compare-matrices -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.155109_sgXuti/compare-matrices_query_matrices.transfac -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt -format2 tf -strand DR -lth cor 0.9 -lth Ncor 0.5 -uth match_rank 50 -return cor,Ncor,logoDP,NsEucl,NSW,match_rank,matrix_id,matrix_name,width,strand,offset,consensus,alignments_1ton -o $RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.155109_sgXuti/compare-matrices.tab Program version 1.118 Slow mode Input files file1 $RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.155109_sgXuti/compare-matrices_query_matrices.transfac file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt Output files html_index $RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.155109_sgXuti/compare-matrices_index.html alignments_1ton $RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.155109_sgXuti/compare-matrices_alignments_1ton.tab match_table_txt $RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.155109_sgXuti/compare-matrices.tab match_table_html $RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.155109_sgXuti/compare-matrices.html prefix $RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.155109_sgXuti/compare-matrices alignments_1ton_html $RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.155109_sgXuti/compare-matrices_alignments_1ton.html Matrices file1 5 matrices $RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.155109_sgXuti/compare-matrices_query_matrices.transfac file1 1 12 15 kyCCTGGGCCmd file1 2 12 26 rwAATTAAAcyy file1 3 11 42 wcCCCAGCChy file1 4 12 15 wvAGTGAGTCaa file1 5 12 17 wrAGTCAAGAar file2 879 matrices $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt file2 1 6 20 CACGTG file2 2 14 43 TTyACGCwTsAvTk file2 3 10 25 wwcwAGGTCA file2 4 15 10 RGGTCAwcGrGTTCA file2 5 10 17 sGGrmwTTCC file2 6 10 18 gGGraTTTCC file2 7 17 25 AAAGGTCAAAGGTCAAc file2 8 15 33 gsmmCCyWrGGkkkm file2 9 14 16 TGGCAssrwGCCAA file2 10 6 16 mTCCAC file2 11 15 1369 ywTTswyATGCAaAt ... 869 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 NSW Normalized Sandelin-Wasserman similarity. NSW = SW/w 9 NsEucl relative Euclidian similarity. NsEucl = (max(dEucl) - dEucl)/max(dEucl) 10 w1 Width of the first matrix 11 w2 Width of the second matrix 12 w Alignment length (number of overlapping columns between matrix 1 and matrix 2, as a function of the offset) 13 W Total alignment length (overlapping + non-overlapping columns). W = w1 + w2 - w 14 Wr Relative alignment length (overlap divided by the total alignemnt length). Wr = w/W 15 wr1 Alignment length relative to the width of the first matrix. wr1 = w/w1 16 wr2 Alignment length relative to the width of the second matrix. wr2 = w/w2 17 strand "strand", i.e. orientation of matrix 2 relative to matrix 1 (D=direct; R=reverse) 18 offset shift of the second matrix relative to the first matrix (negative:left; positive: right) 19 consensus1 IUPAC consensus of matrix 1 (dots represent non-aligned columns) 20 consensus2 IUPAC consensus of matrix 2 (dots represent non-aligned columns) 21 rcor Matching rank for cor 22 rNcor Matching rank for Ncor 23 rlogoDP Matching rank for logoDP 24 rNsEucl Matching rank for NsEucl 25 rNSW Matching rank for NSW 26 rank_mean Mean of the matching ranks on all selected metrics 27 match_rank Rank of the match (sorting by rank_mean)
