Params: ./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc,13,l-CU_-AG,33,l-AG-CU-_,193,r-CU_-AG,192,l-ACU-G_,235,r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc,13,l-ACU-G-_,12,r-AU-C-G-_,33,l-AG-CU-_,32,l-AGU-C-_,31,l-AGU-C-_,193,r-CU_-AG,192,l-ACU-G_,191,l-ACU-G_,190,r-AG-CU-_,235,l-AU_-C-G,234,r-CGU-A_,233,r-AGU-C_,229,r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub,176,75 Build: release Host: bicycle.cs.washington.edu pid: 14797 ----hmm-from-cmFileName: Rfam/cm/RF00017.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-greedy-node 350 76.00 Rfam/cm/RF00017.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 350 76.00 Rfam/cm/RF00017.cm forward-alg-inf 100000 cycling-node cfsqp-elim-gauss 0 1 Build: release Host: recycle.cs.washington.edu ----hmm-from-cmFileName: Rfam/cm/RF00017.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00017.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00017.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu Exploded HMM has 1475 states ----hmm-from-cmFileName: Rfam/cm/RF00017.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --set-input-mm-file data/More_strep_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00017.cm 1 1 100000 1 cfsqp 0 1 Build: release Host: xmen.cs.washington.edu ;Params: ./cmzasha --set-input-mm-file data/Bordetella_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00017.cm 1 1 100000 1 cfsqp 0 1 Build: release Host: xmen.cs.washington.edu ----2struct-info: 1/remember-nuc,13,l-CU_-AG/remember-nuc,33,l-AG-CU-_/remember-nuc,193,r-CU_-AG/remember-nuc,192,l-ACU-G_/remember-nuc,235,r-AGU-C_ Exploded HMM has 4035 states ----hmm-from-cmFileName: Rfam/cm/RF00017.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --set-input-mm-file data/More_strep_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00017.cm 1 1 100000 1 cfsqp 0 1 Build: release Host: xmen.cs.washington.edu ;Params: ./cmzasha --set-input-mm-file data/Bordetella_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00017.cm 1 1 100000 1 cfsqp 0 1 Build: release Host: xmen.cs.washington.edu ----2struct-info: 1/remember-nuc,13,l-ACU-G-_/remember-nuc,12,r-AU-C-G-_/remember-nuc,33,l-AG-CU-_/remember-nuc,32,l-AGU-C-_/remember-nuc,31,l-AGU-C-_/remember-nuc,193,r-CU_-AG/remember-nuc,192,l-ACU-G_/remember-nuc,191,l-ACU-G_/remember-nuc,190,r-AG-CU-_/remember-nuc,235,l-AU_-C-G/remember-nuc,234,r-CGU-A_/remember-nuc,233,r-AGU-C_/remember-nuc,229,r-AGU_-C ----hmm-from-cmFileName: Rfam/cm/RF00017.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --set-input-mm-file data/More_strep_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00017.cm 1 1 100000 1 cfsqp 0 1 Build: release Host: xmen.cs.washington.edu ;Params: ./cmzasha --set-input-mm-file data/Bordetella_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00017.cm 1 1 100000 1 cfsqp 0 1 Build: release Host: xmen.cs.washington.edu ----2struct-info: 1/sub,176,75 ----cmFile: Rfam/cm/RF00017.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/inv01.dat.fasta.gz ----sequence: #4974,sp|AC002512.1|AC002512 Drosophila melanogaster (P1 DS00276 (D13)) DNA sequence, complete sequence. ----isReversed: 0 ----hitSequence: ACUGGAAGGUUGGCAGCUUCUGUAAUCACGCUUCUGUGAGGUCUGAUUGUGGGAUGGCCUGAGGCUGGGAUCUACUGCGUAGCGGACCAGCUCAUGUUGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUCCCGUGGUAGGCAGUAGUGGGAUAGCGUACCGGAGUGGACUGCCGUUAUCAGCCCAACCGAUAUGGUUGGACCACAAUCUU hit 0 : 78113 78409 (fwd) 108.54 bits (((,<<<<__________>>>>,,,,,<<<__....._>>>)))----((((((((---( 1 GCCGGGcgguguGGCGugcgCCUGUAACCCaG.....cGGGGGCcgAAgccugguGgGAg 55 :C:GG::GG +UGGC GC::CUGUAA:C:+G :G::G: :::U:GUGG +: 78113 ACUGGAAGG-UUGGCA-GCUUCUGUAAUCACGcuucuGUGAGGU---CUGAUUGUGG-GA 78166 (--((-..---((--..----((-((----((((------((---------((((((--( 56 uGgcuG..GGucggc..cccgcggggucggcccuggggguaugcUuaUUGaaggcccGCc 111 :GGC:+ GG+ GG+ C + :G+G: + C+: G+U:: +UU GA:GG::CG C 78167 UGGCCUgaGGCUGGGauCUACUGCGUAG--CGGACCAGCUCAUGUU---GACGGAACGUC 78221 (--(((--((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>, 112 CcuuCcaAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuU 171 C +:C:AAGC::::::U ::::::G:::GCC::G::GGAG::C::GGC:::C:::::: 78222 CGCACUAAGCUUGCCAU--CAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGG 78279 ,,,,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))) 172 CUAAAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccg 231 CUAA+G GG:::GAACCG:G:CAGG+::G A A::+AGCA:C:AA A:::CCCG::::: 78280 CUAAGGAGGGAUGAACCGGGCCAGGGGUGAA--AACCAGCAGCCAAGAGUUCCCGUGGUA 78337 )))---)))--))---.-))))))-----))------))))-.-------))-))----- 232 ggCGGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagGcc 289 :GC+GU:G:G GGAUA CG::CC:G AG::+ AC :+G +U :C C:A C 78338 GGCAGUAGUG-GGAUAgCGUACCGG--AGUGG--ACUGCCGUu---AUCAGCCCAA---C 78386 )).---))--))---)))))))): 290 cg.cacagucaaGACCaccaggcU 312 C +A+:GU+:: ACCAC:A:::U 78387 CGaUAUGGUUGG-ACCACAAUCUU 78409 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #4974,sp|AC002512.1|AC002512 Drosophila melanogaster (P1 DS00276 (D13)) DNA sequence, complete sequence. ----isReversed: 1 ----hitSequence: ACUGGAAGGUUGGCAGCUUCUGUAAUCACGCUUCUGUGAGGUCUGAUUGUGGGAUGGCCUGAGGCUGGGAUCUACUGCGUAGCGGACCAGCUCAUGUUGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUCCCGUGGUAGGCAGUAGUGGGAUAGCGUACCGGAGUGGACUGCCGUUAUCAGCCCAACCGAUAUGGUUGGACCACAAUCUU hit 1 : 76040 75744 (rev) 108.54 bits (((,<<<<__________>>>>,,,,,<<<__....._>>>)))----((((((((---( 1 GCCGGGcgguguGGCGugcgCCUGUAACCCaG.....cGGGGGCcgAAgccugguGgGAg 55 :C:GG::GG +UGGC GC::CUGUAA:C:+G :G::G: :::U:GUGG +: 8207 ACUGGAAGG-UUGGCA-GCUUCUGUAAUCACGcuucuGUGAGGU---CUGAUUGUGG-GA 8260 (--((-..---((--..----((-((----((((------((---------((((((--( 56 uGgcuG..GGucggc..cccgcggggucggcccuggggguaugcUuaUUGaaggcccGCc 111 :GGC:+ GG+ GG+ C + :G+G: + C+: G+U:: +UU GA:GG::CG C 8261 UGGCCUgaGGCUGGGauCUACUGCGUAG--CGGACCAGCUCAUGUU---GACGGAACGUC 8315 (--(((--((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>, 112 CcuuCcaAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuU 171 C +:C:AAGC::::::U ::::::G:::GCC::G::GGAG::C::GGC:::C:::::: 8316 CGCACUAAGCUUGCCAU--CAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGG 8373 ,,,,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))) 172 CUAAAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccg 231 CUAA+G GG:::GAACCG:G:CAGG+::G A A::+AGCA:C:AA A:::CCCG::::: 8374 CUAAGGAGGGAUGAACCGGGCCAGGGGUGAA--AACCAGCAGCCAAGAGUUCCCGUGGUA 8431 )))---)))--))---.-))))))-----))------))))-.-------))-))----- 232 ggCGGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagGcc 289 :GC+GU:G:G GGAUA CG::CC:G AG::+ AC :+G +U :C C:A C 8432 GGCAGUAGUG-GGAUAgCGUACCGG--AGUGG--ACUGCCGUu---AUCAGCCCAA---C 8480 )).---))--))---)))))))): 290 cg.cacagucaaGACCaccaggcU 312 C +A+:GU+:: ACCAC:A:::U 8481 CGaUAUGGUUGG-ACCACAAUCUU 8503 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #6331,sp|AC084446.1|AC084446 Caenorhabditis briggsae cosmid CB018G16, complete sequence. ----isReversed: 1 ----hitSequence: ACCGGGUGUCGUGGCGGGCGCCUGUGAGUCAGCUUCUUGACGGUAGACAAGUGUGGAUGGAGUGAAGGGAGGAGUCCUGUGGGUGUUGUCGGCAACGGCGACCGAGCGUCCGUGCCAAGCGCUGCGUCGCCAGGGGUCUCCGGUCGGAAGGCUGGCGGUCCCGGGCGCAUAAGGAGUGGUGCACGGCUCAGGGCCGAAAGGCAGCAGGCAAAAGCCACCGCGCGGUGCAGUGGCCGGAUAGCGCUUGUGAGUUGUCGCUCGCCCACAGCCUCUCUGAUACCUUCAGACCACUUGUC hit 2 : 16506 16211 (rev) 133.97 bits (((,<<<<__________>>>>,,,,,<<<__....._>>>)))----((((((((---( 1 GCCGGGcgguguGGCGugcgCCUGUAACCCaG.....cGGGGGCcgAAgccugguGgGAg 55 :CCGGG:G++GUGGCG GC:CCUGU A::CAG +G::GG: AG:C::GUG G+: 30196 ACCGGGUGUCGUGGCGGGCGCCUGUGAGUCAGcuucuUGACGGU---AGACAAGUGUGGA 30252 (--((----((--.......----((-((----((((------((---------(((((( 56 uGgcuGGGucggc.......cccgcggggucggcccuggggguaugcUuaUUGaaggccc 108 UGG:: U : + +CC+ GGGU : ::+ GG+ A G+ GA::::+C 30253 UGGAG---UGAAGggaggagUCCUGUGGGU---GUUGUCGGCAACGGC----GACCGAGC 30302 --((--(((--((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>> 109 GCcCcuuCcaAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgc 168 G CC U:CCAAGC C:G:GU :G:C:GGG: : CC+G:CGGA+G:C+GG : :CCC:G: 30303 GUCCGUGCCAAGCGCUGCGU--CGCCAGGGGUCUCCGGUCGGAAGGCUGGCGGUCCCGGG 30360 >>,,,.,,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,) 169 cuUCU.AAAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgC 227 C: C AA+G G:GG:G AC G::UCAGG+CCG A AGG+AGCAG::AAAA:CC:CCGC 30361 CG-CAuAAGGAGUGGUGCAC-GGCUCAGGGCCGAA--AGGCAGCAGGCAAAAGCCACCGC 30416 )))))))---)))--))---.-))))))-----))------))))--------))-))-- 228 uccgggCGGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggccuacuGGccucgag 286 :C:G GC+GUGG: GGAUA CG+::::G AG U+ C :: :C ++ GCCU ++ 30417 GCGGUGCAGUGGCC-GGAUAgCGCUUGUG--AGUUGUCGCUCGCCC---ACAGCCUCUCU 30470 ---)).---))--))---)))))))): 287 Gcccg.cacagucaaGACCaccaggcU 312 G : ::UCA: ACCAC::G:C 30471 G-AUAc---CUUCAG-ACCACUUGUC- 30491 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #6748,sp|AC095014.1|AC095014 Drosophila melanogaster, chromosome 3R, region 83F-84A, BAC clone BACR19D23, complete sequence. ----isReversed: 0 ----hitSequence: ACUGGAAGGUUGGCAGCUUCUGUAAUCACGCUUCUGUGAGGUCUGAUUGUGGGAUGGCCUGAGGCUGGGAUCUACUGCGUAGCGGACCAGCUCAUGUUGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUCCCGUGGUAGGCAGUAGUGGGAUAGCGUACCGGAGUGGACUGCCGUUAUCAGCCCAACCGAUAUGGUUGGACCACAAUCUU hit 3 : 156446 156742 (fwd) 108.54 bits (((,<<<<__________>>>>,,,,,<<<__....._>>>)))----((((((((---( 1 GCCGGGcgguguGGCGugcgCCUGUAACCCaG.....cGGGGGCcgAAgccugguGgGAg 55 :C:GG::GG +UGGC GC::CUGUAA:C:+G :G::G: :::U:GUGG +: 156446 ACUGGAAGG-UUGGCA-GCUUCUGUAAUCACGcuucuGUGAGGU---CUGAUUGUGG-GA 156499 (--((-..---((--..----((-((----((((------((---------((((((--( 56 uGgcuG..GGucggc..cccgcggggucggcccuggggguaugcUuaUUGaaggcccGCc 111 :GGC:+ GG+ GG+ C + :G+G: + C+: G+U:: +UU GA:GG::CG C 156500 UGGCCUgaGGCUGGGauCUACUGCGUAG--CGGACCAGCUCAUGUU---GACGGAACGUC 156554 (--(((--((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>, 112 CcuuCcaAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuU 171 C +:C:AAGC::::::U ::::::G:::GCC::G::GGAG::C::GGC:::C:::::: 156555 CGCACUAAGCUUGCCAU--CAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGG 156612 ,,,,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))) 172 CUAAAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccg 231 CUAA+G GG:::GAACCG:G:CAGG+::G A A::+AGCA:C:AA A:::CCCG::::: 156613 CUAAGGAGGGAUGAACCGGGCCAGGGGUGAA--AACCAGCAGCCAAGAGUUCCCGUGGUA 156670 )))---)))--))---.-))))))-----))------))))-.-------))-))----- 232 ggCGGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagGcc 289 :GC+GU:G:G GGAUA CG::CC:G AG::+ AC :+G +U :C C:A C 156671 GGCAGUAGUG-GGAUAgCGUACCGG--AGUGG--ACUGCCGUu---AUCAGCCCAA---C 156719 )).---))--))---)))))))): 290 cg.cacagucaaGACCaccaggcU 312 C +A+:GU+:: ACCAC:A:::U 156720 CGaUAUGGUUGG-ACCACAAUCUU 156742 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #6748,sp|AC095014.1|AC095014 Drosophila melanogaster, chromosome 3R, region 83F-84A, BAC clone BACR19D23, complete sequence. ----isReversed: 1 ----hitSequence: ACUGGAAGGUUGGCAGCUUCUGUAAUCACGCUUCUGUGAGGUCUGAUUGUGGGAUGGCCUGAGGCUGGGAUCUACUGCGUAGCGGACCAGCUCAUGUUGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUCCCGUGGUAGGCAGUAGUGGGAUAGCGUACCGGAGUGGACUGCCGUUAUCAGCCCAACCGAUAUGGUUGGACCACAAUCUU hit 4 : 154373 154077 (rev) 108.54 bits (((,<<<<__________>>>>,,,,,<<<__....._>>>)))----((((((((---( 1 GCCGGGcgguguGGCGugcgCCUGUAACCCaG.....cGGGGGCcgAAgccugguGgGAg 55 :C:GG::GG +UGGC GC::CUGUAA:C:+G :G::G: :::U:GUGG +: 16429 ACUGGAAGG-UUGGCA-GCUUCUGUAAUCACGcuucuGUGAGGU---CUGAUUGUGG-GA 16482 (--((-..---((--..----((-((----((((------((---------((((((--( 56 uGgcuG..GGucggc..cccgcggggucggcccuggggguaugcUuaUUGaaggcccGCc 111 :GGC:+ GG+ GG+ C + :G+G: + C+: G+U:: +UU GA:GG::CG C 16483 UGGCCUgaGGCUGGGauCUACUGCGUAG--CGGACCAGCUCAUGUU---GACGGAACGUC 16537 (--(((--((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>, 112 CcuuCcaAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuU 171 C +:C:AAGC::::::U ::::::G:::GCC::G::GGAG::C::GGC:::C:::::: 16538 CGCACUAAGCUUGCCAU--CAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGG 16595 ,,,,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))) 172 CUAAAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccg 231 CUAA+G GG:::GAACCG:G:CAGG+::G A A::+AGCA:C:AA A:::CCCG::::: 16596 CUAAGGAGGGAUGAACCGGGCCAGGGGUGAA--AACCAGCAGCCAAGAGUUCCCGUGGUA 16653 )))---)))--))---.-))))))-----))------))))-.-------))-))----- 232 ggCGGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagGcc 289 :GC+GU:G:G GGAUA CG::CC:G AG::+ AC :+G +U :C C:A C 16654 GGCAGUAGUG-GGAUAgCGUACCGG--AGUGG--ACUGCCGUu---AUCAGCCCAA---C 16702 )).---))--))---)))))))): 290 cg.cacagucaaGACCaccaggcU 312 C +A+:GU+:: ACCAC:A:::U 16703 CGaUAUGGUUGG-ACCACAAUCUU 16725 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #7416,sp|AE001572.2|AE001572 Drosophila melanogaster Antennapedia complex (ANT-C),complete sequence. ----isReversed: 0 ----hitSequence: ACUGGAAGGUUGGCAGCUUCUGUAAUCACGCUUCUGUGAGGUCUGAUUGUGGGAUGGCCUGAGGCUGGGAUCUACUGCGUAGCGGACCAGCUCAUGUUGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUCCCGUGGUAGGCAGUAGUGGGAUAGCGUACCGGAGUGGACUGCCGUUAUCAGCCCAACCGAUAUGGUUGGACCACAAUCUU hit 5 : 236401 236697 (fwd) 108.54 bits (((,<<<<__________>>>>,,,,,<<<__....._>>>)))----((((((((---( 1 GCCGGGcgguguGGCGugcgCCUGUAACCCaG.....cGGGGGCcgAAgccugguGgGAg 55 :C:GG::GG +UGGC GC::CUGUAA:C:+G :G::G: :::U:GUGG +: 236401 ACUGGAAGG-UUGGCA-GCUUCUGUAAUCACGcuucuGUGAGGU---CUGAUUGUGG-GA 236454 (--((-..---((--..