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 200 40 Rfam/cm/RF00075.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00075_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00075.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,1478,AB016871.1,1,sp|AB016871.1|AB016871 Arabidopsis thaliana genomic DNA; chromosome 5; TAC clone:K16L22.,1,0,77005,76861,62.88,UUUGAGGGGAAUGUUGUCUGGCACGAGGCCCUUAACUUAGAUCUAUAUUUGAUUAUAUAUAUAUGUCUCUUCUUUAUUCAUUAGUCUAUACAUGAAUGAUCAUUUUACGGUUAAUGACGUCGGACCAGGCUUCAUUCCCCUCAAU,AB016871.1/77005-76861,77005-76861,0,144,AB016871.1/77005-76861
./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00075.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00075_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00075.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,1482,AB016875.1,1,sp|AB016875.1|AB016875 Arabidopsis thaliana genomic DNA; chromosome 5; TAC clone:K9D7.,0,1,40211,40311,46.12,GUUCAGGUGAAUGAUGCCUGGCUCGAGACCAUUCAAUCUCAUGAUCUCAUGAUUAUAACGAUGAUGAUGAUGAUGUCGGACCAGGCUUCAUUCCCCUCAAC,AB016875.1/40211-40311,40211-40311,0,100,AB016875.1/40211-40311
./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00075.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00075_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00075.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,8711,AC005819.3,1,sp|AC005819.3|AC005819 Arabidopsis thaliana chromosome 2 clone T3A4 map CIC06C03; complete sequence.,0,2,30684,30829,60.20,UUUGAGGGGACUGUUGUCUGGCUCGAGGACUCUGGCUCGCUCUAUUCAUGUUGGAUCUCUUUCGAUCUAACAAUCGAAUUGAACCUUCAGAUUUCAGAUUUGAUUAGGGUUUUAGCGUCUUCGGACCAGGCUUCAUUCCCCCCAAU,AC005819.3/30684-30829,30684-30829,0,145,AC005819.3/30684-30829
./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00075.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00075_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00075.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,8903,AC007323.5,1,sp|AC007323.5|AC007323 Genomic sequence for Arabidopsis thaliana BAC T25K16 from chromosome I; complete sequence.,1,3,78739,78629,64.68,GUUGAGGGGAAUGUUGUCUGGAUCGAGGAUAUUAUAGAUAUAUACAUGUGUAUGUUAAUGAUUCAAGUGAUCAUAGAGAGUAUCCUCGGACCAGGCUUCAUCCCCCCCAAC,AC023628.3/19945-19835 AC007323.5/78739-78629,78739-78629,0,110,AC007323.5/78739-78629
./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00075.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00075_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00075.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,9152,AC023628.3,1,sp|AC023628.3|AC023628 Arabidopsis thaliana chromosome I BAC F6F3 genomic sequence; complete sequence.,1,4,19945,19835,64.68,GUUGAGGGGAAUGUUGUCUGGAUCGAGGAUAUUAUAGAUAUAUACAUGUGUAUGUUAAUGAUUCAAGUGAUCAUAGAGAGUAUCCUCGGACCAGGCUUCAUCCCCCCCAAC,AC023628.3/19945-19835 AC007323.5/78739-78629,19945-19835,0,110,AC023628.3/19945-19835
./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00075.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00075_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00075.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,9169,AC025296.10,1,sp|AC025296.10|AC025296 Oryza sativa chromosome 10 BAC OSJNBa0076F20 genomic sequence; complete sequence.,0,5,95861,95981,46.06,UCUGAGUGGAAUGUUGUCUGGUUCAAGGUCUCAUGCACCUUGCGGUUUUGAGGAUGAUUUGUGCAAGGUUUUUCAUUCCUCUCAUCCGUGGGAUCUCGGACCAGGCUUCAUUCCCCUCAGA,AC025296.10/95861-95981 AE017112.1/186405-186525,95861-95981,0,120,AC025296.10/95861-95981
./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00075.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00075_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00075.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,9583,AC104428.2,1,sp|AC104428.2|AC104428 Oryza sativa (japonica cultivar-group) chromosome 3 clone OJ1123F12; complete sequence.,1,6,40907,40796,54.91,GUUGAGGGGAAUGUUGUCUGGUCCGAGACCUAACACCGGGCGGAAUGGCGGAUUCAGCUGCAGCUAAGCAAGCUAGGUGGGGGGUUUCGGACCAGGCUUCAUUCCCCCCAAC,AC104428.2/40907-40796,40907-40796,0,111,AC104428.2/40907-40796
