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 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,4974,AC002512.1,1,sp|AC002512.1|AC002512 Drosophila melanogaster (P1 DS00276 (D13)) DNA sequence; complete sequence.,1,0,65196,65121,32.01,CCACGUCUACCCUGUAGAUCCGAAUUUGUUUUAUACUAGCUUUAAGGACAAAUUCGGUUCUAGAGAGGUUUGUGUG,AC095014.1/143527-143452 AC002512.1/65196-65121 AE001572.2/247245-247320 AE003673.3/31404-31329,,0,74 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,6748,AC095014.1,1,sp|AC095014.1|AC095014 Drosophila melanogaster; chromosome 3R; region 83F-84A; BAC clone BACR19D23; complete sequence.,1,1,143527,143452,32.01,CCACGUCUACCCUGUAGAUCCGAAUUUGUUUUAUACUAGCUUUAAGGACAAAUUCGGUUCUAGAGAGGUUUGUGUG,AC095014.1/143527-143452 AC002512.1/65196-65121 AE001572.2/247245-247320 AE003673.3/31404-31329,,0,74 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,6975,AC124817.2,1,sp|AC124817.2|AC124817 Branchiostoma floridae; clone -10F3; complete sequence.,1,2,56096,56022,24.56,CUAUAUGUACCCUGUAGAUCCGAAUUUGUGUGAGGUACCCAAGUCACAAAUUCGUUUCUGCAGGUAUAAUGUAGC,AC124817.2/56096-56022,,0,73 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,7416,AE001572.2,1,sp|AE001572.2|AE001572 Drosophila melanogaster Antennapedia complex (ANT-C);complete sequence.,0,3,247245,247320,32.01,CCACGUCUACCCUGUAGAUCCGAAUUUGUUUUAUACUAGCUUUAAGGACAAAUUCGGUUCUAGAGAGGUUUGUGUG,AC095014.1/143527-143452 AC002512.1/65196-65121 AE001572.2/247245-247320 AE003673.3/31404-31329,,0,76 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,7689,AE003673.3,1,sp|AE003673.3|AE003673 Drosophila melanogaster chromosome 3R; section 11 of 118 of the complete sequence.,1,4,31404,31329,32.01,CCACGUCUACCCUGUAGAUCCGAAUUUGUUUUAUACUAGCUUUAAGGACAAAUUCGGUUCUAGAGAGGUUUGUGUG,AC095014.1/143527-143452 AC002512.1/65196-65121 AE001572.2/247245-247320 AE003673.3/31404-31329,,0,74 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,36735,AF321227.1,1,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 ,0,5,48039,48109,27.26,CUACAUCUACCCUGUAGAUCCGAAUUUGUUUGAAAUCAGGCGACAAAUUCGGUUCUAGAGAGGUUUGUGUG,AF321227.1/48039-48109,,0,71 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,36735,AF321227.1,1,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 ,1,6,86918,86845,24.97,CGUGAUCUACCCUGUAGAUCCGGGCUUUUGUAGAAUUUUUAGAUCAGAAGCUCGUCUCUACAGGUAUCUUACGG,AF321227.1/86918-86845,,0,72 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz,44026,Z68760.2,1,sp|Z68760.2|CEF36H1 Caenorhabditis elegans cosmid F36H1,1,7,2906,2832,23.58,GUCCGUCUACCCGUAGCUCCUAUCCAUGUUACUGGUCAAAAAGUGAACAUGGAAGCAGGUACAGGUGCACGGCGA,Z68760.2/2906-2832,,0,73 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz,45139,Z36753.1,1,sp|Z36753.1|CET09A5 Caenorhabditis elegans cosmid T09A5,1,8,18689,18615,22.55,GCUCGUCUACCCUGUAGAUCGAGCUGUGUGUUUGAAACAAUCAUACACGAGCUAGACUACAAGGUGCACGAACAA,Z36753.1/18689-18615,,0,73 