compare-matrices -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/03/26/compare-matrices_2025-03-26.111727_8jZM1g/compare-matrices_query_matrices.transfac -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_fungi_non-redundant_pfms_transfac.txt -format2 tf -strand DR -lth cor 0.7 -lth Ncor 0.4 -uth match_rank 50 -return cor,Ncor,logoDP,NIcor,NsEucl,SW,NSW,offset,match_rank,matrix_id,matrix_name,width,strand,offset,consensus,alignments_1ton -o $RSAT/public_html/tmp/www-data/2025/03/26/compare-matrices_2025-03-26.111727_8jZM1g/compare-matrices.tab Program version 1.118 Slow mode Input files file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_fungi_non-redundant_pfms_transfac.txt file1 $RSAT/public_html/tmp/www-data/2025/03/26/compare-matrices_2025-03-26.111727_8jZM1g/compare-matrices_query_matrices.transfac Output files match_table_txt $RSAT/public_html/tmp/www-data/2025/03/26/compare-matrices_2025-03-26.111727_8jZM1g/compare-matrices.tab prefix $RSAT/public_html/tmp/www-data/2025/03/26/compare-matrices_2025-03-26.111727_8jZM1g/compare-matrices alignments_1ton_html $RSAT/public_html/tmp/www-data/2025/03/26/compare-matrices_2025-03-26.111727_8jZM1g/compare-matrices_alignments_1ton.html match_table_html $RSAT/public_html/tmp/www-data/2025/03/26/compare-matrices_2025-03-26.111727_8jZM1g/compare-matrices.html alignments_1ton $RSAT/public_html/tmp/www-data/2025/03/26/compare-matrices_2025-03-26.111727_8jZM1g/compare-matrices_alignments_1ton.tab html_index $RSAT/public_html/tmp/www-data/2025/03/26/compare-matrices_2025-03-26.111727_8jZM1g/compare-matrices_index.html Matrices file1 6 matrices $RSAT/public_html/tmp/www-data/2025/03/26/compare-matrices_2025-03-26.111727_8jZM1g/compare-matrices_query_matrices.transfac file1 1 12 392 tgCATrACAAwr file1 2 12 565 wtATGCAAATgw file1 3 11 246 wtATGyTAAtk file1 4 20 233 byCwTTGwyATGCAaATGdr file1 5 21 56 srTATGyGCATATGCAwATrw file1 6 11 663 AAAAAAAAAAA file2 178 matrices $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_fungi_non-redundant_pfms_transfac.txt file2 1 6 301 wGACkC file2 2 8 234 AyyTRAAT file2 3 6 100 CCGGAw file2 4 10 294 CCrrRTcrGG file2 5 9 102 aAAARGAAa file2 6 8 100 GGCGGRGw file2 7 11 9 CAGCrrAAAwG file2 8 9 100 TGACAyAww file2 9 7 101 cGATAAG file2 10 19 203 AAAAGCCGCGGGCGGGATT file2 11 9 101 awwrYGCGc ... 168 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 logoDP Dot product between the logo matrices. 8 NIcor Normalized Pearson correlation between the information content matrices. NIcor = Icor * Wr 9 NSW Normalized Sandelin-Wasserman similarity. NSW = SW/w 10 SW Sandelin-Wasserman similarity. 