUUUGUUUUUAUGAAAUGU hit 75 : 299503 299604 (fwd) 55.47 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 + C::G C:::: GCAA G:+: A+: ::GAA C::GUCAGGUCCGGAAGGAAGCAGC: 299503 CGCAAGGCCAAAAgGCAAGGGUGGAUUUACGAAUCGUGUCAGGUCCGGAAGGAAGCAGCA 299562 >--->>>>---->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 :UAA:: :+ UU:+:C UGUGCC::::++U U::G + + 299563 CUAAGUUUGCUUCAUCUUGUGCCUUUUGUUUUUAUGAAAUGU 299604 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #924,sp|AP001119.1|AP001119 Buchnera aphidicola str. APS (Acyrthosiphon pisum) genomic DNA, complete sequence, segment 2/2. ----isReversed: 1 ----hitSequence: CUGUUAGCUCCAAACACUGCAAUAUUGAAUAGUUGGUCAGAUUCGGAAGGAAGCAGCCAAAUCAAUUGAUACAGGUGUUCUGAUAAAGCUAACAGAAAC hit 76 : 183537 183439 (rev) 48.78 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 +::: G: :C: :CA :G :: + ::G: A :GGUCAG U:CGGAAG:AAGCAGCC: 109645 CUGUUAGCUCCAAACACUGCAA-UAUUGAAUAGUUGGUCAGAUUCGGAAGGAAGCAGCCA 109703 --->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 A:C::UU :: C: GUG: :G:U + :CU ::: A C 109704 A-AUCAAUU-GAUACAGGUGUUCUGAUAAaGCUAACAGAAAC 109743 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #926,sp|AP001507.1|AP001507 Bacillus halodurans genomic DNA, section 1/14. ----isReversed: 0 ----hitSequence: CGCUUGGGUUCUACGCAACGAAAACCCACGAACCCUGUCAGGUCCGGAAGGAAGCAGCAGUAAGUGGCCCCUUUCGUGUGCCGUAGAGUCGCCUGGGCCGAGC hit 77 : 46599 46701 (fwd) 94.24 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +GCUUGG: C::CGCAACG::A ACCC::GAACCC:GUCAGGUCCGGAAGGAAGCAGC: 46599 CGCUUGGGuUCUACGCAACGAAA-ACCCACGAACCCUGUCAGGUCCGGAAGGAAGCAGCA 46657 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 GUAA::GG + U::CGUGUGCCG::G GU :CUGGGCCGA+C 46658 GUAAGUGGCCCCUUUCGUGUGCCGUAGAGUcgCCUGGGCCGAGC 46701 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #943,sp|AP002546.2|AP002546 Chlamydophila pneumoniae J138 genomic DNA, complete sequence, section 2/4. ----isReversed: 1 ----hitSequence: GUUGGGGGCCUUUUAAGAGAAGGAACCUGCGAAUCGGGUCAGGACUGGAAGGUAGCAGCCCUAAGGAGAGUUUUCUUUUGCUAAAAGAAUGUUCUCCAACUUAC hit 78 : 147527 147424 (rev) 63.46 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G::::GG:CC::: +::A ::G:AACC: :GAA C:GGUCAGG:C:GGAA:G:AGCAGCC 153124 GUUGGGGGCCUUUuAAGAGAAGGAACCUGCGAAUCGGGUCAGGACUGGAAGGUAGCAGCC 153183 >--->>>>--.-->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguu.uuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAA: :G+ UU:C:: UG:: :::G U :CU::::C+ C 153184 CUAAGGAGAGuUUUCUUUUGCU-AAAAGAAUguUCUCCAACUUAC 153227 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #947,sp|AP002551.1|AP002551 Escherichia coli O157:H7 DNA, complete genome, section 2/20. ----isReversed: 0 ----hitSequence: CUGUUGGUUCUCCCGCAACGCUACUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCCAAGGCAGAUGACGCGUGUGCCGGGAUGUAGCUGGCAGGGCC hit 79 : 261040 261139 (fwd) 83.14 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +::UUGG: C:C:CGCAACGC : +C:GU ACC GGUCAGGUCCGGAAGGAAGCAGCC 261040 CUGUUGGUuCUCCCGCAACGCUA-CUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCC 261098 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 GC:G+U : GCGUGUGCCG:G:UGU :CUGG:: G+CC 261099 AA-GGCAGAU-GACGCGUGUGCCGGGAUGUaGCUGGCAGGGCC 261139 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #978,sp|AP003006.2|AP003006 Mesorhizobium loti DNA, complete genome, section 13/21. ----isReversed: 0 ----hitSequence: CGGGAGGUUGGUGGUGGACGAUCCACUCGCCAACCGGGUCAGGUCCGGAAGGAAGCAGCCCUAACGAGCCCGGAACGGGUCAUUGUUCCAGCCUCCCACCUC hit 80 : 282608 282709 (fwd) 56.62 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G:::GG: : :+:ACG +: AC:CG: AACC:GGUCAGGUCCGGAAGGAAGCAGCC 282608 CGGGAGGUUGGUGgUGGACGAUCCACUCGCCAACCGGGUCAGGUCCGGAAGGAAGCAGCC 282667 >--->>>>--.-->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguu.uuucgcgUGuGcCgcgguguuCugggccgacC 101 :U A:CG:+ + :+ CG G:+: : +:C+:::C+ C 282668 CU-AACGAGCcCGGAACGGGUCAUUGUUCCAGCCUCCCACCUC 282709 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #992,sp|AP003130.2|AP003130 Staphylococcus aureus subsp. aureus N315 genomic DNA, complete genome, section 2/10. ----isReversed: 0 ----hitSequence: GAUUUCGGUCCUAUGCAAUAUGAACCCAUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCAUCAUAUGUGCCGUAGGGUAGCCGAGAUUUAGC hit 81 : 203537 203639 (fwd) 77.96 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G::U G: CC:::GCAA:::GA ACCC:UGAACC::GUCAGGUCC GA GGAAGCAGC: 203537 GAUUUCGGuCCUAUGCAAUAUGA-ACCCAUGAACCAUGUCAGGUCCUGACGGAAGCAGCA 203595 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:GG+U+ UC:::UGUGCC:::G+GU :C G:: +A+C 203596 UUAAGUGGAUCAUCAUAUGUGCCGUAGGGUagCCGAGAUUUAGC 203639 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #1002,sp|AP003185.1|AP003185 Clostridium perfringens str. 13 DNA, complete genome, section 1/10. ----isReversed: 0 ----hitSequence: GAGUUGGGCCCCACGCAAUGGAAACCUGUGAACCUCGUCAGGUCCGGAAGGAAGCAGCGAUAAGCAGUCAUUUUCAUGUGCCGUGGAUACGUCUGGCUUGAGC hit 82 : 54642 54744 (fwd) 97.02 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G::UUGG: CCC:CGCAA:G::A ACC:GUGAACC::GUCAGGUCCGGAAGGAAGCAGC: 54642 GAGUUGGGcCCCACGCAAUGGAA-ACCUGUGAACCUCGUCAGGUCCGGAAGGAAGCAGCG 54700 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAGC:GU UU::C:UGUGCCG:GG ++ :CUGG:: GA+C 54701 AUAAGCAGUCAUUUUCAUGUGCCGUGGAUAcgUCUGGCUUGAGC 54744 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #1013,sp|AP003359.2|AP003359 Staphylococcus aureus subsp. aureus Mu50 genomic DNA, complete sequence, section 2/9. ----isReversed: 0 ----hitSequence: GAUUUCGGUCCUAUGCAAUAUGAACCCAUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCAUCAUAUGUGCCGUAGGGUAGCCGAGAUUUAGC