compare-matrices -v 1 -mode matches -format1 transfac -file1 W9/regulonW9.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/peaks_oligos_5-7nt_m1.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o W9/regulonW9.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/peaks_oligos_5-7nt_m1_vs_db_footDB Program version 1.118 Quick mode Input files file2 $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf file1 W9/regulonW9.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/peaks_oligos_5-7nt_m1.tf Output files alignments_1ton W9/regulonW9.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/peaks_oligos_5-7nt_m1_vs_db_footDB_alignments_1ton.tab match_table_txt W9/regulonW9.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/peaks_oligos_5-7nt_m1_vs_db_footDB.tab html_index W9/regulonW9.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/peaks_oligos_5-7nt_m1_vs_db_footDB_index.html alignments_1ton_html W9/regulonW9.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/peaks_oligos_5-7nt_m1_vs_db_footDB_alignments_1ton.html match_table_html W9/regulonW9.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/peaks_oligos_5-7nt_m1_vs_db_footDB.html prefix W9/regulonW9.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/peaks_oligos_5-7nt_m1_vs_db_footDB Matrices file1 1 matrices W9/regulonW9.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/peaks_oligos_5-7nt_m1.tf file1 1 24 1 file2 2892 matrices $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf file2 1 16 5 file2 2 8 5 file2 3 8 3 file2 4 8 5 file2 5 8 1 file2 6 8 2 file2 7 8 2 file2 8 8 6 file2 9 8 2 file2 10 8 8 file2 11 8 1 ... 2882 more matrices Column content 1 id1 Identifier of the first matrix 2 id2 Identifier of the second matrix 3 name1 Name of the first matrix 4 name2 Name of the second matrix 5 cor Pearson coefficient of correlation between frequency matrices 6 Ncor Normalized correlation. Ncor = cor * Wr 7 w1 Width of the first matrix 8 w2 Width of the second matrix 9 w Alignment length (number of overlapping columns between matrix 1 and matrix 2, as a function of the offset) 10 W Total alignment length (overlapping + non-overlapping columns). W = w1 + w2 - w 11 Wr Relative alignment length (overlap divided by the total alignemnt length). Wr = w/W 12 wr1 Alignment length relative to the width of the first matrix. wr1 = w/w1 13 wr2 Alignment length relative to the width of the second matrix. wr2 = w/w2 14 strand "strand", i.e. orientation of matrix 2 relative to matrix 1 (D=direct; R=reverse) 15 offset shift of the second matrix relative to the first matrix (negative:left; positive: right) id1 id2 name1 name2 cor Ncor w1 w2 w W Wr wr1 wr2 strand offset Host name baobab.eead.csic.es Job started 2021-02-18.131056 Job done 2021-02-18.131101 Seconds 3.63 user 3.63 system 0.08 cuser 0.7 ; csystem 0.05