11 NsEucl relative Euclidian similarity. NsEucl = (max(dEucl) - dEucl)/max(dEucl) 12 w1 Width of the first matrix 13 w2 Width of the second matrix 14 w Alignment length (number of overlapping columns between matrix 1 and matrix 2, as a function of the offset) 15 W Total alignment length (overlapping + non-overlapping columns). W = w1 + w2 - w 16 Wr Relative alignment length (overlap divided by the total alignemnt length). Wr = w/W 17 wr1 Alignment length relative to the width of the first matrix. wr1 = w/w1 18 wr2 Alignment length relative to the width of the second matrix. wr2 = w/w2 19 strand "strand", i.e. orientation of matrix 2 relative to matrix 1 (D=direct; R=reverse) 20 offset shift of the second matrix relative to the first matrix (negative:left; positive: right) 21 consensus1 IUPAC consensus of matrix 1 (dots represent non-aligned columns) 22 consensus2 IUPAC consensus of matrix 2 (dots represent non-aligned columns) 23 rcor Matching rank for cor 24 rNcor Matching rank for Ncor 25 rlogoDP Matching rank for logoDP 26 rNIcor Matching rank for NIcor 27 rNsEucl Matching rank for NsEucl 28 rSW Matching rank for SW 29 rNSW Matching rank for NSW 30 rank_mean Mean of the matching ranks on all selected metrics 31 match_rank Rank of the match (sorting by rank_mean)
| id1 | id2 | name1 | name2 | cor | Ncor | logoDP | NIcor | NSW | SW | NsEucl | w1 | w2 | w | W | Wr | wr1 | wr2 | strand | offset | consensus1 | consensus2 | rcor | rNcor | rlogoDP | rNIcor | rNsEucl | rSW | rNSW | rank_mean | match_rank |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| positions_7nt_m3 | MA0277.1 | positions_7nt_m3 | AZF1 | 0.782 | 0.640 | 7.566 | 0.637 | 0.871 | 15.68 | 0.88026 | 11 | 9 | 9 | 11 | 0.8182 | 0.8182 | 1.0000 | D | 1 | .AAAAAAAAA. | aAAARGAAa | 4 | 1 | 1 | 1 | 1 | 1 | 4 | 1.8571 | 1 |
| oligos_7nt_mkv5_m2 | MA0355.2 | oligos_7nt_mkv5_m2 | PHD1 | 0.822 | 0.411 | 4.641 | 0.404 | 0.912 | 10.94 | 0.87865 | 12 | 6 | 6 | 12 | 0.5000 | 0.5000 | 1.0000 | D | 1 | .tATGCA..... | smTGCA | 2 | 6 | 4 | 2 | 2 | 4 | 1 | 3.0000 | 2 |
| oligos_7nt_mkv5_m3 | MA0433.2 | oligos_7nt_mkv5_m3 | YOX1 | 0.829 | 0.414 | 5.484 | 0.380 | 0.895 | 10.74 | 0.86760 | 11 | 7 | 6 | 12 | 0.5000 | 0.5455 | 0.8571 | D | 5 | .....yTAAtk | yTAATT. | 1 | 5 | 3 | 4 | 4 | 5 | 2 | 3.4286 | 3 |
| oligos_7nt_mkv5_m2 | MA0274.1 | oligos_7nt_mkv5_m2 | ARR1 | 0.755 | 0.503 | 4.068 | 0.319 | 0.871 | 13.93 | 0.87281 | 12 | 8 | 8 | 12 | 0.6667 | 0.6667 | 1.0000 | R | 2 | ..ATGCAAAT.. | ATTYARRT | 5 | 2 | 5 | 5 | 3 | 2 | 5 | 3.8571 | 4 |
| oligos_7nt_mkv5_m2 | MA0434.2 | oligos_7nt_mkv5_m2 | YPR013C | 0.719 | 0.419 | 5.745 | 0.388 | 0.857 | 12.00 | 0.85710 | 12 | 7 | 7 | 12 | 0.5833 | 0.5833 | 1.0000 | D | 4 | ....GCAAATg. | GymrATC | 6 | 4 | 2 | 3 | 6 | 3 | 6 | 4.2857 | 5 |
| oligos_7nt_mkv5_m3 | MA0417.1 | oligos_7nt_mkv5_m3 | YAP5 | 0.793 | 0.433 | 2.375 | 0.072 | 0.879 | 10.54 | 0.85774 | 11 | 6 | 6 | 11 | 0.5455 | 0.5455 | 1.0000 | R | 2 | ..ATGyTA... | ATGYYT | 3 | 3 | 6 | 6 | 5 | 6 | 3 | 4.5714 | 6 |
Host name rsat Job started 2025-03-26.111728 Job done 2025-03-26.111732 Seconds 2.77 user 2.77 system 0.07 cuser 1.19 ; csystem 0.24