hit 83 : 175906 176008 (fwd) 77.96 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G::U G: CC:::GCAA:::GA ACCC:UGAACC::GUCAGGUCC GA GGAAGCAGC: 175906 GAUUUCGGuCCUAUGCAAUAUGA-ACCCAUGAACCAUGUCAGGUCCUGACGGAAGCAGCA 175964 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:GG+U+ UC:::UGUGCC:::G+GU :C G:: +A+C 175965 UUAAGUGGAUCAUCAUAUGUGCCGUAGGGUagCCGAGAUUUAGC 176008 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #1026,sp|AP003584.1|AP003584 Nostoc sp. PCC 7120 DNA, complete genome, section 4/19. ----isReversed: 1 ----hitSequence: GACCUGGAUCUAUGCGACUGCAACGCCUAAACCUUGUCAGGACCGGAAGGUAGCAGCAACACAGGAUGCUUGUGGUAGGCGUAGUCUCCGGGUCGCCC hit 84 : 338551 338454 (rev) 62.58 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G:C:UGGA C:: GC AC ::A AC:C:+ AACC::GUCAGG:CCGGAAGG:AGCAGC: 9800 GACCUGGA-UCUAuGCGACUGCA-ACGCCUAAACCUUGUCAGGACCGGAAGGUAGCAGCA 9857 >--->>>>---->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 : A +:G:U +UU:: GU GC ::G UC+G:G:CG CC 9858 ACACAGGAUGCUUGUGGUAGGCGUAGUC--UCCGGGUCGCCC 9897 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #1053,sp|AP004174.1|AP004174 Mycoplasma penetrans genomic DNA, complete sequence, section 5/5. ----isReversed: 0 ----hitSequence: UAAUAUAGACGUCAUAACAUUAGAAGUGAAUCGUGUCAGGAUAGAAAUAUAGCAGCACUAAGCAAUAUCUUUUGUGUAUGGCGUCUUUUUUAUUAGAAU hit 85 : 15607 15705 (fwd) 50.70 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +:::: :: :CG: ::AAC: +A : GUGAA C::GUCAGG:::G AA:::AGCAGC: 15607 UAAUAUAG-ACGUcAUAACAUUA--GAAGUGAAUCGUGUCAGGAUAGAAAUAUAGCAGCA 15663 >--->>>>---->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 :UAAGC :U+U U+ :GUGU:: :CG: +U::U::::+GA 15664 CUAAGCAAUAUCUUUUGUGUAUGGCGUCUUUUUUAUUAGAAU 15705 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #1055,sp|AP004593.1|AP004593 Oceanobacillus iheyensis HTE831 genomic DNA, section 1/13. ----isReversed: 0 ----hitSequence: CGCCCGGGUCCUGCGCAACAGGAACCCACGAAUCCUGUCAGGUCCGGAAGGAAGCAGCAGUAAGUGGUUAUUCUUGUGUGCCGCAGGGAAGCCUAGGCCGAGC hit 86 : 30934 31036 (fwd) 92.49 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +GC: GG: CC:GCGCAAC::GA ACCC::GAA CC:GUCAGGUCCGGAAGGAAGCAGC: 30934 CGCCCGGGuCCUGCGCAACAGGA-ACCCACGAAUCCUGUCAGGUCCGGAAGGAAGCAGCA 30992 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 GUAA::GGUU UUC::GUGUGCCGC:G+G+ :CU :GCCGA+C 30993 GUAAGUGGUUAUUCUUGUGUGCCGCAGGGAagCCUAGGCCGAGC 31036 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #1069,sp|AP004823.1|AP004823 Staphylococcus aureus subsp. aureus MW2 DNA, complete genome, strain:MW2, section 2/10. ----isReversed: 0 ----hitSequence: GAUUUCGGUCCUAUGCAAUAUGAACCCAUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCAUCAUAUGUGCCGUAGGGUAGCCGAGAUUUAGC hit 87 : 196716 196818 (fwd) 77.96 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G::U G: CC:::GCAA:::GA ACCC:UGAACC::GUCAGGUCC GA GGAAGCAGC: 196716 GAUUUCGGuCCUAUGCAAUAUGA-ACCCAUGAACCAUGUCAGGUCCUGACGGAAGCAGCA 196774 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:GG+U+ UC:::UGUGCC:::G+GU :C G:: +A+C 196775 UUAAGUGGAUCAUCAUAUGUGCCGUAGGGUagCCGAGAUUUAGC 196818 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #1095,sp|AP005037.1|AP005037 Streptomyces avermitilis genomic DNA, complete genome, section 17/30. ----isReversed: 1 ----hitSequence: GCGCAGCCCCUCACGUGGCGCUAUCUGACUGAACUCCCCCAGGGCCGGAAGUCAGCAAGGGUAGGUUGGCUCUGGCGGGUGCGUGGGGGGCGCUUGCGUUCCC hit 88 : 294403 294301 (rev) 47.03 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G::::G :CC::: G::+CGC+A+ + ::UGAAC C:+ :AGG: CGGAAG :AGCA:+: 5023 GCGCAGCCCCUCAcGUGGCGCUAUCUGACUGAACUCCCCCAGGGCCGGAAGUCAGCAAGG 5082 >--->>>>--.-->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguu.uuucgcgUGuGcCgcggugu.uCugggccgacC 101 GU AG:: + U U+GCG G::C :::G+G : U:::: + CC 5083 GU-AGGUUGGcUCUGGCGGGUGCGUGGGGGGcGCUUGCGUUCCC 5125 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #1112,sp|AP005076.1|AP005076 Vibrio parahaemolyticus DNA, chromosome 1, complete sequence, 4/11. ----isReversed: 0 ----hitSequence: CUCUGGUCCUCUCGCAACAAUAGCUCGUGAACUCGGUCAGGUCCGGAAGGAAGCAGCCGCAGCGUGUGACUUGUGUGCCGGGAUGUGGCUGGGGUCCC hit 89 : 95721 95818 (fwd) 83.08 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 +:CU+G::C:C CGCAAC:: : C:CGUGAAC CGGUCAGGUCCGGAAGGAAGCAGCCG 95721 CUCUGGUCCUCUCGCAACAAUA-GCUCGUGAACUCGGUCAGGUCCGGAAGGAAGCAGCCG 95779 --->>>>---->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 AGCG:+U : ::GUGUGCCG G:UGU::++GG: + CC 95780 C-AGCGUGU-GACUUGUGUGCCGGGAUGUGGCUGGGGUCCC 95818 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #1126,sp|AP005141.1|AP005141 Streptococcus pyogenes SSI-1 DNA, complete genome, section 1/6. ----isReversed: 0 ----hitSequence: UAAUAAUAGGCGGAGCAACACUUGUGCGUGAAGUGGGUCAGGGGAGGAAUCCAGCAGCCCUAAGCGAUUUUCGGGUGUGUGCUCUUUUUUUUGUUGACUUUAC hit 90 : 177237 177339 (fwd) 59.87 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 + U: :A+ :: GCAAC:C+: +:CGUGAA :GGUCAGG: :GGAA: :AGCAGCC 177237 UAAUAAUAGGCGGaGCAACACUU-GUGCGUGAAGUGGGUCAGGGGAGGAAUCCAGCAGCC 177295 >--->>>>--.-->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguu.uuucgcgUGuGcCgcggugu.uCugggccgacC 101 :UAAGCG:UU U :+G:GUGUGC :: U+U U:U:G + C 177296 CUAAGCGAUUuUCGGGUGUGUGCUCUUUUUUuUGUUGACUUUAC 177339 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #1133,sp|AP005214.1|AP005214 Corynebacterium efficiens YS-314 DNA, complete genome, section 1/11. ----isReversed: 0 ----hitSequence: GGAUCCCGUGCGGCGUUUAUCUUGUGAACUCCCCCAGGGCAGGAAUGCAGCAAGGGUCAGCGAGCUCUGACGGGUGCGCGGGAUCCCCU hit 91 : 220057 220145 (fwd) 48.34 bits :<<<<-<<.