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/mam.dat.fasta.gz,7191,AC116664.1,1,sp|AC116664.1|AC116664 Papio hamadryas; clone RP41-57E23; complete sequence.,0,9,138988,139063,33.12,CUGUAUAUACCCUGUAGAUCCGAAUUUGUGUAAGGAAUUUUGUGGUCACAAAUUCGUAUCUAGGGGAAUAUGUAGU,AC011194.15/112960-113035 AC103702.3/109566-109641 AC009789.21/113436-113511 AL606824.13/12219-12294 AC116664.1/138988-139063 AF287967.1/27998-28073,,0,76 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/mam.dat.fasta.gz,7192,AC116665.1,1,sp|AC116665.1|AC116665 Papio hamadryas chromosome ; clone RP41-119J13; complete sequence.,0,10,91344,91418,38.08,CUAUAUAUACCCUGUAGAACCGAAUUUGUGUGGUAUCCAUAUAGUCACAGAUUCGAUUCUAGGGGAAUAUAUGGU,AC116665.1/91344-91418,,0,75 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/mam.dat.fasta.gz,7268,AC129959.6,1,sp|AC129959.6|AC129959 Bos taurus; clone RP42-518P7; complete sequence.,1,11,98422,98347,33.03,CUGUAUAUACCCUGUAGAUCCGAAUUUGUGUAAGGAAUUUUGUGAUCACAAAUUCGUAUCUAGGGGAAUAUGUAGU,AC129959.6/98422-98347,,0,74 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/mus.dat.fasta.gz,4599,AC011194.15,1,sp|AC011194.15|AC011194 Mus musculus chromosome 11; clone RP23-196F5; complete sequence.,0,12,112960,113035,33.12,CUGUAUAUACCCUGUAGAUCCGAAUUUGUGUAAGGAAUUUUGUGGUCACAAAUUCGUAUCUAGGGGAAUAUGUAGU,AC011194.15/112960-113035 AC103702.3/109566-109641 AC009789.21/113436-113511 AL606824.13/12219-12294 AC116664.1/138988-139063 AF287967.1/27998-28073,,0,76 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/mus.dat.fasta.gz,4610,AC015584.18,1,sp|AC015584.18|AC015584 Mus musculus; clone RP23-400H17; complete sequence.,0,13,162939,163013,37.55,CUAUAUAUACCCUGUAGAACCGAAUUUGUGUGGUACCCACAUAGUCACAGAUUCGAUUCUAGGGGAAUAUAUGGU,AC015584.18/162939-163013 AL928644.12/210999-211073 U77364.1/4186-4260,,0,75 ./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 ,Rfam/cm/RF00104.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.,1,14,49344,49273,33.16,UGACAUAAACCCGUAGAUCCGAUCUUGUGGUGAAGUGGACCGCGCAAGCUCGUUUCUAUGGGUCUGUGGCAG,AC122451.3/49344-49273,,0,70 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/mus.dat.fasta.gz,24200,AL606824.13,1,sp|AL606824.13|AL606824 Mouse DNA sequence from clone RP23-9G13 on chromosome 11,0,15,12219,12294,33.12,CUGUAUAUACCCUGUAGAUCCGAAUUUGUGUAAGGAAUUUUGUGGUCACAAAUUCGUAUCUAGGGGAAUAUGUAGU,AC011194.15/112960-113035 AC103702.3/109566-109641 AC009789.21/113436-113511 AL606824.13/12219-12294 AC116664.1/138988-139063 AF287967.1/27998-28073,,0,76 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/mus.dat.fasta.gz,26961,AL928644.12,0,sp|AL928644.12|AL928644 Mouse DNA sequence from clone RP23-313J15 on chromosome 2,0,16,210999,211073,37.55,CUAUAUAUACCCUGUAGAACCGAAUUUGUGUGGUACCCACAUAGUCACAGAUUCGAUUCUAGGGGAAUAUAUGGU,AC015584.18/162939-163013 AL928644.12/210999-211073 U77364.1/4186-4260,,0,75 