compare-matrices -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.092437_5FrWdl/compare-matrices_query_matrices.transfac -file2 $RSAT/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.092437_5FrWdl/custom_motif_file.tf -format2 transfac -strand DR -lth cor 0.7 -lth Ncor 0.4 -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/2026/04/21/compare-matrices_2026-04-21.092437_5FrWdl/compare-matrices.tab Program version 1.118 Slow mode Input files file2 $RSAT/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.092437_5FrWdl/custom_motif_file.tf file1 $RSAT/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.092437_5FrWdl/compare-matrices_query_matrices.transfac Output files match_table_txt $RSAT/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.092437_5FrWdl/compare-matrices.tab alignments_1ton_html $RSAT/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.092437_5FrWdl/compare-matrices_alignments_1ton.html prefix $RSAT/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.092437_5FrWdl/compare-matrices match_table_html $RSAT/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.092437_5FrWdl/compare-matrices.html html_index $RSAT/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.092437_5FrWdl/compare-matrices_index.html alignments_1ton $RSAT/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.092437_5FrWdl/compare-matrices_alignments_1ton.tab Matrices file1 7 matrices $RSAT/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.092437_5FrWdl/compare-matrices_query_matrices.transfac file1 1 11 6 yyGAACCGAks file1 2 10 2 CCCGCTACCG file1 3 14 3 GAGGAGTGAGATTA file1 4 11 6 vbwCTTTCksy file1 5 22 3 CGCCGAACCGATCCGGGACGGC file1 6 11 4 msGAGAGAArG file1 7 13 2 CCGGAAGGCACTC file2 10 matrices $RSAT/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.092437_5FrWdl/custom_motif_file.tf file2 1 10 3 wbCAGCAsrw file2 2 11 7 hmGAGAGGAms file2 3 10 4 vSAAGGAGhW file2 4 10 4 ndMTCGGSSb file2 5 10 4 bsACRTAGrn file2 6 13 4 hnMGAGAGGAAsm file2 7 11 3 hbCAGmTCAvs file2 8 12 1 CAAGGAGCAGCA file2 9 11 2 rsCCCGATCyT file2 10 11 1 GCCGCGTACTG 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| oligos_7nt_mkv1_m3 | oligos_6nt_mkv1_m2 | oligos_7nt_mkv1_m3 | oligos_6nt_mkv1_m2 | 0.759 | 0.759 | 12.071 | 0.861 | 0.88772 | 11 | 11 | 11 | 11 | 1.0000 | 1.0000 | 1.0000 | D | 0 | msGAGAGAArG | hmGAGAGGAms | 1 | 1 | 2 | 1 | 1 | 1.2000 | 1 |
| oligos_7nt_mkv1_m3 | oligos_7nt_mkv1_m1 | oligos_7nt_mkv1_m3 | oligos_7nt_mkv1_m1 | 0.729 | 0.617 | 12.706 | 0.835 | 0.87761 | 11 | 13 | 11 | 13 | 0.8462 | 1.0000 | 0.8462 | D | -1 | msGAGAGAArG | .nMGAGAGGAAs. | 2 | 2 | 1 | 2 | 2 | 1.8000 | 2 |
Host name rsat Job started 2026-04-21.092437 Job done 2026-04-21.092437 Seconds 0.36 user 0.36 system 0.04 cuser 0.34 ; csystem 0.06