-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->> 1 ggcuuGGa.Cccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGC 58 G: CC:: GC:+CG:+ A+C::GUGAAC C:+ :AGG:C:GGAA:G:AGCA:+ 220057 ------GGaUCCCGuGCGGCGUUUAUCUUGUGAACUCCCCCAGGGCAGGAAUGCAGCAAG 220110 >>--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 59 cgUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 :GU AGC::+ U +:CG G:GC ::GG + :CU 220111 GGUCAGCGAGCUCUGACGGGUGCGCGGGAUCcCCU--------- 220145 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #1146,sp|AP005274.1|AP005274 Corynebacterium glutamicum ATCC 13032 DNA, complete genome, section 1/10. ----isReversed: 0 ----hitSequence: GGAUCCCGUGCGGCGUUUAUCUUGUGAACUCCCCCAGGGCAGGAAUGCAGCAAGGGUCAGCGAGCUCUGACGGGUGCGCGGGAUCCCCU hit 92 : 256434 256522 (fwd) 48.34 bits :<<<<-<<.-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->> 1 ggcuuGGa.Cccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGC 58 G: CC:: GC:+CG:+ A+C::GUGAAC C:+ :AGG:C:GGAA:G:AGCA:+ 256434 ------GGaUCCCGuGCGGCGUUUAUCUUGUGAACUCCCCCAGGGCAGGAAUGCAGCAAG 256487 >>--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 59 cgUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 :GU AGC::+ U +:CG G:GC ::GG + :CU 256488 GGUCAGCGAGCUCUGACGGGUGCGCGGGAUCcCCU--------- 256522 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #1156,sp|AP005369.1|AP005369 Thermosynechococcus elongatus BP-1 DNA, complete genome, section 1/9. ----isReversed: 1 ----hitSequence: GGCUCGGAAUCAUGCGAUCGCAACGCCUCAACCUUGUCAGGUCCGGAAGGAAGCAGCAAUACGGGAUGCUUGCGAUAGGCGUGAUCUCCGGGUCACCC hit 93 : 216057 215960 (rev) 64.18 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G CU:GGA :::: GC A::::A AC:C:U AACC::GUCAGGUCCGGAAGGAAGCAGC: 84544 GGCUCGGA-AUCAuGCGAUCGCA-ACGCCUCAACCUUGUCAGGUCCGGAAGGAAGCAGCA 84601 >--->>>>---->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 :UA G:G:U +UU::::U GC :::: UC+:GG C CC 84602 AUACGGGAUGCUUGCGAUAGGCGUGAUC--UCCGGGUCACCC 84641 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #1195,sp|AP005964.1|AP005964 Bradyrhizobium japonicum USDA 110 DNA, complete genome, section 30/31. ----isReversed: 1 ----hitSequence: GGAGAUUGGCGGUGGACGAGCCACUCGCCAACCGGGUCAGGUCCGGAAGGAAGCAGCCCUAACGAGGUCCGGAUCGGGUCGCUCGUCAGUCUCCUACC hit 94 : 208840 208743 (rev) 53.04 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 GG::: ::+ CG :+:ACG: : AC:CG: AACC:GGUCAGGUCCGGAAGGAAGCAGCC: 90911 GGAGAUUGG-CGGUGGACGAGCCACUCGCCAACCGGGUCAGGUCCGGAAGGAAGCAGCCC 90969 --->>>>--..-->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguu..uuucgcgUGuGcCgcgguguuCugggccgacC 101 U A:CG:+ + : :CG G:+:C CG+ :: :::CC+ACC 90970 U-AACGAGGucCGGAUCGGGUCGCUCGU---CAGUCUCCUACC 91008 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #35932,sp|D11422.1|BAALSCR B. alcalophilus gene for small cytoplasmic RNA. ----isReversed: 0 ----hitSequence: CGUUGGGUUCUACGCAACGAAAACCCACGAACCCUGUCAGGUCCGGAAGGAAGCAGCAGUAAGUGGCCCCUUUCGUGUGCCGUAGAGUCGCUGGGCCGAGC hit 95 : 117 217 (fwd) 89.95 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 +G:U GG: C::CGCAACG::A ACCC::GAACCC:GUCAGGUCCGGAAGGAAGCAGC:G 117 CGUUGGGUUCUACGCAACGAAA-ACCCACGAACCCUGUCAGGUCCGGAAGGAAGCAGCAG 175 --->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 UAA::GG + U::CGUGUGCCG::G GU :CU G:CCGA+C 176 UAAGUGGCCCCUUUCGUGUGCCGUAGAGUcGCUGGGCCGAGC 217 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #35944,sp|D11416.1|BAASCR B. amyloliquefaciens gene for small cytoplasmic RNA. ----isReversed: 0 ----hitSequence: CGUUUGGGUCCUGCGCAAUGGGAAUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCAUGUGCCGCAGGGUUGCCUGGGCCGAGC hit 96 : 118 220 (fwd) 97.92 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G:UUGG: CC:GCGCAA:G:GA A+:C:UGAACC::GUCAGGUCCGGAAGGAAGCAGC: 118 CGUUUGGGuCCUGCGCAAUGGGA-AUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCA 176 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:G:+++ UC:C:UGUGCCGC:G+GU :CUGG:CCGA+C 177 UUAAGUGAAACCUCUCAUGUGCCGCAGGGUugCCUGGGCCGAGC 220 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #36363,sp|D13041.1|BASCRNA Bacillus amyloliquefaciens scr gene for scRNA. ----isReversed: 0 ----hitSequence: CGUUUGGGUCCUGCGCAAUGGGAAUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCAUGUGCCGCAGGGUUGCCUGGGCCGAGC hit 97 : 118 220 (fwd) 97.92 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G:UUGG: CC:GCGCAA:G:GA A+:C:UGAACC::GUCAGGUCCGGAAGGAAGCAGC: 118 CGUUUGGGuCCUGCGCAAUGGGA-AUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCA 176 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:G:+++ UC:C:UGUGCCGC:G+GU :CUGG:CCGA+C 177 UUAAGUGAAACCUCUCAUGUGCCGCAGGGUugCCUGGGCCGAGC 220 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #36737,sp|D12926.1|BBD12926 Bacillus brevis scr gene for scRNA. ----isReversed: 0 ----hitSequence: GGAGCGGGUCCUGUGCAACGCGAACCCAUGAACCUGGUCAGGUCCGGAAGGAAGCAGCCAUAAGUGGAUCAUCGCGUGUGCCGCAGGGUAGCCUGCUCUGAGC hit 98 : 388 490 (fwd) 97.51 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 GG:::GG: CC:G:GCAACGCGA ACCC:UGAACC:GGUCAGGUCCGGAAGGAAGCAGCC 388 GGAGCGGGuCCUGUGCAACGCGA-ACCCAUGAACCUGGUCAGGUCCGGAAGGAAGCAGCC 446 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:GG+U+ UCGCGUGUGCC:C:G+GU :CU:::C GA+C 447 AUAAGUGGAUCAUCGCGUGUGCCGCAGGGUagCCUGCUCUGAGC 490 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #37107,sp|D14472.1|BBSCRNA Bacillus brevis gene for scRNA. ----isReversed: 0 ----hitSequence: GGAGCGGGUCCUGUGCAACGCGAACCCAUGAACCUGGUCAGGUCCGGAAGGAAGCAGCCAUAAGUGGAUCAUCGCGUGUGCCGCAGGGUAGCCUGCUCUGAGC hit 99 : 591 693 (fwd) 97.51 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 GG:::GG: CC:G:GCAACGCGA ACCC:UGAACC:GGUCAGGUCCGGAAGGAAGCAGCC 591 