----((-((----((((------((---------((((((--( 56 uGgcuG..GGucggc..cccgcggggucggcccuggggguaugcUuaUUGaaggcccGCc 111 :GGC:+ GG+ GG+ C + :G+G: + C+: G+U:: +UU GA:GG::CG C 236455 UGGCCUgaGGCUGGGauCUACUGCGUAG--CGGACCAGCUCAUGUU---GACGGAACGUC 236509 (--(((--((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>, 112 CcuuCcaAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuU 171 C +:C:AAGC::::::U ::::::G:::GCC::G::GGAG::C::GGC:::C:::::: 236510 CGCACUAAGCUUGCCAU--CAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGG 236567 ,,,,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))) 172 CUAAAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccg 231 CUAA+G GG:::GAACCG:G:CAGG+::G A A::+AGCA:C:AA A:::CCCG::::: 236568 CUAAGGAGGGAUGAACCGGGCCAGGGGUGAA--AACCAGCAGCCAAGAGUUCCCGUGGUA 236625 )))---)))--))---.-))))))-----))------))))-.-------))-))----- 232 ggCGGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagGcc 289 :GC+GU:G:G GGAUA CG::CC:G AG::+ AC :+G +U :C C:A C 236626 GGCAGUAGUG-GGAUAgCGUACCGG--AGUGG--ACUGCCGUu---AUCAGCCCAA---C 236674 )).---))--))---)))))))): 290 cg.cacagucaaGACCaccaggcU 312 C +A+:GU+:: ACCAC:A:::U 236675 CGaUAUGGUUGG-ACCACAAUCUU 236697 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #7416,sp|AE001572.2|AE001572 Drosophila melanogaster Antennapedia complex (ANT-C),complete sequence. ----isReversed: 1 ----hitSequence: ACUGGAAGGUUGGCAGCUUCUGUAAUCACGCUUCUGUGAGGUCUGAUUGUGGGAUGGCCUGAGGCUGGGAUCUACUGCGUAGCGGACCAGCUCAUGUUGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUCCCGUGGUAGGCAGUAGUGGGAUAGCGUACCGGAGUGGACUGCCGUUAUCAGCCCAACCGAUAUGGUUGGACCACAAUCUU hit 6 : 234328 234032 (rev) 108.54 bits (((,<<<<__________>>>>,,,,,<<<__....._>>>)))----((((((((---( 1 GCCGGGcgguguGGCGugcgCCUGUAACCCaG.....cGGGGGCcgAAgccugguGgGAg 55 :C:GG::GG +UGGC GC::CUGUAA:C:+G :G::G: :::U:GUGG +: 195498 ACUGGAAGG-UUGGCA-GCUUCUGUAAUCACGcuucuGUGAGGU---CUGAUUGUGG-GA 195551 (--((-..---((--..----((-((----((((------((---------((((((--( 56 uGgcuG..GGucggc..cccgcggggucggcccuggggguaugcUuaUUGaaggcccGCc 111 :GGC:+ GG+ GG+ C + :G+G: + C+: G+U:: +UU GA:GG::CG C 195552 UGGCCUgaGGCUGGGauCUACUGCGUAG--CGGACCAGCUCAUGUU---GACGGAACGUC 195606 (--(((--((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>, 112 CcuuCcaAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuU 171 C +:C:AAGC::::::U ::::::G:::GCC::G::GGAG::C::GGC:::C:::::: 195607 CGCACUAAGCUUGCCAU--CAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGG 195664 ,,,,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))) 172 CUAAAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccg 231 CUAA+G GG:::GAACCG:G:CAGG+::G A A::+AGCA:C:AA A:::CCCG::::: 195665 CUAAGGAGGGAUGAACCGGGCCAGGGGUGAA--AACCAGCAGCCAAGAGUUCCCGUGGUA 195722 )))---)))--))---.-))))))-----))------))))-.-------))-))----- 232 ggCGGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagGcc 289 :GC+GU:G:G GGAUA CG::CC:G AG::+ AC :+G +U :C C:A C 195723 GGCAGUAGUG-GGAUAgCGUACCGG--AGUGG--ACUGCCGUu---AUCAGCCCAA---C 195771 )).---))--))---)))))))): 290 cg.cacagucaaGACCaccaggcU 312 C +A+:GU+:: ACCAC:A:::U 195772 CGaUAUGGUUGG-ACCACAAUCUU 195794 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #7689,sp|AE003673.3|AE003673 Drosophila melanogaster chromosome 3R, section 11 of 118 of the complete sequence. ----isReversed: 0 ----hitSequence: ACUGGAAGGUUGGCAGCUUCUGUAAUCACGCUUCUGUGAGGUCUGAUUGUGGGAUGGCCUGAGGCUGGGAUCUACUGCGUAGCGGACCAGCUCAUGUUGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUCCCGUGGUAGGCAGUAGUGGGAUAGCGUACCGGAGUGGACUGCCGUUAUCAGCCCAACCGAUAUGGUUGGACCACAAUCUU hit 7 : 44323 44619 (fwd) 108.54 bits (((,<<<<__________>>>>,,,,,<<<__....._>>>)))----((((((((---( 1 GCCGGGcgguguGGCGugcgCCUGUAACCCaG.....cGGGGGCcgAAgccugguGgGAg 55 :C:GG::GG +UGGC GC::CUGUAA:C:+G :G::G: :::U:GUGG +: 44323 ACUGGAAGG-UUGGCA-GCUUCUGUAAUCACGcuucuGUGAGGU---CUGAUUGUGG-GA 44376 (--((-..---((--..----((-((----((((------((---------((((((--( 56 uGgcuG..GGucggc..cccgcggggucggcccuggggguaugcUuaUUGaaggcccGCc 111 :GGC:+ GG+ GG+ C + :G+G: + C+: G+U:: +UU GA:GG::CG C 44377 UGGCCUgaGGCUGGGauCUACUGCGUAG--CGGACCAGCUCAUGUU---GACGGAACGUC 44431 (--(((--((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>, 112 CcuuCcaAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuU 171 C +:C:AAGC::::::U ::::::G:::GCC::G::GGAG::C::GGC:::C:::::: 44432 CGCACUAAGCUUGCCAU--CAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGG 44489 ,,,,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))) 172 CUAAAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccg 231 CUAA+G GG:::GAACCG:G:CAGG+::G A A::+AGCA:C:AA A:::CCCG::::: 44490 CUAAGGAGGGAUGAACCGGGCCAGGGGUGAA--AACCAGCAGCCAAGAGUUCCCGUGGUA 44547 )))---)))--))---.-))))))-----))------))))-.-------))-))----- 232 ggCGGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagGcc 289 :GC+GU:G:G GGAUA CG::CC:G AG::+ AC :+G +U :C C:A C 44548 GGCAGUAGUG-GGAUAgCGUACCGG--AGUGG--ACUGCCGUu---AUCAGCCCAA---C 44596 )).---))--))---)))))))): 290 cg.cacagucaaGACCaccaggcU 312 C +A+:GU+:: ACCAC:A:::U 44597 CGaUAUGGUUGG-ACCACAAUCUU 44619 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #7689,sp|AE003673.3|AE003673 Drosophila melanogaster chromosome 3R, section 11 of 118 of the complete sequence. ----isReversed: 1 ----hitSequence: ACUGGAAGGUUGGCAGCUUCUGUAAUCACGCUUCUGUGAGGUCUGAUUGUGGGAUGGCCUGAGGCUGGGAUCUACUGCGUAGCGGACCAGCUCAUGUUGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUCCCGUGGUAGGCAGUAGUGGGAUAGCGUACCGGAGUGGACUGCCGUUAUCAGCCCAACCGAUAUGGUUGGACCACAAUCUU hit 8 : 42250 41954 (rev) 108.54 bits (((,<<<<__________>>>>,,,,,<<<__....._>>>)))----((((((((---( 1 GCCGGGcgguguGGCGugcgCCUGUAACCCaG.....cGGGGGCcgAAgccugguGgGAg 55 :C:GG::GG +UGGC GC::CUGUAA:C:+G :G::G: :::U:GUGG +: 265897 ACUGGAAGG-UUGGCA-GCUUCUGUAAUCACGcuucuGUGAGGU---CUGAUUGUGG-GA 265950 (--((-..---((--..----((-((----((((------((---------((((((--( 56 uGgcuG..GGucggc..cccgcggggucggcccuggggguaugcUuaUUGaaggcccGCc 111 :GGC:+ GG+ GG+ C + :G+G: + C+: G+U:: +UU GA:GG::CG C 265951 UGGCCUgaGGCUGGGauCUACUGCGUAG--CGGACCAGCUCAUGUU---GACGGAACGUC 266005 (--(((--((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>, 112 CcuuCcaAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuU 171 C +:C:AAGC::::::U ::::::G:::GCC::G::GGAG::C::GGC:::C:::::: 266006 CGCACUAAGCUUGCCAU--CAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGG 266063 ,,,,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))) 172 CUAAAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccg 231 CUAA+G GG:::GAACCG:G:CAGG+::G A A::+AGCA:C:AA A:::CCCG::::: 266064 CUAAGGAGGGAUGAACCGGGCCAGGGGUGAA--AACCAGCAGCCAAGAGUUCCCGUGGUA 266121 )))---)))--))---.-))))))-----))------))))-.-------))-))----- 232 ggCGGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagGcc 289 :GC+GU:G:G GGAUA CG::CC:G AG::+ AC :+G +U :C C:A C 266122 GGCAGUAGUG-GGAUAgCGUACCGG--AGUGG--ACUGCCGUu---AUCAGCCCAA---C 266170 )).---))--))---)))))))): 290 cg.cacagucaaGACCaccaggcU 312 C +A+:GU+:: ACCAC:A:::U 266171 CGaUAUGGUUGG-ACCACAAUCUU 266193 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #43107,sp|Z30973.1|CEB0284 Caenorhabditis elegans cosmid B0284 ----isReversed: 1 ----hitSequence: ACCGAGCGUCGUGGCGGGCGCUUGUGAGUCAGCUUCUUGACGGUAGAUAAGUGUGGAUGGAGUGAGAGGAGGAGUCCUGUGUAUGUCGUUGUCAACGUCGACCGAGCGUCCGUGCCAAGCGCUGCGUCACCAGGGGAUGACUGUCGGAAGAUGGUCAGUCCCGGGUGCAUAAGGAGUGGUGGAUGGUUCAGGACCGAAAGGUAGCAGACAAAAGCCACCGCGCGGUGCAGUGGCCGGACUGCGCUUGUGAGUUGACACGUAUACACAGCCUUCUCAAUACCUUCAGACCACUUGUUU hit 9 : 7231 6935 (rev) 127.35 bits (((,<<<<__________>>>>,,,,,<<<__....._>>>)))----((((((((---( 1 GCCGGGcgguguGGCGugcgCCUGUAACCCaG.....cGGGGGCcgAAgccugguGgGAg 55 :CCG:GCG++GUGGCG GCGC:UGU A::CAG +G::GG: A:::::GUG G+: 13959 ACCGAGCGUCGUGGCGGGCGCUUGUGAGUCAGcuucuUGACGGU---AGAUAAGUGUGGA 14015 (--((----((------((-((---.-((((------((-----.----((((((--((- 56 uGgcuGGGucggccccgcggggucg.gcccuggggguaugcUua.UUGaaggcccGCcCc 113 UGG:: U :G G:GG:GUC G +::+G+ GU C + U GA::::+CG CC 14016 UGGAG---UGAG--AGGAGGAGUCCuGUGUAUGUCGUUGUCAACgUCGACCGAGCGUCCG 14070 -(((--((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,, 114 uuCcaAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCU 173 U:CCAAGC C:G:GU :::C:GGG:: ::C:::CGGA+G:::G:: ::CCC:G::: C 14071 UGCCAAGCGCUGCGU--CACCAGGGGAUGACUGUCGGAAGAUGGUCAGUCCCGGGUG-CA 14127 .,,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,)))))) 174 .AAAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgg 232 AA+G G:GG:G+A G::UCAGG:CCG A AGG:AGCAG::AAAA:CC:CCGC:C:G 14128 uAAGGAGUGGUGGAU-GGUUCAGGACCGAA--AGGUAGCAGACAAAAGCCACCGCGCGGU 14184 ))---)))--))---.-))))))-----))------))))-.-------))-))-----) 233 gCGGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagGccc 290 GC+GUGG: GGA CG+::::G AG +A AC ::+ C C G C:UC:+ : 14185 GCAGUGGCC-GGACUgCGCUUGUG--AGUUGACACGUAUACa---CAGCCUUCUCA--AU 14236 ).---))--))---)))))))): 291 g.cacagucaaGACCaccaggcU 312 ::UCA: ACCAC:::::U 14237 Ac---CUUCAG-ACCACUUGUUU 14255 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #43108,sp|Z34533.1|CEB0285 Caenorhabditis elegans cosmid B0285 ----isReversed: 0 ----hitSequence: ACCGAGCGUCGUGGCGGGCGCUUGUGAGUCAGCUUCUUGACGGUAGAUGAGUGUGGAUGGAGUGAGAGGAGGAGUCCUGUGUAUGUCGUUGUCAACGUCGACCGAGCGUCCGUGCCAAGCGCUGCGUCACCAGGGGAUGACUGUCGGAAGAUGGUCAGUCCCGGGUGCAUAAGGAGUGGUGGAUGGUUCAGGACCGAAAGGUAGCAGACAAAAGCCACCGCGCGGUGCAGUGGCCGGACAGCGCUUGUGAGUUGACACGUAUACACAGCCUUCUCAAUACCUUCAGACCACUUGUC hit 10 : 38786 39081 (fwd) 127.45 bits (((,<<<<__________>>>>,,,,,<<<__....._>>>)))----((((((((---( 1 GCCGGGcgguguGGCGugcgCCUGUAACCCaG.....cGGGGGCcgAAgccugguGgGAg 55 :CCG:GCG++GUGGCG GCGC:UGU A::CAG +G::GG: AG::::GUG G+: 38786 ACCGAGCGUCGUGGCGGGCGCUUGUGAGUCAGcuucuUGACGGU---AGAUGAGUGUGGA 38842 (--((----((------((-((---.-((((------((-----.----((((((--((- 56 uGgcuGGGucggccccgcggggucg.gcccuggggguaugcUua.UUGaaggcccGCcCc 113 UGG:: U :G G:GG:GUC G +::+G+ GU C + U GA::::+CG CC 38843 UGGAG---UGAG--AGGAGGAGUCCuGUGUAUGUCGUUGUCAACgUCGACCGAGCGUCCG 38897 -(((--((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,, 114 uuCcaAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCU 173 U:CCAAGC C:G:GU :::C:GGG:: ::C:::CGGA+G:::G:: ::CCC:G::: C 38898 UGCCAAGCGCUGCGU--CACCAGGGGAUGACUGUCGGAAGAUGGUCAGUCCCGGGUG-CA 38954 .,,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,)))))) 174 .AAAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgg 232 AA+G G:GG:G+A G::UCAGG:CCG A AGG:AGCAG::AAAA:CC:CCGC:C:G 38955 uAAGGAGUGGUGGAU-GGUUCAGGACCGAA--AGGUAGCAGACAAAAGCCACCGCGCGGU 39011 ))---)))--))---.-))))))-----))------))))-.-------))-))-----) 233 gCGGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagGccc 290 GC+GUGG: GGA A CG+::::G AG +A AC ::+ C C G C:UC:+ : 39012 GCAGUGGCC-GGACAgCGCUUGUG--AGUUGACACGUAUACa---CAGCCUUCUCA--AU 39063 ).---))--))---)))))))): 291 g.cacagucaaGACCaccaggcU 312 ::UCA: ACCAC::::C 39064 Ac---CUUCAG-ACCACUUGUC- 39081 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #44091,sp|U41993.1|CEF44A2 Caenorhabditis elegans cosmid F44A2, complete sequence. ----isReversed: 1 ----hitSequence: ACCGGGCGUCGUGGCGGGCGUCUGUAAGCCAGCUUCUUGGCGGUAGAUAAGUGUGGAUGGAGUGAAGGGAGGAGCCCUUUGGGUGUUGCUGGCAACGGCGACCGAGCGUCCGUGCCAAGCGCUGCGUCGCUAGGGGUCAUCUGGCGGAAGGCGGGCGGUCCCGGGCGCAUAAGGAGCGGUAUACGGCUCAGGGCCGAAAGGCAGCAGGCAAAAGCCUCCGCGCGGUGCAGUGGCCGGAUAGCGCUUGCGAGUUGUCGCUCACCCACUGCCUCUCUGAUACCUUUAGACCACUUAUC hit 11 : 1858 1563 (rev) 117.29 bits (((,<<<<__________>>>>,,,,,<<<__....._>>>)))----((((((((---( 1 GCCGGGcgguguGGCGugcgCCUGUAACCCaG.....cGGGGGCcgAAgccugguGgGAg 55 :CCGG CG++GUGGCG GCG CUGUAA:CCAG +GG:GG: AG::::GUG G+: 36783 ACCGGGCGUCGUGGCGGGCGUCUGUAAGCCAGcuucuUGGCGGU---AGAUAAGUGUGGA 36839 (--((----((--.......----((-((----((((------((---------(((((( 56 uGgcuGGGucggc.......cccgcggggucggcccuggggguaugcUuaUUGaaggccc 108 UGG:: U : + CCC+ GGGU : :: GG+ A G+ GA :::+C 36840 UGGAG---UGAAGggaggagCCCUUUGGGU---GUUGCUGGCAACGGC----GACCGAGC 36889 --((--(((--((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>> 109 GCcCcuuCcaAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgc 168 G CC U:CCAAGC C:G:GU :G:::GGG: : :C:G CGGA+G C:G: : :CCC::: 36890 GUCCGUGCCAAGCGCUGCGU--CGCUAGGGGUCAUCUGGCGGAAGGCGGGCGGUCCCGGG 36947 >>,,,.,,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,) 169 cuUCU.AAAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgC 227 C: C AA+G G GG: AC G::UCAGG+CCG A AGG+AGCAG::AAAA:CC CCGC 36948 CG-CAuAAGGAGCGGUAUAC-GGCUCAGGGCCGAA--AGGCAGCAGGCAAAAGCCUCCGC 37003 )))))))---)))--))---.-))))))-----))------))))--------))-))-- 228 uccgggCGGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggccuacuGGccucgag 286 :C:G GC+GUGG: GGAUA CG+::: G AG U+ C :: :C ++ GCCU ++ 37004 GCGGUGCAGUGGCC-GGAUAgCGCUUGCG--AGUUGUCGCUCACCC---ACUGCCUCUCU 37057 ---)).---))--))---)))))))): 287 Gcccg.cacagucaaGACCaccaggcU 312 G : ::U+A: ACCAC::::C 37058 G-AUAc---CUUUAG-ACCACUUAUC- 37078 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #44947,sp|U23515.1|CER144 Caenorhabditis elegans cosmid R144, complete sequence. ----isReversed: 1 ----hitSequence: ACCGAGCGUCGUGGCGGGCGCUUGUGAGUCAGCUUCUUGACGGUAGAUAAGUGUGGAUGGAGUGAGAGGAGGAGUCCUGUGUAUGUCGUCGUCUACGUCGACCGAGCGUCCGUGCCAAGCGCUACGUCACCAGGGGAUAACUGUCGGAAGGCGGUUAGUCCCGGGUGCAUAAGGAGUCGUGGAUGGUUCAGGACCGAAAGGUAGCAGACAAAAGCGACCGCGUGGUGCAGUGGCCGGACCGCGCUUGUAAGUUGACACACAUACACAGCCUUCUCGAUACCUUCAGACCACUUAUC hit 12 : 33862 33567 (rev) 116.17 bits (((,<<<<__________>>>>,,,,,<<<__....._>>>)))----((((((((---( 1 GCCGGGcgguguGGCGugcgCCUGUAACCCaG.....cGGGGGCcgAAgccugguGgGAg 55 :CCG:GCG++GUGGCG GCGC:UGU A::CAG +G::GG: AG::::GUG G+: 4826 ACCGAGCGUCGUGGCGGGCGCUUGUGAGUCAGcuucuUGACGGU---AGAUAAGUGUGGA 4882 (--((----((------((-((---.-((((------((-----..----((((((--(( 56 uGgcuGGGucggccccgcggggucg.gcccuggggguaugcUua..UUGaaggcccGCcC 112 UGG:: U :G G:GG:GUC +::U G++ :G UA U GA::::+CG CC 4883 UGGAG---UGAG--AGGAGGAGUCCu-GUGUAUGUCGUCGUCUAcgUCGACCGAGCGUCC 4936 --(((--((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,, 113 cuuCcaAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUC 172 U:CCAAGC C:::GU :::C:GGG:: ::C:G:CGGA+G:C:G:: ::CCC:G::: C 4937 GUGCCAAGCGCUACGU--CACCAGGGGAUAACUGUCGGAAGGCGGUUAGUCCCGGGUG-C 4993 ,.,,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))) 173 U.AAAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccg 231 AA+G G::G:G+A G::UCAGG:CCG A AGG:AGCAG::AAAA:C::CCGC:::G 4994 AuAAGGAGUCGUGGAU-GGUUCAGGACCGAA--AGGUAGCAGACAAAAGCGACCGCGUGG 5050 )))---)))--))---.