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 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 ,Rfam/cm/RF00103.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,4965,AC002442.1,1,sp|AC002442.1|AC002442 Drosophila melanogaster DNA sequence (P1 DS08416 (D52)); complete sequence.,0,0,20529,20604,29.33,UUGAGAGUUCCAUGCUUCCUUGCAUUCAAUAGUUAUAUUCAAGCAUAUGGAAUGUAAAGAAGUAUGGAGCGAAAUC,AC093198.2/177303-177378 AC002442.1/20529-20604 AC093440.1/41821-41896 AE003667.3/4813-4888,20529-20604,0,75,AC002442.1/20529-20604 ./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 ,Rfam/cm/RF00103.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,6573,AC087074.1,1,sp|AC087074.1|AC087074 Caenorhabditis briggsae cosmid CB010J11; complete sequence.,0,1,69936,70014,36.14,UGCCGAGCUGCAUACUUCCUUACAUGCCCAUACUGUACUGUGAAUGGAUAUGGAAUGUAAAGAAGUAUGUAGAACGGAA,AC087074.1/69936-70014,69936-70014,0,78,AC087074.1/69936-70014 ./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 ,Rfam/cm/RF00103.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,6718,AC093198.2,1,sp|AC093198.2|AC093198 Drosophila melanogaster; chromosome 2L; region 38B-38C; BAC clone BACR03G24; complete sequence.,0,2,177303,177378,29.33,UUGAGAGUUCCAUGCUUCCUUGCAUUCAAUAGUUAUAUUCAAGCAUAUGGAAUGUAAAGAAGUAUGGAGCGAAAUC,AC093198.2/177303-177378 AC002442.1/20529-20604 AC093440.1/41821-41896 AE003667.3/4813-4888,177303-177378,0,75,AC093198.2/177303-177378 ./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 ,Rfam/cm/RF00103.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,6725,AC093440.1,1,sp|AC093440.1|AC093440 Drosophila melanogaster; chromosome 2L; region 38C-38D; BAC clone BACR34H03; complete sequence.,0,3,41821,41896,29.33,UUGAGAGUUCCAUGCUUCCUUGCAUUCAAUAGUUAUAUUCAAGCAUAUGGAAUGUAAAGAAGUAUGGAGCGAAAUC,AC093198.2/177303-177378 AC002442.1/20529-20604 AC093440.1/41821-41896 AE003667.3/4813-4888,41821-41896,0,75,AC093440.1/41821-41896 ./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 ,Rfam/cm/RF00103.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,7683,AE003667.3,1,sp|AE003667.3|AE003667 Drosophila melanogaster chromosome 2L section 76 of 83 of the complete sequence.,0,4,4813,4888,29.33,UUGAGAGUUCCAUGCUUCCUUGCAUUCAAUAGUUAUAUUCAAGCAUAUGGAAUGUAAAGAAGUAUGGAGCGAAAUC,AC093198.2/177303-177378 AC002442.1/20529-20604 AC093440.1/41821-41896 AE003667.3/4813-4888,4813-4888,0,75,AE003667.3/4813-4888 ./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 ,Rfam/cm/RF00103.cm (global),/projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz,45659,U97405.1,1,sp|U97405.1|CEUT09B4 Caenorhabditis elegans cosmid T09B4; complete sequence.,1,5,23097,23019,40.34,UACCGAGCUGCAUACUUCCUUACAUGCCCAUACUAUAUCAUAAAUGGAUAUGGAAUGUAAAGAAGUAUGUAGAACGGGG,U97405.1/23097-23019,23097-23019,0,78,U97405.1/23097-23019 ./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 ,Rfam/cm/RF00103.cm (global),/projects/bio/zasha/seqs/embl/mus.dat.fasta.gz,25238,AL672157.5,1,sp|AL672157.5|AL672157 Mouse DNA sequence from clone RP24-499M12 on chromosome 2,0,6,42188,42264,41.62,GCUUGGGACACAUACUUCUUUAUAUGCCCAUAUGAACCUGCUAAGCUAUGGAAUGUAAAGAAGUAUGUAUUUCAGGC,AL672157.5/42188-42264,42188-42264,0,76,AL672157.5/42188-42264 ./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 ,Rfam/cm/RF00103.cm (global),/projects/bio/zasha/seqs/embl/rod.dat.fasta.gz,17595,L33721.1,1,sp|L33721.1|RNNCRNAA Rattus norvegicus synapse-specific noncoding RNA (7H4) gene; clone RG1; repeat region and enhancers.,0,7,66,141,22.21,CCCCAGGCCACAUGCUUCUUUAUAUCCUCAUAGAUAUCACUGCGCUAUGGAAUGUAAGGAAGUGUGUGGUUUUGGC,L33721.1/66-141,66-141,0,75,L33721.1/66-141 ./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 ,Rfam/cm/RF00103.cm (global),/projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz,24334,AL929326.9,1,sp|AL929326.9|AL929326 Zebrafish DNA sequence from clone BUSM1-SL11 in linkage group 20,0,8,101067,101144,30.22,ACUUGGUGUACAUACUUCUUUAUGUGCCCAUAUGAACAUAUAAAAGCUAUGGAAUGUAAAGAAGUAUGUAUUCUUGGU,AL929326.9/101067-101144,101067-101144,0,77,AL929326.9/101067-101144 ./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 ,Rfam/cm/RF00103.cm (global),/projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz,2668,AC103987.5,1,sp|AC103987.5|AC103987 Homo sapiens chromosome 18; clone RP11-268I9; complete sequence.,1,9,56357,56281,38.10,ACUCAGAGUACAUACUUCUUUAUGUACCCAUAUGAACAUACAAUGCUAUGGAAUGUAAAGAAGUAUGUAUUUUUGGU,AC103987.5/56357-56281 AC116916.2/49716-49640,56357-56281,0,76,AC103987.5/56357-56281 ./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 ,Rfam/cm/RF00103.cm (global),/projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz,5152,AC116916.2,1,sp|AC116916.2|AC116916 Homo sapiens chromosome 18; clone CTD-3070B10; complete sequence.,1,10,49716,49640,38.10,ACUCAGAGUACAUACUUCUUUAUGUACCCAUAUGAACAUACAAUGCUAUGGAAUGUAAAGAAGUAUGUAUUUUUGGU,AC103987.5/56357-56281 AC116916.2/49716-49640,49716-49640,0,76,AC116916.2/49716-49640 ./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 ,Rfam/cm/RF00103.cm (global),/projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz,3151,AL391221.15,1,sp|AL391221.15|AL391221 Human DNA sequence from clone RP11-771D21 on chromosome 6,0,11,79486,79562,37.95,UCCCGAGGCCACAUGCUUCUUUAUAUCCCCAUAUGGAUUACUUUGCUAUGGAAUGUAAGGAAGUGUGUGGUUUCGGC,AL391221.15/79486-79562,79486-79562,0,76,AL391221.15/79486-79562 ./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 ,Rfam/cm/RF00103.cm (global),/projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz,3618,AL449263.5,1,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,1,12,25754,25678,41.33,GCUUGGGAAACAUACUUCUUUAUAUGCCCAUAUGGACCUGCUAAGCUAUGGAAUGUAAAGAAGUAUGUAUCUCAGGC,AL449263.5/25754-25678,25754-25678,0,76,AL449263.5/25754-25678 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)