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 150 16 Rfam/cm/RF00043.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00043_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00043.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,17966,AF325537.2,1,sp|AF325537.2|AF325537 Acidithiobacillus caldus plasmid pTC-F14 replicon; complete sequence.,0,0,5765,5838,39.39,CGGCGCGAGCCGGAGUGUCAGUCCCCGGCAGCGCCUAACCACGCCAGUUCUGGAAAGGAGAACAGCAUGGCUUU,AF325537.2/5765-5838,5765-5838,0,73,AF325537.2/5765-5838
./cmzasha --no-stderr --filter 150 16 Rfam/cm/RF00043.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00043_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00043.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,6851,AY043298.1,1,sp|AY043298.1|AY043298 Aeromonas salmonicida subsp. salmonicida plasmid pRAS3.1; complete sequence.,1,1,7823,7750,16.12,CGGCGCGGCAGGGUGCGGGAACACCCGGCAGCGCCUAACCAUAACCGUUCUACACAGGAGAACAGCAUGGCUUU,AY043298.1/7823-7750 AY043299.1/7801-7728,7823-7750,0,73,AY043298.1/7823-7750
./cmzasha --no-stderr --filter 150 16 Rfam/cm/RF00043.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00043_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00043.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,6852,AY043299.1,1,sp|AY043299.1|AY043299 Aeromonas salmonicida plasmid pRAS3.2; complete sequence.,1,2,7801,7728,16.12,CGGCGCGGCAGGGUGCGGGAACACCCGGCAGCGCCUAACCAUAACCGUUCUACACAGGAGAACAGCAUGGCUUU,AY043298.1/7823-7750 AY043299.1/7801-7728,7801-7728,0,73,AY043299.1/7801-7728
./cmzasha --no-stderr --filter 150 16 Rfam/cm/RF00043.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00043_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00043.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,41041,Z78058.1,1,sp|Z78058.1|BSPCAC Bacteria sp. plasmid pIE1024 (partial).,0,3,1759,1831,34.00,UAGCGCUUAUGGGGUAGUGACCCCGCCAGCGCCUAACCACCAACUGCCUGCAAAGGAGGCAAUCAAUGGCUAC,Z78058.1/1759-1831,1759-1831,0,72,Z78058.1/1759-1831
./cmzasha --no-stderr --filter 150 16 Rfam/cm/RF00043.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00043_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00043.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,47748,Y19120.1,1,sp|Y19120.1|DN1Y19120 Dichelobacter nodosus plasmid DN1,0,4,3371,3442,36.79,CGGCGCAUGGCGGGGCAUCCCCGCCAGCGCUUGACCAUCAACCGCCUGCAAAGGAGGCAAACCAAUGGCUAC,Y19120.1/3371-3442,3371-3442,0,71,Y19120.1/3371-3442
./cmzasha --no-stderr --filter 150 16 Rfam/cm/RF00043.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00043_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00043.cm (global),/projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz,825,Z47410.1,1,sp|Z47410.1|ECINCQAAT E.coli IncQ plasmid aadB gene for aminoglycoside adenylyltransferase.,0,5,1220,1294,47.12,CGGCGCAGGGCGGGGGUAGUGACCCCGCCAGCGCCUAACCACCAACUGCCUGCAAAGGAGGCAAUCAAUGGCUAC,Z47410.1/1220-1294,1220-1294,0,74,Z47410.1/1220-1294
./cmzasha --no-stderr --filter 150 16 Rfam/cm/RF00043.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00043_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00043.cm (global),/projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz,45465,AJ271879.1,1,sp|AJ271879.1|UEU271879 Uncultured eubacterium plasmid pIE1130 DNA for repA gene; repC gene; repB gene; mobA gene; mobB gene; mobC gene; cac gene; catI,0,6,3249,3322,42.53,CGGCGCAGGGCGGGGGUGGUGACCCCGCCAGCGCCUAACCACCAACUGCCUGAACAGGAGGCAAUCAUGGCUAC,AJ271879.1/3249-3322,3249-3322,0,73,AJ271879.1/3249-3322
./cmzasha --no-stderr --filter 150 16 Rfam/cm/RF00043.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00043_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00043.cm (global),/projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz,45782,AJ293027.1,1,sp|AJ293027.1|UEU293027 Uncultured eubacterium pIE1115 plasmid pIE1115; complete sequence,0,7,2887,2958,38.39,CGGCGCAUGGCGGGGAUGCCCCGCCAGCGCCUGACCAUCAACCGCCUGCAAAGGAGGCAAACCAAUGGCUAC,AJ293027.1/2887-2958,2887-2958,0,71,AJ293027.1/2887-2958



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)