Params: ./cmzasha --no-stderr --filter 120 22 Rfam/cm/RF00104.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00104_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin Build: release Host: recycle.cs.washington.edu ----cmFile: Rfam/cm/RF00104.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: 1 ----hitSequence: CCACGUCUACCCUGUAGAUCCGAAUUUGUUUUAUACUAGCUUUAAGGACAAAUUCGGUUCUAGAGAGGUUUGUGUG hit 0 : 65196 65121 (rev) 32.01 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<________._______>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaauc.Aaacaugcacaaguucguauc 58 C+AC:+:UA:C: GUAGA:+CGAA:UUGU:UUA+A U+ ++A G:ACAA:UUCG+:UC 19051 CCACGUCUACCCuGUAGAUCCGAAUUUGUUUUAUACUAgCUUUAAGGACAAAUUCGGUUC 19110 >-->>>-->>>>>>:: 59 uAgggguguaugucgg 74 UAG:G:+G:+:GU+ G 19111 UAGAGAGGUUUGUGUG 19126 ----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: CCACGUCUACCCUGUAGAUCCGAAUUUGUUUUAUACUAGCUUUAAGGACAAAUUCGGUUCUAGAGAGGUUUGUGUG hit 1 : 143527 143452 (rev) 32.01 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<________._______>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaauc.Aaacaugcacaaguucguauc 58 C+AC:+:UA:C: GUAGA:+CGAA:UUGU:UUA+A U+ ++A G:ACAA:UUCG+:UC 27275 CCACGUCUACCCuGUAGAUCCGAAUUUGUUUUAUACUAgCUUUAAGGACAAAUUCGGUUC 27334 >-->>>-->>>>>>:: 59 uAgggguguaugucgg 74 UAG:G:+G:+:GU+ G 27335 UAGAGAGGUUUGUGUG 27350 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #6975,sp|AC124817.2|AC124817 Branchiostoma floridae, clone -10F3, complete sequence. ----isReversed: 1 ----hitSequence: CUAUAUGUACCCUGUAGAUCCGAAUUUGUGUGAGGUACCCAAGUCACAAAUUCGUUUCUGCAGGUAUAAUGUAGC hit 2 : 56096 56022 (rev) 24.56 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<_______________>>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaaucAaacaugcacaaguucguaucu 59 C:A:AU:UACC: GUAGA:CCGAA:UUGUGU AG + C +A +CACAA:UUCGU:UCU 77885 CUAUAUGUACCCuGUAGAUCCGAAUUUGUGUGAGGUAC-CCAAGUCACAAAUUCGUUUCU 77943 -->>>--.>>>>>>:: 60 Aggggug.uaugucgg 74 :GGU :AU:U:G 77944 GCAGGUAuAAUGUAGC 77959 ----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: CCACGUCUACCCUGUAGAUCCGAAUUUGUUUUAUACUAGCUUUAAGGACAAAUUCGGUUCUAGAGAGGUUUGUGUG hit 3 : 247245 247320 (fwd) 32.01 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<________._______>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaauc.Aaacaugcacaaguucguauc 58 C+AC:+:UA:C: GUAGA:+CGAA:UUGU:UUA+A U+ ++A G:ACAA:UUCG+:UC 247245 CCACGUCUACCCuGUAGAUCCGAAUUUGUUUUAUACUAgCUUUAAGGACAAAUUCGGUUC 247304 >-->>>-->>>>>>:: 59 uAgggguguaugucgg 74 UAG:G:+G:+:GU+ G 247305 UAGAGAGGUUUGUGUG 247320 ----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: CCACGUCUACCCUGUAGAUCCGAAUUUGUUUUAUACUAGCUUUAAGGACAAAUUCGGUUCUAGAGAGGUUUGUGUG hit 4 : 31404 31329 (rev) 32.01 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<________._______>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaauc.Aaacaugcacaaguucguauc 58 C+AC:+:UA:C: GUAGA:+CGAA:UUGU:UUA+A U+ ++A G:ACAA:UUCG+:UC 276743 CCACGUCUACCCuGUAGAUCCGAAUUUGUUUUAUACUAgCUUUAAGGACAAAUUCGGUUC 276802 >-->>>-->>>>>>:: 