GGAGCGGGuCCUGUGCAACGCGA-ACCCAUGAACCUGGUCAGGUCCGGAAGGAAGCAGCC 649 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:GG+U+ UCGCGUGUGCC:C:G+GU :CU:::C GA+C 650 AUAAGUGGAUCAUCGCGUGUGCCGCAGGGUagCCUGCUCUGAGC 693 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #37494,sp|D11419.1|BCCISCR B. circulans gene for small cytoplasmic RNA. ----isReversed: 0 ----hitSequence: CGUCCGGGUCCUGCGCAAUGGGAAUCCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGGACACCCCCAUGUGCCGCAGGGUUACCUGGACUGAGC hit 100 : 119 221 (fwd) 90.30 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G:::GG: CC:GCGCAA:G:G A+CC:UGAACC::GUCAGGUCCGGAAGGAAGCAGC: 119 CGUCCGGGuCCUGCGCAAUGGGA-AUCCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCA 177 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:GG+ C:C:UGUGCCGC:G+GU :CU:::C GA+C 178 UUAAGUGGACACCCCCAUGUGCCGCAGGGUuaCCUGGACUGAGC 221 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #37497,sp|D11413.1|BCCSCR B. cereus gene for small cytoplasmic RNA. ----isReversed: 0 ----hitSequence: CGUUUGGGUCCUGCGCAACGGGACCCGUGAACCUUGUCAGGUCCGGAAGGAAGCAGCAAUAAGCGGUCUUCUCGUGUGCCGAGAGUGCCUGAACCGAGC hit 101 : 118 216 (fwd) 89.62 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G::UGG: CC:GCGCAACG:GA CCCGUGAACC::GUCAGGUCCGGAAGGAAGCAGC: 118 CGUUUGGGuCCUGCGCAACGGGA--CCCGUGAACCUUGUCAGGUCCGGAAGGAAGCAGCA 175 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 :UAAGCGGU UUC:CGUGUGCCG :G GU :CUG::CCGA+C 176 AUAAGCGGUC-UUCUCGUGUGCCG-AGAGUgCCUGAACCGAGC 216 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #38901,sp|D11420.1|BMMASCR B. macerans gene for small cytoplasmic RNA. ----isReversed: 0 ----hitSequence: CGUCUGGGUCCUGCGCAAUGGGAAUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCAUGUGCCGCAGGGUUGCCUGGGCUGAGC hit 102 : 119 221 (fwd) 95.55 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G::UGG: CC:GCGCAA:G:GA A+:C:UGAACC::GUCAGGUCCGGAAGGAAGCAGC: 119 CGUCUGGGuCCUGCGCAAUGGGA-AUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCA 177 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:G:+++ UC:C:UGUGCCGC:G+GU :CUG::C GA+C 178 UUAAGUGAAACCUCUCAUGUGCCGCAGGGUugCCUGGGCUGAGC 221 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #38904,sp|D11414.1|BMMSCR B. megaterium gene for small cytoplasmic RNA. ----isReversed: 0 ----hitSequence: CGUUUGGGUCCUACGCAAUGGGAAUCUGUGAACCCUGUCAGGUCCGGAAGGAAGCAGCAGUAAGCAGAACCUCUCAUGUGCCAUGGGGUCGCCUGAACCGAGC hit 103 : 117 219 (fwd) 95.35 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G::UGG: CC:: GCAA:G:GA A+C:GUGAACCC:GUCAGGUCCGGAAGGAAGCAGC: 117 CGUUUGGGuCCUACGCAAUGGGA-AUCUGUGAACCCUGUCAGGUCCGGAAGGAAGCAGCA 175 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 GUAAGC:G+++ UC:C:UGUGCC ::G+GU :CUG::CCGA+C 176 GUAAGCAGAACCUCUCAUGUGCCAUGGGGUcgCCUGAACCGAGC 219 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #39340,sp|D11421.1|BPPOSCR B. polymyxa gene for small cytoplasmic RNA. ----isReversed: 0 ----hitSequence: CGUUUGGGUCCUGCGCAAUGGGAAUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCAUGUGCCGCAGGGUUGCCUGGGCCGAGC hit 104 : 119 221 (fwd) 97.92 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G:UUGG: CC:GCGCAA:G:GA A+:C:UGAACC::GUCAGGUCCGGAAGGAAGCAGC: 119 CGUUUGGGuCCUGCGCAAUGGGA-AUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCA 177 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:G:+++ UC:C:UGUGCCGC:G+GU :CUGG:CCGA+C 178 UUAAGUGAAACCUCUCAUGUGCCGCAGGGUugCCUGGGCCGAGC 221 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #39342,sp|D11415.1|BPPSCR B. pumilus gene for small cytoplasmic RNA. ----isReversed: 0 ----hitSequence: CGUCUGGGUCCUGCGCAAUGGGAAUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCAUGUGCCGCAGGGUUGCCUGGGCCGAGC hit 105 : 117 219 (fwd) 96.82 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G::UGG: CC:GCGCAA:G:GA A+:C:UGAACC::GUCAGGUCCGGAAGGAAGCAGC: 117 CGUCUGGGuCCUGCGCAAUGGGA-AUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCA 175 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:G:+++ UC:C:UGUGCCGC:G+GU :CUG::CCGA+C 176 UUAAGUGAAACCUCUCAUGUGCCGCAGGGUugCCUGGGCCGAGC 219 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #40452,sp|X52144.1|BSORF17 Bacillus subtilis DNA for ORF17, small cytoplasmic RNA and partial dnaX gene ----isReversed: 0 ----hitSequence: CGUUUGGGUCCUGCGCAAUGGGAAUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCAUGUGCCGCAGGGUUGCCUGGGCCGAGC hit 106 : 810 912 (fwd) 97.92 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G:UUGG: CC:GCGCAA:G:GA A+:C:UGAACC::GUCAGGUCCGGAAGGAAGCAGC: 810 CGUUUGGGuCCUGCGCAAUGGGA-AUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCA 868 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:G:+++ UC:C:UGUGCCGC:G+GU :CUGG:CCGA+C 869 UUAAGUGAAACCUCUCAUGUGCCGCAGGGUugCCUGGGCCGAGC 912 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #41326,sp|D26185.1|BSPURA1 B. subtilis DNA, 180 kilobase region of replication origin. ----isReversed: 0 ----hitSequence: CGUUUGGGUCCUGCGCAAUGGGAAUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCAUGUGCCGCAGGGUUGCCUGGGCCGAGC hit 107 : 90133 90235 (fwd) 97.92 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G:UUGG: CC:GCGCAA:G:GA A+:C:UGAACC::GUCAGGUCCGGAAGGAAGCAGC: 90133 CGUUUGGGuCCUGCGCAAUGGGA-AUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCA 90191 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:G:+++ UC:C:UGUGCCGC:G+GU :CUGG:CCGA+C 90192 UUAAGUGAAACCUCUCAUGUGCCGCAGGGUugCCUGGGCCGAGC 90235 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #41996,sp|X15523.1|BSSCR Bacillus stearothermophilus small cytoplasmic RNA ----isReversed: 0 ----hitSequence: CGUCUGGGUCCCGCGCAAUGGGAUUCCGUGAACCCUGUCAGGUCCGGAAGGAAGCAGCAGUUAGCGGAUGCUCCCAUGUGCCGCGGGGGCGCCUGGGCUGAGC hit 108 : 115 217 (fwd) 92.44 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G::UGG: CCCGCGCAA:G:GA ++CCGUGAACCC:GUCAGGUCCGGAAGGAAGCAGC: 115 CGUCUGGGuCCCGCGCAAUGGGA-UUCCGUGAACCCUGUCAGGUCCGGAAGGAAGCAGCA 173 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 GU AGCGG+U UC:C:UGUGCCGCGG+G :CUG::C GA+C 174 GUUAGCGGAUGCUCCCAUGUGCCGCGGGGGcgCCUGGGCUGAGC 217 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #41997,sp|X14796.1|BSSCRNA B.subtilis small cytoplasmic RNA gene and dnaZX-like gene (partial). ----isReversed: 0 ----hitSequence: CGUUUGGGUCCUGCGCAAUGGGAAUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCAUGUGCCGCAGGGUUGCCUGGGCCGAGC hit 109 : 404 506 (fwd) 97.92 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G:UUGG: CC:GCGCAA:G:GA A+:C:UGAACC::GUCAGGUCCGGAAGGAAGCAGC: 404 CGUUUGGGuCCUGCGCAAUGGGA-AUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCA 462 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:G:+++ UC:C:UGUGCCGC:G+GU :CUGG:CCGA+C 463 UUAAGUGAAACCUCUCAUGUGCCGCAGGGUugCCUGGGCCGAGC 506 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #41998,sp|X06802.1|BSSCRNA1 Bacillus subtilis small cytoplasmic RNA (scRNA) ----isReversed: 0 ----hitSequence: CGUUUGGGUCCUGCGCAAUGGGAAUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCAUGUGCCGCAGGGUUGCCUGGGCCGAGC hit 110 : 118 220 (fwd) 97.92 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G:UUGG: CC:GCGCAA:G:GA A+:C:UGAACC::GUCAGGUCCGGAAGGAAGCAGC: 118 CGUUUGGGuCCUGCGCAAUGGGA-AUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCA 176 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:G:+++ UC:C:UGUGCCGC:G+GU :CUGG:CCGA+C 177 UUAAGUGAAACCUCUCAUGUGCCGCAGGGUugCCUGGGCCGAGC 220 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #41999,sp|X12642.1|BSSCRNAA Bacillus subtilis scRNA gene ----isReversed: 0 ----hitSequence: CGUUUGGGUCCUGCGCAAUGGGAAUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCAUGUGCCGCAGGGUUGCCUGGGCCGAGC hit 111 : 405 507 (fwd) 97.92 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G:UUGG: CC:GCGCAA:G:GA A+:C:UGAACC::GUCAGGUCCGGAAGGAAGCAGC: 405 CGUUUGGGuCCUGCGCAAUGGGA-AUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCA 463 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:G:+++ UC:C:UGUGCCGC:G+GU :CUGG:CCGA+C 464 UUAAGUGAAACCUCUCAUGUGCCGCAGGGUugCCUGGGCCGAGC 507 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #42127,sp|D11418.1|BSSPSCR B. sphaericus gene for small cytoplasmic RNA. ----isReversed: 0 ----hitSequence: CGUUUGGGUCCUGCGCAAUGGGAAUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCAUGUGCCGCAGGUUGCCUUGGGCCGAGC hit 112 : 118 220 (fwd) 92.97 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G:UUG : CC:GCGCAA:G:GA A+:C:UGAACC::GUCAGGUCCGGAAGGAAGCAGC: 118 CGUUUGGGuCCUGCGCAAUGGGA-AUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCA 176 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:G:+++ UC:C:UGUGCCGC:G++U : UGG:CCGA+C 177 UUAAGUGAAACCUCUCAUGUGCCGCAGGUUgcCUUGGGCCGAGC 220 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #42138,sp|D11417.1|BSSSCR B. subtilis gene for small cytoplasmic RNA. ----isReversed: 0 ----hitSequence: CGUUUGGGUCCUGCGCAAUGGGAAUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCAUGUGCCGCAGGGUUGCCUGGGCCGAGC hit 113 : 118 220 (fwd) 97.92 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G:UUGG: CC:GCGCAA:G:GA A+:C:UGAACC::GUCAGGUCCGGAAGGAAGCAGC: 118 CGUUUGGGuCCUGCGCAAUGGGA-AUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCA 176 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:G:+++ UC:C:UGUGCCGC:G+GU :CUGG:CCGA+C 177 UUAAGUGAAACCUCUCAUGUGCCGCAGGGUugCCUGGGCCGAGC 220 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #42381,sp|Z99104.2|BSUB0001 Bacillus subtilis complete genome (section 1 of 21): from 1 to 213080. ----isReversed: 0 ----hitSequence: CGUUUGGGUCCUGCGCAAUGGGAAUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCAUGUGCCGCAGGGUUGCCUGGGCCGAGC hit 114 : 26531 26633 (fwd) 97.92 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G:UUGG: CC:GCGCAA:G:GA A+:C:UGAACC::GUCAGGUCCGGAAGGAAGCAGC: 26531 CGUUUGGGuCCUGCGCAAUGGGA-AUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCA 26589 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAG:G:+++ UC:C:UGUGCCGC:G+GU :CUGG:CCGA+C 26590 UUAAGUGAAACCUCUCAUGUGCCGCAGGGUugCCUGGGCCGAGC 26633 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #42855,sp|D11412.1|BTTSCR B. thuringiensis gene for small cytoplasmic RNA. ----isReversed: 0 ----hitSequence: CGUUUGGGUCCUGCGCAACGGGACCCCGUGAACCUUGUCAGGUCCGGAAGGAAGCAGCAAUAAGCGGGUCUUCUCGUGUGCCGCAGGAGUGCCUGAACCGAGC hit 115 : 117 219 (fwd) 97.57 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G::UGG: CC:GCGCAACG:GA CCCGUGAACC::GUCAGGUCCGGAAGGAAGCAGC: 117 CGUUUGGGuCCUGCGCAACGGGA-CCCCGUGAACCUUGUCAGGUCCGGAAGGAAGCAGCA 175 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAGCGG+U+UUC:CGUGUGCCGC:G+ :CUG::CCGA+C 176 AUAAGCGGGUCUUCUCGUGUGCCGCAGGAGugCCUGAACCGAGC 219 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #42972,sp|BX248347.1|BX248347 Mycobacterium bovis subsp. bovis AF2122/97 complete genome; segment 14/14 ----isReversed: 1 ----hitSequence: CACGGUGGACCCCGCGCGGCGUCUAUCCUGUGAACUCCCCCAGGGCUGGAAGGCAGCAAGGGUCAACGGGCUCUGUCGGGUGCGCGGGGUCCCCUUCAGCC hit 116 : 38747 38647 (rev) 48.93 bits :<<<<-<<.