-))))))-----))------))))--------))-))-----) 232 ggCGGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggccuacuGGccucgagGccc 290 GC+GUGG: GGA CG+:::: A : +A+ CA::++C+ C G C:UC:+G : 5051 UGCAGUGGCC-GGACCgCGCUUGU---AAGUUGACACACAUACA-CAGCCUUCUCG--AU 5103 ).---))--))---)))))))): 291 g.cacagucaaGACCaccaggcU 312 ::UCA: ACCAC::::C 5104 Ac---CUUCAG-ACCACUUAUC- 5121 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #46068,sp|U00064.1|CEZC155 Caenorhabditis elegans cosmid ZC155, complete sequence. ----isReversed: 0 ----hitSequence: ACCGAGCGUCGUGGCGGGCGCUUGUGAGUCAGCUUCUUGACGGUAGAUAAGUGUGGAUGGAGUGAGAGGAGGAGUCCUGUGUAUGUCGUUGUCUACGUCGACCGAGCGUCCGUGCCAAGCGCUACGUCACCAGGGGAUAACUGUCGGAAGGCGGUUAGUCCCGGGUGCAUAAGGAGUCGUGGAUGGUUCAGGACCGAAAGGUAGCAGACAAAAGCGACCGCGUGGUGCAGUGGCCGGACCGCGCUUGUGAGUUGACACACAUACGCAGCCUUCUCGAUACCUUCAGACCACUUAUC hit 13 : 12850 13145 (fwd) 121.37 bits (((,<<<<__________>>>>,,,,,<<<__....._>>>)))----((((((((---( 1 GCCGGGcgguguGGCGugcgCCUGUAACCCaG.....cGGGGGCcgAAgccugguGgGAg 55 :CCG:GCG++GUGGCG GCGC:UGU A::CAG +G::GG: AG::::GUG G+: 12850 ACCGAGCGUCGUGGCGGGCGCUUGUGAGUCAGcuucuUGACGGU---AGAUAAGUGUGGA 12906 (--((----((------((-((---.-((((------((-----.----((((((--((- 56 uGgcuGGGucggccccgcggggucg.gcccuggggguaugcUua.UUGaaggcccGCcCc 113 UGG:: U :G G:GG:GUC G:+::+G+ GU: CU+ U GA::::+CG CC 12907 UGGAG---UGAG--AGGAGGAGUCCuGUGUAUGUCGUUGUCUACgUCGACCGAGCGUCCG 12961 -(((--((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,, 114 uuCcaAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCU 173 U:CCAAGC C:::GU :::C:GGG:: ::C:G:CGGA+G:C:G:: ::CCC:G::: C 12962 UGCCAAGCGCUACGU--CACCAGGGGAUAACUGUCGGAAGGCGGUUAGUCCCGGGUG-CA 13018 .,,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,)))))) 174 .AAAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgg 232 AA+G G::G:G+A G::UCAGG:CCG A AGG:AGCAG::AAAA:C::CCGC:::G 13019 uAAGGAGUCGUGGAU-GGUUCAGGACCGAA--AGGUAGCAGACAAAAGCGACCGCGUGGU 13075 ))---)))--))---.-))))))-----))------))))--------))-))-----)) 233 gCGGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggccuacuGGccucgagGcccg 291 GC+GUGG: GGA CG+::::G G :CA AC ::+: C G C:UC:+G : 13076 GCAGUGGCC-GGACCgCGCUUGUGAGUUGACACACAUACG----CAGCCUUCUCG--AUA 13128 .---))--))---)))))))): 292 .cacagucaaGACCaccaggcU 312 ::UCA: ACCAC::::C 13129 c---CUUCAG-ACCACUUAUC- 13145 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----sequence: #213,sp|X01056.1|DM7SL Drosophila melanogaster 7SL RNA gene ----isReversed: 0 ----hitSequence: ACUGGAAGGUUGGCAGCUUCUGUAAUCACGCUUCUGUGAGGUCUGAUUGUGGGAUGGCCUGAGGCUGGGAUCUACUGCGUAGCGGACCAGCUCAUGUUCGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAACCAAGAGUUCCCGUGGUAGGCAGUAGUGGGAUAGCGUACCGGAGUGGACUGCCGUUAUCAGCCCAACCGAUAUGGUUGGACCACAAUCU hit 14 : 2 295 (fwd) 99.85 bits (((,<<<<__________>>>>,,,,,<<<__....._>>>)))----((((((((---( 1 GCCGGGcgguguGGCGugcgCCUGUAACCCaG.....cGGGGGCcgAAgccugguGgGAg 55 :C:GG::GG +UGGC GC::CUGUAA:C:+G :G::G:C G::UG::GG : 2 ACUGGAAGG-UUGGCA-GCUUCUGUAAUCACGcuucuGUGAGGUC--UGAUUGUGGG--A 55 (--((-..---((--..----((-((----((((------((---------((((((--( 56 uGgcuG..GGucggc..cccgcggggucggcccuggggguaugcUuaUUGaaggcccGCc 111 :GGC:+ GG+ GG+ C + :G+G: + G+:C G ++ : :GG::CG C 56 UGGCCUgaGGCUGGGauCUACUGCGUAGCGGACCAGCUCAUG-------UUCGGAACGUC 108 (--(((--((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>, 112 CcuuCcaAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuU 171 C +:C:AAGC::::::U ::::::G:::GCC::G::GGAG::C::GGC:::C:::::: 109 CGCACUAAGCUUGCCAU--CAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGG 166 ,,,,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))) 172 CUAAAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccg 231 CUAA+G GG:::GAACCG:G:CAGG+::G A A::+AGCA:C:AA A:::CCCG::::: 167 CUAAGGAGGGAUGAACCGGGCCAGGGGUGAA--AACCAGCAACCAAGAGUUCCCGUGGUA 224 )))---)))--))---.-))))))-----))------))))--------))-))-----) 232 ggCGGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggccuacuGGccucgagGccc 290 :GC+GU:G:G GGAUA CG::CC:G AG :+A + C G:+ +U :C C:A CC 225 GGCAGUAGUG-GGAUAgCGUACCGG--AGUGGACUGCCGUU----AUCAGCCCAA---CC 274 ).---))--))---)))))))): 291 g.cacagucaaGACCaccaggcU 312 +A+:GU+:: C::CA::CU 275 GaUAUGGUUGG--ACCACAAUCU 295 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----sequence: #3159,sp|K01755.1|DMKSG7SL D. melanogaster 7SL RNA gene. ----isReversed: 0 ----hitSequence: ACUGGAAGGUUGGCAGCUUCUGUAAUCACGCUUCUGUGAGGUCUGAUUGUGGGAUGGCCUGAGGCUGGGAUCUACUGCGUAGCGGACCAGCUCAUGUUCGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAACCAACAGUUCCCGUGGUAGGCAGUAGUGGGAUAGCGUACCGGAGUGGACUGCCGUUAUCAGCCCAACCGAUAUGGUUGGACCACAAUCU hit 15 : 2 295 (fwd) 101.58 bits (((,<<<<__________>>>>,,,,,<<<__....._>>>)))----((((((((---( 1 GCCGGGcgguguGGCGugcgCCUGUAACCCaG.....cGGGGGCcgAAgccugguGgGAg 55 :C:GG::GG +UGGC GC::CUGUAA:C:+G :G::G:C G::UG::GG : 2 ACUGGAAGG-UUGGCA-GCUUCUGUAAUCACGcuucuGUGAGGUC--UGAUUGUGGG--A 55 (--((-..---((--..----((-((----((((------((---------((((((--( 56 uGgcuG..GGucggc..cccgcggggucggcccuggggguaugcUuaUUGaaggcccGCc 111 :GGC:+ GG+ GG+ C + :G+G: + G+:C G ++ : :GG::CG C 56 UGGCCUgaGGCUGGGauCUACUGCGUAGCGGACCAGCUCAUG-------UUCGGAACGUC 108 (--(((--((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>, 112 CcuuCcaAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuU 171 C +:C:AAGC::::::U ::::::G:::GCC::G::GGAG::C::GGC:::C:::::: 109 CGCACUAAGCUUGCCAU--CAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGG 166 ,,,,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))) 172 CUAAAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccg 231 CUAA+G GG:::GAACCG:G:CAGG+::G A A::+AGCA:C:AA A:::CCCG::::: 167 CUAAGGAGGGAUGAACCGGGCCAGGGGUGAA--AACCAGCAACCAACAGUUCCCGUGGUA 224 )))---)))--))---.-))))))-----))------))))--------))-))-----) 232 ggCGGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggccuacuGGccucgagGccc 290 :GC+GU:G:G GGAUA CG::CC:G AG :+A + C G:+ +U :C C:A CC 225 GGCAGUAGUG-GGAUAgCGUACCGG--AGUGGACUGCCGUU----AUCAGCCCAA---CC 274 ).---))--))---)))))))): 291 g.cacagucaaGACCaccaggcU 312 +A+:GU+:: C::CA::CU 275 GaUAUGGUUGG--ACCACAAUCU 295 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----sequence: #3956,sp|X00952.1|DMRN7S Drosophila 7SL RNA sequence of signal recognition particle ----isReversed: 0 ----hitSequence: GACUGGAAGGUUGGCAGCUUCUGUAACUCACGCUUCUGUGAGGUCUGAUUGUGGGAUGGCCUGAGGCUGGGAUCUACUGCGUAGCGGACCAGCUCAUGUUGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUCCCGUGGUAGGCAGUAGUGGGAUAGCGUACCGGAGUGGACUGCCGUUAUCAGCCCAACCGAUAUGGUUGGACCACAAUCU hit 16 : 2 299 (fwd) 110.27 bits (((.,<<<<__________>>>>,,,,,<<<.__......_>>>)))----((((((((- 1 GCC.GGGcgguguGGCGugcgCCUGUAACCC.aG......cGGGGGCcgAAgccugguGg 52 G C GG::GG +UGGC GC::CUGUAAC:C +G +G:GG C G::UG::GG 2 GACuGGAAGG-UUGGCA-GCUUCUGUAACUCaCGcuucugUGAGGUC---UGAUUGUGGG 56 --((--((-..---((--..----((-((----((((------((---------(((((( 53 GAguGgcuG..GGucggc..cccgcggggucggcccuggggguaugcUuaUUGaaggccc 108 ::GGC:+ GG+ GG+ C + :G+G: + C+: G+U:: +UU GA:GG::C 57 --AUGGCCUgaGGCUGGGauCUACUGCGUAG--CGGACCAGCUCAUGUU---GACGGAAC 109 --((--(((--((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>> 109 GCcCcuuCcaAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgc 168 G CC +:C:AAGC::::::U ::::::G:::GCC::G::GGAG::C::GGC:::C:::: 110 GUCCGCACUAAGCUUGCCAU--CAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGU 167 >>,,,,,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,)) 169 cuUCUAAAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCu 228 :: CUAA+G GG:::GAACCG:G:CAGG+::G A A::+AGCA:C:AA A:::CCCG:: 168 UGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAA--AACCAGCAGCCAAGAGUUCCCGUG 225 ))))))---)))--))---.-))))))-----))------))))-.-------))-))-- 229 ccgggCGGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgag 286 ::::GC+GU:G:G GGAUA CG::CC:G AG::+ AC :+G +U :C C:A 226 GUAGGCAGUAGUG-GGAUAgCGUACCGG--AGUGG--ACUGCCGUu---AUCAGCCCAA- 276 ---)).---))--))---)))))))): 287 Gcccg.cacagucaaGACCaccaggcU 312 CC +A+:GU+:: C::CA::CU 277 --CCGaUAUGGUUGG--ACCACAAUCU 299 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----sequence: #24707,sp|X56981.1|TT7SL T.thermophilus gene for 7SL RNA ----isReversed: 0 ----hitSequence: GCCAGGGUAGCAAUACCUGUGUCUAUAUGUGGCAUAAACAAUGUAGGUUGUGAUAGAUAGGAUAUGAGAGUUUGAUGAGACAGUUUGCUAAGAGUGUGCCCGCUCCAAACAAUGAGUUGCUAUGGUGGUAACCUAGUAAUAGGACUCCACCAGGGCAUUAAAGAGCUAAGGAAACGCCUCAGGCUGGCAACAGAACAGGGAAAACUUGCCGCUUGUUGUGGUGGAAGGAUAACAUACUCAUUAACUGUCAAACUAAUCGUUCUACUAUCAAAGCCAGACAUUGCUUUU hit 17 : 102 389 (fwd) 76.41 bits (((.,<<<<__________>>>>,,,,,<<<___>>>)))----((((((((---((--( 1 GCC.GGGcgguguGGCGugcgCCUGUAACCCaGcGGGGGCcgAAgccugguGgGAguGgc 59 GCC GGG: +GC + :CCUGU :: :: GGC A::: :: :G : GG: 102 GCCaGGGU-----AGCAAU-ACCUGUGUCUAUA-UGUGGC---AUAAACAAUG--UAGGU 149 (-....---((------((-((---.-((((------((---------((((((--((-- 60 uG....GGucggccccgcggggucg.gcccuggggguaugcUuaUUGaaggcccGCcCcu 114 UG G ::G+ : :: G::::G GU: GCU+ A+:G: :GCCC + 150 UGugauAGAUAGG-AUAUGAGAGUUuGAUGAGACAGUUUGCUA----AGAGUGUGCCCGC 204 (((--((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,. 115 uCcaAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCU. 173 UCCAA:C::::AGU +G::::GGUGG:::C:::G A+:::G:::CCACC::::C+ U 205 UCCAAACAAUGAGU--UGCUAUGGUGGUAACCUAGUAAUAGGACUCCACCAGGGCA-UUa 261 ,,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))) 174 AAAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccggg 233 AA+ ::GGAA+CGC:UCAGGC::G A A::GA CAG:GAAAAC:: CGCU::::G 262 AAGAGCUAAGGAAACGCCUCAGGCUGGCA--ACAGAACAGGGAAAACUUGCCGCUUGUUG 319 )---)))--))---.-))))))-----))------))))--------))-))-----)). 234 CGGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggccuacuGGccucgagGcccg. 291 :GGUGGA+ GGAUA C: :C:+ A : ++ ::::+CUA+U G:: :++ :: 320 UGGUGGAA-GGAUAaCAUACUC---AUUAA--CUGUCAAACUAAUCGUUCUACU--AUCa 371 ---))--))---)))))))): 292 cacagucaaGACCaccaggcU 312 A: C :GAC: :: :::U 372 ---AAGCCAGACAUUGCUUUU 389 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----sequence: #543,sp|AB021174.1|AB021174 Oryctolagus cuniculus transforming scRNA. ----isReversed: 0 ----hitSequence: GCCGGGCGCGGUGGCGCGCGCCUGUAGUCCCAGCUACUCGGGAGGCUGAGGCCGGAGGAUCGCUUGAGUCCAGGAGUUCUGGGCUGUCGUGCGCUAUGCCGAUCGGGUGUCCGCACUAAGUUCGGCAUCAAUAUGGUGACCUCCCGGGAGCGGGGGACCACCAGGUUGCCUAAGGAGGGGUGAACCGGCCCAGGUCGGAAACGGAGCAGGUCAAAACUCCCGUGCUGAUCAGUAGUGGGAUCGCGCCUGUGAAUAGCCACUGCACUCCAGCCUGGGCAACAUAGCGAGACCCUGUCUC hit 18 : 1 298 (fwd) 126.12 bits (((,<<<<__________>>>>,,,,,<<<.__......_>>>)))----((((((((-- 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aG......cGGGGGCcgAAgccugguGgG 53 GCCGGGCG GUGGCG GCGCCUGUA :CC AG GG:GGC G:::: :G G 1 GCCGGGCGCGGUGGCGCGCGCCUGUAGUCCcAGcuacucGGGAGGC---UGAGGCCGGAG 57 -((--((-..---((--...----((-((----((((------((---------(((((( 54 AguGgcuG..GGucggc...cccgcggggucggcccuggggguaugcUuaUUGaaggccc 108 +:U GCU+ G + G+ +C G:G+:GUC G+ G G+UAUGC GA:::++: 58 GAUCGCUUgaGUCCAGGaguUCUGGGCUGUC-GU----GCGCUAUGCC----GAUCGGGU 108 --((--(((--((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>> 109 GCcCcuuCcaAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgc 168 G CC +:C:AAG::C:G::U ::::::GGUG: C:C:C GGAG G:G:G :CACC:::: 109 GUCCGCACUAAGUUCGGCAU--CAAUAUGGUGACCUCCCGGGAGCGGGGGACCACCAGGU 166 >>,,,.,,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,) 169 cuUCU.AAAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgC 227 :: C+ AA+G GG:G:GAACCG ::CAGG:C:G A A:G:AGCA:: AAA:C:CCCG: 167 UG-CCuAAGGAGGGGUGAACCGGCCCAGGUCGGAA--ACGGAGCAGGUCAAAACUCCCGU 223 )))))))---)))--))---.-))))))-----))------))))--------))-))-- 228 uccgggCGGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggccuacuGGccucgag 286 :C:G::C+GU:G:G GGAU C:++:::G A AU + + C+G ++ C:+C: G 224 GCUGAUCAGUAGUG-GGAUCgCGCCUGUG--A-AUAGCCACUGC-----ACUCCAGCCUG 274 ---)).---))--))---)))))))): 287 Gcccg.cacagucaaGACCaccaggcU 312 G + CA+AG A: ACC: ::::C 275 G-GCAaCAUAGCGAG-ACCCUGUCUC- 298 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #6983,sp|AC126244.3|AC126244 Mus musculus chromosome 12 clone RP24-319A6, complete sequence. ----isReversed: 0 ----hitSequence: GCCGGGCGCGGUGGCGCACGCCUGUAGUCCCAGCUACUCGGGAGGCUGAGACAGGAGGAUCGCUUGAGUCCAGGAGUUCUGGGCUGUAGUGCGCUAUGCCGAUCGGGUGUCCGCACUAAGUUCGGCAUCAAUAUGGUGACCUCCCGGGAGCGGGGGACCACCAGGUUGCCUAAGGAGGGGUGAACCGGCCCAGGUCGGAAACGGAGCAGGUCAAAACUCCCGUGCUGAUCAGUAGUGGGAUCGCGCCUGUGAAUAGCCACUGCACUCCAGCCUGGGCAACAUAGCGAGACCCCGUCUCU hit 19 : 141259 141557 (fwd) 130.23 bits (((,<<<<__________>>>>,,,,,<<<.__......_>>>)))----((((((((-- 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aG......cGGGGGCcgAAgccugguGgG 53 GCCGGGCG GUGGCG CGCCUGUA :CC AG GG:GGC G::::::G G 141259 GCCGGGCGCGGUGGCGCACGCCUGUAGUCCcAGcuacucGGGAGGC---UGAGACAGGAG 141315 -((--((-..---((------((-((----((((------((---------((((((--( 54 AguGgcuG..GGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCc 111 +:U GCU+ G + G+ +C GGG+ G:::UG G+UAUGC GA:::++:G C 141316 GAUCGCUUgaGUCCAGGAGUUCUGGGCU-GUAGUGC-GCUAUGCC----GAUCGGGUGUC 141369 (--(((--((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>, 112 CcuuCcaAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuU 171 C +:C:AAG::C:G::U ::::::GGUG: C:C:C GGAG G:G:G :CACC:::::: 141370 CGCACUAAGUUCGGCAU--CAAUAUGGUGACCUCCCGGGAGCGGGGGACCACCAGGUUG- 141426 ,,.,,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,)))) 172 CU.AAAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCucc 230 C+ AA+G GG:G:GAACCG ::CAGG:C:G A A:G:AGCA:: AAA:C:CCCG::C: 141427 CCuAAGGAGGGGUGAACCGGCCCAGGUCGGAA--ACGGAGCAGGUCAAAACUCCCGUGCU 141484 ))))---)))--))---.-))))))-----))------))))-.-------))-))---- 231 gggCGGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagGc 288 G::C+GU:G:G GGAU C:++:::G A AU CCA:::C CU C+ GCCU G + 141485 GAUCAGUAGUG-GGAUCgCGCCUGUG--A-AUA--GCCACUGCaCU-CCAGCCUGGGC-A 141536 -)).