59 uAgggguguaugucgg 74 UAG:G:+G:+:GU+ G 276803 UAGAGAGGUUUGUGUG 276818 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #36735,sp|AF321227.1|AF321227 Tribolium castaneum Ftz (ftz), Scr (scr), Dfd (dfd), Zen (zen), and Zen2 (zen2) genes, complete cds; and Pb (pb) gene, partial ----isReversed: 0 ----hitSequence: CUACAUCUACCCUGUAGAUCCGAAUUUGUUUGAAAUCAGGCGACAAAUUCGGUUCUAGAGAGGUUUGUGUG hit 5 : 48039 48109 (fwd) 27.26 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<_______________>>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaaucAaacaugcacaaguucguaucu 59 C:ACA+:UA:C: GUAGA:+CGAA:UUGU UU++AAUC A ++G ACAA:UUCG+:UCU 48039 CUACAUCUACCCuGUAGAUCCGAAUUUGU-UUGAAAUC--AGGCG-ACAAAUUCGGUUCU 48094 -->>>-->>>>>>:: 60 Agggguguaugucgg 74 AG:G:+G:+UGU: G 48095 AGAGAGGUUUGUGUG 48109 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #36735,sp|AF321227.1|AF321227 Tribolium castaneum Ftz (ftz), Scr (scr), Dfd (dfd), Zen (zen), and Zen2 (zen2) genes, complete cds; and Pb (pb) gene, partial ----isReversed: 1 ----hitSequence: CGUGAUCUACCCUGUAGAUCCGGGCUUUUGUAGAAUUUUUAGAUCAGAAGCUCGUCUCUACAGGUAUCUUACGG hit 6 : 86918 86845 (rev) 24.97 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<_______________>>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaaucAaacaugcacaaguucguaucu 59 CG: A::UACC: GUAGA+CCG::CUU:UGU ++A+U +++ +CA:AAG::CGU+UCU 46489 CGUGAUCUACCCuGUAGAUCCGGGCUUUUGUAGAAUUU-UUAGAUCAGAAGCUCGUCUCU 46547 -->>>-->>>>>>:: 60 Agggguguaugucgg 74 A :GGU ::U :CGG 46548 ACAGGUAUCUUACGG 46562 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #44026,sp|Z68760.2|CEF36H1 Caenorhabditis elegans cosmid F36H1 ----isReversed: 1 ----hitSequence: GUCCGUCUACCCGUAGCUCCUAUCCAUGUUACUGGUCAAAAAGUGAACAUGGAAGCAGGUACAGGUGCACGGCGA hit 7 : 2906 2832 (rev) 23.58 bits :<<<<<<--<<<--<<<<<<<<<<<<.<<<_______________>>>>>>>>>>>>>>> 1 cgacauaUAcccGUagauccgaacuu.guguuagaaucAaacaugcacaaguucguaucu 59 +::C:U:UACC:GUA+:U:C:::C:+ GU: +G +++AAA++UG:AC+:G:::G:A:+U 35703 GUCCGUCUACCCGUAGCUCCUAUCCAuGUUACUGGUCAAAAAGUGAACAUGGAAGCAGGU 35762 -->>>-->>>>>>:: 60 Agggguguaugucgg 74 A :GGUG:A:G::G+ 35763 ACAGGUGCACGGCGA 35777 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #45139,sp|Z36753.1|CET09A5 Caenorhabditis elegans cosmid T09A5 ----isReversed: 1 ----hitSequence: GCUCGUCUACCCUGUAGAUCGAGCUGUGUGUUUGAAACAAUCAUACACGAGCUAGACUACAAGGUGCACGAACAA hit 8 : 18689 18615 (rev) 22.55 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<_______________>>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaaucAaacaugcacaaguucguaucu 59 ++::::+UA:CC GU:+A+++::::::GUGUU+GAA CAA+CAU+CAC::::::+++U+: 20012 GCUCGUCUACCCuGUAGAUCGAGCUGUGUGUUUGAAACAAUCAUACACGAGCUAGACUAC 20071 -->>>-->>>>>>:: 60 Agggguguaugucgg 74 A GG:+++::::+++ 20072 AAGGUGCACGAACAA 20086 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----sequence: #7191,sp|AC116664.1|AC116664 Papio hamadryas, clone RP41-57E23, complete sequence. ----isReversed: 0 ----hitSequence: CUGUAUAUACCCUGUAGAUCCGAAUUUGUGUAAGGAAUUUUGUGGUCACAAAUUCGUAUCUAGGGGAAUAUGUAGU hit 9 : 138988 139063 (fwd) 33.12 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<________._______>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaauc.Aaacaugcacaaguucguauc 58 C:::AUAUACCC GUAGAUCCGAA:UUGUGU AG A +++ +CACAA:UUCGUAUC 138988 CUGUAUAUACCCuGUAGAUCCGAAUUUGUGUAAGGAAUuUUGUGGUCACAAAUUCGUAUC 139047 >-->>>-->>>>>>:: 59 uAgggguguaugucgg 74 UAGGGG+ UAU:::G+ 139048 UAGGGGAAUAUGUAGU 139063 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----sequence: #7192,sp|AC116665.1|AC116665 Papio hamadryas chromosome , clone RP41-119J13, complete sequence. ----isReversed: 0 ----hitSequence: CUAUAUAUACCCUGUAGAACCGAAUUUGUGUGGUAUCCAUAUAGUCACAGAUUCGAUUCUAGGGGAAUAUAUGGU hit 10 : 91344 91418 (fwd) 38.08 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<_______________>>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaaucAaacaugcacaaguucguaucu 59 C:A:AUAUACCC GUAGA:+CGAA:+UGUGU ++A++CA A+A +CACA+:UUCG+:UCU 91344 CUAUAUAUACCCuGUAGAACCGAAUUUGUGUGGUAUCCAUAUAGUCACAGAUUCGAUUCU 91403 -->>>-->>>>>>:: 60 Agggguguaugucgg 74 AGGGG+ UAU:U:G+ 91404 AGGGGAAUAUAUGGU 91418 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----sequence: #7268,sp|AC129959.6|AC129959 Bos taurus, clone RP42-518P7, complete sequence. ----isReversed: 1 ----hitSequence: CUGUAUAUACCCUGUAGAUCCGAAUUUGUGUAAGGAAUUUUGUGAUCACAAAUUCGUAUCUAGGGGAAUAUGUAGU hit 11 : 98422 98347 (rev) 33.03 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<________._______>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaauc.Aaacaugcacaaguucguauc 58 C:::AUAUACCC GUAGAUCCGAA:UUGUGU AG A +++ +CACAA:UUCGUAUC 113567 CUGUAUAUACCCuGUAGAUCCGAAUUUGUGUAAGGAAUuUUGUGAUCACAAAUUCGUAUC 113626 >-->>>-->>>>>>:: 59 uAgggguguaugucgg 74 UAGGGG+ UAU:::G+ 113627 UAGGGGAAUAUGUAGU 113642 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #4599,sp|AC011194.15|AC011194 Mus musculus chromosome 11, clone RP23-196F5, complete sequence. ----isReversed: 0 ----hitSequence: CUGUAUAUACCCUGUAGAUCCGAAUUUGUGUAAGGAAUUUUGUGGUCACAAAUUCGUAUCUAGGGGAAUAUGUAGU hit 12 : 112960 113035 (fwd) 33.12 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<________._______>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaauc.Aaacaugcacaaguucguauc 58 C:::AUAUACCC GUAGAUCCGAA:UUGUGU AG A +++ +CACAA:UUCGUAUC 112960 CUGUAUAUACCCuGUAGAUCCGAAUUUGUGUAAGGAAUuUUGUGGUCACAAAUUCGUAUC 113019 >-->>>-->>>>>>:: 59 uAgggguguaugucgg 74 UAGGGG+ UAU:::G+ 113020 UAGGGGAAUAUGUAGU 113035 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #4610,sp|AC015584.18|AC015584 Mus musculus, clone RP23-400H17, complete sequence. ----isReversed: 0 ----hitSequence: CUAUAUAUACCCUGUAGAACCGAAUUUGUGUGGUACCCACAUAGUCACAGAUUCGAUUCUAGGGGAAUAUAUGGU hit 13 : 162939 163013 (fwd) 37.55 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<_______________>>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaaucAaacaugcacaaguucguaucu 59 C:A:AUAUACCC GUAGA:+CGAA:+UGUGU ++A +CA A+A +CACA+:UUCG+:UCU 162939 CUAUAUAUACCCuGUAGAACCGAAUUUGUGUGGUACCCACAUAGUCACAGAUUCGAUUCU 162998 -->>>-->>>>>>:: 60 Agggguguaugucgg 