-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->> 1 ggcuuGGa.Cccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGC 58 +: :: G: CCC:: GC:+CG : A+CC:G+GAAC C:+ :AGG:C:GGAA:G:AGCA:+ 239746 CACGGUGGaCCCCGcGCGGCGUCUAUCCUGUGAACUCCCCCAGGGCUGGAAGGCAGCAAG 239805 >>--->>>>---->>>>>-->>>->>>>--->>->>>>::::: 59 cgUAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 :GU A+C:G+ U : CG G:GC ::GG+ :C+:: :C +CC 239806 GGUCAACGGGCUCUGUCGGGUGCGCGGGG--UCCCCUUCAGCC 239846 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #42978,sp|BX251412.1|BX251412 Tropheryma whipplei TW08/27, complete genome; segment 3/3 ----isReversed: 1 ----hitSequence: UAGUUUGCCUCCGCGCGGCGUUACCCGGGUGAACUCCCCCAGGUUAGGAAUAAAGCAAGGGUAGCUCGGCUCUGGCGGGUGUGCGGGGGUCUUGCGGGCUCCGUU hit 117 : 198570 198466 (rev) 49.01 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +::UU G:C:C:: :C:+CG:+A C GUGAAC C:+ :AGGU::GGAA::AAGCA:+: 104369 UAGUUUGCCUCCGcGCGGCGUUACCCGGGUGAACUCCCCCAGGUUAGGAAUAAAGCAAGG 104428 >--->>>>--.-->>>>>-->>>->>>>---...>>->>>>::::: 60 gUAAgcgguu.uuucgcgUGuGcCgcggugu...uCugggccgacC 101 GU AGC + U U+:CG G:G: ::G:+GU :C GG::C + 104429 GU-AGCUCGGcUCUGGCGGGUGUGCGGGGGUcuuGCGGGCUCCGUU 104473 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #42990,sp|BX294144.1|BX294144 Pirellula sp. strain 1 complete genome; segment 12/24 ----isReversed: 1 ----hitSequence: GGUGGCGACCCUUGCGACUGUGAGUCGUGAACCUGGUCAGGCCUUAACUGGAGCAGCCAUAAGCGGUGUAACUUUGUGUGAGGGUUGCCGCCACCGAGC hit 118 : 110364 110266 (rev) 48.35 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 GG::: G CCC ::C:A :+ A :CGUGAACC:GGUCAGG:C A G:AGCAGCC: 194487 GGUGGCGACCCUUGCGACUGUG-AGUCGUGAACCUGGUCAGGCCUUAACUGGAGCAGCCA 194545 --->>>>---->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 UAAGCG:U U +: UG:G: : GGU+ C :::CCGA+C 194546 UAAGCGGUG-UAACUUUGUGUGAGGGUUGCCGCCACCGAGC 194585 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #43004,sp|BX321857.1|BX321857 Nitrosomonas europaea ATCC 19718, complete genome; segment 2/10 ----isReversed: 0 ----hitSequence: UGGCGGGCCUCCCCGCAUUGUGAGGUAGUGAAUCUGGUCAGAUCCGGAAGGAAGCAGCCACAGCUAUUUUUCGCAAGUGCCGGGGGUUCGGCUCGCCACCCG hit 119 : 168385 168486 (fwd) 75.49 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G:::GG: CC:CGCA :G:GA ::GUGAA C:GGUCAG UCCGGAAGGAAGCAGCC 168385 UGGCGGGCcUCCCCGCAUUGUGA-GGUAGUGAAUCUGGUCAGAUCCGGAAGGAAGCAGCC 168443 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 : AGC::UUUUUC:C: GUGCCG:GG++U :CU:::C+ C 168444 AC-AGCUAUUUUUCGCAAGUGCCGGGGGUUcgGCUCGCCACCCG 168486 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #43017,sp|BX569693.1|BX569693 Synechococcus sp. WH8102 complete genome; segment 5/7 ----isReversed: 1 ----hitSequence: GACUCGGGCCAUGCGGCUCGGACGCCCAAAUCUGGUCAGGACCGGAAGGGAGCAGCCACACGGGAUGCUCAGAGCAGGCGUGGACUCCGGGUCACCC hit 120 : 191291 191195 (rev) 50.36 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 G:CU:GG: CC::GC +C C : AC:C:: AA C:GGUCAGG CCGGAAGG AGCAGCC: 157923 GACUCGGG-CCAUGCGGCUCGG-ACGCCCAAAUCUGGUCAGGACCGGAAGGGAGCAGCCA 157980 --->>>>---->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 A ::G:U +U: G G GC ::GG :C+:GG:C CC 157981 CACGGGAUGCUCAGAGCAGGC-GUGGAC-UCCGGGUCACCC 158019 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #43023,sp|BX572093.1|BX572093 Prochlorococcus marinus MED4 complete genome; segment 4/5 ----isReversed: 1 ----hitSequence: GACUCGGCCUUUCGCGGUUUUAACGCCCAAACCUGGUCAGGAUCGGAAGGUAGCAGCCACAAGGGAUGCUUGAGGCAGGCGAGAUAACCGAGUCACUU hit 121 : 216574 216477 (rev) 52.10 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 G:C::GG C:::C C +: :+A AC:C:: AACC:GGUCAGG::CGGAAG::AGCAGCC: 132413 GACUCGGCCUUUCGCGGUUUUA-ACGCCCAAACCUGGUCAGGAUCGGAAGGUAGCAGCCA 132471 --->>>>---->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 AA::G:U U+: : G CG:::U C+::G:C 132472 CAAGGGAUG-CUUGAGGCAGGCGAGAUA-ACCGAGUCACUU 132510 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #43026,sp|BX572096.1|BX572096 Prochlorococcus marinus MIT9313 complete genome; segment 2/7 ----isReversed: 0 ----hitSequence: GACUCGGACCCAUGCGGCCGCGACGCCUAAAUCUGGUCAGGACCGGAAGGGAGCAGCCACACGGGAUGCUCGUGACAGGCGUGGACUCCGGGUCACCC hit 122 : 15940 16037 (fwd) 53.55 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G:CU:GGA :C :+:+: C:: AC:C:U AA C:GGUCAGG CCGGAAGG AGCAGCC 15940 GACUCGGA--CCCaUGCGGCCGCGACGCCUAAAUCUGGUCAGGACCGGAAGGGAGCAGCC 15997 >--->>>>--.-->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguu.uuucgcgUGuGcCgcgguguuCugggccgacC 101 : A G:G:U U ::G : G:+: G: UC+:GG:C CC 15998 ACACGGGAUGcUCGUGACAGGCGUGGAC---UCCGGGUCACCC 16037 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #43036,sp|BX640415.1|BX640415 Bordetella pertussis strain Tohama I, complete genome; segment 5/12 ----isReversed: 0 ----hitSequence: GGCGGGCCCCUUCGCAUGGUUCGGCGGUGAAUCUGGUCAGGUCGGGAACGAAGCAGCCAUAGUCGUUCAGAACCAGUGCCGGAGUAAGGCUCGCCUACC hit 123 : 240569 240667 (fwd) 71.60 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 GGC:+G :CC: CGCA :G:+: C:+UGAA C:GGUCAGGUC GGAA GAAGCAGCC: 240569 GGCGGGCCCCUUCGCAUGGUUC-GGCGGUGAAUCUGGUCAGGUCGGGAACGAAGCAGCCA 240627 --->>>>---->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 U AG+:GUU+ :+:C: GUGCCG :GU +: ++:GCC+ACC 240628 U-AGUCGUUCAGAACCAGUGCCGGAGUAAGGCUCGCCUACC 240667 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #43047,sp|BX640426.1|BX640426 Bordetella parapertussis strain 12822, complete genome; segment 4/14 ----isReversed: 0 ----hitSequence: GGCGGGCCCCUUCGCAUGGUUCGGCGGUGAAUCUGGUCAGGUCGGGAACGAAGCAGCCAUAGUCGUUCAGAACCAGUGCCGGAGUAAGGCUCGCCUACC hit 124 : 255860 255958 (fwd) 71.60 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 GGC:+G :CC: CGCA :G:+: C:+UGAA C:GGUCAGGUC GGAA GAAGCAGCC: 255860 GGCGGGCCCCUUCGCAUGGUUC-GGCGGUGAAUCUGGUCAGGUCGGGAACGAAGCAGCCA 255918 --->>>>---->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 