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/mus.dat.fasta.gz,75905,U77364.1,1,sp|U77364.1|MMU77364 Mus musculus homeodomain-containing transcription factor (Hoxd4) gene; complete cds.,0,17,4186,4260,37.55,CUAUAUAUACCCUGUAGAACCGAAUUUGUGUGGUACCCACAUAGUCACAGAUUCGAUUCUAGGGGAAUAUAUGGU,AC015584.18/162939-163013 AL928644.12/210999-211073 U77364.1/4186-4260,,0,75 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz,23845,AL645782.2,1,sp|AL645782.2|AL645782 Zebrafish DNA sequence from clone BUSM1-254O17 in linkage group 3 Contains the hoxb1a; hoxb2a; hoxb3a; hoxb4a; hoxb5a; hoxb6a; ,0,18,32556,32631,36.95,CUAUAUAUACCCUGUAGAUCCGGAUUUGUGUAAACAGACGCACAGUCACAAAUUCGUAUCUAGGGGAGUAUGUAGU,AL645782.2/32556-32631,,0,76 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz,23854,AL645798.2,1,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,0,19,23515,23586,32.43,CUAUAUAUACCCUGUAGAUCCGAAUUUGUGUGAAUAUACAGUCGCAAAUUCGUGUCUUGGGGAAUAUGUAGU,AL645798.2/23515-23586,,0,72 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz,29105,AY168642.1,1,sp|AY168642.1|AY168642 Danio rerio homeodomain protein Hoxd4A (hoxd4a) gene; complete cds.,0,20,1778,1850,26.56,CUAUAUAUACCCUGUAGAACCGAAUUUGUGUGAAAAAAUAACAUCACAGAUUCGAUUCAGGGGAGUAUAUGGU,AY168642.1/1778-1850,,0,73 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz,36467,BX005254.9,0,sp|BX005254.9|BX005254 Zebrafish DNA sequence from clone DKEY-81P22 in linkage group 23,1,21,84183,84108,23.89,CUAUAUGUACCCUGUAGAACCGAAUUUGUGUCCAAAACAUCAAAAUCGCAAAUACGUCUCUACAGGAAUACAUGGG,BX005254.9/84183-84108,,0,74 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz,38819,U92575.1,1,sp|U92575.1|FRU92575 Fugu rubripes homeobox protein HOXB-4 (FrHOXB-4) gene; complete cds.,0,22,1530,1608,37.64,CUAUAUCUACCCUGUAGAUCCGGAUUUGUGUAAAAAUCAUUAAAGCAAUCACAAAUUCGCUUCUAGGGGAGUAUAUAGU,U92575.1/1530-1608,,0,79 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz,2801,AC009336.13,1,sp|AC009336.13|AC009336 Homo sapiens chromosome 2; clone RP11-387A1; complete sequence.,0,23,134311,134385,36.21,CUAUAUAUACCCUGUAGAACCGAAUUUGUGUGGUAUCCGUAUAGUCACAGAUUCGAUUCUAGGGGAAUAUAUGGU,AC009336.13/134311-134385 X17360.1/308-382,,0,75 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz,2967,AC009789.21,1,sp|AC009789.21|AC009789 Homo sapiens chromosome 17; clone RP11-361K8; complete sequence.,0,24,113436,113511,33.12,CUGUAUAUACCCUGUAGAUCCGAAUUUGUGUAAGGAAUUUUGUGGUCACAAAUUCGUAUCUAGGGGAAUAUGUAGU,AC011194.15/112960-113035 AC103702.3/109566-109641 AC009789.21/113436-113511 AL606824.13/12219-12294 AC116664.1/138988-139063 AF287967.1/27998-28073,,0,76 ./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 ,Rfam/cm/RF00104.