---))--))---)))))))): 289 ccg.cacagucaaGACCaccaggcU 312 AG A: ACC::::::CU 141537 ACAu---AGCGAG-ACCCCGUCUCU 141557 ----endhit ----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/pln.dat.fasta.gz ----sequence: #2031,sp|AB020752.1|AB020752 Arabidopsis thaliana genomic DNA, chromosome 5, P1 clone:MTH16. ----isReversed: 0 ----hitSequence: GUCGAGCUAUGUAACGAGAGCUUGUAACCCAAGUGGGGACUAUAAGAUGGUGGAACACUGGAUCGGCCCACGGGUCGGAUUUGUUGUUGGCAUAGGUCUGGACUGCCCAAUCCAAGCUGUGAGUGAACCGUAUGAACCAAGCGAAGGUUUGAUCCGUACGGUUGCUAAAGGUUGAGGGUAUUGCGUUAGGCUGGCUUCACAGAGCAGCGACUACCUCCCGCUCUCAGCAGUGGACGGACAACGGUUCGACGCCACACAAAUCCACUAUGGUCCGCUGGCUCGUAACCCGCUUGAACCACCAUUUU hit 20 : 35792 36096 (fwd) 158.22 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 G:CG:GC: UGU+ CG G:GC:UGUAACCC AG+GGGG:C ++A:::UGGUGG+A:: C 35792 GUCGAGCUAUGUAACGAGAGCUUGUAACCCaAGUGGGGACUAUAAGAUGGUGGAACA--C 35849 (----((------((-((----((((------((---------((((((--((--(((-- 60 uGGGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCcaA 119 GG UCGGC CC CG G+UC G:::U+G++GU::GC UA +:G::C:GCCC UCCAA 35850 UGGAUCGGC-CCACG-GGUC-GGAUUUGUUGUUGGCAUAGGUCUGGACUGCCCAAUCCAA 35906 ((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,.,,,,, 120 GcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCU.AAAGu 178 GC:: GAGU ::C:G::+G:: C:: CG+AGG ::G ::C+::C:G:: CU AA+GU 35907 GCUGUGAGU--GAACCGUAUGAACCAAGCGAAGGUUUGAUCCGUACGGUUG-CUaAAGGU 35963 <<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))---) 179 gggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGUg 238 :G:GGG A GCGU AGGC::G +UCA::GAGCAGCGA+ ACC:C:CGCUC ::GC+GUG 35964 UGAGGGUAUUGCGUUAGGCUGGCUUCACAGAGCAGCGACUACCUCCCGCUCUCAGCAGUG 36023 ))--))---.-))))))-----))------))))-.-------))-))---.--))...- 239 GagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagG.cccg...c 292 GA GGA A C:G::C: G +::C AC A:::C CU +UGG+C CG++G C CG 36024 GAC-GGACAaCGGUUCGACG-CCAC--ACAAAUCCaCU-AUGGUC-CGCUGgCUCGuaa- 36076 --))--))---)))))))): 293 acagucaaGACCaccaggcU 312 +C G +::+ACCACCA:::U 36077 CCCGCUUGAACCACCAUUUU 36096 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #2649,sp|AB026661.1|AB026661 Arabidopsis thaliana genomic DNA, chromosome 5, BAC clone:T30G6. ----isReversed: 1 ----hitSequence: UUCCAAAUCAGUAACGAGGGCUUGUUAACCAAGUGGGGACAAUAAGUUGGUGGAACACUGACUCGGUCCACGGGUCAGAUCUGUUGUGGCAUUGUUCUGGGCUGCCCAGUCCAAGCUGUGAGUGAUCUGUGUGUGUUGAGCGAAGGCUUGGCUCAGGCGGUUCUUACAUUGGUGGGCAAUGCGUGAGGCUGGUUUCAUAGAGCAGCGAUCACCUCCCGCUCUCGGCAGUGGACGGAUCACAGCUCGACACCACUCAGAUUCACUAUGGCUUGCUCGCUCGUUCCCAGCUGGACCACCAAUUU hit 21 : 49999 49698 (rev) 105.63 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 :C :: : +GU+ CG G: ::UGU A:CC AG+GG:G: +++A:::UGGUGG+A:: C 26996 UUCCAAAUCAGUAACGAGGGCUUGUUAACCaAGUGGGGACAAUAAGUUGGUGGAACA--C 27053 (----((------((-((----((((------((---------((((((--((--(((-- 60 uGGGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCcaA 119 UG UCGG C :G:GUC +:::+G++GU: + UU U +:G:+C:GCCC UCCAA 27054 UGACUCGG--UCCACGGGUC-AGAUCUGUUGUGGCAUU-GUUCUGGGCUGCCCAGUCCAA 27109 ((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,,,,< 120 GcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCUAAAGug 179 GC:: GAGU :: C:G UG :::+::CG+AGG::+::: CA C:G :: UA A UG 27110 GCUGUGAGU--GAUCUGUGUGUGUUGAGCGAAGGCUUGGCUCAGGCGGUUC-UUACAUUG 27166 <<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))---)) 180 ggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGUgG 239 G GGG A+ GCGU+AGGC: G +UCA :GAGCAGCGA+ ACC CCCGCUC ::GC+GUGG 27167 GUGGGCAAUGCGUGAGGCUGGUUUCAUAGAGCAGCGAUCACCUCCCGCUCUCGGCAGUGG 27226 )--))---.-))))))-----))------))))-.-------))-))---.--))..--- 240 agGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagG.cccg..cac 294 A GGAU C:G+:C: A+ :CA +C :::+C CU +UGGC:U: G CG C+C 27227 AC-GGAUCaCAGCUCG---ACACCACUCAGAUUCaCU-AUGGCUUGCUCGc-UCGuuCCC 27280 ))--))---)))))))): 295 agucaaGACCaccaggcU 312 AG +:: ACCACCA:::U 27281 AGCUGG-ACCACCAAUUU 27297 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #8675,sp|AC005275.1|AC005275 Arabidopsis thaliana BAC F4C21 from chromosome IV, top arm, near 17 cM, complete sequence. ----isReversed: 0 ----hitSequence: GUCGAGCUAAGUAACAUGAGCUUGUAACCCAUGUGGGGACAUUUAGAUGGUGGAACACUGGUUCGGGUCCACGGGCCGGUUCUGUUGUUGGCAUGUUUCUGGGCUGCCCAGUCCAAGCUGUGAGUAAGACGUGUGUGUCAAGCGAAGGCUUGGCUCAAACGGCUUCUAAAGUUGGAGGGUAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGUGGACGGAUCACAGUUUAGCGUCGCUCAGAACCACUAUGGCCUGCUGGUCCGAUCUCAUAUGAACCACCAUUUU hit 22 : 105500 105804 (fwd) 164.81 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 G:CG:GC: +GU+ C UG:GC:UGUAACCC G+GGGG:C+++ :::UGGUGG+A:: : 105500 GUCGAGCUAAGUAACAUGAGCUUGUAACCCaUGUGGGGACAUUUAGAUGGUGGAACAC-U 105558 (----((------((-((----((((------((---------((((((--((--(((-- 60 uGGGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCcaA 119 : G UCGG++CC C GG+C G::::+G++GU::GC U UU +::: C:GCCC UCCAA 105559 G-GUUCGGGUCCACG-GGCC-GGUUCUGUUGUUGGCAUGUUUCUGGGCUGCCCAGUCCAA 105615 ((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,,,., 120 GcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCUAAAG.u 178 GC:: :AGU ::G::G: UG ::C:::CG+AGG:::G:: CA :C::C:: CUAAAG U 105616 GCUGUGAGU--AAGACGUGUGUGUCAAGCGAAGGCUUGGCUCAAACGGCUU-CUAAAGuU 105672 <<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))---) 179 gggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGUg 238 GG::GG A+ GCGU+AGGC::G +UCA::GAGCAGCGA+ AC::CCCGCU: ::GC+GUG 105673 GGAGGGUAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGUG 105732 ))--))---.-))))))-----))------))))-.-------))-))---..--)).-- 239 GagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagG..cccg.ca 293 GA GGAU C:G :::G G ::C +C ::::C CU +UGGCC G++G CCG ++ 105733 GAC-GGAUCaCAGUUUAGCG-UCGC--UCAGAACCaCU-AUGGCC-UGCUGgu-CCGaUC 105785 -))--))---)))))))): 294 cagucaaGACCaccaggcU 312 +::U ::+ACCACCA:::U 105786 UCAUAUGAACCACCAUUUU 105804 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #8675,sp|AC005275.1|AC005275 Arabidopsis thaliana BAC F4C21 from chromosome IV, top arm, near 17 cM, complete sequence. ----isReversed: 0 ----hitSequence: GUCGAGCGAAGUAACAUGAGCUUGUAACCCAUGUGGGGACAUUAAGAUGGUGGAACACUGGUUCGGGUCCACGGGCCGGUUCUGUUGCUGGCAUGUUUCUGGGCUGCCCAGUCCAAGCUGUGAGUAAGACGUGUGUGUCAAGCGAAGGCUUGGCUCAAACGGCUGCUAAAGUUGGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGAUUACUUCCCGCUUACAGCAGUGGACGGAUCACAGUUUGGCGUCGCUCAGAACCACUAUGGCCUGCUGGUCCGAUCUCAUCUGAACCACCAUUUU hit 23 : 109058 109362 (fwd) 164.56 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 G:CG:GC +GU+ C UG GC:UGUAACCC G+GGGG:C+++A:::UGGUGG+A:: : 109058 GUCGAGCGAAGUAACAUGAGCUUGUAACCCaUGUGGGGACAUUAAGAUGGUGGAACAC-U 109116 (----((------((-((----((((------((---------((((((--((--(((-- 60 uGGGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCcaA 119 : G UCGG++CC C GG+C G::::+G++G+::GC U UU +::: C:GCCC UCCAA 109117 G-GUUCGGGUCCACG-GGCC-GGUUCUGUUGCUGGCAUGUUUCUGGGCUGCCCAGUCCAA 109173 ((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,,,., 120 GcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCUAAAG.u 178 GC:: :AGU ::G::G: UG ::C:::CG+AGG:::G:: CA :C::C:: CUAAAG U 109174 GCUGUGAGU--AAGACGUGUGUGUCAAGCGAAGGCUUGGCUCAAACGGCUG-CUAAAGuU 109230 <<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))---) 179 gggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGUg 238 GG::GG A+ GCGU+AGGC::G +UCA::GAGCAGCGA+ AC::CCCGCU: ::GC+GUG 109231 GGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGAUUACUUCCCGCUUACAGCAGUG 109290 ))--))---.-))))))-----))------))))-.-------))-))---..--)).-- 239 GagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagG..cccg.ca 293 GA GGAU C:G :::G G ::C +C ::::C CU +UGGCC G++G CCG ++ 109291 GAC-GGAUCaCAGUUUGGCG-UCGC--UCAGAACCaCU-AUGGCC-UGCUGgu-CCGaUC 109343 -))--))---)))))))): 294 cagucaaGACCaccaggcU 312 +::UC::+ACCACCA:::U 109344 UCAUCUGAACCACCAUUUU 109362 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #8681,sp|AC005311.3|AC005311 Arabidopsis thaliana chromosome 2 clone T16B12 map m283, complete sequence. ----isReversed: 0 ----hitSequence: GUCGAGCUAAGUAACGAGAGCUUGUGACCCGAGUGGGGACAAUAAGGUGGUGGAACAGUGGUUCAAUUCCUCGGGUCGGACCUGAUGCUGACAUAUAUCUGAGCUGCCCAGUCCAAGCUGUGAGUAAUCUGUGUGGGUCAGGCGAAGGCUUGACUCAGGCGGAUUCUAAAGUCGGAGGGUAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACUACUUCCCUCUUACAGCAGUGGAUGGAUCAUAGUUCGAAGUCUCUCAGAUCCACUAUGGCCCGCUGGUUCGAUCUCUCCUGGACCACCACUUU hit 24 : 17031 17335 (fwd) 145.77 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 G:CG:GC: +GU+ CG G:GC:UGU ACCC AG+GGGG:C+++A:::UGGUGG :: : 17031 GUCGAGCUAAGUAACGAGAGCUUGUGACCCgAGUGGGGACAAUAAGGUGGUGG--AAC-A 17087 (-.---((------((-((----((((------((---------((((((--((--(((- 60 uG.GGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCca 118 :+ G U : +CC+CG GGUCGG: CUG +G+U::+ U+ U +:G: C:GCCC UCCA 17088 GUgGUUCAAUUCCUCG-GGUCGGACCUGAUGCUGACAUA-UAUCUGAGCUGCCCAGUCCA 17145 -((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,,,. 119 AGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCUAAAG. 177 AGC:: :AGU :::C:G UG+::C:::CG+AGG:::G::+CA C:G::: CUAAAG 17146 AGCUGUGAGU--AAUCUGUGUGGGUCAGGCGAAGGCUUGACUCAGGCGGAUU-CUAAAGu 17202 ,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))--- 178 ugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGU 237 +GG::GG A+ GCGU+AGGC::G +UCA::GAGCAGCGA+ AC::CCC CU: ::GC+GU 17203 CGGAGGGUAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACUACUUCCCUCUUACAGCAGU 17262 )))--))---.-))))))-----))------))))---.-----))-))---.--))..- 238 gGagGGgAUa.CgggccgGUGAgaucaaaccagggccu.acuGGccucgagG.cccg..c 292 GGA GGAU :G :C: AG:: ++CAG :CC+ +UGGCC CG++G : + 17263 GGAU-GGAUCaUAGUUCGA--AGUCU--CUCAGAUCCAcUAUGGCC-CGCUGg-UUCgaU 17315 --))--))---)))))))): 293 acagucaaGACCaccaggcU 312 ++:: C::GACCACCA:::U 17316 CUCUCCUGGACCACCACUUU 17335 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #8702,sp|AC005662.3|AC005662 Arabidopsis thaliana chromosome 2 clone F13H10 map CIC11C08, complete sequence. ----isReversed: 1 ----hitSequence: GUCGAACUCAGUAACGCGGGCUUGUGAUCCAAGUGGAGACAAUAAGGGGAUGGGACGUUGGGUCGAUCUCAUUGGGCCGGGUUCGGGUUGGGCUAUAUUCUGGCCCGCCCAUUCCAAGUUGGGAGUUGAGGCAUGGGCUUCGAGCGAAGGCUCGGGUCUCAUGUCUUCUAGAGUGGGGGAGACCGCGUGAGGCUGGUUUCACAGAGCAGCGUCCACCUCCCGCUCUUGACGGUGGAAGGAUUACGGGCCAUUGCCUUCCGAGCCCACUAUGACCCAAUAAGCCGCUCCGAUUGGACCAUCACUUU hit 25 : 47366 47062 (rev) 165.66 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 G:CG::C: +GU+ CG G:G::UGU A:CC AG+GG:G:C+++A::: G:UGGGA:: : 48701 GUCGAACUCAGUAACGCGGGCUUGUGAUCCaAGUGGAGACAAUAAGGGGAUGGGACG--U 48758 (----((--.----((-((----((((------((---------((((((--((--(((- 60 uGGGucggc.cccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCca 118 GGGUCG +C++:G GG+C G:+:U GGG U::GCU+ U +:GGCCCGCCC UUCCA 48759 UGGGUCGAUcUCAUUG-GGCC-GGGUUCGGGUUGGGCUAUAUUCUGGCCCGCCCAUUCCA 48816 -((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,,,, 119 AGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCUAAAGu 178 AG:: :GAGUU :G+:::G:G +:C:::CG+AGG:::G:+ C:C:::+C: CUA+AGU 48817 AGUUGGGAGUU-GAGGCAUGGGCUUCGAGCGAAGGCUCGGGUCUCAUGUCUU-CUAGAGU 48874 <<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))---) 179 gggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGUg 238 GG:GG +ACCGCGU+AGGC::G +UCA::GAGCAGCG + ACC:CCCGCUC: ::CGGUG 48875 GGGGGAGACCGCGUGAGGCUGGUUUCACAGAGCAGCGUCCACCUCCCGCUCUUGACGGUG 48934 ))--))---.-))))))-----))------))))-.-------))-))---.--)).--- 239 GagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagG.cccg.cac 294 GA+ GGAU CGGGCC: UG +:: +C A:+:C CU +UG CC C:A+ +CCG ++C 48935 GAA-GGAUUaCGGGCCAUUG-CCUU--CCGAGCCCaCU-AUGACC-CAAUAaGCCGcUCC 48988 ))--))---)))))))): 295 agucaaGACCaccaggcU 312 : +::GACCA:C :::U 48989 GA-UUGGACCAUCACUUU 49005 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #8921,sp|AC007591.2|AC007591 Arabidopsis thaliana chromosome 1 BAC F9L1 sequence, complete sequence. ----isReversed: 1 ----hitSequence: GUCGAGCUCAGUAACGUGGGCUUGUGACCCGUGUGGGGACAAUAAGUUGGUGGAACACUGGCUCGGCCCACGGGUCGGAUCUGUUGUGGCAUUGUUCCGGGCUGCCCAGUCCAAGCUGAGAGUGAUCCGUGUGUGUUAAGCGAAGGCUUGGCUCAGGCGGUUCUUGCAGUGGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGAUCACCUCCCGCUCUCAGCAGUGGACGGAUCACAGCUCGACGCCACUCAGAUUCACCAUGGCCUGCUGGCUCGUUCCCAGCUGGACCACCAAUUU hit 26 : 113708 113407 (rev) 159.55 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 G:CG:GC: +GU+ CGUG:GC:UGU ACCC G+GGGG:C+++A:::UGGUGG+A:: C 28277 GUCGAGCUCAGUAACGUGGGCUUGUGACCCgUGUGGGGACAAUAAGUUGGUGGAACA--C 28334 (----((------((-((----((((------((---------((((((--((--(((-- 60 uGGGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCcaA 119 UGG UCGGC CC C GGUC G+:::+G++GU: + UU U +:G:+C:GCCC UCCAA 28335 UGGCUCGGC-CCACG-GGUC-GGAUCUGUUGUGGCAUU-GUUCCGGGCUGCCCAGUCCAA 28390 ((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,.,,, 120 GcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCUAA.AGu 178 GC:::GAGU :: C:G UG ::::::CG+AGG:::::: CA C:G ::U + AGU 28391 GCUGAGAGU--GAUCCGUGUGUGUUAAGCGAAGGCUUGGCUCAGGCGGUUCU--UGcAGU 28446 <<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))---) 179 gggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGUg 238 GG:GGG A+ GCGU+AGGC::G +UCA::GAGCAGCGA+ ACC:CCCGCUC:::GC+GUG 28447 GGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGAUCACCUCCCGCUCUCAGCAGUG 28506 ))--))---.-))))))-----))------))))--------))-))---.--))..