U AG+:GUU+ :+:C: GUGCCG :GU +: ++:GCC+ACC 255919 U-AGUCGUUCAGAACCAGUGCCGGAGUAAGGCUCGCCUACC 255958 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #43062,sp|BX640441.1|BX640441 Bordetella bronchiseptica strain RB50, complete genome; segment 5/16 ----isReversed: 0 ----hitSequence: GGCGGGCCCCUUCGCAUGGUUCGGCGGUGAAUCUGGUCAGGUCGGGAACGAAGCAGCCAUAGUCGUUCAGAACCAGUGCCGGAGUAAGGCUCGCCUACC hit 125 : 143442 143540 (fwd) 71.60 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 GGC:+G :CC: CGCA :G:+: C:+UGAA C:GGUCAGGUC GGAA GAAGCAGCC: 143442 GGCGGGCCCCUUCGCAUGGUUC-GGCGGUGAAUCUGGUCAGGUCGGGAACGAAGCAGCCA 143500 --->>>>---->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 U AG+:GUU+ :+:C: GUGCCG :GU +: ++:GCC+ACC 143501 U-AGUCGUUCAGAACCAGUGCCGGAGUAAGGCUCGCCUACC 143540 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #43574,sp|U22036.1|CC22036 Caulobacter crescentus 4.5S RNA homolog (ffs) gene, partial sequence, and DNA polymerase III tau subunit (dnaX) gene, partial cds. ----isReversed: 0 ----hitSequence: CGGAGAUCGGCGCGGACGGAGUCCUCGCCAACCUGGUCAGGGCCGAGAGGCAGCAGCCACAACGAGAUCACCUCUGGGUCGUCUGCCGGUCUCCACCUC hit 126 : 384 482 (fwd) 53.36 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +G::: ::+ :C :::+::: C:CG: AACC:GGUCAGG:CCG AGG:AGCAGCC 384 CGGAGAUCGGCGCgGACGGAGU--CCUCGCCAACCUGGUCAGGGCCGAGAGGCAGCAGCC 441 >--->>>>---->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 : A:CG:++U + :::UG:::CG: + ::U:::C+ C 442 AC-AACGAGAUCACCUCUGGGUCGUCUGCCGGUCUCCACCUC 482 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #43593,sp|U49738.1|CC49738 Caulobacter crescentus DNA polymerase III tau homolog DnaX (dnaX) gene, complete cds. ----isReversed: 0 ----hitSequence: GAGAUCGGCGCGGACGGAGUCCUCGCCAACCUGGUCAGGGCCGAGAGGCAGCAGCCACAACGAGAUCACCUCUGGGUCGUCUGCCGGUCUCCACC hit 127 : 1 95 (fwd) 52.77 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G:::U G: :C :::+::: C:CG: AACC:GGUCAGG:CCG AGG:AGCAGCC 1 GAGAUCGG--CGCgGACGGAGU--CCUCGCCAACCUGGUCAGGGCCGAGAGGCAGCAGCC 56 >--->>>>---->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 : A:CG:++U + :::UG:::CG: ++ :C G:::C ACC 57 AC-AACGAGAUCACCUCUGGGUCGUCUG--CCGGUCUCCACC 95 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #44364,sp|AL139074.2|CJ11168X1 Campylobacter jejuni subsp. jejuni NCTC 11168 complete genome; segment 1/6 ----isReversed: 0 ----hitSequence: UUCUUAGACCUGUGCAAUGCUAUUUUUAAGCACCGCUUCAGGGUGGGAACACAGCAGAGCACUUGAUUUUAGUGUGUGCCGCAGUUAUCUGGGGAAGGG hit 128 : 66646 66744 (fwd) 60.99 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 +:CUU GACC:G:GCAA::C+A+++::::G ACC:::UCAGG:: GGAA ::AGCAG::: 66646 UUCUUAGACCUGUGCAAUGCUAUUUUUAAGCACCGCUUCAGGGUGGGAACACAGCAGAGC 66705 --->>>>---->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 ::::UU UU+G::UGUGCC:C:GU++UCUGGG:+ ++ 66706 A-CUUGAUU-UUAGUGUGUGCCGCAGUUAUCUGGGGAAGGG 66744 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #45566,sp|D49784.1|CPSERTRNA Clostridium perfringens genes for tRNA-Ser, scRNA, Orf1 and sodium-coupled branched-chain amino acid carrier. ----isReversed: 0 ----hitSequence: GAGUUGGGCCCCACGCAAUGGAAACCUGUGAACCUCGUCAGGUCCGGAAGGAAGCAGCGAUAAGCAGUCAUUUUCAUGUGCCGUGGAUACGUCUGGCUUGAGC hit 129 : 399 501 (fwd) 97.02 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G::UUGG: CCC:CGCAA:G::A ACC:GUGAACC::GUCAGGUCCGGAAGGAAGCAGC: 399 GAGUUGGGcCCCACGCAAUGGAA-ACCUGUGAACCUCGUCAGGUCCGGAAGGAAGCAGCG 457 >--->>>>---->>>>>-->>>->>>>---..>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu..uCugggccgacC 101 :UAAGC:GU UU::C:UGUGCCG:GG ++ :CUGG:: GA+C 458 AUAAGCAGUCAUUUUCAUGUGCCGUGGAUAcgUCUGGCUUGAGC 501 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #48868,sp|AE000151.1|ECAE151 Escherichia coli K12 MG1655 section 41 of 400 of the complete genome. ----isReversed: 0 ----hitSequence: CUGUUGGUUCUCCCGCAACGCUACUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCCAAGGCAGAUGACGCGUGUGCCGGGAUGUAGCUGGCAGGGCC hit 130 : 10906 11005 (fwd) 83.14 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +::UUGG: C:C:CGCAACGC : +C:GU ACC GGUCAGGUCCGGAAGGAAGCAGCC 10906 CUGUUGGUuCUCCCGCAACGCUA-CUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCC 10964 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 GC:G+U : GCGUGUGCCG:G:UGU :CUGG:: G+CC 10965 AA-GGCAGAU-GACGCGUGUGCCGGGAUGUaGCUGGCAGGGCC 11005 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz ----sequence: #2470,sp|X01074.1|ECRNA45 E. coli 4.5S rRNA gene ----isReversed: 0 ----hitSequence: CUGUUGGUUCUCCCGCAACGCUACUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCCAAGGCAGAUGACGCGUGUGCCGGGAUGUAGCUGGCAGGGCC hit 131 : 169 268 (fwd) 83.14 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +::UUGG: C:C:CGCAACGC : +C:GU ACC GGUCAGGUCCGGAAGGAAGCAGCC 169 CUGUUGGUuCUCCCGCAACGCUA-CUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCC 227 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 GC:G+U : GCGUGUGCCG:G:UGU :CUGG:: G+CC 228 AA-GGCAGAU-GACGCGUGUGCCGGGAUGUaGCUGGCAGGGCC 268 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz ----sequence: #2581,sp|M17993.1|ECRRKP E.coli 4.5S ribosomal RNA (rRNA) precursor RNA. ----isReversed: 0 ----hitSequence: CUGUUGGUUCUCCCGCAACGUCACUCUGUUUACCAGGUCAGGUCCGGAAGCCAAGGCAGCAGAUGACGCGUGUGCCGGGAUGUAGCUGGCAGGGCC hit 132 : 29 124 (fwd) 43.90 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +::UUGG: C:C:CGCAACG: : +C:GU ACC U:AGGUCC GGAAGC : 29 CUGUUGGUuCUCCCGCAACGUCA-CUCUGUUUACCAGGUCAGGUCC----GGAAGCCAAG 83 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 AGC:G+U : :CGUGUGCCG:G:UGU :CUGG:: G+CC 84 GC-AGCAGAU-GACGCGUGUGCCGGGAUGUaGCUGGCAGGGCC 