; compare-matrices -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.093227_5guD2o/compare-matrices_query_matrices.transfac -file2 $RSAT/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.093227_5guD2o/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_2026-04-21.093227_5guD2o/compare-matrices.tab ; Program version 1.118 ; Slow mode ; Input files ; file2 /var/www/html/rsat/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.093227_5guD2o/custom_motif_file.tf ; file1 /var/www/html/rsat/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.093227_5guD2o/compare-matrices_query_matrices.transfac ; Output files ; prefix /var/www/html/rsat/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.093227_5guD2o/compare-matrices ; match_table_txt /var/www/html/rsat/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.093227_5guD2o/compare-matrices.tab ; match_table_html /var/www/html/rsat/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.093227_5guD2o/compare-matrices.html ; alignments_1ton /var/www/html/rsat/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.093227_5guD2o/compare-matrices_alignments_1ton.tab ; html_index /var/www/html/rsat/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.093227_5guD2o/compare-matrices_index.html ; alignments_1ton_html /var/www/html/rsat/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.093227_5guD2o/compare-matrices_alignments_1ton.html ; Matrices ; file1 7 matrices /var/www/html/rsat/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.093227_5guD2o/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 /var/www/html/rsat/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.093227_5guD2o/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 2026-04-21.093228 ; Job done 2026-04-21.093228 ; Seconds 0.32 ; user 0.32 ; system 0.04 ; cuser 0.41 ; csystem 0.05