--- 239 GagGGgAUa.CgggccgGUGAgaucaaaccagggccuacuGGccucgagG.cccg..cac 294 GA GGAU C:G+:C: A+ :CA +C :::+C ++UGGCC G++G C CG C+C 28507 GAC-GGAUCaCAGCUCG---ACGCCACUCAGAUUCACCAUGGCC-UGCUGgCUCGuuCCC 28561 ))--))---)))))))): 295 agucaaGACCaccaggcU 312 AG +:: ACCACCA:::U 28562 AGCUGG-ACCACCAAUUU 28578 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #9034,sp|AC011807.4|AC011807 Arabidopsis thaliana chromosome I BAC F14J22 genomic sequence, complete sequence. ----isReversed: 0 ----hitSequence: GUCGAACCUAGUAACGUGGGUUUAUGAUCCGAGUGGAGACAACAAGGUGAUGGUACAUUGGGUCGGAUCUCAAUGGGCCGGGUUCGGCUUGGGCUCUUUACUGGCCUGCCCAUUCCAAGUCGGGAGUUGAGAUAUCUUCUGAGCGAAGGUUCGGAGCCAAUAUCUCUUUAGAGCGGAGGAGACCGCGUGAGGCUGGUUUCACAGAGCAGCGUCCACCUUCCGUUCUCGACGGUGGAAGGAUAACGGGCCCGUUGUCUUCCGAGCCCACUAUGACCCAUUAGGCCGACUCCAACUGAGCCAUCACUUU hit 27 : 47784 48090 (fwd) 146.14 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 G:CG::C:++GU+ CGUG:G::U U A:CC AG+GG:G:C++ A:::UG:UGG :: : 47784 GUCGAACCUAGUAACGUGGGUUUAUGAUCCgAGUGGAGACAACAAGGUGAUGG--UACAU 47841 (----((--.----((-((----((((------((---------((((((--((--(((- 60 uGGGucggc.cccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCca 118 UGGGUCGG C C ::GGG+C G:+:U GG U:+GCU UU + GGCC:GCCC UUCCA 47842 UGGGUCGGAuCUCAAUGGGCC-GGGUUCGGCUUGGGCUCUUUACUGGCCUGCCCAUUCCA 47900 -((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>.>>>>>>,,,,,,, 119 AGcccggaGUUGuggcgggguggccccgccGgAGggcggggccacc.ccgccuUCUAAAG 177 AG:C::GA UU ::G::: ::C::: CG+AGG :::G:: + :::C::U UA+AG 47901 AGUCGGGAGUU-GAGAUA--UCUUCUGAGCGAAGGUUCGGAGCCA-aUAUCUCUUUAGAG 47956 ,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))--- 178 ugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGU 237 +G::GG +ACCGCGU+AGGC::G +UCA::GAGCAGCG + ACC::CCG UC::G:CGGU 47957 CGGAGGAGACCGCGUGAGGCUGGUUUCACAGAGCAGCGUCCACCUUCCGUUCUCGACGGU 48016 )))--))---.-))))))-----))------))))-.-------))-))---.--))..- 238 gGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagG.cccg..c 292 GGA+ GGAUA C:GGCC GU G :C +C A:+:C CU +UG CC :: G CCG + 48017 GGAA-GGAUAaCGGGCCCGUU-G-UCUUCCGAGCCCaCU-AUGACCCAUUAGg-CCGacU 48071 --))--))---)))))))): 293 acagucaaGACCaccaggcU 312 +CA: +::G CCA:CA:::U 48072 CCAACUGAG-CCAUCACUUU 48090 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #9070,sp|AC013453.1|AC013453 Arabidopsis thaliana chromosome I BAC T16N11 genomic sequence, complete sequence. ----isReversed: 1 ----hitSequence: GUCGAGCUCAGUAACGUGGGCUUGUGACCCGUGUGGGGACAAUAAGUUGGUGGAACACUGGCUCGGCCCACGGGUCGGAUCUGUUGUGGCAUUGUUCCGGGCUGCCCAGUCCAAGCUGAGAGUGAUCCGUGUGUGUUAAGCGAAGGCUUGGCUCAGGCGGUUCUUGCAGUGGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGAUCACCUCCCGCUCUCAGCAGUGGACGGAUCACAGCUCGACGCCACUCAGAUUCACCAUGGCCUGCUGGCUCGUUCCCAGCUGGACCACCAAUUU hit 28 : 1552 1251 (rev) 159.55 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 G:CG:GC: +GU+ CGUG:GC:UGU ACCC G+GGGG:C+++A:::UGGUGG+A:: C 89450 GUCGAGCUCAGUAACGUGGGCUUGUGACCCgUGUGGGGACAAUAAGUUGGUGGAACA--C 89507 (----((------((-((----((((------((---------((((((--((--(((-- 60 uGGGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCcaA 119 UGG UCGGC CC C GGUC G+:::+G++GU: + UU U +:G:+C:GCCC UCCAA 89508 UGGCUCGGC-CCACG-GGUC-GGAUCUGUUGUGGCAUU-GUUCCGGGCUGCCCAGUCCAA 89563 ((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,.,,, 120 GcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCUAA.AGu 178 GC:::GAGU :: C:G UG ::::::CG+AGG:::::: CA C:G ::U + AGU 89564 GCUGAGAGU--GAUCCGUGUGUGUUAAGCGAAGGCUUGGCUCAGGCGGUUCU--UGcAGU 89619 <<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))---) 179 gggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGUg 238 GG:GGG A+ GCGU+AGGC::G +UCA::GAGCAGCGA+ ACC:CCCGCUC:::GC+GUG 89620 GGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGAUCACCUCCCGCUCUCAGCAGUG 89679 ))--))---.-))))))-----))------))))--------))-))---.--))..--- 239 GagGGgAUa.CgggccgGUGAgaucaaaccagggccuacuGGccucgagG.cccg..cac 294 GA GGAU C:G+:C: A+ :CA +C :::+C ++UGGCC G++G C CG C+C 89680 GAC-GGAUCaCAGCUCG---ACGCCACUCAGAUUCACCAUGGCC-UGCUGgCUCGuuCCC 89734 ))--))---)))))))): 295 agucaaGACCaccaggcU 312 AG +:: ACCACCA:::U 89735 AGCUGG-ACCACCAAUUU 89751 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #9379,sp|AC079888.9|AC079888 Oryza sativa chromosome 10 BAC OSJNBa0078O01 genomic sequence, complete sequence. ----isReversed: 0 ----hitSequence: GCCGAGCCAAGUAGCGAUGGCUUGUCACCCGAGCGGGGGCAAUAAGGUGGUGCGGAUGCCUGGUCGUUUGCGCUUUGGCCUGGGCCUGUGGUUCGCUCUAUGCGGCCCGCCCGUUCCAAGUUGCGUAGCGUGUAUGGGGCGCCCUGGCGAAAGCUAGAGCGUCCCUGCACCUAGAGUGGCGGGUAUUGCGUGAGGCUGGUUUCACAGAGCAGCGAGUACCGCCCGCUUCCAACGGUGGAAGGAUAACGGGCCGCUGCAGCCCUGGCCCGCUUCCGGCCCAUGUGCCUUCCAUGGCAGACCCCCAUCUU hit 29 : 142244 142551 (fwd) 156.20 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 GCCG:GC: +GU+GCG +:GC:UGU ACCC AGCGGGGGC+++A::+UGG G G+:UG C 142244 GCCGAGCCAAGUAGCGAUGGCUUGUCACCCgAGCGGGGGCAAUAAGGUGGUGCGGAUG-C 142302 (----((--..----((-((----((((------((---------((((((--((--((( 60 uGGGucggc..cccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCc 117 :+GGU G+ C C+: GG+C G:+C:+G+GGU::GCU U :GGCCCGCCC UUCC 142303 CUGGUCGUUugCGCUUU-GGCCUGGGCCUGUGGUUCGCUC-UAUGCGGCCCGCCCGUUCC 142360 --((((.((((,,,<<<<<.<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,, 118 aAGccc.ggaGUUGuggcg.ggguggccccgccGgAGggcggggccaccccgccuUCUAA 175 AAG::: G:AG ::G:: GGG::GC C:::CG+A+G:::G GC::CCC::C:: CUA+ 142361 AAGUUGcGUAG--CGUGUAuGGGGCGCCCUGGCGAAAGCUAGAGCGUCCCUGCAC-CUAG 142417 ,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))- 176 AGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCG 235 AGUGG:GGG A GCGU+AGGC::G +UCA::GAGCAGCGA ACC:CCCGCU:C:::CG 142418 AGUGGCGGGUAUUGCGUGAGGCUGGUUUCACAGAGCAGCGAGUACCGCCCGCUUCCAACG 142477 --)))--))---.-))))))-----))------))))-.-------))-))---.--)). 236 GUgGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagG.cccg. 291 GUGGA+ GGAUA CGGGCC: UG +::C +C :G+:C CU C+GGCC : G CC 142478 GUGGAA-GGAUAaCGGGCCGCUG-CAGC--CCUGGCCCgCUUCCGGCC-CAUGUg-CCUu 142531 .---))--))---)))))))): 292 .cacagucaaGACCaccaggcU 312 CA+:G CA: ACC CCA+::U 142532 cCAUGG-CAG-ACCCCCAUCUU 142551 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #9379,sp|AC079888.9|AC079888 Oryza sativa chromosome 10 BAC OSJNBa0078O01 genomic sequence, complete sequence. ----isReversed: 1 ----hitSequence: GCCGAGCCAGGUAGCGUUGGCUUGUCACCCGAGCGGGGGCAAUAAGGUGGUGUUGGAUGCCUGGUCGUUUGCGCUUGGGGUCUGCGCCUGUGGUUUGCACUAUGCGGCCCGCCCGUUCCAAGUUGCGUAGCGUGUGUGGGGCGCCUGGGCGAAGGCUCGAGCGUCCCUGCACCUAGAGUGGCGGGUAUUGCGUGAGGCUGGUUUCACAGAGCAGCGAGUACCGCCCGCUUCCAACGGUGGAAGGAUAACGGGCCGCUGCAGCCCUGGCCCGCUUCCGGCCCAAGUGCCUUCCAUGGCAGACCACCACCUU hit 30 : 27802 27493 (rev) 162.33 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((-.--((-- 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGg.GAguGg 58 GCCG:GC: GU+GCGU+:GC:UGU ACCC AGCGGGGGC+++A:::UGGUG G+:UG 120201 GCCGAGCCAGGUAGCGUUGGCUUGUCACCCgAGCGGGGGCAAUAAGGUGGUGUuGGAUG- 120259 ((----((--..----((-((----((((------((---------((((((--((--(( 59 cuGGGucggc..cccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuC 116 C:+GGU G+ C C+: GGGUC G +C:+G+GGU:UGC U :GGCCCGCCC UUC 120260 CCUGGUCGUUugCGCUUGGGGUCUGCGCCUGUGGUUUGCAC-UAUGCGGCCCGCCCGUUC 120318 (--((((.((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>.>>>>>>,,,, 117 caAGccc.ggaGUUGuggcgggguggccccgccGgAGggcggggccacc.ccgccuUCUA 174 CAAG::: G:AG ::G: G G::GC ::::CG+AGG:::: GC::C C :C:: CUA 120319 CAAGUUGcGUAGCGUGUGUGG-GGCGCCUGGGCGAAGGCUCGAGCGUC-cCUGCAC-CUA 120375 ,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,)))))))) 175 AAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggC 234 +AGUGG:GGG A GCGU+AGGC::G +UCA::GAGCAGCGA ACC:CCCGCU:C:::C 120376 GAGUGGCGGGUAUUGCGUGAGGCUGGUUUCACAGAGCAGCGAGUACCGCCCGCUUCCAAC 120435 ---)))--))---.-))))))-----))------))))-.-------))-))-----)). 235 GGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagGcccg. 291 GGUGGA+ GGAUA CGGGCC: UG +A:C +C :G+ C CU C+GGCC : +G CC 120436 GGUGGAA-GGAUAaCGGGCCGCUG-CAGC--CCUGGCCCgCUUCCGGCCCAAGUG-CCUu 120490 .---))--))---)))))))): 292 .cacagucaaGACCaccaggcU 312 CA+:G CA: ACCACCA:::U 120491 cCAUGG-CAG-ACCACCACCUU 120510 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #9694,sp|AC121489.2|AC121489 Oryza sativa (japonica cultivar-group) chromosome 3 clone OJ1217B09, complete sequence. ----isReversed: 0 ----hitSequence: GCCGAGCUCAGUAGCGAGAGCUUGUAACCCAUGUGGGGGCAUCAGGUGGUGUGGAUGAUCGGUGCUGAAUUUGGGCCUGGGUCCAUGUGUUGUUAACUAUGCUGGCUUGCGUAGUGGGUGGAGGGGCUUCGGCGAAAGCCUUGGUCUCUCCGGCCCUGAAGUUGGCAGACACGGCGUGAGGCUGGCUUCACAGAGCAGCGAUCACUGCCCGCUUCCAACGGUGGAAGGAUAACAGGCCGCUGCACCAUGGGCCCGCUUCUGGCCCCACUAUUACAGACCACCAUCAU hit 31 : 123851 124137 (fwd) 100.98 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 GCCG:GC: +GU+GCG G:GC:UGUAACCC G+GGGGGC++ ::+UGGUG G: : 123851 GCCGAGCUCAGUAGCGAGAGCUUGUAACCCaUGUGGGGGCAU-CAGGUGGUGU--GG--A 123905 (----((------((-((----((((------((---------((((((--((--(((-- 60 uGGGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCcaA 119 UG +:G+ C+ : : U+ :+C:+GGG +:+ +U : G::: C: U C:++ 123906 UGAUCGGU--GCUGAAUUUG--GGCCUGGGUCCAUGU-----GUUGUUAA-CUAUGCUGG 123955 ((((.((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,.,,,, 120 Gccc.ggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCU.AAAG 177 ::: G:AGU :G :GG G:G+C:: G:CG+A+G:C ::G+C:C CC: C: CU AA+ 123956 CUUGcGUAGU--GGGUGGAGGGGCUUCGGCGAAAGCCUUGGUCUCUCCGGCC-CUgAAGU 124012 ,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))--- 178 ugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGU 237 UGG::G AC GCGU+AGGC::G +UCA::GAGCAGCGA+ AC::CCCGCU:C::: GGU 124013 UGGCAGACACGGCGUGAGGCUGGCUUCACAGAGCAGCGAUCACUGCCCGCUUCCAACGGU 124072 )))--))---.-))))))-----))------))))--------))-))---.--)).--- 238 gGagGGgAUa.CgggccgGUGAgaucaaaccagggccuacuGGccucgagG.cccg.cac 294 :G + :GAUA C:::C : UG ++:C A+ :G+: : : ++G CCC: ++ 124073 GGAA-GGAUAaCAGGCCGCUG-CACC--AUGGGCC--------CGCUUCUGgCCCCa-CU 124119 ))--))---)))))))): 295 agucaaGACCaccaggcU 312 A:U :AGACCACCA+::U 124120 AUUACAGACCACCAUCAU 124137 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #9721,sp|AC123570.4|AC123570 Medicago truncatula clone mth2-33l22, complete sequence. ----isReversed: 0 ----hitSequence: GCUGAGUUGGGUAGUGCCAACUUGGGACCCAAGUGAGAGCACUAAAAUAAUGGGACAUGGCUAUGGCUUGUCUUGGCUGAGCUGGUUUCUGCAAUAUGCUGGCUUGUCCGCUCCAAGUUGAGAGUUGUGCCAUGGGACUUUGGCAUACGCCUUCGUCUCAUGGCUCCUAGACUAGAGGGCACUGCGUGAGGCUCUGCUCACAGAGCAGCGAAGACCUCUCCCUCCUGACAGUGGAGGGAUUACAAGCUGCUGUACUUCUAGUCUACUAAGCCGGUGAGCCUAGCCUUUGAACCAUCAUUUU hit 32 : 87824 88124 (fwd) 88.82 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 GC:G:G::G GU+G G ::C:UG AC C AG+G G:GC+ +A:::U :UGGGA:: +: 87824 GCUGAGUUGGGUAGUGCCAACUUGGGACCCaAGUGAGAGCACUAAAAUAAUGGGACA-UG 87882 (----((------((-((---..-((((------((---------((((((--((--((( 60 uGGGucggccccgcggggucg..gcccuggggguaugcUuaUUGaaggcccGCcCcuuCc 117 : +::++ C+: : U+G G:+CUGG + U:UGC + UG+::GC::G CC +UCC 87883 G---CUAUG-GCUUGUCUUGGcuGAGCUGG-UUUCUGCAAUAUGCUGGCUUGUCCGCUCC 87937 --((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,,, 118 aAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCUAAAG 177 AAG:: :GAGUU : GC:::G:G:C : G:C A G:C : G:C:C:::GC : CUA+A 87938 AAGUUGAGAGUU-GUGCCAUGGGACUUUGGCAUACGCCUUCGUCUCAUGGCUC-CUAGAC 87995 ,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))--- 178 ugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGU 237 U:G:GGG AC GCGU+AGGC: G UCA :GAGCAGCGAA ACC:C:C CUC: ::C+GU 87996 UAGAGGGCACUGCGUGAGGCUCUGCUCACAGAGCAGCGAAGACCUCUCCCUCCUGACAGU 88055 )))--))---.-))))))-----))------))))-.-------))-))-----)).--- 238 gGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagGcccg.cac 294 GGAG GGAU C::GC:: UG A: +C AG+: CU + G :+ :AG CC:: 88056 GGAG-GGAUUaCAAGCUGCUG-UACU--UCUAGUCUaCU-AAGCCGGUGAG-CCUAg--- 88106 ))--))---)))))))): 295 agucaaGACCaccaggcU 312 ::U+::+ACCA: A:::U 88107 CCUUUGAACCAUCAUUUU 88124 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #9905,sp|AC137997.2|AC137997 Oryza sativa chromosome 3 BAC clone OJ1499_D04, complete sequence. ----isReversed: 1 ----hitSequence: GCCGAGCUCAGCAGCGCGAGCUUGUAACCCGAGCGGGGGCAUUAAGGUGGUGUGGACGUUGCCGUAUGGCUGCGGGCCUGGGUUGGCAGUGCCAUAGAUGGCCCGCCCGUUCCAAGUUGCGUAGUUGGGCCGGCGGGGCUUGAGCGAAAGCUCUGGCCUCACGUUUCCCUAGAGUGGCAGGCAUUGCGUGAGGCUGGCUUCACAGAGCAGCGAAUACUGUCCGCUUCCAACGGUGGAAGGAUAACGGGCCGCCGCACUGCUGGCCCGCUUGGGUCUCGCAGCCUACUCCAACGGACCACCACUUU hit 33 : 82646 82342 (rev) 159.61 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 GCCG:GC: +G++GCG G:GC:UGUAACCC AGCGGGGGC+++A:::UGGUG G+: G+: 8439 GCCGAGCUCAGCAGCGCGAGCUUGUAACCCgAGCGGGGGCAUUAAGGUGGUGUGGACGUU 8498 (-.---((------((-((----((((------((---------((((((--((--(((- 60 uG.GGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCca 118 : G :GG C GCG :G+C G:+::GG GU::+ U+ GA:GGCCCGCCC UUCCA 8499 GCcGUAUGG--CUGCG-GGCCUGGGUUGGCAGUGCCAUA---GAUGGCCCGCCCGUUCCA 8552 -((((.((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,.,,, 119 AGccc.ggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCU.AAA 176 AG::: G:AGUUG:: G G:GGC:::::CG+A+G:::::GCC:C C :: C+ A+A 8553 AGUUGcGUAGUUGGGCCGGCGGGGCUUGAGCGAAAGCUCUGGCCUCACGUUUC-CCuAGA 8611 ,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))-- 177 GugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGG 236 GUG:::GG A GCGU+AGGC::G +UCA::GAGCAGCGAA AC:::CCGCU:C:::CGG 8612 GUGGCAGGCAUUGCGUGAGGCUGGCUUCACAGAGCAGCGAAUACUGUCCGCUUCCAACGG 8671 -)))--))---.-))))))-----))------))))-.-------))-))-----)).-- 237 UgGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagGcccg.ca 293 UGGA+ GGAUA CGGGCC: +:: C ::+:C CU G C: CG+ G CC: C 8672 UGGAA-GGAUAaCGGGCCGC---CGCACUGCUGGCCCgCUUGGGUCU-CGCAG-CCUaCU 8725 -))--))---)))))))): 294 cagucaaGACCaccaggcU 312 C:: C : ACCACCA:::U 8726 CCAACGG-ACCACCACUUU 8743 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #10389,sp|AE017109.1|AE017109 Oryza sativa (japonica cultivar-group) chromosome 10, section 63 of 77 of the complete sequence. ----isReversed: 0 ----hitSequence: GCCGAGCCAAGUAGCGAUGGCUUGUCACCCGAGCGGGGGCAAUAAGGUGGUGCGGAUGCCUGGUCGUUUGCGCUUUGGCCUGGGCCUGUGGUUCGCUCUAUGCGGCCCGCCCGUUCCAAGUUGCGUAGCGUGUAUGGGGCGCCCUGGCGAAAGCUAGAGCGUCCCUGCACCUAGAGUGGCGGGUAUUGCGUGAGGCUGGUUUCACAGAGCAGCGAGUACCGCCCGCUUCCAACGGUGGAAGGAUAACGGGCCGCUGCAGCCCUGGCCCGCUUCCGGCCCAUGUGCCUUCCAUGGCAGACCCCCAUCUU hit 34 : 257283 257590 (fwd) 156.20 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 GCCG:GC: +GU+GCG +:GC:UGU ACCC AGCGGGGGC+++A::+UGG G G+:UG C 257283 GCCGAGCCAAGUAGCGAUGGCUUGUCACCCgAGCGGGGGCAAUAAGGUGGUGCGGAUG-C 257341 (----((--..