74 AGGGG+ UAU:U:G+ 162999 AGGGGAAUAUAUGGU 163013 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #6187,sp|AC122451.3|AC122451 Mus musculus clone RP24-252G15, complete sequence. ----isReversed: 1 ----hitSequence: UGACAUAAACCCGUAGAUCCGAUCUUGUGGUGAAGUGGACCGCGCAAGCUCGUUUCUAUGGGUCUGUGGCAG hit 14 : 49344 49273 (rev) 33.16 bits :<<<<<<--<<<--<<<<<<<<<<<<<<<_______________>>>>>>>>>>>>>>>- 1 cgacauaUAcccGUagauccgaacuuguguuagaaucAaacaugcacaaguucguaucuA 60 +G CA+A ACCCGUAGA:CCGA:CUUG:G+U++A U ++ +GC:CAAG:UCGU:UCUA 110913 UGACAUAAACCCGUAGAUCCGAUCUUGUGGUGAAGUG--GACCGCGCAAGCUCGUUUCUA 110970 ->>>-->>>>>>:: 61 gggguguaugucgg 74 +GGGU+U+UG C+G 110971 UGGGUCUGUGGCAG 110984 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #24200,sp|AL606824.13|AL606824 Mouse DNA sequence from clone RP23-9G13 on chromosome 11 ----isReversed: 0 ----hitSequence: CUGUAUAUACCCUGUAGAUCCGAAUUUGUGUAAGGAAUUUUGUGGUCACAAAUUCGUAUCUAGGGGAAUAUGUAGU hit 15 : 12219 12294 (fwd) 33.12 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<________._______>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaauc.Aaacaugcacaaguucguauc 58 C:::AUAUACCC GUAGAUCCGAA:UUGUGU AG A +++ +CACAA:UUCGUAUC 12219 CUGUAUAUACCCuGUAGAUCCGAAUUUGUGUAAGGAAUuUUGUGGUCACAAAUUCGUAUC 12278 >-->>>-->>>>>>:: 59 uAgggguguaugucgg 74 UAGGGG+ UAU:::G+ 12279 UAGGGGAAUAUGUAGU 12294 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #26961,sp|AL928644.12|AL928644 Mouse DNA sequence from clone RP23-313J15 on chromosome 2 ----isReversed: 0 ----hitSequence: CUAUAUAUACCCUGUAGAACCGAAUUUGUGUGGUACCCACAUAGUCACAGAUUCGAUUCUAGGGGAAUAUAUGGU hit 16 : 210999 211073 (fwd) 37.55 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<_______________>>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaaucAaacaugcacaaguucguaucu 59 C:A:AUAUACCC GUAGA:+CGAA:+UGUGU ++A +CA A+A +CACA+:UUCG+:UCU 210999 CUAUAUAUACCCuGUAGAACCGAAUUUGUGUGGUACCCACAUAGUCACAGAUUCGAUUCU 211058 -->>>-->>>>>>:: 60 Agggguguaugucgg 74 AGGGG+ UAU:U:G+ 211059 AGGGGAAUAUAUGGU 211073 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #75905,sp|U77364.1|MMU77364 Mus musculus homeodomain-containing transcription factor (Hoxd4) gene, complete cds. ----isReversed: 0 ----hitSequence: CUAUAUAUACCCUGUAGAACCGAAUUUGUGUGGUACCCACAUAGUCACAGAUUCGAUUCUAGGGGAAUAUAUGGU hit 17 : 4186 4260 (fwd) 37.55 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<_______________>>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaaucAaacaugcacaaguucguaucu 59 C:A:AUAUACCC GUAGA:+CGAA:+UGUGU ++A +CA A+A +CACA+:UUCG+:UCU 4186 CUAUAUAUACCCuGUAGAACCGAAUUUGUGUGGUACCCACAUAGUCACAGAUUCGAUUCU 4245 -->>>-->>>>>>:: 60 Agggguguaugucgg 74 AGGGG+ UAU:U:G+ 4246 AGGGGAAUAUAUGGU 4260 ----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/pro01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro05.