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.,0,25,119760,119832,29.67,UGGCACCCACCCGUAGAACCGACCUUGCGGGGCCUUCGCCGCACACAAGCUCGUGUCUGUGGGUCCGUGUCGG,AC018755.3/119760-119832,,0,73 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz,2555,AC103702.3,1,sp|AC103702.3|AC103702 Homo sapiens chromosome 17; clone RP11-357H14; complete sequence.,0,26,109566,109641,33.12,CUGUAUAUACCCUGUAGAUCCGAAUUUGUGUAAGGAAUUUUGUGGUCACAAAUUCGUAUCUAGGGGAAUAUGUAGU,AC011194.15/112960-113035 AC103702.3/109566-109641 AC009789.21/113436-113511 AL606824.13/12219-12294 AC116664.1/138988-139063 AF287967.1/27998-28073,,0,76 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/hum06.dat.fasta.gz,4653,AF287967.1,1,sp|AF287967.1|AF287967 Homo sapiens homeobox B7 (HOXB7) gene; partial cds; and homeobox B6 (HOXB6); homeobox B5 (HOXB5); homeobox B4 (HOXB4); and home,0,27,27998,28073,33.12,CUGUAUAUACCCUGUAGAUCCGAAUUUGUGUAAGGAAUUUUGUGGUCACAAAUUCGUAUCUAGGGGAAUAUGUAGU,AC011194.15/112960-113035 AC103702.3/109566-109641 AC009789.21/113436-113511 AL606824.13/12219-12294 AC116664.1/138988-139063 AF287967.1/27998-28073,,0,76 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/hum07.dat.fasta.gz,3702,AF480538.1,1,sp|AF480538.1|AF480538 Homo sapiens miR-100-precursor-11 micro RNA; complete sequence.,0,28,6,75,30.51,UGCCACAAACCCGUAGAUCCGAACUUGUGGUAUUAGUCCGCACAAGCUUGUAUCUAUAGGUAUGUGUCUG,AF480538.1/6-75 AP001359.4/120261-120192,,0,70 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/hum07.dat.fasta.gz,3735,AF480571.1,1,sp|AF480571.1|AF480571 Homo sapiens miR-99-precursor-21 micro RNA; complete sequence.,0,29,6,77,35.75,UGGCAUAAACCCGUAGAUCCGAUCUUGUGGUGAAGUGGACCGCACAAGCUCGCUUCUAUGGGUCUGUGUCAG,AP000962.2/117355-117426 AF480571.1/6-77 AP001667.1/185811-185882,,0,72 ./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 ,Rfam/cm/RF00104.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.,0,30,117355,117426,35.75,UGGCAUAAACCCGUAGAUCCGAUCUUGUGGUGAAGUGGACCGCACAAGCUCGCUUCUAUGGGUCUGUGUCAG,AP000962.2/117355-117426 AF480571.1/6-77 AP001667.1/185811-185882,,0,72 ./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 ,Rfam/cm/RF00104.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.,1,31,120261,120192,30.51,UGCCACAAACCCGUAGAUCCGAACUUGUGGUAUUAGUCCGCACAAGCUUGUAUCUAUAGGUAUGUGUCUG,AF480538.1/6-75 AP001359.4/120261-120192,,0,68 ./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 ,Rfam/cm/RF00104.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.,0,32,185811,185882,35.75,UGGCAUAAACCCGUAGAUCCGAUCUUGUGGUGAAGUGGACCGCACAAGCUCGCUUCUAUGGGUCUGUGUCAG,AP000962.2/117355-117426 AF480571.1/6-77 AP001667.1/185811-185882,,0,72 ./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 ,Rfam/cm/RF00104.cm (global),/projects/bio/zasha/seqs/embl/hum21.dat.fasta.gz,8999,X17360.1,1,sp|X17360.1|HSHOX51 Human HOX 5.1 gene for HOX 5.1 protein,0,33,308,382,36.21,CUAUAUAUACCCUGUAGAACCGAAUUUGUGUGGUAUCCGUAUAGUCACAGAUUCGAUUCUAGGGGAAUAUAUGGU,AC009336.13/134311-134385 X17360.1/308-382,,0,75 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) # 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)