; matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_sites.tab ; Quick counting mode ; Input files ; input /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta ; bg /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt ; Matrix files ; matrix 1 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2.tf ; Sequence format fasta ; Output files ; output /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_sites.tab ; Pseudo counts 1 ; Background model ; Method file ; Markov order 1 ; Strand undef ; Background pseudo-frequency 0.01 ; Residue probabilities ; a 0.29011 ; c 0.21156 ; g 0.20757 ; t 0.29076 ; Thresholds lower upper ; score 7.5 NA ; Output columns ; 1 seq_id ; 2 ft_type ; 3 ft_name ; 4 strand ; 5 start ; 6 end ; 7 sequence ; 8 weight #seq_id ft_type ft_name strand start end sequence weight ?_gi|49175990|ref|NC_000913.2|_281330_281431_+ site oligos_8nt_mkv2 R 8 19 GAAGAGGGAGTG 12.4 ?_gi|49175990|ref|NC_000913.2|_1655944_1656045_+ site oligos_8nt_mkv2 R 22 33 ATAGAGGGAGTC 13.2 ?_gi|49175990|ref|NC_000913.2|_1797306_1797407_+ site oligos_8nt_mkv2 D 27 38 AAAGAGGGAGAC 12.6 ; ; Matrices ; matrix name ncol nrow pseudo Wmin Wmax Wrange ; 1 oligos_8nt_mkv2 12 4 0 -16.700 12.700 29.400 a:0.290 c:0.212 g:0.208 t:0.291 ; Number of sequences scanned 109 ; Sum of sequence lengths 11009 ; N residues 0 ; Matches per matrix ; matrix name matches scored ; 1 oligos_8nt_mkv2 3 0 ; TOTAL 3 0 ; Host name biow ; Job started 2014-09-06.012147 ; Job done 2014-09-06.012148 ; Seconds 0.28 ; user 0.28 ; system 0.02 ; cuser 0.23 ; csystem 0.02