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----sequence: #23845,sp|AL645782.2|AL645782 Zebrafish DNA sequence from clone BUSM1-254O17 in linkage group 3 Contains the hoxb1a, hoxb2a, hoxb3a, hoxb4a, hoxb5a, hoxb6a, ----isReversed: 0 ----hitSequence: CUAUAUAUACCCUGUAGAUCCGGAUUUGUGUAAACAGACGCACAGUCACAAAUUCGUAUCUAGGGGAGUAUGUAGU hit 18 : 32556 32631 (fwd) 36.95 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<________._______>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaauc.Aaacaugcacaaguucguauc 58 C:A:AUAUACCC GUAGAUCCG:A:UUGUGU A+ A + ACA +CACAA:U:CGUAUC 32556 CUAUAUAUACCCuGUAGAUCCGGAUUUGUGUAAACAGAcGCACAGUCACAAAUUCGUAUC 32615 >-->>>-->>>>>>:: 59 uAgggguguaugucgg 74 UAGGGG+GUAU:U:G+ 32616 UAGGGGAGUAUGUAGU 32631 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----sequence: #23854,sp|AL645798.2|AL645798 Zebrafish DNA sequence from clone BUSM1-227H09 in linkage group 3 Contains the hoxb8b, hoxb6b, hoxb5b and hoxb1b genes, a novel ----isReversed: 0 ----hitSequence: CUAUAUAUACCCUGUAGAUCCGAAUUUGUGUGAAUAUACAGUCGCAAAUUCGUGUCUUGGGGAAUAUGUAGU hit 19 : 23515 23586 (fwd) 32.43 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<_______________>>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaaucAaacaugcacaaguucguaucu 59 C:A:AUAUACCC GUAGA CCGAA:UUG:GU A+ AU ACA +C:CAA:UUCGU UCU 23515 CUAUAUAUACCCuGUAGAUCCGAAUUUGUGUGAAUAU---ACAGUCGCAAAUUCGUGUCU 23571 -->>>-->>>>>>:: 60 Agggguguaugucgg 74 GGGG+ UAU:U:G+ 23572 UGGGGAAUAUGUAGU 23586 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----sequence: #29105,sp|AY168642.1|AY168642 Danio rerio homeodomain protein Hoxd4A (hoxd4a) gene, complete cds. ----isReversed: 0 ----hitSequence: CUAUAUAUACCCUGUAGAACCGAAUUUGUGUGAAAAAAUAACAUCACAGAUUCGAUUCAGGGGAGUAUAUGGU hit 20 : 1778 1850 (fwd) 26.56 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<_______________>>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaaucAaacaugcacaaguucguaucu 59 C:A:AUAUACCC GUAGA:+CGAA:+UGUGU A+AA + A+ +CACA+:UUCG+:UC 1778 CUAUAUAUACCCuGUAGAACCGAAUUUGUGUGAAAAAA-UAACAUCACAGAUUCGAUUC- 1835 -->>>-->>>>>>:: 60 Agggguguaugucgg 74 AGGGG+GUAU:U:G+ 1836 AGGGGAGUAUAUGGU 1850 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----sequence: #36467,sp|BX005254.9|BX005254 Zebrafish DNA sequence from clone DKEY-81P22 in linkage group 23 ----isReversed: 1 ----hitSequence: CUAUAUGUACCCUGUAGAACCGAAUUUGUGUCCAAAACAUCAAAAUCGCAAAUACGUCUCUACAGGAAUACAUGGG hit 21 : 84183 84108 (rev) 23.89 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<________._______>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaauc.Aaacaugcacaaguucguauc 58 C:A: U:UACC: GUAGA CCG:A:UUG:GU +AA C A+A +C:CAA:U:CGU UC 75830 CUAUAUGUACCCuGUAGAACCGAAUUUGUGUCCAAAACaUCAAAAUCGCAAAUACGUCUC 75889 >-->>>-->>>>>>:: 59 uAgggguguaugucgg 74 UA :GG+ :A :U:GG 75890 UACAGGAAUACAUGGG 75905 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----sequence: #38819,sp|U92575.1|FRU92575 Fugu rubripes homeobox protein HOXB-4 (FrHOXB-4) gene, complete cds. ----isReversed: 0 ----hitSequence: CUAUAUCUACCCUGUAGAUCCGGAUUUGUGUAAAAAUCAUUAAAGCAAUCACAAAUUCGCUUCUAGGGGAGUAUAUAGU hit 22 : 1530 1608 (fwd) 37.64 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<________...._______>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaauc....Aaacaugcacaaguucgu 