Params: ./cmzasha --no-stderr --filter 120 22 Rfam/cm/RF00103.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00103_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin Build: release Host: recycle.cs.washington.edu pid: 13268 ----cmFile: Rfam/cm/RF00103.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: #4965,sp|AC002442.1|AC002442 Drosophila melanogaster DNA sequence (P1 DS08416 (D52)), complete sequence. ----isReversed: 0 ----hitSequence: UUGAGAGUUCCAUGCUUCCUUGCAUUCAAUAGUUAUAUUCAAGCAUAUGGAAUGUAAAGAAGUAUGGAGCGAAAUC hit 0 : 20529 20604 (fwd) 29.33 bits :::::::<<<<<<<<<<<<<<<<<<<<<-<<<______________>>>>>>>>>>>>>> 1 UcccGAGcuacauacuuccuuauaugccCauauggACaUaCaagGcuauggaauguaaag 60 U GAG:U:CAU:CUUCCUU::AU:C: AUA + A AU CAAG +UAU:G:AU::AAAG 20529 UUGAGAGUUCCAUGCUUCCUUGCAUUCA-AUAGUUAUAUUCAAGCAUAUGGAAUGUAAAG 20587 >>>>>>>>>>::::::: 61 aaguauguaguucaGGc 77 AAG:AUG:A:+ A C 20588 AAGUAUGGAGCGAAAUC 20604 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #6573,sp|AC087074.1|AC087074 Caenorhabditis briggsae cosmid CB010J11, complete sequence. ----isReversed: 0 ----hitSequence: UGCCGAGCUGCAUACUUCCUUACAUGCCCAUACUGUACUGUGAAUGGAUAUGGAAUGUAAAGAAGUAUGUAGAACGGAA hit 1 : 69936 70014 (fwd) 36.14 bits :::::::<<<<<<<<<<<<<<<<<<<<<-<<<____..__________>>>>>>>>>>>> 1 UcccGAGcuacauacuuccuuauaugccCauauggA..CaUaCaagGcuauggaauguaa 58 U CCGAGCU:CAUACUUCCUUA:AUGCCCAUA++G+ U++A+GG+UAUGGAAU:UAA 69936 UGCCGAGCUGCAUACUUCCUUACAUGCCCAUACUGUacUGUGAAUGGAUAUGGAAUGUAA 69995 >>>>>>>>>>>>::::::: 59 agaaguauguaguucaGGc 77 AGAAGUAUG:AG++C+G 69996 AGAAGUAUGUAGAACGGAA 70014 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #6718,sp|AC093198.2|AC093198 Drosophila melanogaster, chromosome 2L, region 38B-38C, BAC clone BACR03G24, complete sequence. ----isReversed: 0 ----hitSequence: UUGAGAGUUCCAUGCUUCCUUGCAUUCAAUAGUUAUAUUCAAGCAUAUGGAAUGUAAAGAAGUAUGGAGCGAAAUC hit 2 : 177303 177378 (fwd) 29.33 bits :::::::<<<<<<<<<<<<<<<<<<<<<-<<<______________>>>>>>>>>>>>>> 1 UcccGAGcuacauacuuccuuauaugccCauauggACaUaCaagGcuauggaauguaaag 60 U GAG:U:CAU:CUUCCUU::AU:C: AUA + A AU CAAG +UAU:G:AU::AAAG 177303 UUGAGAGUUCCAUGCUUCCUUGCAUUCA-AUAGUUAUAUUCAAGCAUAUGGAAUGUAAAG 177361 >>>>>>>>>>::::::: 61 aaguauguaguucaGGc 77 AAG:AUG:A:+ A C 177362 AAGUAUGGAGCGAAAUC 177378 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #6725,sp|AC093440.1|AC093440 Drosophila melanogaster, chromosome 2L, region 38C-38D, BAC clone