./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00075.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00075_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00075.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,10392,AE017112.1,1,sp|AE017112.1|AE017112 Oryza sativa (japonica cultivar-group) chromosome 10; section 66 of 77 of the complete sequence.,0,7,186405,186525,46.06,UCUGAGUGGAAUGUUGUCUGGUUCAAGGUCUCAUGCACCUUGCGGUUUUGAGGAUGAUUUGUGCAAGGUUUUUCAUUCCUCUCAUCCGUGGGAUCUCGGACCAGGCUUCAUUCCCCUCAGA,AC025296.10/95861-95981 AE017112.1/186405-186525,186405-186525,0,120,AE017112.1/186405-186525
./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00075.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00075_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00075.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,101358,AB005234.1,1,sp|AB005234.1|ATAB5234 Arabidopsis thaliana genomic DNA; chromosome 5; P1 clone:MBK5.,0,8,57935,58034,43.70,GUUUAGAGGAAUGUUGUUUGGCUCGAGGUCAUGGAGAGUAAUUCGUUAACCCAACUCAAAACUCUAAAUGAUUCUCGGACCAGGCUUCAUUCCCCUCAAC,AB005234.1/57935-58034,57935-58034,0,99,AB005234.1/57935-58034
./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00075.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00075_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00075.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,101473,AF013294.1,1,sp|AF013294.1|ATAF13294 Arabidopsis thaliana BAC TM018A10.,0,9,57881,58026,55.13,GUUGUGGGGAAUGUUGUUUGGAUCGAGGAUAUCAUAAACGCAUACACAUGUUUAUAUGUUAUGAUGCAUUAUAUGACUGAUGUAAUGUACAUAUAUAUACAUACAUGCCACAUGGUAUCGUCGGACCAGGCUUCAUCCCCCUCAAC,AL161472.2/176684-176539 AF013294.1/57881-58026,57881-58026,0,145,AF013294.1/57881-58026
./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00075.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00075_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00075.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,101871,AL161472.2,1,sp|AL161472.2|ATCHRIV2 Arabidopsis thaliana DNA chromosome 4; contig fragment No. 2,1,10,176684,176539,55.13,GUUGUGGGGAAUGUUGUUUGGAUCGAGGAUAUCAUAAACGCAUACACAUGUUUAUAUGUUAUGAUGCAUUAUAUGACUGAUGUAAUGUACAUAUAUAUACAUACAUGCCACAUGGUAUCGUCGGACCAGGCUUCAUCCCCCUCAAC,AL161472.2/176684-176539 AF013294.1/57881-58026,176684-176539,0,145,AL161472.2/176684-176539
./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00075.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00075_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00075.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,102241,AL138642.1,1,sp|AL138642.1|ATF21F14 Arabidopsis thaliana DNA chromosome 3; BAC clone F21F14,0,11,84877,84998,61.08,UUUGAGGGGACUGUUGUCUGGCUCGAGGACUCUUAUUCUAAUACAAUCUCAUUUGAAUACAUUCAGAUCUGAUGAUUGAUUAGGGUUUUAGUGUCGUCGGACCAGGCUUCAUUCCCCCCAAU,AL138642.1/84877-84998,84877-84998,0,121,AL138642.1/84877-84998
./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00075.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00075_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00075.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,119366,AL590346.1,1,sp|AL590346.1|ATT2K12 Arabidopsis thaliana DNA chromosome 5; BAC clone T2K12 (ESSA project),0,12,40100,40217,59.11,GUUGAGAGGAUUGUUGUCUGGCUCGAGGUCAUGAAGAAGAGAAUCACUCGAAUUAAUUUGGAAGAACAAAUUAAGAAAACCCUAGAUGAUUCUCGGACCAGGCUUCAUUCCCCCUAAC,AL590346.1/40100-40217,40100-40217 42078-42188,0,117,AL590346.1/40100-40217
./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00075.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00075_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00075.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,119366,AL590346.1,1,sp|AL590346.1|ATT2K12 Arabidopsis thaliana DNA chromosome 5; BAC clone T2K12 (ESSA project),0,13,42078,42188,65.47,GUUGAGAGGAAUAUUGUCUGGCUCGAGGUCAUGAAGAAGAUCGGUAGAUUGAUUCAUUUUAAAGAGUGAAAUCCCUAAAUGAUUCUCGGACCAGGCUUCAUUCCCCCCAAC,AL590346.1/42078-42188,40100-40217 42078-42188,0,110,AL590346.1/42078-42188



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)