55 C:A:AU:UACCC GUAGA::CG:A:UUGUGU A+AAUC AA+CA +CACAA:U:CG: 1530 CUAUAUCUACCCuGUAGAUCCGGAUUUGUGUAAAAAUCauuaAAGCAAUCACAAAUUCGC 1589 >>>>-->>>-->>>>>>:: 56 aucuAgggguguaugucgg 74 :UCUAGGGG+G:AU:U:G+ 1590 UUCUAGGGGAGUAUAUAGU 1608 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----sequence: #2801,sp|AC009336.13|AC009336 Homo sapiens chromosome 2, clone RP11-387A1, complete sequence. ----isReversed: 0 ----hitSequence: CUAUAUAUACCCUGUAGAACCGAAUUUGUGUGGUAUCCGUAUAGUCACAGAUUCGAUUCUAGGGGAAUAUAUGGU hit 23 : 134311 134385 (fwd) 36.21 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<_______________>>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaaucAaacaugcacaaguucguaucu 59 C:A:AUAUACCC GUAGA:+CGAA:+UGUGU ++A++C A+A +CACA+:UUCG+:UCU 134311 CUAUAUAUACCCuGUAGAACCGAAUUUGUGUGGUAUCCGUAUAGUCACAGAUUCGAUUCU 134370 -->>>-->>>>>>:: 60 Agggguguaugucgg 74 AGGGG+ UAU:U:G+ 134371 AGGGGAAUAUAUGGU 134385 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----sequence: #2967,sp|AC009789.21|AC009789 Homo sapiens chromosome 17, clone RP11-361K8, complete sequence. ----isReversed: 0 ----hitSequence: CUGUAUAUACCCUGUAGAUCCGAAUUUGUGUAAGGAAUUUUGUGGUCACAAAUUCGUAUCUAGGGGAAUAUGUAGU hit 24 : 113436 113511 (fwd) 33.12 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<________._______>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaauc.Aaacaugcacaaguucguauc 58 C:::AUAUACCC GUAGAUCCGAA:UUGUGU AG A +++ +CACAA:UUCGUAUC 113436 CUGUAUAUACCCuGUAGAUCCGAAUUUGUGUAAGGAAUuUUGUGGUCACAAAUUCGUAUC 113495 >-->>>-->>>>>>:: 59 uAgggguguaugucgg 74 UAGGGG+ UAU:::G+ 113496 UAGGGGAAUAUGUAGU 113511 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----sequence: #5062,sp|AC018755.3|AC018755 Homo sapiens chromosome 19, BAC BC330783 (CIT-HSPC_470E3), complete sequence. ----isReversed: 0 ----hitSequence: UGGCACCCACCCGUAGAACCGACCUUGCGGGGCCUUCGCCGCACACAAGCUCGUGUCUGUGGGUCCGUGUCGG hit 25 : 119760 119832 (fwd) 29.67 bits :<<<<<<--<<<--<<<<<<<<<<<<<<<_______________>>>>>>>>>>>>>>>- 1 cgacauaUAcccGUagauccgaacuuguguuagaaucAaacaugcacaaguucguaucuA 60 +G:CA:: ACCCGUAGA:CCGA:CUUG:G+ + +UC C+++C:CAAG:UCGU:UCU 119760 UGGCACCCACCCGUAGAACCGACCUUGCGGGGCCUUC-GCCGCACACAAGCUCGUGUCUG 119818 ->>>-->>>>>>:: 61 gggguguaugucgg 74 +GGGU+::UG:CGG 119819 UGGGUCCGUGUCGG 119832 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz ----sequence: #2555,sp|AC103702.3|AC103702 Homo sapiens chromosome 17, clone RP11-357H14, complete sequence. ----isReversed: 0 ----hitSequence: CUGUAUAUACCCUGUAGAUCCGAAUUUGUGUAAGGAAUUUUGUGGUCACAAAUUCGUAUCUAGGGGAAUAUGUAGU hit 26 : 109566 109641 (fwd) 33.12 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<________._______>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaauc.Aaacaugcacaaguucguauc 58 C:::AUAUACCC GUAGAUCCGAA:UUGUGU AG A +++ +CACAA:UUCGUAUC 109566 CUGUAUAUACCCuGUAGAUCCGAAUUUGUGUAAGGAAUuUUGUGGUCACAAAUUCGUAUC 109625 >-->>>-->>>>>>:: 59 uAgggguguaugucgg 74 UAGGGG+ UAU:::G+ 109626 UAGGGGAAUAUGUAGU 109641 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum04.