compare-matrices -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/03/26/compare-matrices_2025-03-26.111958_MPJhvm/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,NsEucl,NSW,offset,matrix_id,matrix_name,width,strand,offset,consensus,alignments_1ton -o $RSAT/public_html/tmp/www-data/2025/03/26/compare-matrices_2025-03-26.111958_MPJhvm/compare-matrices.tab Program version 1.118 Slow mode Input files file1 $RSAT/public_html/tmp/www-data/2025/03/26/compare-matrices_2025-03-26.111958_MPJhvm/compare-matrices_query_matrices.transfac file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_fungi_non-redundant_pfms_transfac.txt Output files alignments_1ton $RSAT/public_html/tmp/www-data/2025/03/26/compare-matrices_2025-03-26.111958_MPJhvm/compare-matrices_alignments_1ton.tab match_table_html $RSAT/public_html/tmp/www-data/2025/03/26/compare-matrices_2025-03-26.111958_MPJhvm/compare-matrices.html html_index $RSAT/public_html/tmp/www-data/2025/03/26/compare-matrices_2025-03-26.111958_MPJhvm/compare-matrices_index.html alignments_1ton_html $RSAT/public_html/tmp/www-data/2025/03/26/compare-matrices_2025-03-26.111958_MPJhvm/compare-matrices_alignments_1ton.html match_table_txt $RSAT/public_html/tmp/www-data/2025/03/26/compare-matrices_2025-03-26.111958_MPJhvm/compare-matrices.tab prefix $RSAT/public_html/tmp/www-data/2025/03/26/compare-matrices_2025-03-26.111958_MPJhvm/compare-matrices Matrices file1 6 matrices $RSAT/public_html/tmp/www-data/2025/03/26/compare-matrices_2025-03-26.111958_MPJhvm/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 NSW Normalized Sandelin-Wasserman similarity. NSW = SW/w 8 NsEucl relative Euclidian similarity. NsEucl = (max(dEucl) - dEucl)/max(dEucl) 9 w1 Width of the first matrix 10 w2 Width of the second matrix 11 w Alignment length (number of overlapping columns between matrix 1 and matrix 2, as a function of the offset) 12 W Total alignment length (overlapping + non-overlapping columns). W = w1 + w2 - w 13 Wr Relative alignment length (overlap divided by the total alignemnt length). Wr = w/W 14 wr1 Alignment length relative to the width of the first matrix. wr1 = w/w1 15 wr2 Alignment length relative to the width of the second matrix. wr2 = w/w2 16 strand "strand", i.e. orientation of matrix 2 relative to matrix 1 (D=direct; R=reverse) 17 offset shift of the second matrix relative to the first matrix (negative:left; positive: right) 18 consensus1 IUPAC consensus of matrix 1 (dots represent non-aligned columns) 19 consensus2 IUPAC consensus of matrix 2 (dots represent non-aligned columns)
| id1 | id2 | name1 | name2 | cor | Ncor | NSW | NsEucl | w1 | w2 | w | W | Wr | wr1 | wr2 | strand | offset | consensus1 | consensus2 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| positions_7nt_m3 | MA0277.1 | positions_7nt_m3 | AZF1 | 0.782 | 0.640 | 0.871 | 0.88026 | 11 | 9 | 9 | 11 | 0.8182 | 0.8182 | 1.0000 | D | 1 | .AAAAAAAAA. | aAAARGAAa |
| oligos_7nt_mkv5_m2 | MA0274.1 | oligos_7nt_mkv5_m2 | ARR1 | 0.755 | 0.503 | 0.871 | 0.87281 | 12 | 8 | 8 | 12 | 0.6667 | 0.6667 | 1.0000 | R | 2 | ..ATGCAAAT.. | ATTYARRT |
| oligos_7nt_mkv5_m3 | MA0417.1 | oligos_7nt_mkv5_m3 | YAP5 | 0.793 | 0.433 | 0.879 | 0.85774 | 11 | 6 | 6 | 11 | 0.5455 | 0.5455 | 1.0000 | R | 2 | ..ATGyTA... | ATGYYT |
| oligos_7nt_mkv5_m2 | MA0434.2 | oligos_7nt_mkv5_m2 | YPR013C | 0.719 | 0.419 | 0.857 | 0.85710 | 12 | 7 | 7 | 12 | 0.5833 | 0.5833 | 1.0000 | D | 4 | ....GCAAATg. | GymrATC |
| oligos_7nt_mkv5_m3 | MA0433.2 | oligos_7nt_mkv5_m3 | YOX1 | 0.829 | 0.414 | 0.895 | 0.86760 | 11 | 7 | 6 | 12 | 0.5000 | 0.5455 | 0.8571 | D | 5 | .....yTAAtk | yTAATT. |
| oligos_7nt_mkv5_m2 | MA0355.2 | oligos_7nt_mkv5_m2 | PHD1 | 0.822 | 0.411 | 0.912 | 0.87865 | 12 | 6 | 6 | 12 | 0.5000 | 0.5000 | 1.0000 | D | 1 | .tATGCA..... | smTGCA |
Host name rsat Job started 2025-03-26.111958 Job done 2025-03-26.112001 Seconds 1.69 user 1.69 system 0.11 cuser 1.06 ; csystem 0.18