----((-((----((((------((---------((((((--((--((( 60 uGGGucggc..cccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCc 117 :+GGU G+ C C+: GG+C G:+C:+G+GGU::GCU U :GGCCCGCCC UUCC 257342 CUGGUCGUUugCGCUUU-GGCCUGGGCCUGUGGUUCGCUC-UAUGCGGCCCGCCCGUUCC 257399 --((((.((((,,,<<<<<.<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,, 118 aAGccc.ggaGUUGuggcg.ggguggccccgccGgAGggcggggccaccccgccuUCUAA 175 AAG::: G:AG ::G:: GGG::GC C:::CG+A+G:::G GC::CCC::C:: CUA+ 257400 AAGUUGcGUAG--CGUGUAuGGGGCGCCCUGGCGAAAGCUAGAGCGUCCCUGCAC-CUAG 257456 ,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))- 176 AGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCG 235 AGUGG:GGG A GCGU+AGGC::G +UCA::GAGCAGCGA ACC:CCCGCU:C:::CG 257457 AGUGGCGGGUAUUGCGUGAGGCUGGUUUCACAGAGCAGCGAGUACCGCCCGCUUCCAACG 257516 --)))--))---.-))))))-----))------))))-.-------))-))---.--)). 236 GUgGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagG.cccg. 291 GUGGA+ GGAUA CGGGCC: UG +::C +C :G+:C CU C+GGCC : G CC 257517 GUGGAA-GGAUAaCGGGCCGCUG-CAGC--CCUGGCCCgCUUCCGGCC-CAUGUg-CCUu 257570 .---))--))---)))))))): 292 .cacagucaaGACCaccaggcU 312 CA+:G CA: ACC CCA+::U 257571 cCAUGG-CAG-ACCCCCAUCUU 257590 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #10389,sp|AE017109.1|AE017109 Oryza sativa (japonica cultivar-group) chromosome 10, section 63 of 77 of the complete sequence. ----isReversed: 1 ----hitSequence: GCCGAGCCAGGUAGCGUUGGCUUGUCACCCGAGCGGGGGCAAUAAGGUGGUGUUGGAUGCCUGGUCGUUUGCGCUUGGGGUCUGCGCCUGUGGUUUGCACUAUGCGGCCCGCCCGUUCCAAGUUGCGUAGCGUGUGUGGGGCGCCUGGGCGAAGGCUCGAGCGUCCCUGCACCUAGAGUGGCGGGUAUUGCGUGAGGCUGGUUUCACAGAGCAGCGAGUACCGCCCGCUUCCAACGGUGGAAGGAUAACGGGCCGCUGCAGCCCUGGCCCGCUUCCGGCCCAAGUGCCUUCCAUGGCAGACCACCACCUU hit 35 : 142841 142532 (rev) 162.33 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((-.--((-- 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGg.GAguGg 58 GCCG:GC: GU+GCGU+:GC:UGU ACCC AGCGGGGGC+++A:::UGGUG G+:UG 157189 GCCGAGCCAGGUAGCGUUGGCUUGUCACCCgAGCGGGGGCAAUAAGGUGGUGUuGGAUG- 157247 ((----((--..----((-((----((((------((---------((((((--((--(( 59 cuGGGucggc..cccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuC 116 C:+GGU G+ C C+: GGGUC G +C:+G+GGU:UGC U :GGCCCGCCC UUC 157248 CCUGGUCGUUugCGCUUGGGGUCUGCGCCUGUGGUUUGCAC-UAUGCGGCCCGCCCGUUC 157306 (--((((.((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>.>>>>>>,,,, 117 caAGccc.ggaGUUGuggcgggguggccccgccGgAGggcggggccacc.ccgccuUCUA 174 CAAG::: G:AG ::G: G G::GC ::::CG+AGG:::: GC::C C :C:: CUA 157307 CAAGUUGcGUAGCGUGUGUGG-GGCGCCUGGGCGAAGGCUCGAGCGUC-cCUGCAC-CUA 157363 ,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,)))))))) 175 AAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggC 234 +AGUGG:GGG A GCGU+AGGC::G +UCA::GAGCAGCGA ACC:CCCGCU:C:::C 157364 GAGUGGCGGGUAUUGCGUGAGGCUGGUUUCACAGAGCAGCGAGUACCGCCCGCUUCCAAC 157423 ---)))--))---.-))))))-----))------))))-.-------))-))-----)). 235 GGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagGcccg. 291 GGUGGA+ GGAUA CGGGCC: UG +A:C +C :G+ C CU C+GGCC : +G CC 157424 GGUGGAA-GGAUAaCGGGCCGCUG-CAGC--CCUGGCCCgCUUCCGGCCCAAGUG-CCUu 157478 .---))--))---)))))))): 292 .cacagucaaGACCaccaggcU 312 CA+:G CA: ACCACCA:::U 157479 cCAUGG-CAG-ACCACCACCUU 157498 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #16313,sp|AF069442.1|AF069442 Arabidopsis thaliana BAC T4I9, chromosome IV, near 17 cM, complete sequence. ----isReversed: 0 ----hitSequence: GUCGAGCUAAGUAACAAUAGCUUGUAACCCAUGUGGGGACAUUAAGAUGGUGGGACACUGGUUCGGUUCCUCGGAUCGGUUCUGAUGUGGGCAUGUUUCUGAGCUGCCCAGUCCAAGCUGUGAGUAAUUAGUGUUGAGUUGAGCGAAGGCUUGGCUCAUGCAGGUUCUAGAGUCGGAGGGUAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGUGGACGGAUCACGGUUUAGCGUCGCUCAGAACCACUAUGGCCUGCUGGUCCGAUCUCAUAUGAACCACCAUUUU hit 36 : 64156 64461 (fwd) 142.97 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 G:CG:GC: +GU+ C +:GC:UGUAACCC G+GGGG:C+++A:::UGGUGGGA:: : 64156 GUCGAGCUAAGUAACAAUAGCUUGUAACCCaUGUGGGGACAUUAAGAUGGUGGGACAC-U 64214 (----((------((-((----((((------((---------((((((--((--(((-- 60 uGGGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCcaA 119 : G UCGG +CC+C G UC G::::+G +GU :GC U UU +::: C:GCCC UCCAA 64215 G-GUUCGGUUCCUCG-GAUC-GGUUCUGAUGUGGGCAUGUUUCUGAGCUGCCCAGUCCAA 64271 ((((((((,,,<<<<<<<<.<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,,,. 120 GcccggaGUUGuggcgggg.uggccccgccGgAGggcggggccaccccgccuUCUAAAG. 177 GC:: :AGU :: : G : UG::::+::CG+AGG::+::::CA: C : :: CUA+AG 64272 GCUGUGAGU--AAUUAGUGuUGAGUUGAGCGAAGGCUUGGCUCAUGCAGGUU-CUAGAGu 64328 ,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))--- 178 ugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGU 237 +GG::GG A+ GCGU+AGGC::G +UCA::GAGCAGCGA+ AC::CCCGCU: ::GC+GU 64329 CGGAGGGUAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGU 64388 )))--))---.-))))))-----))------))))-.-------))-))---..--)).- 238 gGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagG..cccg.c 292 GGA GGAU C:G :::G G : C +C ::::C CU +UGG C G++G CCG + 64389 GGAC-GGAUCaCGGUUUAGCG-UCGC--UCAGAACCaCU-AUGGCC-UGCUGgu-CCGaU 64441 --))--))---)))))))): 293 acagucaaGACCaccaggcU 312 ++::U ::+ACCACCA:::U 64442 CUCAUAUGAACCACCAUUUU 64461 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #99211,sp|AP003253.3|AP003253 Oryza sativa (japonica cultivar-group) genomic DNA, chromosome 1, PAC clone:P0451D05. ----isReversed: 0 ----hitSequence: GCCGAGCUCAGUAGCGAGAGCCUGUAACCCAAGCGGGGGCACUAAAGGUGGCUGCGGAUGUUUGGUGUGGAUUCUGAUCCUGGGCCCCAUGUUGUUGUAAUCUUGCUGGCUUGCCCGUUCCAAGUUGCGUAGUGGGCCGGAGGGGCUUUGGCGAAGGCCUUUGCUUUGCUUCUCCGGCCCUAAAGUGGCAGGCACAGCGUGAGGCUGGCUUCACAGAGCAGCGAUCACUGCCCGCUUCCAUCGGUGGAAGGAUAACAGGCUGCUGCACCUUGGGCCCGCUUCUGGCCCAGAGUCCCUCUACAACAGACCACCAUCUU hit 37 : 106424 106740 (fwd) 143.70 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))--.--((((((.((---((- 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcg.AAgccugg.uGgGAguG 57 GCCG:GC: +GU+GCG G:GC:UGUAACCC AGCGGGGGC+ AA::+UGG UG G+:UG 106424 GCCGAGCUCAGUAGCGAGAGCCUGUAACCCaAGCGGGGGCACuAAAGGUGGcUGCGGAUG 106483 -((----((------((-((---.-((((------((-----..----((((((--((-- 58 gcuGGGucggccccgcggggucg.gcccuggggguaugcUua..UUGaaggcccGCcCcu 114 +:UGG :GG +C:G +C G: C: +G U:U +U+A UUG+::GC::GCCC U 106484 UUUGGUGUGG--AUUCUGAUCCUgGGCCCCAUGUUGUUGUAAucUUGCUGGCUUGCCCGU 106541 (((--((((.((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>.....>>>>>> 115 uCcaAGccc.ggaGUUGuggcgggguggccccgccGgAGggcggggcca.....ccccgc 168 UCCAAG::: G:AGU G:G:CGG G::GC : G:CG+AGG:C : GC:: C CCG: 106542 UCCAAGUUGcGUAGU-GGGCCGGAGGGGCUUUGGCGAAGGCCUUUGCUUugcuuCUCCGG 106600 >>,,,,,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,)) 169 cuUCUAAAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCu 228 C: CUAAAGUGG::GG AC GCGU+AGGC::G +UCA::GAGCAGCGA+ AC::CCCGCU 106601 CC-CUAAAGUGGCAGGCACAGCGUGAGGCUGGCUUCACAGAGCAGCGAUCACUGCCCGCU 106659 ))))))---)))--))---.-))))))-----))------))))-.-------))-))-- 229 ccgggCGGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgag 286 :C:::CGGUGGA+ GGAUA C::GC:: UG +A:C ++ :G :C CU CUGG :GAG 106660 UCCAUCGGUGGAA-GGAUAaCAGGCUGCUG-CACC--UUGGGCCCgCUUCUGGCCCAGAG 106715 -.--)).---))--))---)))))))): 287 G.cccg.cacagucaaGACCaccaggcU 312 CCC: +ACA: CA: ACCACCA+::U 106716 -uCCCUcUACAA-CAG-ACCACCAUCUU 106740 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #99274,sp|AP003333.4|AP003333 Oryza sativa (japonica cultivar-group) genomic DNA, chromosome 1, BAC clone:B1103C09. ----isReversed: 0 ----hitSequence: GCCGAGCUCAGUAGCGAGAGCCUGUAACCCAAGCGGGGGCACUAAAGGUGGCUGCGGAUGUUUGGUGUGGAUUCUGAUCCUGGGCCCCAUGUUGUUGUAAUCUUGCUGGCUUGCCCGUUCCAAGUUGCGUAGUGGGCCGGAGGGGCUUUGGCGAAGGCCUUUGCUUUGCUUCUCCGGCCCUAAAGUGGCAGGCACAGCGUGAGGCUGGCUUCACAGAGCAGCGAUCACUGCCCGCUUCCAUCGGUGGAAGGAUAACAGGCUGCUGCACCUUGGGCCCGCUUCUGGCCCAGAGUCCCUCUACAACAGACCACCAUCUU hit 38 : 45380 45696 (fwd) 143.70 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))--.--((((((.((---((- 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcg.AAgccugg.uGgGAguG 57 GCCG:GC: +GU+GCG G:GC:UGUAACCC AGCGGGGGC+ AA::+UGG UG G+:UG 45380 GCCGAGCUCAGUAGCGAGAGCCUGUAACCCaAGCGGGGGCACuAAAGGUGGcUGCGGAUG 45439 -((----((------((-((---.-((((------((-----..----((((((--((-- 58 gcuGGGucggccccgcggggucg.gcccuggggguaugcUua..UUGaaggcccGCcCcu 114 +:UGG :GG +C:G +C G: C: +G U:U +U+A UUG+::GC::GCCC U 45440 UUUGGUGUGG--AUUCUGAUCCUgGGCCCCAUGUUGUUGUAAucUUGCUGGCUUGCCCGU 45497 (((--((((.((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>.....>>>>>> 115 uCcaAGccc.ggaGUUGuggcgggguggccccgccGgAGggcggggcca.....ccccgc 168 UCCAAG::: G:AGU G:G:CGG G::GC : G:CG+AGG:C : GC:: C CCG: 45498 UCCAAGUUGcGUAGU-GGGCCGGAGGGGCUUUGGCGAAGGCCUUUGCUUugcuuCUCCGG 45556 >>,,,,,,,,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,)) 169 cuUCUAAAGugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCu 228 C: CUAAAGUGG::GG AC GCGU+AGGC::G +UCA::GAGCAGCGA+ AC::CCCGCU 45557 CC-CUAAAGUGGCAGGCACAGCGUGAGGCUGGCUUCACAGAGCAGCGAUCACUGCCCGCU 45615 ))))))---)))--))---.-))))))-----))------))))-.-------))-))-- 229 ccgggCGGUgGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgag 286 :C:::CGGUGGA+ GGAUA C::GC:: UG +A:C ++ :G :C CU CUGG :GAG 45616 UCCAUCGGUGGAA-GGAUAaCAGGCUGCUG-CACC--UUGGGCCCgCUUCUGGCCCAGAG 45671 -.--)).---))--))---)))))))): 287 G.cccg.cacagucaaGACCaccaggcU 312 CCC: +ACA: CA: ACCACCA+::U 45672 -uCCCUcUACAA-CAG-ACCACCAUCUU 45696 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #100168,sp|AP006123.1|AP006123 Lotus corniculatus var. japonicus genomic DNA, chromosome 1, clone:LjT41E18, TM0207. ----isReversed: 0 ----hitSequence: GCCGAGCUUGCACGAUAGCUUGUAACCCGAAUGGGGGCACCAAGAUGGUGGAACAUGGCUAUGACUUCACUGGGUUGGUCUGGUGGUUGCACCUUGUUGGCCUGCCCGCUCCAAGUCGAGAGGUGGGCCAUGUGUCUUUAGUGAAAGCUAAGGUCUUGUGGUUCCUAGACAGGAGGGCAAAGCGUGAGGCUGGUGUCACAGAGCAGCGAACACUUCUGGCUCCUGACAGUGGAGGGAUAACAGGCUGCUGCACCUUCAGCCCACAAAUGCCUAGUGAACCCAGCUACCUGAACUAUCAUUUU hit 39 : 43412 43713 (fwd) 120.99 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 GCCG:GC: UG++ +:GC:UGUAACCC A +GGGGGC+ A:::UG U G+A:: : 43412 GCCGAGCU-UGCACGA-UAGCUUGUAACCCgAAUGGGGGCACCAAGAUGGUGGAACA--U 43467 (----((------((-((----((((------((---------((((((--((--(((-- 60 uGGGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCcaA 119 G :G C+ C C:GGGU G: CUGG+GG UGC UUG ::GCC:GCCC +UCCAA 43468 GGCUAUGACUUCACUGGGUU-GGUCUGGUGG-UUGCACCUUGUUGGCCUGCCCGCUCCAA 43525 ((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,,,,< 120 GcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCUAAAGug 179 G:C :GAG U :: C:: : G C::::::G+A+::::::G C : ::G :: CUA+A 43526 GUCGAGAGGU-GGGCCAUGUGUCUUUAGUGAAAGCUAAGGUCUUGUGGUUC-CUAGACAG 43583 <<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))---)) 180 ggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGUgG 239 G::GG A+ GCGU+AGGC::G UCA::GAGCAGCGAA AC::C +GCUC: G:C+GUGG 43584 GAGGGCAAAGCGUGAGGCUGGUGUCACAGAGCAGCGAACACUUCUGGCUCCUGACAGUGG 43643 )--))---.-))))))-----))------))))--------))-))---.--))..---) 240 agGGgAUa.CgggccgGUGAgaucaaaccagggccuacuGGccucgagG.cccg..caca 295 AG GGAUA C:GGC:: UG +A C ++CAG :C A+ GCCU:G G CCC: 43644 AG-GGAUAaCAGGCUGCUG-CACC--UUCAGCCCACAAAUGCCUAGUGAaCCCAgc---U 43696 )--))---)))))))): 296 gucaaGACCaccaggcU 312 : C::+AC A CA:::U 43697 ACCUGAACUAUCAUUUU 43713 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #100222,sp|AP006364.1|AP006364 Lotus corniculatus var. japonicus genomic DNA, chromosome 4, clone:LjT28B04, TM0170. ----isReversed: 1 ----hitSequence: GCCGAGUUGGGUUACUCCAGCUUGUGACCCAAGUGGGGGCACCAGGUUGAUGGAACAUGGUUCUGGCUUUCGUUAGGCUGGGCUGUUAGAUGCAAUAUUCUGGCCUGCCCACUCCAAGUUGAGAGUUGGACCGUGGGGCUUGGGCGAAGGCCCUUGUCUCUCGGCCCCUAAACUGGAGGGCAAAGCGUGAGGCUGGUUUCACAGAGCAGCGAAUACCUCUGGCUCCUGACAGUGGAGGGAUAACAGGCUGAUGCACUCUCAGCCCAUUGUGCCUAGUGGGCCUGGCCUCUUGAACCAUCAUCUU hit 40 : 60840 60537 (rev) 129.92 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 GCCG:G::G GU C ::C:UGU ACCC AG+GGGGGC+ A:: UG:UGG+A:: G: 40333 GCCGAGUUGGGUUACUCCAGCUUGUGACCCaAGUGGGGGCACCAGGUUGAUGGAACAUGG 40392 (----((--..----((-((----((((------((---------((((((--((--((( 60 uGGGucggc..cccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCc 117 + UC G+ + CG:: GG+ :+::+G++ AUGC + U +::GCC:GCCC +UCC 40393 U---UCUGGcuUUCGUUAGGCU--GGGCUGUUAGAUGCAAUAUUCUGGCCUGCCCACUCC 40447 --((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,,, 118 aAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCUAAAG 177 AAG:: :GAGUU :G C:G:G:G+C ::G:CG+AGG:C:: G+C:C:C:G C: CUAAA 40448 AAGUUGAGAGUU-GGACCGUGGGGCUUGGGCGAAGGCCCUUGUCUCUCGGCCC-CUAAAC 40505 ,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))--- 178 ugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGU 237 U G:GGG A+ GCGU+AGGC::G +UCA::GAGCAGCGAA ACC:C +GCUC: ::C+GU 40506 UGGAGGGCAAAGCGUGAGGCUGGUUUCACAGAGCAGCGAAUACCUCUGGCUCCUGACAGU 40565 )))--))---.-))))))-----))------))))--------))-))---.--)).--- 238 gGagGGgAUa.CgggccgGUGAgaucaaaccagggccuacuGGccucgagG.cccg.cac 294 GGAG GGAUA C:GGC:: UG +A C +C ::+:+ U UG CCU:: GG CC G +C 40566 GGAG-GGAUAaCAGGCUGAUG-CA-CUCUCAGCCCAUU-GUG-CCUAGUGGgCCUGg-CC 40619 ))--))---)))))))): 295 agucaaGACCaccaggcU 312 +: +::+ACCA:CA ::U 40620 UC-UUGAACCAUCAUCUU 40636 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #101245,sp|X72228.1|AT7SL1A A.thaliana gene At7SL-1 for 7SL RNA ----isReversed: 0 ----hitSequence: GUCGAGCUAAGUAACAAUAGCUUGUAACCCAUGUGGGGACAUUAAGAUGGUGGGACACUGGUUCGGUUCCUCGGAUCGGUUCUGAUGUGGGCAUGUUUCUGAGCUGCCCAGUCCAAGCUGUGAGUAAUUAGUGUUGAGUUGAGCGAAGGCUUGGCUCAUGCAGGUUCUAGAGUCGGAGGGUAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGUGGACGGAUCACGGUUUAGCGUCGCUCAGAACCACUAUGGCCUGCUGGUCCGAUCUCAUAUGAACCACCAUUUU hit 41 : 320 625 (fwd) 142.97 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 G:CG:GC: +GU+ C +:GC:UGUAACCC G+GGGG:C+++A:::UGGUGGGA:: : 320 GUCGAGCUAAGUAACAAUAGCUUGUAACCCaUGUGGGGACAUUAAGAUGGUGGGACAC-U 378 (----((------((-((----((((------((---------((((((--((--(((-- 60 uGGGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCcaA 119 : G UCGG +CC+C G UC G::::+G +GU :GC U UU +::: C:GCCC UCCAA 379 G-GUUCGGUUCCUCG-GAUC-GGUUCUGAUGUGGGCAUGUUUCUGAGCUGCCCAGUCCAA 435 ((((((((,,,<<<<<<<<.