124 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz ----sequence: #2717,sp|M17994.1|ECSRAKA E.coli (MRE 600) 4.5S RNA. ----isReversed: 0 ----hitSequence: CUGUUGGUUCUCCCGCAACGUCACUCUGUUUACCAGGUCAGGUCCGGAAGCCAAGGCAGCAGAUGACGCGUGUGCCGGGAUGUAGCUGGCAAGGCC hit 133 : 7 102 (fwd) 44.25 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +::UUGG: C:C:CGCAACG: : +C:GU ACC U:AGGUCC GGAAGC : 7 CUGUUGGUuCUCCCGCAACGUCA-CUCUGUUUACCAGGUCAGGUCC----GGAAGCCAAG 61 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 AGC:G+U : :CGUGUGCCG:G:UGU :CUGG::+G+CC 62 GC-AGCAGAU-GACGCGUGUGCCGGGAUGUaGCUGGCAAGGCC 102 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz ----sequence: #3196,sp|U82664.1|ECU82664 Escherichia coli minutes 9 to 11 genomic sequence. ----isReversed: 0 ----hitSequence: CUGUUGGUUCUCCCGCAACGCUACUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCCAAGGCAGAUGACGCGUGUGCCGGGAUGUAGCUGGCAGGGCC hit 134 : 55903 56002 (fwd) 83.14 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +::UUGG: C:C:CGCAACGC : +C:GU ACC GGUCAGGUCCGGAAGGAAGCAGCC 55903 CUGUUGGUuCUCCCGCAACGCUA-CUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCC 55961 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 GC:G+U : GCGUGUGCCG:G:UGU :CUGG:: G+CC 55962 AA-GGCAGAU-GACGCGUGUGCCGGGAUGUaGCUGGCAGGGCC 56002 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz ----sequence: #5448,sp|U32175.1|HD32175 Haemophilus ducreyi hemolytic cytotoxin HhdA and HhdB precursors (hhdA, hhdB) genes, complete cds. ----isReversed: 1 ----hitSequence: UUAUUGGUUUCUCGCAGCAGAAUUCAGCUUACUUAGUCAGGGCCGGAAGGAAGCAGCUUGGGUUGAAUUUCUGGGUGCCGGGAGUCGCUGGUAAUACC hit 135 : 5757 5660 (rev) 68.26 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 +::UUGG: :C CGCA+C:::A ++C:+: AC :GUCAGG CCGGAAGG AGCAGC: 714 UUAUUGGUUUCUCGCAGCAGAA-UUCAGCUUACUUAGUCAGGGCCGGAAGGAAGCAGCUU 772 --->>>>---->>>>>-->>>->>>>--->>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 :+:G++ UU:::G GUGCCG G:++ :CUGG::++ACC 773 G-GGUUGAA-UUUCUGGGUGCCGGGAGUCGCUGGUAAUACC 811 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz ----sequence: #5822,sp|U32795.1|HI32795 Haemophilus influenzae Rd section 110 of 163 of the complete genome. ----isReversed: 0 ----hitSequence: UUCUCGGUCUCUCGCAACGGUGUCUGGUUUACUCGGUCAGGUCCGGAAGGAAGCAGCCAAAGUCGGAAUUACUGUGUGCCGAGAAGAAGCUGGGAAGGUU hit 136 : 4504 4603 (fwd) 77.44 bits :<<<<-<<-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>>> 1 ggcuuGGaCccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCcg 60 +:CU:GG:C:C:CGCAAC::+: +C::+U AC GGUCAGGUCCGGAAGGAAGCAGCC 4504 UUCUCGGUCUCUCGCAACGGUG-UCUGGUUUACUCGGUCAGGUCCGGAAGGAAGCAGCCA 4562 --->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 61 UAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 AG+::++ U:+::GUGUGCCG:G: G+ :CU:GG:+G+ 4563 A-AGUCGGAAUUACUGUGUGCCGAGAAGAaGCUGGGAAGGUU 4603 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz ----sequence: #9764,sp|U15684.1|LM15684 Listeria monocytogenes signal recognition particle scRNA. ----isReversed: 0 ----hitSequence: AGGUUGGGUCUUGCGCAAUGGGAACCUUGUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGCAGUGUUCUCAUGUGCCGCGAGUCGCCUGGCCCGAGC hit 137 : 123 224 (fwd) 94.23 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 G:UUGG: C::GCGCAA:G:GAA C::GUGAACC::GUCAGGUCCGGAAGGAAGCAGC: 123 AGGUUGGGuCUUGCGCAAUGGGAACCUUGUGAACCAUGUCAGGUCCGGAAGGAAGCAGCA 182 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 :UAAGC::U UUC:C:UGUGCCGC::++ :CUGG:CCGA+C 183 UUAAGCAGUG-UUCUCAUGUGCCGCGAGUCgCCUGGCCCGAGC 224 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz ----sequence: #10319,sp|M31830.1|LP45SRNA L.pneumophila 4.5S RNA homolog. ----isReversed: 0 ----hitSequence: CUAUUGGUCCCCUCGCGACGAUAGAUUGUGAACCCCGUCAGGCCCGGAAGGGAGCAGCGGUAGCAGUUGAUGCGGGCGCCGGGGUGUGGCUCUUAGAGUC hit 138 : 30 129 (fwd) 75.68 bits :<<<<-<<.-<<<<<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGa.CccgcgCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 +:: GG: CCC CGC:ACG +: ::GUGAACCC:GUCAGG:CCGGAAGG:AGCAGC: 30 CUAUUGGUcCCCUCGCGACGAUA-GAUUGUGAACCCCGUCAGGCCCGGAAGGGAGCAGCG 88 >--->>>>---->>>>>-->>>->>>>---.>>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcggugu.uCugggccgacC 101 GU AGC::UU :+ CG G:GCCG GGUGU :CU :: + C 89 GU-AGCAGUU-GAUGCGGGCGCCGGGGUGUgGCUCUUAGAGUC 129 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz ----sequence: #12139,sp|D00560.1|MCSRNA Mycoplasma capricolum gene for small RNA. ----isReversed: 0 ----hitSequence: AUUAUAAAGCCGCGAUAAGAAUAACAUCUGAAUGAGUUAGGACCGGAAGGUAGCAGCUAUAAGGAAAAGUGUUCUGUAUUGCGGUUUUUUAUUUGGAGA hit 139 : 60 158 (fwd) 51.48 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 : :A+CCGC ::AA:::+A AC:::UGAA :GU:AGG:CCGGAAGG:AGCA:C: 60 AUUAUAAAGCCGCgAUAAGAAUA-ACAUCUGAAU-GAGUUAGGACCGGAAGGUAGCAGCU 117 >--->>>>---->>>>>-->>>->>>>--->>->>>>::::: 60 gUAAgcgguuuuucgcgUGuGcCgcgguguuCugggccgacC 101 UAAG:::++ U+:::UGU:: GCGGU+UU:U : GA+ 118 AUAAGGAAAA-GUGUUCUGUAUUGCGGUUUUUUAUUUGGAGA 158 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz ----sequence: #12794,sp|U39706.1|MG39706 Mycoplasma genitalium section 28 of 51 of the complete genome. ----isReversed: 1 ----hitSequence: UUUAGAACCAUCACAUCAUUAGAGUCGAAUCAUGUCAGGCCAGAAAUGGAGCAGCAUUAAGACUUGUCAGUGAGUGUGAUGGUUUUUUAUUA hit 140 : 5921 5830 (rev) 48.30 bits :<<<<-<<-<<<<.<<<-<<<<<---<<<<-----<<<-<-<-<<<____>>>-->->>> 1 ggcuuGGaCccgc.gCaAcgcgaaacccguGAACCcgGUCAGGuCCGGAAGGaAGCAGCc 59 ::G:A CC:: :CA C::+ A :::GAA C::GUCAGG:C:G AA:G:AGCAGC: 5132 -UUUAGAA-CCAUcACAUCAUU--AGAGUCGAAUCAUGUCAGGCCAGAAAUGGAGCAGCA 5187 >--->>>>---->>>>>-->>>->>>>--->>->>>>::::: 60 g