BACR34H03, complete sequence. ----isReversed: 0 ----hitSequence: UUGAGAGUUCCAUGCUUCCUUGCAUUCAAUAGUUAUAUUCAAGCAUAUGGAAUGUAAAGAAGUAUGGAGCGAAAUC hit 3 : 41821 41896 (fwd) 29.33 bits :::::::<<<<<<<<<<<<<<<<<<<<<-<<<______________>>>>>>>>>>>>>> 1 UcccGAGcuacauacuuccuuauaugccCauauggACaUaCaagGcuauggaauguaaag 60 U GAG:U:CAU:CUUCCUU::AU:C: AUA + A AU CAAG +UAU:G:AU::AAAG 41821 UUGAGAGUUCCAUGCUUCCUUGCAUUCA-AUAGUUAUAUUCAAGCAUAUGGAAUGUAAAG 41879 >>>>>>>>>>::::::: 61 aaguauguaguucaGGc 77 AAG:AUG:A:+ A C 41880 AAGUAUGGAGCGAAAUC 41896 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #7683,sp|AE003667.3|AE003667 Drosophila melanogaster chromosome 2L section 76 of 83 of the complete sequence. ----isReversed: 0 ----hitSequence: UUGAGAGUUCCAUGCUUCCUUGCAUUCAAUAGUUAUAUUCAAGCAUAUGGAAUGUAAAGAAGUAUGGAGCGAAAUC hit 4 : 4813 4888 (fwd) 29.33 bits :::::::<<<<<<<<<<<<<<<<<<<<<-<<<______________>>>>>>>>>>>>>> 1 UcccGAGcuacauacuuccuuauaugccCauauggACaUaCaagGcuauggaauguaaag 60 U GAG:U:CAU:CUUCCUU::AU:C: AUA + A AU CAAG +UAU:G:AU::AAAG 4813 UUGAGAGUUCCAUGCUUCCUUGCAUUCA-AUAGUUAUAUUCAAGCAUAUGGAAUGUAAAG 4871 >>>>>>>>>>::::::: 61 aaguauguaguucaGGc 77 AAG:AUG:A:+ A C 4872 AAGUAUGGAGCGAAAUC 4888 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #45659,sp|U97405.1|CEUT09B4 Caenorhabditis elegans cosmid T09B4, complete sequence. ----isReversed: 1 ----hitSequence: UACCGAGCUGCAUACUUCCUUACAUGCCCAUACUAUAUCAUAAAUGGAUAUGGAAUGUAAAGAAGUAUGUAGAACGGGG hit 5 : 23097 23019 (rev) 40.34 bits :::::::<<<<<<<<<<<<<<<<<<<<<-<<<____..__________>>>>>>>>>>>> 1 UcccGAGcuacauacuuccuuauaugccCauauggA..CaUaCaagGcuauggaauguaa 58 U CCGAGCU:CAUACUUCCUUA:AUGCCCAUA++++ CAUA+A+GG+UAUGGAAU:UAA 15240 UACCGAGCUGCAUACUUCCUUACAUGCCCAUACUAUauCAUAAAUGGAUAUGGAAUGUAA 15299 >>>>>>>>>>>>::::::: 59 agaaguauguaguucaGGc 77 AGAAGUAUG:AG++C+GG 15300 AGAAGUAUGUAGAACGGGG 15318 ----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/mus.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #25238,sp|AL672157.5|AL672157 Mouse DNA sequence from clone RP24-499M12 on chromosome 2 ----isReversed: 0 ----hitSequence: GCUUGGGACACAUACUUCUUUAUAUGCCCAUAUGAACCUGCUAAGCUAUGGAAUGUAAAGAAGUAUGUAUUUCAGGC hit 6 : 42188 42264 (fwd) 41.62 bits :::::::<<<<<<<<<<<<<<<<<<<<<-<<<______________>>>>>>>>>>>>>> 1 UcccGAGcuacauacuuccuuauaugccCauauggACaUaCaagGcuauggaauguaaag 60 C+ G+G::ACAUACUUC:UUAUAUGCCCAUAUG+AC U+C+A GCUAUGGAAUGUAA:G 42188 