params (warning: commas chnged to semicolons),CM file,fastaFile,sequence #,EMBL accession,is in RFAMSEQ,sequence description (warning: commas chnged to semicolons),is reversed?,hit #,start nuc,end nuc,score (bits),hit sequence,hit Id(s) in Rfam with same seq,hit ranges within the same EMBL id,new hitness (0=in Rfam; 1=overlaps hit in Rfam;2=entirely new),amount of overlap with Rfam,this hit in Rfam format ./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 ,Rfam/cm/RF00052.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,5206,AC006590.11,1,sp|AC006590.11|AC006590 Drosophila melanogaster; chromosome 2L; region 36E-; BAC clone BACR13N02; complete sequence.,0,0,38290,38358,36.18,GCUGAUUCCCUGAGACCCUAACUUGUGACUUUUAAUACCAGUUUCACAAGUUUUGAUCUCCGGUAUUGG,AC006590.11/38290-38358 AC008184.4/115811-115879 AE003659.2/55202-55270,38290-38358,0,68,AC006590.11/38290-38358 ./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 ,Rfam/cm/RF00052.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,5562,AC008184.4,1,sp|AC008184.4|AC008184 Drosophila melanogaster; chromosome 2L; region 36E5-36F2; BAC clone BACR04D05; complete sequence.,0,1,115811,115879,36.18,GCUGAUUCCCUGAGACCCUAACUUGUGACUUUUAAUACCAGUUUCACAAGUUUUGAUCUCCGGUAUUGG,AC006590.11/38290-38358 AC008184.4/115811-115879 AE003659.2/55202-55270,115811-115879,0,68,AC008184.4/115811-115879 ./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 ,Rfam/cm/RF00052.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,7675,AE003659.2,1,sp|AE003659.2|AE003659 Drosophila melanogaster chromosome 2L section 68 of 83 of the complete sequence.,0,2,55202,55270,36.18,GCUGAUUCCCUGAGACCCUAACUUGUGACUUUUAAUACCAGUUUCACAAGUUUUGAUCUCCGGUAUUGG,AC006590.11/38290-38358 AC008184.4/115811-115879 AE003659.2/55202-55270,55202-55270,0,68,AE003659.2/55202-55270 ./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 ,Rfam/cm/RF00052.cm (global),/projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz,42287,U01829.1,1,sp|U01829.1|CB01829 Caenorhabditis briggsae lin-4 gene sequence.,0,3,524,593,42.43,GCCUGUUCCCUGAGACCUCAAGUGUGAGCGUUCUGAACAUGCUUCACGCCUGGGCUCUCCGGGUACCAGG,U01829.1/524-593,524-593,0,69,U01829.1/524-593 ./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 ,Rfam/cm/RF00052.cm (global),/projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz,42744,U01830.1,1,sp|U01830.1|CE01830 Caenorhabditis elegans lin-4 gene sequence.,0,4,508,577,43.14,GCCUGUUCCCUGAGACCUCAAGUGUGAGUGUACUAUUGAUGCUUCACACCUGGGCUCUCCGGGUACCAGG,U53332.2/6165-6234 U01830.1/508-577,508-577,0,69,U01830.1/508-577 ./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 ,Rfam/cm/RF00052.cm (global),/projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz,44290,U53332.2,1,sp|U53332.2|CEF59G1 Caenorhabditis elegans cosmid F59G1; complete sequence.,0,5,6165,6234,43.14,GCCUGUUCCCUGAGACCUCAAGUGUGAGUGUACUAUUGAUGCUUCACACCUGGGCUCUCCGGGUACCAGG,U53332.2/6165-6234 U01830.1/508-577,6165-6234,0,69,U53332.2/6165-6234 ./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 ,Rfam/cm/RF00052.cm (global),/projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz,47233,U01838.1,1,sp|U01838.1|CR01838 Caenorhabditis remanei lin-4 gene sequence.,0,6,544,613,40.99,GCCUGCUCCCUGAGACCUCAAGUGUGAGCGUACUGUAGAUGCUUCACACCUGGGCUCUCUGGGUACCAGG,U01838.1/544-613,544-613,0,69,U01838.1/544-613 ./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 ,Rfam/cm/RF00052.cm (global),/projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz,47736,U01837.1,1,sp|U01837.1|CV01837 Caenorhabditis vulgaris lin-4 gene sequence.,0,7,538,607,38.04,GCCUGCUCCCUGAGACCUCAAGUGUGAGCGCACUGUUGAUGCUUCACGCCUGGGCUCUCUGGGUACCAGG,U01837.1/538-607,538-607,0,69,U01837.1/538-607 ./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 ,Rfam/cm/RF00052.cm (global),/projects/bio/zasha/seqs/embl/mus.dat.fasta.gz,6187,AC122451.3,1,sp|AC122451.3|AC122451 Mus musculus clone RP24-252G15; complete sequence.,1,8,2004,1935,45.14,GCCUAGUCCCUGAGACCCUAACUUGUGAGGUAUUUUAGUAACAUCACAAGUCAGGUUCUUGGGACCUAGG,AC122451.3/2004-1935,2004-1935,0,69,AC122451.3/2004-1935 ./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 ,Rfam/cm/RF00052.cm (global),/projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz,5062,AC018755.3,1,sp|AC018755.3|AC018755 Homo sapiens chromosome 19; BAC BC330783 (CIT-HSPC_470E3); complete sequence.,0,9,120411,120479,33.12,UCUAGGUCCCUGAGACCCUUUAACCUGUGAGGACAUCCAGGGUCACAGGUGAGGUUCUUGGGAGCCUGG,AC018755.3/120411-120479,120411-120479,0,68,AC018755.3/120411-120479 ./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 ,Rfam/cm/RF00052.cm (global),/projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz,6765,AP000962.2,1,sp|AP000962.2|AP000962 Homo sapiens genomic DNA; chromosome 21q21.1-q21.2; clone:B821P16; LL56-APP region.,0,10,168508,168577,45.62,UCCUAGUCCCUGAGACCCUAACUUGUGAGGUAUUUUAGUAACAUCACAAGUCAGGCUCUUGGGACCUAGG,AP000962.2/168508-168577 AP001667.1/236964-237033,168508-168577,0,69,AP000962.2/168508-168577 ./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 ,Rfam/cm/RF00052.cm (global),/projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz,6963,AP001359.4,1,sp|AP001359.4|AP001359 Homo sapiens genomic DNA; chromosome 11q clone:RP11-820L6; complete sequences.,1,11,67794,67724,38.85,UCUCAGUCCCUGAGACCCUAACUUGUGAUGUUUACCGUUUAAAUCCACGGGUUAGGCUCUUGGGAGCUGCG,AP001924.5/149434-149364 AP001359.4/67794-67724,67794-67724,0,70,AP001359.4/67794-67724 ./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 ,Rfam/cm/RF00052.cm (global),/projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz,7108,AP001667.1,1,sp|AP001667.1|AP001667 Homo sapiens genomic DNA; chromosome 21q; section 11/105.,0,12,236964,237033,45.62,UCCUAGUCCCUGAGACCCUAACUUGUGAGGUAUUUUAGUAACAUCACAAGUCAGGCUCUUGGGACCUAGG,AP000962.2/168508-168577 AP001667.1/236964-237033,236964-237033,0,69,AP001667.1/236964-237033 ./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 ,Rfam/cm/RF00052.cm (global),/projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz,7236,AP001924.5,1,sp|AP001924.5|AP001924 Homo sapiens genomic DNA; chromosome 11 clone:RP11-166D19; complete sequence.,1,13,149434,149364,38.85,UCUCAGUCCCUGAGACCCUAACUUGUGAUGUUUACCGUUUAAAUCCACGGGUUAGGCUCUUGGGAGCUGCG,AP001924.5/149434-149364 AP001359.4/67794-67724,149434-149364,0,70,AP001924.5/149434-149364 THINGS IN Rfam THAT WEREN'T FOUND: # hits found that weren't in Rfam: 0 (totally new = 0, overlaps hit in Rfam = 0, overlap hits with more than 10 nucs = 0, total # hits with 0 overlap with Rfam (ignoring sequence matching) = 0) # Rfam hits not found: 0 (no overlap of >= 10 nucs: 0) # Rfam seqs not found: 0 (no overlap of >= 10 nucs: too tricky to calculate)