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum05.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum06.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum06.dat.fasta.gz ----sequence: #4653,sp|AF287967.1|AF287967 Homo sapiens homeobox B7 (HOXB7) gene, partial cds; and homeobox B6 (HOXB6), homeobox B5 (HOXB5), homeobox B4 (HOXB4), and home ----isReversed: 0 ----hitSequence: CUGUAUAUACCCUGUAGAUCCGAAUUUGUGUAAGGAAUUUUGUGGUCACAAAUUCGUAUCUAGGGGAAUAUGUAGU hit 27 : 27998 28073 (fwd) 33.12 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<________._______>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaauc.Aaacaugcacaaguucguauc 58 C:::AUAUACCC GUAGAUCCGAA:UUGUGU AG A +++ +CACAA:UUCGUAUC 27998 CUGUAUAUACCCuGUAGAUCCGAAUUUGUGUAAGGAAUuUUGUGGUCACAAAUUCGUAUC 28057 >-->>>-->>>>>>:: 59 uAgggguguaugucgg 74 UAGGGG+ UAU:::G+ 28058 UAGGGGAAUAUGUAGU 28073 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum07.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum07.dat.fasta.gz ----sequence: #3702,sp|AF480538.1|AF480538 Homo sapiens miR-100-precursor-11 micro RNA, complete sequence. ----isReversed: 0 ----hitSequence: UGCCACAAACCCGUAGAUCCGAACUUGUGGUAUUAGUCCGCACAAGCUUGUAUCUAUAGGUAUGUGUCUG hit 28 : 6 75 (fwd) 30.51 bits :<<<<<<--<<<--<<<<<<<<<<<<<<<_______________>>>>>>>>>>>>>>>- 1 cgacauaUAcccGUagauccgaacuuguguuagaaucAaacaugcacaaguucguaucuA 60 +G:CA:A ACC:GUAGAUCC:A:CUUGUG+UA+ A ++ +GCACAAG:U:GUAUCUA 6 UGCCACAAACCCGUAGAUCCGAACUUGUGGUAUUA----GUCCGCACAAGCUUGUAUCUA 61 ->>>-->>>>>>:: 61 gggguguaugucgg 74 +:GGU U:UG:C G 62 UAGGUAUGUGUCUG 75 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum07.dat.fasta.gz ----sequence: #3735,sp|AF480571.1|AF480571 Homo sapiens miR-99-precursor-21 micro RNA, complete sequence. ----isReversed: 0 ----hitSequence: UGGCAUAAACCCGUAGAUCCGAUCUUGUGGUGAAGUGGACCGCACAAGCUCGCUUCUAUGGGUCUGUGUCAG hit 29 : 6 77 (fwd) 35.75 bits :<<<<<<--<<<--<<<<<<<<<<<<<<<_______________>>>>>>>>>>>>>>>- 1 cgacauaUAcccGUagauccgaacuuguguuagaaucAaacaugcacaaguucguaucuA 60 +G:CA+A ACCCGUAGA::CGA:CUUGUG+U++A U ++ +GCACAAG:UCG::UCUA 6 UGGCAUAAACCCGUAGAUCCGAUCUUGUGGUGAAGUG--GACCGCACAAGCUCGCUUCUA 63 ->>>-->>>>>>:: 61 gggguguaugucgg 74 +GGGU+U+UG:C+G 64 UGGGUCUGUGUCAG 77 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum08.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum09.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz ----sequence: #6765,sp|AP000962.2|AP000962 Homo sapiens genomic DNA, chromosome 21q21.1-q21.2, clone:B821P16, LL56-APP region. ----isReversed: 0 ----hitSequence: UGGCAUAAACCCGUAGAUCCGAUCUUGUGGUGAAGUGGACCGCACAAGCUCGCUUCUAUGGGUCUGUGUCAG hit 30 : 117355 117426 (fwd) 35.75 bits :<<<<<<--<<<--<<<<<<<<<<<<<<<_______________>>>>>>>>>>>>>>>- 1 cgacauaUAcccGUagauccgaacuuguguuagaaucAaacaugcacaaguucguaucuA 60 +G:CA+A ACCCGUAGA::CGA:CUUGUG+U++A U ++ +GCACAAG:UCG::UCUA 117355 UGGCAUAAACCCGUAGAUCCGAUCUUGUGGUGAAGUG--GACCGCACAAGCUCGCUUCUA 117412 ->>>-->>>>>>:: 61 gggguguaugucgg 74 +GGGU+U+UG:C+G 117413 UGGGUCUGUGUCAG 