GCUUGGGACACAUACUUCUUUAUAUGCCCAUAUGAACCUGCUAAGCUAUGGAAUGUAAAG 42247 >>>>>>>>>>::::::: 61 aaguauguaguucaGGc 77 AAGUAUGU::UUCAGGC 42248 AAGUAUGUAUUUCAGGC 42264 ----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/rod.dat.fasta.gz ----sequence: #17595,sp|L33721.1|RNNCRNAA Rattus norvegicus synapse-specific noncoding RNA (7H4) gene, clone RG1, repeat region and enhancers. ----isReversed: 0 ----hitSequence: CCCCAGGCCACAUGCUUCUUUAUAUCCUCAUAGAUAUCACUGCGCUAUGGAAUGUAAGGAAGUGUGUGGUUUUGGC hit 7 : 66 141 (fwd) 22.21 bits :::::::<<<<<<<<<<<<<<<<<<<<<-<<<______________>>>>>>>>>>>>>> 1 UcccGAGcuacauacuuccuuauaugccCauauggACaUaCaagGcuauggaauguaaag 60 CCC +GC:ACA::CUUC:UUAUAU:C:CAUA A AC+ GCUAU:G:AUGUAA:G 66 CCCCAGGCCACAUGCUUCUUUAUAUCCUCAUAGAUA-UCACUGCGCUAUGGAAUGUAAGG 124 >>>>>>>>>>::::::: 61 aaguauguaguucaGGc 77 AAG::UGU:GUU+ GGC 125 AAGUGUGUGGUUUUGGC 141 ----endhit ----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: #24334,sp|AL929326.9|AL929326 Zebrafish DNA sequence from clone BUSM1-SL11 in linkage group 20 ----isReversed: 0 ----hitSequence: ACUUGGUGUACAUACUUCUUUAUGUGCCCAUAUGAACAUAUAAAAGCUAUGGAAUGUAAAGAAGUAUGUAUUCUUGGU hit 8 : 101067 101144 (fwd) 30.22 bits :::::::<<<<<<<<<<<<<<<<<<<<<-<<<________.______>>>>>>>>>>>>> 1 UcccGAGcuacauacuuccuuauaugccCauauggACaUa.CaagGcuauggaauguaaa 59 C+ G+ :UACAUACUUC:UUAU:UGCCCAUAUG+ACAUA +AA GCUAUGGAA:GUAA: 101067 ACUUGGUGUACAUACUUCUUUAUGUGCCCAUAUGAACAUAuAAAAGCUAUGGAAUGUAAA 101126 >>>>>>>>>>>::::::: 60 gaaguauguaguucaGGc 77 GAAGUAUGUA:U + GG 101127 GAAGUAUGUAUUCUUGGU 101144 ----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/hum03.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz ----sequence: #2668,sp|AC103987.5|AC103987 Homo sapiens chromosome 18, clone RP11-268I9, complete sequence. ----isReversed: 1 ----hitSequence: ACUCAGAGUACAUACUUCUUUAUGUACCCAUAUGAACAUACAAUGCUAUGGAAUGUAAAGAAGUAUGUAUUUUUGGU hit 9 : 56357 56281 (rev) 38.10 bits :::::::<<<<<<<<<<<<<<<<<<<<<-<<<______________>>>>>>>>>>>>>> 1 UcccGAGcuacauacuuccuuauaugccCauauggACaUaCaagGcuauggaauguaaag 60 C+C + :UACAUACUUC:UUAU:U+CCCAUAUG+ACAUACAA+GCUAUGG+A:GUAA:G 107616 ACUCAGAGUACAUACUUCUUUAUGUACCCAUAUGAACAUACAAUGCUAUGGAAUGUAAAG 107675 >>>>>>>>>>::::::: 61 aaguauguaguucaGGc 77 AAGUAUGUA:UU+ GG 107676 AAGUAUGUAUUUUUGGU 107692 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz ----sequence: #5152,sp|AC116916.2|AC116916 Homo sapiens chromosome 18, clone CTD-3070B10, complete sequence. ----isReversed: 