<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,,,. 120 GcccggaGUUGuggcgggg.uggccccgccGgAGggcggggccaccccgccuUCUAAAG. 177 GC:: :AGU :: : G : UG::::+::CG+AGG::+::::CA: C : :: CUA+AG 436 GCUGUGAGU--AAUUAGUGuUGAGUUGAGCGAAGGCUUGGCUCAUGCAGGUU-CUAGAGu 492 ,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))--- 178 ugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGU 237 +GG::GG A+ GCGU+AGGC::G +UCA::GAGCAGCGA+ AC::CCCGCU: ::GC+GU 493 CGGAGGGUAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGU 552 )))--))---.-))))))-----))------))))-.-------))-))---..--)).- 238 gGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagG..cccg.c 292 GGA GGAU C:G :::G G : C +C ::::C CU +UGG C G++G CCG + 553 GGAC-GGAUCaCGGUUUAGCG-UCGC--UCAGAACCaCU-AUGGCC-UGCUGgu-CCGaU 605 --))--))---)))))))): 293 acagucaaGACCaccaggcU 312 ++::U ::+ACCACCA:::U 606 CUCAUAUGAACCACCAUUUU 625 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #101246,sp|X72229.1|AT7SL2A A.thaliana gene At7SL-2 for 7SL RNA ----isReversed: 0 ----hitSequence: GUCGAGCUAAGUAACAUGAGCUUGUAACCCAUGUGGGGACAUUUAGAUGGUGGAACACUGGUUCGGGUCCACGGGCCGGUUCUGUUGUUGGCAUGUUUCUGGGCUGCCCAGUCCAAGCUGUGAGUAAGACGUGUGUGUCAAGCGAAGGCUUGGCUCAAACGGCUUCUAAAGUUGGAGGGUAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGUGGACGGAUCACAGUUUAGCGUCGCUCAGAACCACUAUGGCCUGCUGGUCCGAUCUCAUAUGAACCACCAUUUU hit 42 : 323 627 (fwd) 164.81 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 G:CG:GC: +GU+ C UG:GC:UGUAACCC G+GGGG:C+++ :::UGGUGG+A:: : 323 GUCGAGCUAAGUAACAUGAGCUUGUAACCCaUGUGGGGACAUUUAGAUGGUGGAACAC-U 381 (----((------((-((----((((------((---------((((((--((--(((-- 60 uGGGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCcaA 119 : G UCGG++CC C GG+C G::::+G++GU::GC U UU +::: C:GCCC UCCAA 382 G-GUUCGGGUCCACG-GGCC-GGUUCUGUUGUUGGCAUGUUUCUGGGCUGCCCAGUCCAA 438 ((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,,,., 120 GcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCUAAAG.u 178 GC:: :AGU ::G::G: UG ::C:::CG+AGG:::G:: CA :C::C:: CUAAAG U 439 GCUGUGAGU--AAGACGUGUGUGUCAAGCGAAGGCUUGGCUCAAACGGCUU-CUAAAGuU 495 <<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))---) 179 gggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGUg 238 GG::GG A+ GCGU+AGGC::G +UCA::GAGCAGCGA+ AC::CCCGCU: ::GC+GUG 496 GGAGGGUAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGUG 555 ))--))---.-))))))-----))------))))-.-------))-))---..--)).-- 239 GagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagG..cccg.ca 293 GA GGAU C:G :::G G ::C +C ::::C CU +UGGCC G++G CCG ++ 556 GAC-GGAUCaCAGUUUAGCG-UCGC--UCAGAACCaCU-AUGGCC-UGCUGgu-CCGaUC 608 -))--))---)))))))): 294 cagucaaGACCaccaggcU 312 +::U ::+ACCACCA:::U 609 UCAUAUGAACCACCAUUUU 627 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #101247,sp|X55111.1|AT7SLRNA A. thaliana 7SL RNA gene ----isReversed: 0 ----hitSequence: GUCGAGCUAAGUAACAAUAGCUUGUAACCCAUGUGGGGACAUUAAGAUGGUGGGACACUGGUUCGGUUCCUCGGAUCGGUUCUGAUGUGGGCAUGUUUCUGAGCUGCCCAGUCCAAGCUGUGAGUAAUUAGUGUUGAGUUGAGCGAAGGCUUGGCUCAUGCAGGUUCUAGAGUCGGAGGGUAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGUGGACGGAUCACGGUUUAGCGUCGCUCAGAACCACUAUGGCCUGCUGGUCCGAUCUCAUAUGAACCACCAUUUU hit 43 : 801 1106 (fwd) 142.97 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 G:CG:GC: +GU+ C +:GC:UGUAACCC G+GGGG:C+++A:::UGGUGGGA:: : 801 GUCGAGCUAAGUAACAAUAGCUUGUAACCCaUGUGGGGACAUUAAGAUGGUGGGACAC-U 859 (----((------((-((----((((------((---------((((((--((--(((-- 60 uGGGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCcaA 119 : G UCGG +CC+C G UC G::::+G +GU :GC U UU +::: C:GCCC UCCAA 860 G-GUUCGGUUCCUCG-GAUC-GGUUCUGAUGUGGGCAUGUUUCUGAGCUGCCCAGUCCAA 916 ((((((((,,,<<<<<<<<.<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,,,. 120 GcccggaGUUGuggcgggg.uggccccgccGgAGggcggggccaccccgccuUCUAAAG. 177 GC:: :AGU :: : G : UG::::+::CG+AGG::+::::CA: C : :: CUA+AG 917 GCUGUGAGU--AAUUAGUGuUGAGUUGAGCGAAGGCUUGGCUCAUGCAGGUU-CUAGAGu 973 ,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))--- 178 ugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGU 237 +GG::GG A+ GCGU+AGGC::G +UCA::GAGCAGCGA+ AC::CCCGCU: ::GC+GU 974 CGGAGGGUAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGU 1033 )))--))---.-))))))-----))------))))-.-------))-))---..--)).- 238 gGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagG..cccg.c 292 GGA GGAU C:G :::G G : C +C ::::C CU +UGG C G++G CCG + 1034 GGAC-GGAUCaCGGUUUAGCG-UCGC--UCAGAACCaCU-AUGGCC-UGCUGgu-CCGaU 1086 --))--))---)))))))): 293 acagucaaGACCaccaggcU 312 ++::U ::+ACCACCA:::U 1087 CUCAUAUGAACCACCAUUUU 1106 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #101759,sp|X69901.1|ATAUXIN A.thaliana gene for auxin-binding protein ----isReversed: 0 ----hitSequence: GUCGAGCUAAGUAACAAUAGCUUGUAACCCAUGUGGGGACAUUAAGAUGGUGGGACACUGGUUCGGUUCCUCGGAUCGGUUCUGAUGUGGGCAUGUUUCUGAGCUGCCCAGUCCAAGCUGUGAGUAAUUAGUGUUGAGUUGAGCGAAGGCUUGGCUCAUGCAGGUUCUAGAGUCGGAGGGUAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGUGGACGGAUCACGGUUUAGCGUCGCUCAGAACCACUAUGGCCUGCUGGUCCGAUCUCAUAUGAACCACCAUUUU hit 44 : 3886 4191 (fwd) 142.97 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 G:CG:GC: +GU+ C +:GC:UGUAACCC G+GGGG:C+++A:::UGGUGGGA:: : 3886 GUCGAGCUAAGUAACAAUAGCUUGUAACCCaUGUGGGGACAUUAAGAUGGUGGGACAC-U 3944 (----((------((-((----((((------((---------((((((--((--(((-- 60 uGGGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCcaA 119 : G UCGG +CC+C G UC G::::+G +GU :GC U UU +::: C:GCCC UCCAA 3945 G-GUUCGGUUCCUCG-GAUC-GGUUCUGAUGUGGGCAUGUUUCUGAGCUGCCCAGUCCAA 4001 ((((((((,,,<<<<<<<<.<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,,,. 120 GcccggaGUUGuggcgggg.uggccccgccGgAGggcggggccaccccgccuUCUAAAG. 177 GC:: :AGU :: : G : UG::::+::CG+AGG::+::::CA: C : :: CUA+AG 4002 GCUGUGAGU--AAUUAGUGuUGAGUUGAGCGAAGGCUUGGCUCAUGCAGGUU-CUAGAGu 4058 ,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))--- 178 ugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGU 237 +GG::GG A+ GCGU+AGGC::G +UCA::GAGCAGCGA+ AC::CCCGCU: ::GC+GU 4059 CGGAGGGUAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGU 4118 )))--))---.-))))))-----))------))))-.-------))-))---..--)).- 238 gGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagG..cccg.c 292 GGA GGAU C:G :::G G : C +C ::::C CU +UGG C G++G CCG + 4119 GGAC-GGAUCaCGGUUUAGCG-UCGC--UCAGAACCaCU-AUGGCC-UGCUGgu-CCGaU 4171 --))--))---)))))))): 293 acagucaaGACCaccaggcU 312 ++::U ::+ACCACCA:::U 4172 CUCAUAUGAACCACCAUUUU 4191 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #101926,sp|AL161495.2|ATCHRIV7 Arabidopsis thaliana DNA chromosome 4, contig fragment No. 7 ----isReversed: 1 ----hitSequence: GUCGAGCUAAGUAACAAUAGCUUGUAACCCAUGUGGGGACAUUAAGAUGGUGGGACACUGGUUCGGUUCCUCGGAUCGGUUCUGAUGUGGGCAUGUUUCUGAGCUGCCCAGUCCAAGCUGUGAGUAAUUAGUGUUGAGUUGAGCGAAGGCUUGGCUCAUGCAGGUUCUAGAGUCGGAGGGUAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGUGGACGGAUCACGGUUUAGCGUCGCUCAGAACCACUAUGGCCUGCUGGUCCGAUCUCAUAUGAACCACCAUUUU hit 45 : 164946 164641 (rev) 142.97 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 G:CG:GC: +GU+ C +:GC:UGUAACCC G+GGGG:C+++A:::UGGUGGGA:: : 34670 GUCGAGCUAAGUAACAAUAGCUUGUAACCCaUGUGGGGACAUUAAGAUGGUGGGACAC-U 34728 (----((------((-((----((((------((---------((((((--((--(((-- 60 uGGGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCcaA 119 : G UCGG +CC+C G UC G::::+G +GU :GC U UU +::: C:GCCC UCCAA 34729 G-GUUCGGUUCCUCG-GAUC-GGUUCUGAUGUGGGCAUGUUUCUGAGCUGCCCAGUCCAA 34785 ((((((((,,,<<<<<<<<.<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,,,. 120 GcccggaGUUGuggcgggg.uggccccgccGgAGggcggggccaccccgccuUCUAAAG. 177 GC:: :AGU :: : G : UG::::+::CG+AGG::+::::CA: C : :: CUA+AG 34786 GCUGUGAGU--AAUUAGUGuUGAGUUGAGCGAAGGCUUGGCUCAUGCAGGUU-CUAGAGu 34842 ,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))--- 178 ugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGU 237 +GG::GG A+ GCGU+AGGC::G +UCA::GAGCAGCGA+ AC::CCCGCU: ::GC+GU 34843 CGGAGGGUAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGU 34902 )))--))---.-))))))-----))------))))-.-------))-))---..--)).- 238 gGagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagG..cccg.c 292 GGA GGAU C:G :::G G : C +C ::::C CU +UGG C G++G CCG + 34903 GGAC-GGAUCaCGGUUUAGCG-UCGC--UCAGAACCaCU-AUGGCC-UGCUGgu-CCGaU 34955 --))--))---)))))))): 293 acagucaaGACCaccaggcU 312 ++::U ::+ACCACCA:::U 34956 CUCAUAUGAACCACCAUUUU 34975 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #101937,sp|AL161496.2|ATCHRIV8 Arabidopsis thaliana DNA chromosome 4, contig fragment No. 8 ----isReversed: 0 ----hitSequence: GUCGAGCUAAGUAACAUGAGCUUGUAACCCAUGUGGGGACAUUUAGAUGGUGGAACACUGGUUCGGGUCCACGGGCCGGUUCUGUUGUUGGCAUGUUUCUGGGCUGCCCAGUCCAAGCUGUGAGUAAGACGUGUGUGUCAAGCGAAGGCUUGGCUCAAACGGCUUCUAAAGUUGGAGGGUAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGUGGACGGAUCACAGUUUAGCGUCGCUCAGAACCACUAUGGCCUGCUGGUCCGAUCUCAUAUGAACCACCAUUUU hit 46 : 123872 124176 (fwd) 164.81 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 G:CG:GC: +GU+ C UG:GC:UGUAACCC G+GGGG:C+++ :::UGGUGG+A:: : 123872 GUCGAGCUAAGUAACAUGAGCUUGUAACCCaUGUGGGGACAUUUAGAUGGUGGAACAC-U 123930 (----((------((-((----((((------((---------((((((--((--(((-- 60 uGGGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCcaA 119 : G UCGG++CC C GG+C G::::+G++GU::GC U UU +::: C:GCCC UCCAA 123931 G-GUUCGGGUCCACG-GGCC-GGUUCUGUUGUUGGCAUGUUUCUGGGCUGCCCAGUCCAA 123987 ((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,,,., 120 GcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCUAAAG.u 178 GC:: :AGU ::G::G: UG ::C:::CG+AGG:::G:: CA :C::C:: CUAAAG U 123988 GCUGUGAGU--AAGACGUGUGUGUCAAGCGAAGGCUUGGCUCAAACGGCUU-CUAAAGuU 124044 <<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))---) 179 gggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGUg 238 GG::GG A+ GCGU+AGGC::G +UCA::GAGCAGCGA+ AC::CCCGCU: ::GC+GUG 124045 GGAGGGUAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGUG 124104 ))--))---.-))))))-----))------))))-.-------))-))---..--)).-- 239 GagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagG..cccg.ca 293 GA GGAU C:G :::G G ::C +C ::::C CU +UGGCC G++G CCG ++ 124105 GAC-GGAUCaCAGUUUAGCG-UCGC--UCAGAACCaCU-AUGGCC-UGCUGgu-CCGaUC 124157 -))--))---)))))))): 294 cagucaaGACCaccaggcU 312 +::U ::+ACCACCA:::U 124158 UCAUAUGAACCACCAUUUU 124176 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #101937,sp|AL161496.2|ATCHRIV8 Arabidopsis thaliana DNA chromosome 4, contig fragment No. 8 ----isReversed: 0 ----hitSequence: GUCGAGCGAAGUAACAUGAGCUUGUAACCCAUGUGGGGACAUUAAGAUGGUGGAACACUGGUUCGGGUCCACGGGCCGGUUCUGUUGCUGGCAUGUUUCUGGGCUGCCCAGUCCAAGCUGUGAGUAAGACGUGUGUGUCAAGCGAAGGCUUGGCUCAAACGGCUGCUAAAGUUGGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGAUUACUUCCCGCUUACAGCAGUGGACGGAUCACAGUUUGGCGUCGCUCAGAACCACUAUGGCCUGCUGGUCCGAUCUCAUCUGAACCACCAUUUU hit 47 : 127430 127734 (fwd) 164.56 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 G:CG:GC +GU+ C UG GC:UGUAACCC G+GGGG:C+++A:::UGGUGG+A:: : 127430 GUCGAGCGAAGUAACAUGAGCUUGUAACCCaUGUGGGGACAUUAAGAUGGUGGAACAC-U 127488 (----((------((-((----((((------((---------((((((--((--(((-- 60 uGGGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCcaA 119 : G UCGG++CC C GG+C G::::+G++G+::GC U UU +::: C:GCCC UCCAA 127489 G-GUUCGGGUCCACG-GGCC-GGUUCUGUUGCUGGCAUGUUUCUGGGCUGCCCAGUCCAA 127545 ((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,,,., 120 GcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCUAAAG.u 178 GC:: :AGU ::G::G: UG ::C:::CG+AGG:::G:: CA :C::C:: CUAAAG U 127546 GCUGUGAGU--AAGACGUGUGUGUCAAGCGAAGGCUUGGCUCAAACGGCUG-CUAAAGuU 127602 <<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))---) 179 gggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGUg 238 GG::GG A+ GCGU+AGGC::G +UCA::GAGCAGCGA+ AC::CCCGCU: ::GC+GUG 127603 GGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGAUUACUUCCCGCUUACAGCAGUG 127662 ))--))---.-))))))-----))------))))-.-------))-))---..--)).-- 239 GagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagG..cccg.ca 293 GA GGAU C:G :::G G ::C +C ::::C CU +UGGCC G++G CCG ++ 127663 GAC-GGAUCaCAGUUUGGCG-UCGC--UCAGAACCaCU-AUGGCC-UGCUGgu-CCGaUC 127715 -))--))---)))))))): 294 cagucaaGACCaccaggcU 312 +::UC::+ACCACCA:::U 127716 UCAUCUGAACCACCAUUUU 127734 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #102211,sp|AL353994.1|ATF17I14 Arabidopsis thaliana DNA chromosome 5, BAC clone F17I14 (ESSA project) ----isReversed: 1 ----hitSequence: GUCGAGCUAUGUAACGAGAGCUUGUAACCCAAGUGGGGACUAUAAGAUGGUGGAACACUGGAUCGGCCCACGGGUCGGAUUUGUUGUUGGCAUAGGUCUGGACUGCCCAAUCCAAGCUGUGAGUGAACCGUAUGAACCAAGCGAAGGUUUGAUCCGUACGGUUGCUAAAGGUUGAGGGUAUUGCGUUAGGCUGGCUUCACAGAGCAGCGACUACCUCCCGCUCUCAGCAGUGGACGGACAACGGUUCGACGCCACACAAAUCCACUAUGGUCCGCUGGCUCGUAACCCGCUUGAACCACCAUUUU hit 48 : 33792 33488 (rev) 158.22 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 G:CG:GC: UGU+ CG G:GC:UGUAACCC AG+GGGG:C ++A:::UGGUGG+A:: C 58700 GUCGAGCUAUGUAACGAGAGCUUGUAACCCaAGUGGGGACUAUAAGAUGGUGGAACA--C 58757 (----((------((-((----((((------((---------((((((--((--(((-- 60 uGGGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCcaA 119 GG UCGGC CC CG G+UC G:::U+G++GU::GC UA +:G::C:GCCC UCCAA 58758 UGGAUCGGC-CCACG-GGUC-GGAUUUGUUGUUGGCAUAGGUCUGGACUGCCCAAUCCAA 58814 ((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,.,,,,, 120 GcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCU.AAAGu 178 GC:: GAGU ::C:G::+G:: C:: CG+AGG ::G ::C+::C:G:: CU AA+GU 58815 GCUGUGAGU--GAACCGUAUGAACCAAGCGAAGGUUUGAUCCGUACGGUUG-CUaAAGGU 58871 <<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))---) 179 gggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGUg 238 :G:GGG A GCGU AGGC::G +UCA::GAGCAGCGA+ ACC:C:CGCUC ::GC+GUG 58872 UGAGGGUAUUGCGUUAGGCUGGCUUCACAGAGCAGCGACUACCUCCCGCUCUCAGCAGUG 58931 ))--))---.