117426 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz ----sequence: #6963,sp|AP001359.4|AP001359 Homo sapiens genomic DNA, chromosome 11q clone:RP11-820L6, complete sequences. ----isReversed: 1 ----hitSequence: UGCCACAAACCCGUAGAUCCGAACUUGUGGUAUUAGUCCGCACAAGCUUGUAUCUAUAGGUAUGUGUCUG hit 31 : 120261 120192 (rev) 30.51 bits :<<<<<<--<<<--<<<<<<<<<<<<<<<_______________>>>>>>>>>>>>>>>- 1 cgacauaUAcccGUagauccgaacuuguguuagaaucAaacaugcacaaguucguaucuA 60 +G:CA:A ACC:GUAGAUCC:A:CUUGUG+UA+ A ++ +GCACAAG:U:GUAUCUA 101275 UGCCACAAACCCGUAGAUCCGAACUUGUGGUAUUA----GUCCGCACAAGCUUGUAUCUA 101330 ->>>-->>>>>>:: 61 gggguguaugucgg 74 +:GGU U:UG:C G 101331 UAGGUAUGUGUCUG 101344 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz ----sequence: #7108,sp|AP001667.1|AP001667 Homo sapiens genomic DNA, chromosome 21q, section 11/105. ----isReversed: 0 ----hitSequence: UGGCAUAAACCCGUAGAUCCGAUCUUGUGGUGAAGUGGACCGCACAAGCUCGCUUCUAUGGGUCUGUGUCAG hit 32 : 185811 185882 (fwd) 35.75 bits :<<<<<<--<<<--<<<<<<<<<<<<<<<_______________>>>>>>>>>>>>>>>- 1 cgacauaUAcccGUagauccgaacuuguguuagaaucAaacaugcacaaguucguaucuA 60 +G:CA+A ACCCGUAGA::CGA:CUUGUG+U++A U ++ +GCACAAG:UCG::UCUA 185811 UGGCAUAAACCCGUAGAUCCGAUCUUGUGGUGAAGUG--GACCGCACAAGCUCGCUUCUA 185868 ->>>-->>>>>>:: 61 gggguguaugucgg 74 +GGGU+U+UG:C+G 185869 UGGGUCUGUGUCAG 185882 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum11.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum12.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum13.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum14.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum15.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum16.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum17.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum18.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum19.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum20.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum21.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum21.dat.fasta.gz ----sequence: #8999,sp|X17360.1|HSHOX51 Human HOX 5.1 gene for HOX 5.1 protein ----isReversed: 0 ----hitSequence: CUAUAUAUACCCUGUAGAACCGAAUUUGUGUGGUAUCCGUAUAGUCACAGAUUCGAUUCUAGGGGAAUAUAUGGU hit 33 : 308 382 (fwd) 36.21 bits :<<<<<<--<<<.--<<<<<<<<<<<<<<<_______________>>>>>>>>>>>>>>> 1 cgacauaUAccc.GUagauccgaacuuguguuagaaucAaacaugcacaaguucguaucu 59 C:A:AUAUACCC GUAGA:+CGAA:+UGUGU ++A++C A+A +CACA+:UUCG+:UCU 308 CUAUAUAUACCCuGUAGAACCGAAUUUGUGUGGUAUCCGUAUAGUCACAGAUUCGAUUCU 367 -->>>-->>>>>>:: 60 Agggguguaugucgg 74 AGGGG+ UAU:U:G+ 368 AGGGGAAUAUAUGGU 382 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum22.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum23.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum24.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum25.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum26.dat.fasta.gz fracLetsThru=3.78469e-07 (# nucs lets thru=6279/total nucs=1.65905e+10 CPU time: 210619.10u 112.89s 58:32:11.99 Elapsed: 58:31:13