| id1 | id2 | name1 | name2 | cor | Ncor | logoDP | NSW | NsEucl | w1 | w2 | w | W | Wr | wr1 | wr2 | strand | offset | consensus1 | consensus2 | rcor | rNcor | rlogoDP | rNsEucl | rNSW | rank_mean | match_rank |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| assembly_4 | MA0835.3 | assembly_4 | BATF3 | 0.952 | 0.555 | 4.935 | 0.970 | 0.93480 | 12 | 7 | 7 | 12 | 0.5833 | 0.5833 | 1.0000 | R | 4 | ....TGAGTCa. | TGAGTCA | 1 | 4 | 9 | 1 | 1 | 3.2000 | 1 |
| assembly_4 | MA1988.2 | assembly_4 | Atf3 | 0.947 | 0.552 | 4.839 | 0.969 | 0.93356 | 12 | 7 | 7 | 12 | 0.5833 | 0.5833 | 1.0000 | R | 4 | ....TGAGTCa. | TGAGTCA | 2 | 5 | 11 | 2 | 2 | 4.4000 | 2 |
| assembly_5 | MA0676.1 | assembly_5 | Nr2e1 | 0.930 | 0.572 | 5.991 | 0.964 | 0.93319 | 12 | 9 | 8 | 13 | 0.6154 | 0.6667 | 0.8889 | D | -1 | wrAGTCAA.... | .aAAGTCAA | 6 | 3 | 4 | 3 | 6 | 4.4000 | 3 |
| assembly_4 | MA0462.3 | assembly_4 | BATF::JUN | 0.946 | 0.552 | 4.945 | 0.968 | 0.93266 | 12 | 7 | 7 | 12 | 0.5833 | 0.5833 | 1.0000 | R | 4 | ....TGAGTCa. | TGAGTCA | 3 | 6 | 8 | 4 | 3 | 4.8000 | 4 |
| assembly_4 | MA1928.2 | assembly_4 | BNC2 | 0.945 | 0.551 | 5.252 | 0.968 | 0.93248 | 12 | 7 | 7 | 12 | 0.5833 | 0.5833 | 1.0000 | D | 4 | ....TGAGTCa. | TGAGTCA | 4 | 7 | 6 | 5 | 4 | 5.2000 | 5 |
| assembly_4 | MA1634.2 | assembly_4 | BATF | 0.944 | 0.551 | 4.891 | 0.968 | 0.93198 | 12 | 7 | 7 | 12 | 0.5833 | 0.5833 | 1.0000 | R | 4 | ....TGAGTCa. | TGAGTCA | 5 | 8 | 10 | 6 | 5 | 6.8000 | 6 |
| assembly_3 | MA2341.1 | assembly_3 | FEZF2 | 0.916 | 0.666 | 5.165 | 0.957 | 0.92664 | 11 | 8 | 8 | 11 | 0.7273 | 0.7273 | 1.0000 | D | 2 | ..CCCAGCCh. | CCCAGCCT | 10 | 1 | 7 | 8 | 9 | 7.0000 | 7 |
| assembly_1 | MA1986.2 | assembly_1 | ZNF692 | 0.930 | 0.620 | 2.948 | 0.960 | 0.92941 | 12 | 8 | 8 | 12 | 0.6667 | 0.6667 | 1.0000 | R | 3 | ...CTGGGCCm. | STGGGCCC | 7 | 2 | 13 | 7 | 7 | 7.2000 | 8 |
| assembly_2 | MA1519.2 | assembly_2 | LHX5 | 0.926 | 0.540 | 6.723 | 0.958 | 0.92281 | 12 | 7 | 7 | 12 | 0.5833 | 0.5833 | 1.0000 | D | 0 | rwAATTA..... | sYAATTA | 8 | 9 | 2 | 9 | 8 | 7.2000 | 9 |
| assembly_2 | MA0889.2 | assembly_2 | GBX1 | 0.920 | 0.536 | 6.393 | 0.957 | 0.92146 | 12 | 7 | 7 | 12 | 0.5833 | 0.5833 | 1.0000 | D | 0 | rwAATTA..... | syAATTA | 9 | 10 | 3 | 10 | 10 | 8.4000 | 10 |
| assembly_2 | MA0075.4 | assembly_2 | PRRX2 | 0.908 | 0.530 | 6.754 | 0.948 | 0.91412 | 12 | 7 | 7 | 12 | 0.5833 | 0.5833 | 1.0000 | D | 0 | rwAATTA..... | cyAATTA | 11 | 11 | 1 | 12 | 12 | 9.4000 | 11 |
| assembly_2 | MA0644.3 | assembly_2 | ESX1 | 0.908 | 0.530 | 5.860 | 0.953 | 0.91824 | 12 | 7 | 7 | 12 | 0.5833 | 0.5833 | 1.0000 | D | 0 | rwAATTA..... | yyAATTA | 12 | 12 | 5 | 11 | 11 | 10.2000 | 12 |
| assembly_2 | MA0621.2 | assembly_2 | mix-a | 0.903 | 0.527 | 3.905 | 0.939 | 0.90661 | 12 | 7 | 7 | 12 | 0.5833 | 0.5833 | 1.0000 | R | 1 | .wAATTAA.... | TAATTAA | 13 | 13 | 12 | 13 | 13 | 12.8000 | 13 |
Host name rsat Job started 2026-03-29.155110 Job done 2026-03-29.155126 Seconds 9.95 user 9.95 system 0.52 cuser 5.15 ; csystem 0.68