compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/positions_7nt_m7/peak-motifs_positions_7nt_m7.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/idmmpmm_PCM.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 $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/positions_7nt_m7/peak-motifs_positions_7nt_m7_vs_db_IDMMPMM_drosophila Program version 1.118 Quick mode Input files file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/idmmpmm_PCM.tf file1 $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/positions_7nt_m7/peak-motifs_positions_7nt_m7.tf Output files html_index $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/positions_7nt_m7/peak-motifs_positions_7nt_m7_vs_db_IDMMPMM_drosophila_index.html match_table_txt $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/positions_7nt_m7/peak-motifs_positions_7nt_m7_vs_db_IDMMPMM_drosophila.tab alignments_1ton $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/positions_7nt_m7/peak-motifs_positions_7nt_m7_vs_db_IDMMPMM_drosophila_alignments_1ton.tab alignments_1ton_html $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/positions_7nt_m7/peak-motifs_positions_7nt_m7_vs_db_IDMMPMM_drosophila_alignments_1ton.html prefix $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/positions_7nt_m7/peak-motifs_positions_7nt_m7_vs_db_IDMMPMM_drosophila match_table_html $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/positions_7nt_m7/peak-motifs_positions_7nt_m7_vs_db_IDMMPMM_drosophila.html Matrices file1 1 matrices $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/positions_7nt_m7/peak-motifs_positions_7nt_m7.tf file1 1 24 11268 file2 39 matrices $RSAT/public_html/motif_databases/DMMPMM_drosophila/idmmpmm_PCM.tf file2 1 8 64.00006 file2 2 10 28.000033 file2 3 9 31.000094 file2 4 14 33.000041 file2 5 7 328.0003 file2 6 14 22.00003 file2 7 10 156.00013 file2 8 10 134.00035 file2 9 8 40.00004 file2 10 11 203.00042 file2 11 11 25.00004 ... 29 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 rsat Job started 2025-11-26.210858 Job done 2025-11-26.210858 Seconds 0.22 user 0.22 system 0.03 cuser 0.02 ; csystem 0