-))))))-----))------))))-.-------))-))---.--))...- 239 GagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagG.cccg...c 292 GA GGA A C:G::C: G +::C AC A:::C CU +UGG+C CG++G C CG 58932 GAC-GGACAaCGGUUCGACG-CCAC--ACAAAUCCaCU-AUGGUC-CGCUGgCUCGuaa- 58984 --))--))---)))))))): 293 acagucaaGACCaccaggcU 312 +C G +::+ACCACCA:::U 58985 CCCGCUUGAACCACCAUUUU 59004 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #102940,sp|AJ290403.1|ATH290403 Arabidopsis thaliana 7SL-3 gene for signal recognition particle ----isReversed: 0 ----hitSequence: GUCGAGCUAAGUAACAGUAGCUUGUAACCCAUGUGGGGACAAUAAGAUCGAGGGACACUGGUCGGUUCCUCGGGUCGGUUCUGGUGUUGGCAUGUUUCUGAGCUGCCCAGUCCAAGCUGUGGUAAUCCGUGUGAAUCAAGCGAAGGCUUGGCUCAGUCGGUUUCUAAAGGCGGAAGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGUGGACGGGAUCACAGUUUGGCGUCGCUCAGAACCACUAUGGCCUGAUGGUCCGAUCUCAUAUGAACCACCAUUUU hit 49 : 66 369 (fwd) 153.59 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 G:CG:GC: +GU+ C +:GC:UGUAACCC G+GGGG:C+++A:::U G GGGA:: : 66 GUCGAGCUAAGUAACAGUAGCUUGUAACCCaUGUGGGGACAAUAAGAUCGAGGGACAC-U 124 (----((------((-((----((((------((---------((((((--((--(((-- 60 uGGGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCcaA 119 : GUCGG C ::GGGUC G::::+GG+GU::GC U UU +::: C:GCCC UCCAA 125 G--GUCGGU-UCCUCGGGUC-GGUUCUGGUGUUGGCAUGUUUCUGAGCUGCCCAGUCCAA 180 ((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,.,,,,, 120 GcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCU.AAAGu 178 GC:: : GU :: C:G: UG: :C:::CG+AGG:::G: :CA :C:G :: CU AA+G+ 181 GCUG-UGGU--AAUCCGUGUGAAUCAAGCGAAGGCUUGGCUCAGUCGGUUU-CUaAAGGC 236 <<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))---) 179 gggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGUg 238 GG::GG A+ GCGU+AGGC::G +UCA::GAGCAGCGA+ AC::CCCGC :+::GC+GUG 237 GGAAGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGUG 296 ))--))---.-))))))-----))------))))-.-------))-))---.--)).--- 239 GagGGgAUa.CgggccgGUGAgaucaaaccagggc.cuacuGGccucgagG.cccg.cac 294 GA GGGAU C:G :::G G ::C +C ::::C CU +UGGCCU:: GG CCG +++ 297 GACGGGAUCaCAGUUUGGCG-UCGC--UCAGAACCaCU-AUGGCCUGAUGGu-CCGaUCU 351 ))--))---)))))))): 295 agucaaGACCaccaggcU 312 ::U ::+ACC C A:::U 352 CAUAUGAACCACCAUUUU 369 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #103568,sp|AJ505697.1|ATH505697 Arabidopsis thaliana partial small cytoplasmic putative RNA 7SL (7SL RNA gene), clone Ath-29, 5' end incomplete ----isReversed: 0 ----hitSequence: GUGGGCUUGUGACCCGUGUGGGGACAAUAAGUUGGUGGAACACUGGCUCGGCCCACGGGUCGGAUCUGUYGUGGCAUUGUUCCGGGCUGCCCAGUCCAAGCUGAGAGUGAUCCGUGUGUGUUAAGCGAAGGCUUGGCUCAGGCGGUUCUUGCAGUGGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGAUCACCUCCCGCUCUCAGCAGUGGACGGAUCACAGCUCGACGCCACUCAGAUUCACCAUGGCCUGCUGGCUCGUUCCCAGCUGGACCACCAAUUU hit 50 : 4 290 (fwd) 130.45 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 G: G GC + UGU ACCC G+GGG :C+++A:::UGGUGG+A:: C 4 GUGG---------GC--U----UGUGACCCgUGUGGGGACAAUAAGUUGGUGGAACA--C 46 (----((------((-((----((((------((---------((((((--((--(((-- 60 uGGGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCcaA 119 UGG UCGGC CC C GGUC G+:::+G++GU: + UU U +:G:+C:GCCC UCCAA 47 UGGCUCGGC-CCACG-GGUC-GGAUCUGUYGUGGCAUU-GUUCCGGGCUGCCCAGUCCAA 102 ((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,.,,, 120 GcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCUAA.AGu 178 GC:::GAGU :: C:G UG ::::::CG+AGG:::::: CA C:G ::U + AGU 103 GCUGAGAGU--GAUCCGUGUGUGUUAAGCGAAGGCUUGGCUCAGGCGGUUCU--UGcAGU 158 <<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))---) 179 gggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGUg 238 GG:GGG A+ GCGU+AGGC::G +UCA::GAGCAGCGA+ ACC:CCCGCUC:::GC+GUG 159 GGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGAUCACCUCCCGCUCUCAGCAGUG 218 ))--))---.-))))))-----))------))))--------))-))---.--))..--- 239 GagGGgAUa.CgggccgGUGAgaucaaaccagggccuacuGGccucgagG.cccg..cac 294 GA GGAU C:G+:C: A+ :CA +C :::+C ++UGGCC G++G C CG C+C 219 GAC-GGAUCaCAGCUCG---ACGCCACUCAGAUUCACCAUGGCC-UGCUGgCUCGuuCCC 273 ))--))---)))))))): 295 agucaaGACCaccaggcU 312 AG +:: ACCACCA:::U 274 AGCUGG-ACCACCAAUUU 290 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #182773,sp|X71484.1|CRRNASC7 C.reinhardtii 7S(L) small cytoplasmic RNA ----isReversed: 0 ----hitSequence: GCCGGCUGGAGUCACGUCCAGUUGUCACCCAUGUGGGGGCCAAGCGGAUGAAGGAACAUAUGGCUCUCCGGUCGUGAACGCUUCCGUCGAUAGCGUGUCCUCUUCGAGUCCACAGUCGGCAAGGUCGCUGCCCUGAUGGGUGGCUGACCUGGUUGAUGAUUAGUCCCGCACCGCGUGAGGCAGGAAACUGAGCAGCGAAAAGGGACAGCUGCGGACGGCGAAAGGAUCGCAUGCUUGAGGAGGUGCCACGACCACCCGGGGGGUCCUCUGUGGGACCAACUACCG hit 51 : 3 287 (fwd) 79.90 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((-.--((-- 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGg.GAguGg 58 GCCG: :GG+GU CGU C: :UGU ACCC G+GGGGGCC A : :G UG G+:: 3 GCCGGCUGGAGUCACGUCCAGUUGUCACCCaUGUGGGGGCC--AAGCGGAUGAaGGAA-- 58 ((----((------((-((---.-((((------((---------((((((--((--((( 59 cuGGGucggccccgcggggucg.gcccuggggguaugcUuaUUGaaggcccGCcCcuuCc 117 C: U: G+C C+C: +G C+:: G+U::++U GA::GC :G CC +U:C 59 CA---UAUGGCUCUCC----GGu-CGUGAACGCUUCCGUC---GAUAGCGUGUCCUCUUC 107 --((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,,, 118 aAGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCUAAAG 177 +AG:CC::AGU :: C::GGU:+ C:+:CC GA GG:+:G +:ACC::G :: +A 108 GAGUCCACAGU--CGGCAAGGUCG-CUGCCCUGAUGGGUGGCUGACCUGGUUGA--UGAU 162 .,<<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))-- 178 .ugggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGG 236 G::::G ACCGCGU+AGGC::G A A::GAGCAGCGAAAA::::C GCU::GG:CGG 163 uAGUCCCGCACCGCGUGAGGCAGGAA--ACUGAGCAGCGAAAAGGGACAGCUGCGGACGG 220 -)))--))---.-))))))-----))------))))--------))-))---.--)).-- 237 UgGagGGgAUa.CgggccgGUGAgaucaaaccagggccuacuGGccucgagG.cccg.ca 293 G:A+ GGAU C: GC::G AG::++ + C::+G+C AC+ G :G GG C : 221 CGAAA-GGAUCgCAUGCUUG--AGGAGG-UGCCACGACCACCCG---GGGGGu-CCUc-- 270 -))--))---)))))))): 294 cagucaaGACCaccaggcU 312 :G +::GACCA C: : + 271 -UG-UGGGACCAACUACCG 287 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #188807,sp|X65988.1|HJ7SRPA Humulus japonicus small cytoplasmic RNA 7S (7S RNA gene), clone_lib Z10o ----isReversed: 0 ----hitSequence: GCCUAGCAACGUGGGCCUGUGACCCAAGUGGGGGGAUGUGGGAAAUGGGACUCUGGCGCAGCCGGUUGGCAUCGGGUCCAGUGUUAGCUGCUUCCUGGCCUGCCCAUUCCAAGCCGAGACUUGGGCUGUCUGAGCCGGACGAAGGUCUGGCUUGCUCAGCUCCUAAAGCGGAGGGCAAUGCCGUGAGGCUGGCUUCACAGAGCAGCGACCACCUCCCGGUCCCGGCAGUGGCAAGGAUAACGGGCCGUGCUACUUGGGUCCACCAUGUUCACUGGUGGACUCUAAAUAGGACCAUUUCUUU hit 52 : 1 301 (fwd) 123.35 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 G C: +G++ CGUG:G CUGU ACCC AG+GGGGG ++ ::::::UGGGA:U 1 ----GCCU-AGCAACGUGGGCCUGUGACCCaAGUGGGGGGAUGUGGGAAAUGGGACU--C 53 (----((------((-((---.-((((------((---------((((((--((--(((- 60 uGGGucggccccgcggggucg.gcccuggggguaugcUuaUUGaaggcccGCcCcuuCca 118 UGG C:G CCG:: :++ G:+:: G+GU::GCU UU +:GGCC:GCCC U CCA 54 UGGCGCAG--CCGGUUGGCAUcGGGUCCAGUGUUAGCUGCUUCCUGGCCUGCCCAUUCCA 111 -((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,,,, 119 AGcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCUAAAGu 178 AGCC::GA UU ::GC:G: +:::CC+G:CG+AGG:C+GG:::+ :C:GC:: CUAAAG+ 112 AGCCGAGACUU-GGGCUGUCUGAGCCGGACGAAGGUCUGGCUUGCUCAGCUC-CUAAAGC 169 <<<<<------.<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))--- 179 gggggGaACCG.cGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGU 237 GG:GGG A+ G CGU+AGGC::G +UCA::GAGCAGCGA+ ACC:CCCG UC::GGC+GU 170 GGAGGGCAAUGcCGUGAGGCUGGCUUCACAGAGCAGCGACCACCUCCCGGUCCCGGCAGU 229 )))--))---.-))))))-----))------))))--------))-))-----))...-- 238 gGagGGgAUa.CgggccgGUGAgaucaaaccagggccuacuGGccucgagGcccg...ca 293 GG + GGAUA C:GGCC: UG +::C ++ ::+:C C G+: :: G +:G ++ 230 GGCAAGGAUAaCGGGCCG-UG-CUAC--UUGGGUCCAC-CAUGUUCACUG--GUGgacUC 282 -))--))---)))))))): 294 cagucaaGACCaccaggcU 312 +A +A:GACCA::::::U 283 UAAAUAGGACCAUUUCUUU 301 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #188808,sp|X65989.1|HJ7SRPB Humulus japonicus small cytoplasmic RNA 7S (7S RNA gene), clone_lib Z11o ----isReversed: 0 ----hitSequence: GCGUGGUAACGCGAGCCUGUAACCCGAGUGGGGGCAUUAAGGUGAUGGAACGUCAGUUCGGCCCAAUGGCCCGGAUUCGAUGUAGCUGUCUACUGGCUUGCCCGUUCCAAGCCGGGAGUUGAGCCGUGCGANAUUGAGCGGAGGCUCGGCUCGCACCUCUGCUGGAGUGGAGGGUACCGCGUGAGCUGGCUUCACAGAGCAGCGCUUACCUCCCGGUCCUGGCAGUGGAAGGAUAACGGCCCGGUGCUAGGUGGCUCCAAUAUGUUCUACUGGCUAAACAUGAUUGGGCAUACCUUU hit 53 : 1 297 (fwd) 106.14 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 GC G G : + CG G: C UGUAACCC AG+GGGGGC+++A::: :UGG :: G: 1 GC-GUGGU----AACGCGAGCCUGUAACCCgAGUGGGGGCAUUAAGGUGAUGG--AACGU 53 (----((------((-((----((((------((---------((((((--((--(((-- 60 uGGGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCcaA 119 : G U GGCCC+ : G +C G:: : G +G ::GCU U +:GG ::GCCC UUCCAA 54 CAGUUCGGCCCAAUG-GCCC-GGAUUCGAUG-UAGCUGUCUACUGGCUUGCCCGUUCCAA 110 ((((((((,,,<<<<<<<<<<<<.<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,,,, 120 GcccggaGUUGuggcgggguggc.cccgccGgAGggcggggccaccccgccuUCUAAAGu 178 GCC GGA UU :G G:G:G: :::::CGGAGG::::: :C:C:C C: CU +AGU 111 GCCGGGAGUU-GAGCCGUGCGANaUUGAGCGGAGGCUCGGCUCGCACCUCUG-CUGGAGU 168 <<<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))---) 179 gggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGUg 238 GG:GGG ACCGCGU+AG C::G +UCA::GAGCAGCG + ACC:CCCG UCC GGC+GUG 169 GGAGGGUACCGCGUGAG-CUGGCUUCACAGAGCAGCGCUUACCUCCCGGUCCUGGCAGUG 227 ))--))---.-))))))-----))------))))--------))-))-----))...--- 239 GagGGgAUa.CgggccgGUGAgaucaaaccagggccuacuGGccucgagGcccg...cac 294 GA+ GGAUA C:: CC:GUG +::+ + : ::C + +UG C :++G +C CA+ 228 GAA-GGAUAaCGGCCCGGUG-CUAG--GUGGCUCCAAUAUGUUC-UACUG-GCUaaaCAU 281 ))--))---)))))))): 295 agucaaGACCaccaggcU 312 ::U+:: CA: :::U 282 GAUUGG--GCAUACCUUU 297 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #188809,sp|X65990.1|HJ7SRPC Humulus japonicus small cytoplasmic RNA 7S (7S RNA gene), clone_lib Z13o ----isReversed: 0 ----hitSequence: GGCCUAGCAACGUGGGCCUGUAACCCAAGUGGGGGCAUGUGGGAGAUGGGACUUUGGGUCAGCCCAUUGGAUCGGGUCCAGUGUUAGCUGCUUGCUGGUCUGCCCAUUCCAAGCCGAGAGUUGGGCUGUGUGAUCUGGGCGAAGGCUGGGGUCGCACAGCUCCUAAAGAGGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACCACCUCCCGCUCUCGGCAGUGGAAGGAUAACGGGUCGGUGCUACUUGGGCCACCAUGGUCACUGCAUGCACUCUUAAUCAGACCAUCUCUUU hit 54 : 1 300 (fwd) 178.71 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 GGC:++G++ CGUG:GCCUGUAACCC AG+GGGGGC++ ::::G:UGGGA:U : 1 ----GGCCUAGCAACGUGGGCCUGUAACCCaAGUGGGGGCAUGUGGGAGAUGGGACU--U 54 (----((------((-((----((((------((---------((((((--((--(((-- 60 uGGGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCcaA 119 UGGGUC:GCCC++ G:UC G:+:: G+GU::GCU UUG+:G::C:GCCC UUCCAA 55 UGGGUCAGCCCAUUG-GAUC-GGGUCCAGUGUUAGCUGCUUGCUGGUCUGCCCAUUCCAA 112 ((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,,,,< 120 GcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCUAAAGug 179 GCC::GAGUU ::GC:G:G+G:+C: ::CG+AGG:: :G+:C+C:C:GC:: CUAAAG G 113 GCCGAGAGUU-GGGCUGUGUGAUCUGGGCGAAGGCUGGGGUCGCACAGCUC-CUAAAGAG 170 <<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))---)) 180 ggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGUgG 239 G:GGG A+ GCGU+AGGC::G +UCA::GAGCAGCGA+ ACC:CCCGCUC::GGC+GUGG 171 GAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACCACCUCCCGCUCUCGGCAGUGG 230 )--))---.-))))))-----))------))))--------))-))-----))....--- 240 agGGgAUa.CgggccgGUGAgaucaaaccagggccuacuGGccucgagGcccg....cac 294 A+ GGAUA C:G::C:GUG +::C ++ ::+:+C +UGG:C G C :G C + 231 AA-GGAUAaCGGGUCGGUG-CUAC--UUGGGCCACC-AUGGUC-ACUG-CAUGcacuCUU 283 ))--))---)))))))): 295 agucaaGACCaccaggcU 312 A:UCA: ACCA:C::::U 284 AAUCAG-ACCAUCUCUUU 300 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #188810,sp|X65991.1|HJ7SRPD Humulus japonicus small cytoplasmic RNA 7S (7S RNA gene), clone_lib Z20p ----isReversed: 0 ----hitSequence: GGCCUAGCAACGUGGGCCUGUAACCCAAGUGGGGGCAUGUGGGAAAUGGGACUUUAGUUCGGCCCAUUGGAUCGGAUCCAGUGUUAGCUGCUUGCUGGGCUGCCCAUUCCAAGCCGAGAGUUGAGCUGUGUGAGCCGGACGAAGGUCUGGCUUGGUCAGCUCCUAAAGCGGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACAACCUCCCGCUCUCGGCAGUGGAAGGAUAACGGGCCGGUGCUGCUUGGACCCACCAUGGUUCACUGAGCUGACUCUUAAUAGGACCAUUUCUUU hit 55 : 1 302 (fwd) 178.01 bits (((,<<<<__________>>>>,,,,,<<<.___>>>)))----((((((((---((--( 1 GCCGGGcgguguGGCGugcgCCUGUAACCC.aGcGGGGGCcgAAgccugguGgGAguGgc 59 GGC:++G++ CGUG:GCCUGUAACCC AG+GGGGGC++ ::::::UGGGA:U : 1 ----GGCCUAGCAACGUGGGCCUGUAACCCaAGUGGGGGCAUGUGGGAAAUGGGACU--U 54 (----((------((-((----((((------((---------((((((--((--(((-- 60 uGGGucggccccgcggggucggcccuggggguaugcUuaUUGaaggcccGCcCcuuCcaA 119 + G UC GCCC++:G ::UC G:::: G+GU::GCU UUG+:GG C:GCCC UUCCAA 55 UAGUUCGGCCCAUUG-GAUC-GGAUCCAGUGUUAGCUGCUUGCUGGGCUGCCCAUUCCAA 112 ((((((((,,,<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>,,,,,,,,< 120 GcccggaGUUGuggcgggguggccccgccGgAGggcggggccaccccgccuUCUAAAGug 179 GCC::GAGUU ::GC:G: +:::CC+G:CG+AGG:C+GG:::+ :C:GC:: CUAAAG+G 113 GCCGAGAGUU-GAGCUGUGUGAGCCGGACGAAGGUCUGGCUUGGUCAGCUC-CUAAAGCG 170 <<<<------<<<--<-<<<______>>>-->->>>---->>>>>,,))))))))---)) 180 ggggGaACCGcGucAGGCccGgAUCAggGAGCAgCgaaaAccccccgCuccgggCGGUgG 239 G:GGG A+ GCGU+AGGC::G +UCA::GAGCAGCGA+AACC:CCCGCUC::GGC+GUGG 171 GAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACAACCUCCCGCUCUCGGCAGUGG 230 )--))---.-))))))-----))------))))--------))-))---.--))..---) 240 agGGgAUa.CgggccgGUGAgaucaaaccagggccuacuGGccucgagG.cccg..caca 295 A+ GGAUA C:G CC:GUG +::C ++ ::::C ++UGG:: C:++G +C G ++++ 231 AA-GGAUAaCGGGCCGGUG-CUGC--UUGGACCCACCAUGGUU-CACUGaGCUGacUCUU 285 )--))---)))))))): 296 gucaaGACCaccaggcU 312 : +A:GACCA::::::U 286 AAUAGGACCAUUUCUUU 302 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.