Params: ./cmzasha --no-stderr --filter 120 30 Rfam/cm/RF00052.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00052_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin Build: release Host: tricycle.cs.washington.edu pid: 27085 ----cmFile: Rfam/cm/RF00052.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: #5206,sp|AC006590.11|AC006590 Drosophila melanogaster, chromosome 2L, region 36E-, BAC clone BACR13N02, complete sequence. ----isReversed: 0 ----hitSequence: GCUGAUUCCCUGAGACCCUAACUUGUGACUUUUAAUACCAGUUUCACAAGUUUUGAUCUCCGGUAUUGG hit 0 : 38290 38358 (fwd) 36.18 bits :<<<<--<<<-<<<<-<<<-<<<<<<<<________________>>>>>>>>->>>->>> 1 gccuagUcccUgagaCccuAacuugugaGguUUcucuaccAGcUucacaaguuaggcucu 60 GC::A+UCCCU:AGACC::AACUUGUGA +UUU ++UACCAG UUCACAAGUU::G UCU 38290 GCUGAUUCCCUGAGACCCUAACUUGUGACUUUU-AAUACCAGUUUCACAAGUUUUGAUCU 38348 >->>>--->>>> 61 uCgggaaCuagg 72 :C GG+A U::G 38349 CC-GGUA-UUGG 38358 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #5562,sp|AC008184.4|AC008184 Drosophila melanogaster, chromosome 2L, region 36E5-36F2, BAC clone BACR04D05, complete sequence. ----isReversed: 0 ----hitSequence: GCUGAUUCCCUGAGACCCUAACUUGUGACUUUUAAUACCAGUUUCACAAGUUUUGAUCUCCGGUAUUGG hit 1 : 115811 115879 (fwd) 36.18 bits :<<<<--<<<-<<<<-<<<-<<<<<<<<________________>>>>>>>>->>>->>> 1 gccuagUcccUgagaCccuAacuugugaGguUUcucuaccAGcUucacaaguuaggcucu 60 GC::A+UCCCU:AGACC::AACUUGUGA +UUU ++UACCAG UUCACAAGUU::G UCU 115811 GCUGAUUCCCUGAGACCCUAACUUGUGACUUUU-AAUACCAGUUUCACAAGUUUUGAUCU 115869 >->>>--->>>> 61 uCgggaaCuagg 72 :C GG+A U::G 115870 CC-GGUA-UUGG 115879 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #7675,sp|AE003659.2|AE003659 Drosophila melanogaster chromosome 2L section 68 of 83 of the complete sequence. ----isReversed: 0 ----hitSequence: GCUGAUUCCCUGAGACCCUAACUUGUGACUUUUAAUACCAGUUUCACAAGUUUUGAUCUCCGGUAUUGG hit 2 : 55202 55270 (fwd) 36.18 bits :<<<<--<<<-<<<<-<<<-<<<<<<<<________________>>>>>>>>->>>->>> 1 gccuagUcccUgagaCccuAacuugugaGguUUcucuaccAGcUucacaaguuaggcucu 60 GC::A+UCCCU:AGACC::AACUUGUGA +UUU ++UACCAG UUCACAAGUU::G UCU 55202 GCUGAUUCCCUGAGACCCUAACUUGUGACUUUU-AAUACCAGUUUCACAAGUUUUGAUCU 55260 >->>>--->>>> 61 uCgggaaCuagg 72 :C GG+A U::G 55261 CC-GGUA-UUGG 55270 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #42287,sp|U01829.1|CB01829 Caenorhabditis briggsae lin-4 gene sequence. ----isReversed: 0 ----hitSequence: GCCUGUUCCCUGAGACCUCAAGUGUGAGCGUUCUGAACAUGCUUCACGCCUGGGCUCUCCGGGUACCAGG hit 3 : 524 593 (fwd) 42.43 bits :<<<<--<<<-<<<<-<<<-<<<<<<<<________________>>>>>>>>->>>->>> 1 gccuagUcccUgagaCccuAacuugugaGguUUcucuaccAGcUucacaaguuaggcucu 60 GCCU:+UCCCU:AGACC::AA: :GUGAG +UUCU +AC++GCUUCAC:+:U ::GCUCU 524 GCCUGUUCCCUGAGACCUCAAG-UGUGAGCGUUCUGAACAUGCUUCACGCCU-GGGCUCU 581 >->>>--->>>> 61 uCgggaaCuagg 72 :CGGG+AC:AGG 582 CCGGGUACCAGG 593 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #42744,sp|U01830.1|CE01830 Caenorhabditis elegans lin-4 gene sequence. ----isReversed: 0 ----hitSequence: GCCUGUUCCCUGAGACCUCAAGUGUGAGUGUACUAUUGAUGCUUCACACCUGGGCUCUCCGGGUACCAGG hit 4 : 508 577 (fwd) 43.14 bits :<<<<--<<<-<<<<-<<<-<<<<<<<<________________>>>>>>>>->>>->>> 1 gccuagUcccUgagaCccuAacuugugaGguUUcucuaccAGcUucacaaguuaggcucu 60 GCCU:+UCCCU:AGACC::AA: UGUGAG++U+CU+U++++GCUUCACA+:U ::GCUCU 508 GCCUGUUCCCUGAGACCUCAAG-UGUGAGUGUACUAUUGAUGCUUCACACCU-GGGCUCU 565 >->>>--->>>> 61 uCgggaaCuagg 72 :CGGG+AC:AGG 566 CCGGGUACCAGG 577 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #44290,sp|U53332.2|CEF59G1 Caenorhabditis elegans cosmid F59G1, complete sequence. ----isReversed: 0 ----hitSequence: GCCUGUUCCCUGAGACCUCAAGUGUGAGUGUACUAUUGAUGCUUCACACCUGGGCUCUCCGGGUACCAGG hit 5 : 6165 6234 (fwd) 43.14 bits :<<<<--<<<-<<<<-<<<-<<<<<<<<________________>>>>>>>>->>>->>> 1 gccuagUcccUgagaCccuAacuugugaGguUUcucuaccAGcUucacaaguuaggcucu 60 GCCU:+UCCCU:AGACC::AA: UGUGAG++U+CU+U++++GCUUCACA+:U ::GCUCU 6165 GCCUGUUCCCUGAGACCUCAAG-UGUGAGUGUACUAUUGAUGCUUCACACCU-GGGCUCU 6222 >->>>--->>>> 61 uCgggaaCuagg 72 :CGGG+AC:AGG 6223 CCGGGUACCAGG 6234 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #47233,sp|U01838.1|CR01838 Caenorhabditis remanei lin-4 gene sequence. ----isReversed: 0 ----hitSequence: GCCUGCUCCCUGAGACCUCAAGUGUGAGCGUACUGUAGAUGCUUCACACCUGGGCUCUCUGGGUACCAGG hit 6 : 544 613 (fwd) 40.99 bits :<<<<--<<<-<<<<-<<<-<<<<<<<<________________>>>>>>>>->>>->>> 1 gccuagUcccUgagaCccuAacuugugaGguUUcucuaccAGcUucacaaguuaggcucu 60 GCCU: UCCCU:AGACC::AA: UGUGAG +U+CU UA+++GCUUCACA+:U ::GCUCU 544 GCCUGCUCCCUGAGACCUCAAG-UGUGAGCGUACUGUAGAUGCUUCACACCU-GGGCUCU 601 >->>>--->>>> 61 uCgggaaCuagg 72 :+GGG+AC:AGG 602 CUGGGUACCAGG 613 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #47736,sp|U01837.1|CV01837 Caenorhabditis vulgaris lin-4 gene sequence. ----isReversed: 0 ----hitSequence: GCCUGCUCCCUGAGACCUCAAGUGUGAGCGCACUGUUGAUGCUUCACGCCUGGGCUCUCUGGGUACCAGG hit 7 : 538 607 (fwd) 38.04 bits :<<<<--<<<-<<<<-<<<-<<<<<<<<________________>>>>>>>>->>>->>> 1 gccuagUcccUgagaCccuAacuugugaGguUUcucuaccAGcUucacaaguuaggcucu 60 GCCU: UCCCU:AGACC::AA: :GUGAG + +CU U++++GCUUCAC:+:U ::GCUCU 538 GCCUGCUCCCUGAGACCUCAAG-UGUGAGCGCACUGUUGAUGCUUCACGCCU-GGGCUCU 595 >->>>--->>>> 61 uCgggaaCuagg 72 :+GGG+AC:AGG 596 CUGGGUACCAGG 607 ----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: #6187,sp|AC122451.3|AC122451 Mus musculus clone RP24-252G15, complete sequence. ----isReversed: 1 ----hitSequence: GCCUAGUCCCUGAGACCCUAACUUGUGAGGUAUUUUAGUAACAUCACAAGUCAGGUUCUUGGGACCUAGG hit 8 : 2004 1935 (rev) 45.14 bits :<<<<--<<<-<<<<-<<<-<<<<<<<<________________>>>>>>>>->>>->>> 1 gccuagUcccUgagaCccuAacuugugaGguUUcucuaccAGcUucacaaguuaggcucu 60 GCCUAGUCCCUGAGACCCUAACUUGUGAGGU U U UA++A+C UCACAAGU+AGG+UCU 158253 GCCUAGUCCCUGAGACCCUAACUUGUGAGGUAU-UUUAGUAACAUCACAAGUCAGGUUCU 158311 >->>>--->>>> 61 uCgggaaCuagg 72 U GGGA CUAGG 158312 U-GGGACCUAGG 158322 ----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/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: #5062,sp|AC018755.3|AC018755 Homo sapiens chromosome 19, BAC BC330783 (CIT-HSPC_470E3), complete sequence. ----isReversed: 0 ----hitSequence: UCUAGGUCCCUGAGACCCUUUAACCUGUGAGGACAUCCAGGGUCACAGGUGAGGUUCUUGGGAGCCUGG hit 9 : 120411 120479 (fwd) 33.12 bits :<<<<--<<<-<<<<-<<<..