; compare-matrices -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.151802_2ev0Km/compare-matrices_query_matrices.transfac -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf -format2 tf -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/2026/05/29/compare-matrices_2026-05-29.151802_2ev0Km/compare-matrices.tab ; Program version 1.118 ; Slow mode ; Input files ; file1 /var/www/html/rsat/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.151802_2ev0Km/compare-matrices_query_matrices.transfac ; file2 /var/www/html/rsat/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf ; Output files ; html_index /var/www/html/rsat/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.151802_2ev0Km/compare-matrices_index.html ; match_table_txt /var/www/html/rsat/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.151802_2ev0Km/compare-matrices.tab ; match_table_html /var/www/html/rsat/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.151802_2ev0Km/compare-matrices.html ; alignments_1ton_html /var/www/html/rsat/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.151802_2ev0Km/compare-matrices_alignments_1ton.html ; prefix /var/www/html/rsat/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.151802_2ev0Km/compare-matrices ; alignments_1ton /var/www/html/rsat/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.151802_2ev0Km/compare-matrices_alignments_1ton.tab ; Matrices ; file1 1 matrices /var/www/html/rsat/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.151802_2ev0Km/compare-matrices_query_matrices.transfac ; file1 1 19 21 gmkGCATGwrwcakGCCkw ; file2 3463 matrices /var/www/html/rsat/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf ; file2 1 8 5 awmAGTTr ; file2 2 8 3 rkTAGTTr ; file2 3 8 5 wamaGTTr ; file2 4 8 1 GTTAGTTA ; file2 5 8 2 kwCwGTTr ; file2 6 8 2 GTTAGTTr ; file2 7 8 6 wwmaGTTr ; file2 8 8 2 rsTkGTTr ; file2 9 8 8 RkTwGKTr ; file2 10 8 1 TACTGTTG ; file2 11 8 4 WhhWGTTr ; ... 3453 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 dyads_test_vs_ctrl_m1 LEC2_MA0581.1_JASPAR dyads_test_vs_ctrl_m1 LEC2:MA0581.1:JASPAR 0.878 0.439 0.350 0.952 0.93072 19 11 10 20 0.5000 0.5263 0.9091 R -1 gmkGCATGwr......... .WGYGCATGSA 1 4 4 1 1 2.2000 1 dyads_test_vs_ctrl_m1 AtLEC2_AtLEC2_Athamap dyads_test_vs_ctrl_m1 AtLEC2:AtLEC2:Athamap 0.851 0.448 0.235 0.926 0.91408 19 10 10 19 0.5263 0.5263 1.0000 R 0 gmkGCATGwr......... TTTGCATGRM 2 2 5 3 2 2.8000 2 dyads_test_vs_ctrl_m1 FUS3.DAP_M0003_AthalianaCistrome dyads_test_vs_ctrl_m1 FUS3.DAP:M0003:AthalianaCistrome 0.741 0.459 0.378 0.907 0.91557 19 15 13 21 0.6190 0.6842 0.8667 R -2 gmkGCATGwrwca...... ..YWTGCATGYATDT 4 1 3 2 4 2.8000 3 dyads_test_vs_ctrl_m1 FUS3_MA0565.2_JASPAR dyads_test_vs_ctrl_m1 FUS3:MA0565.2:JASPAR 0.849 0.447 3.776 0.923 0.91217 19 10 10 19 0.5263 0.5263 1.0000 R 1 .mkGCATGwrw........ WTGCATGTDW 3 3 2 4 3 3.0000 4 dyads_test_vs_ctrl_m1 ABI19_B73_1_m1_EEAD0171_EEADannot dyads_test_vs_ctrl_m1 ABI19_B73_1_m1:EEAD0171:EEADannot 0.728 0.421 5.250 0.873 0.89235 19 11 11 19 0.5789 0.5789 1.0000 D 0 gmkGCATGwrw........ CwTGCATGCry 5 5 1 5 5 4.2000 5 ; Host name rsat ; Job started 2026-05-29.151802 ; Job done 2026-05-29.151819 ; Seconds 15.42 ; user 15.42 ; system 0.28 ; cuser 0.75 ; csystem 0.27