1 ----hitSequence: ACUCAGAGUACAUACUUCUUUAUGUACCCAUAUGAACAUACAAUGCUAUGGAAUGUAAAGAAGUAUGUAUUUUUGGU hit 10 : 49716 49640 (rev) 38.10 bits :::::::<<<<<<<<<<<<<<<<<<<<<-<<<______________>>>>>>>>>>>>>> 1 UcccGAGcuacauacuuccuuauaugccCauauggACaUaCaagGcuauggaauguaaag 60 C+C + :UACAUACUUC:UUAU:U+CCCAUAUG+ACAUACAA+GCUAUGG+A:GUAA:G 4921 ACUCAGAGUACAUACUUCUUUAUGUACCCAUAUGAACAUACAAUGCUAUGGAAUGUAAAG 4980 >>>>>>>>>>::::::: 61 aaguauguaguucaGGc 77 AAGUAUGUA:UU+ GG 4981 AAGUAUGUAUUUUUGGU 4997 ----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/hum07.dat.fasta.gz ----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: #3151,sp|AL391221.15|AL391221 Human DNA sequence from clone RP11-771D21 on chromosome 6 ----isReversed: 0 ----hitSequence: UCCCGAGGCCACAUGCUUCUUUAUAUCCCCAUAUGGAUUACUUUGCUAUGGAAUGUAAGGAAGUGUGUGGUUUCGGC hit 11 : 79486 79562 (fwd) 37.95 bits :::::::.<<<<<<<<<<<<<<<<<<<<<-<<<______________>>>>>>>>>>>>> 1 UcccGAG.cuacauacuuccuuauaugccCauauggACaUaCaagGcuauggaauguaaa 59 UCCCGAG C:ACA::CUUC:UUAUAU:CCCAUAUGGA UAC+++GCUAUGG:AUGUAA: 79486 UCCCGAGgCCACAUGCUUCUUUAUAUCCCCAUAUGGA-UUACUUUGCUAUGGAAUGUAAG 79544 >>>>>>>>>>>::::::: 60 gaaguauguaguucaGGc 77 GAAG::UGU:GUU+ GGC 79545 GAAGUGUGUGGUUUCGGC 79562 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz ----sequence: #3618,sp|AL449263.5|AL449263 Human DNA sequence from clone RP3-353C17 on chromosome 20 Contains ESTs, STSs, GSSs and a CpG island. Contains a novel gene and ----isReversed: 1 ----hitSequence: GCUUGGGAAACAUACUUCUUUAUAUGCCCAUAUGGACCUGCUAAGCUAUGGAAUGUAAAGAAGUAUGUAUCUCAGGC hit 12 : 25754 25678 (rev) 41.33 bits :::::::<<<<<<<<<<<<<<<<<<<<<-<<<______________>>>>>>>>>>>>>> 1 UcccGAGcuacauacuuccuuauaugccCauauggACaUaCaagGcuauggaauguaaag 60 C+ G+G:+ACAUACUUC:UUAUAUGCCCAUAUGGAC U+C+A GCUAUGGAAUGUAA:G 10073 GCUUGGGAAACAUACUUCUUUAUAUGCCCAUAUGGACCUGCUAAGCUAUGGAAUGUAAAG 10132 >>>>>>>>>>::::::: 61 aaguauguaguucaGGc 77 AAGUAUGU+:+UCAGGC 10133 AAGUAUGUAUCUCAGGC 10149 ----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/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 done 1.65905e+10 nucs (frac lets thru so far=1.12474e-07, 2d-fracLetsThru=6.29351e-08). Filter report: done 1.65905e+10 nucs (frac lets thru so far=1.12474e-07, 2d-fracLetsThru=6.29351e-08). done 1.65905e+10 nucs (frac lets thru so far=1.12474e-07, 2d-fracLetsThru=6.29351e-08). CPU time: 259241.10u 339.45s 72:06:20.55 Elapsed: 72:14:03