-<<<<<<<<________________>>>>>>>>->>>-> 1 gccuagUcccUgagaCccu..AacuugugaGguUUcucuaccAGcUucacaaguuaggcu 58 +C:::GUCCCUGAGACCCU AAC:UGUGAGG +C++CCAG UCACA:GU AGG+U 120411 UCUAGGUCCCUGAGACCCUuuAACCUGUGAGG----ACAUCCAGGGUCACAGGUGAGGUU 120466 >>>->>>--->>>> 59 cuuCgggaaCuagg 72 CUU GGGA+C:::G 120467 CUU-GGGAGCCUGG 120479 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz ----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: #6765,sp|AP000962.2|AP000962 Homo sapiens genomic DNA, chromosome 21q21.1-q21.2, clone:B821P16, LL56-APP region. ----isReversed: 0 ----hitSequence: UCCUAGUCCCUGAGACCCUAACUUGUGAGGUAUUUUAGUAACAUCACAAGUCAGGCUCUUGGGACCUAGG hit 10 : 168508 168577 (fwd) 45.62 bits :<<<<--<<<-<<<<-<<<-<<<<<<<<________________>>>>>>>>->>>->>> 1 gccuagUcccUgagaCccuAacuugugaGguUUcucuaccAGcUucacaaguuaggcucu 60 +CCUAGUCCCUGAGACCCUAACUUGUGAGGU U U UA++A+C UCACAAGU+AGGCUCU 168508 UCCUAGUCCCUGAGACCCUAACUUGUGAGGUAU-UUUAGUAACAUCACAAGUCAGGCUCU 168566 >->>>--->>>> 61 uCgggaaCuagg 72 U GGGA CUAGG 168567 U-GGGACCUAGG 168577 ----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: UCUCAGUCCCUGAGACCCUAACUUGUGAUGUUUACCGUUUAAAUCCACGGGUUAGGCUCUUGGGAGCUGCG hit 11 : 67794 67724 (rev) 38.85 bits :<<<<--<<<-<<<<-<<<-<<<<<<<<________________>>>>>>>>->>>->>> 1 gccuagUcccUgagaCccuAacuugugaGguUUcucuaccAGcUucacaaguuaggcucu 60 +C::AGUCCCUGAGACCCUAAC::GUG: GUUU+ C + +A+ U:CAC::GUUAGGCUCU 153742 UCUCAGUCCCUGAGACCCUAACUUGUGAUGUUUACCGUUUAAAUCCACGGGUUAGGCUCU 153801 >->>>--->>>> 61 uCgggaaCuagg 72 U GGGA+CU::G 153802 U-GGGAGCUGCG 153812 ----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: UCCUAGUCCCUGAGACCCUAACUUGUGAGGUAUUUUAGUAACAUCACAAGUCAGGCUCUUGGGACCUAGG hit 12 : 236964 237033 (fwd) 45.62 bits :<<<<--<<<-<<<<-<<<-<<<<<<<<________________>>>>>>>>->>>->>> 1 gccuagUcccUgagaCccuAacuugugaGguUUcucuaccAGcUucacaaguuaggcucu 60 +CCUAGUCCCUGAGACCCUAACUUGUGAGGU U U UA++A+C UCACAAGU+AGGCUCU 236964 UCCUAGUCCCUGAGACCCUAACUUGUGAGGUAU-UUUAGUAACAUCACAAGUCAGGCUCU 237022 >->>>--->>>> 61 uCgggaaCuagg 72 U GGGA CUAGG 237023 U-GGGACCUAGG 237033 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz ----sequence: #7236,sp|AP001924.5|AP001924 Homo sapiens genomic DNA, chromosome 11 clone:RP11-166D19, complete sequence. ----isReversed: 1 ----hitSequence: UCUCAGUCCCUGAGACCCUAACUUGUGAUGUUUACCGUUUAAAUCCACGGGUUAGGCUCUUGGGAGCUGCG hit 13 : 149434 149364 (rev) 38.85 bits :<<<<--<<<-<<<<-<<<-<<<<<<<<________________>>>>>>>>->>>->>> 1 gccuagUcccUgagaCccuAacuugugaGguUUcucuaccAGcUucacaaguuaggcucu 60 +C::AGUCCCUGAGACCCUAAC::GUG: GUUU+ C + +A+ U:CAC::GUUAGGCUCU 40927 UCUCAGUCCCUGAGACCCUAACUUGUGAUGUUUACCGUUUAAAUCCACGGGUUAGGCUCU 40986 >->>>--->>>> 61 uCgggaaCuagg 72 U GGGA+CU::G 40987 U-GGGAGCUGCG 40997 ----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=1.10846e-07, 2d-fracLetsThru=6.129e-08). Filter report: done 1.65905e+10 nucs (frac lets thru so far=1.10846e-07, 2d-fracLetsThru=6.129e-08). done 1.65905e+10 nucs (frac lets thru so far=1.10846e-07, 2d-fracLetsThru=6.129e-08). CPU time: 215122.42u 235.73s 59:49:18.15 Elapsed: 59:50:50