compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/positions_7nt_m10/peak-motifs_positions_7nt_m10.tf -format2 tf -file2 $RSAT/public_html/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey_2016.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.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/positions_7nt_m10/peak-motifs_positions_7nt_m10_vs_db_FlyFactorSurvey Program version 1.118 Quick mode Input files file2 $RSAT/public_html/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey_2016.tf file1 $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/positions_7nt_m10/peak-motifs_positions_7nt_m10.tf Output files alignments_1ton_html $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/positions_7nt_m10/peak-motifs_positions_7nt_m10_vs_db_FlyFactorSurvey_alignments_1ton.html match_table_txt $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/positions_7nt_m10/peak-motifs_positions_7nt_m10_vs_db_FlyFactorSurvey.tab html_index $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/positions_7nt_m10/peak-motifs_positions_7nt_m10_vs_db_FlyFactorSurvey_index.html alignments_1ton $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/positions_7nt_m10/peak-motifs_positions_7nt_m10_vs_db_FlyFactorSurvey_alignments_1ton.tab prefix $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/positions_7nt_m10/peak-motifs_positions_7nt_m10_vs_db_FlyFactorSurvey match_table_html $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/positions_7nt_m10/peak-motifs_positions_7nt_m10_vs_db_FlyFactorSurvey.html Matrices file1 1 matrices $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/positions_7nt_m10/peak-motifs_positions_7nt_m10.tf file1 1 24 11119 file2 652 matrices $RSAT/public_html/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey_2016.tf file2 1 21 20 file2 2 26 461 file2 3 8 37 file2 4 8 7 file2 5 7 18 file2 6 8 662 file2 7 9 21 file2 8 8 2704 file2 9 8 19 file2 10 8 19 file2 11 7 23 ... 642 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 2025-11-26.210154 Job done 2025-11-26.210155 Seconds 0.38 user 0.38 system 0.03 cuser 0.04 ; csystem 0