compare-matrices -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.163848_zCfwD2/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/2026/01/09/compare-matrices_2026-01-09.163848_zCfwD2/compare-matrices.tab Program version 1.118 Slow mode Input files file1 $RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.163848_zCfwD2/compare-matrices_query_matrices.transfac file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf Output files alignments_1ton_html $RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.163848_zCfwD2/compare-matrices_alignments_1ton.html html_index $RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.163848_zCfwD2/compare-matrices_index.html match_table_html $RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.163848_zCfwD2/compare-matrices.html match_table_txt $RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.163848_zCfwD2/compare-matrices.tab prefix $RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.163848_zCfwD2/compare-matrices alignments_1ton $RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.163848_zCfwD2/compare-matrices_alignments_1ton.tab Matrices file1 1 matrices $RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.163848_zCfwD2/compare-matrices_query_matrices.transfac file1 1 12 1476 wwATACGTATww file2 3346 matrices $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 ... 3336 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| cluster_5 | bZIP65_EEAD0071_EEADannot | cluster_5 | bZIP65:EEAD0071:EEADannot | 0.988 | 0.494 | 6.670 | 0.982 | 0.94554 | 12 | 6 | 6 | 12 | 0.5000 | 0.5000 | 1.0000 | D | 3 | ...TACGTA... | TACGTA | 1 | 4 | 1 | 1 | 1 | 1.6000 | 1 |
| cluster_5 | ANAC55_ANAC55_2_ArabidopsisPBM | cluster_5 | ANAC55:ANAC55_2:ArabidopsisPBM | 0.740 | 0.617 | 3.436 | 0.896 | 0.89809 | 12 | 10 | 10 | 12 | 0.8333 | 0.8333 | 1.0000 | D | 1 | .wATACGTATw. | rwTACGTAwy | 4 | 1 | 4 | 2 | 4 | 3.0000 | 2 |
| cluster_5 | ARR18_MA0948.2_JASPAR | cluster_5 | ARR18:MA0948.2:JASPAR | 0.818 | 0.477 | 3.426 | 0.918 | 0.89209 | 12 | 7 | 7 | 12 | 0.5833 | 0.5833 | 1.0000 | D | 0 | wwATACG..... | AGATAcG | 2 | 5 | 5 | 3 | 2 | 3.4000 | 3 |
| cluster_5 | ZFHD10-3_EEAD0065_EEADannot | cluster_5 | ZFHD10-3:EEAD0065:EEADannot | 0.710 | 0.592 | 5.719 | 0.851 | 0.87787 | 12 | 10 | 10 | 12 | 0.8333 | 0.8333 | 1.0000 | D | 1 | .wATACGTATw. | TATATATATA | 5 | 2 | 2 | 6 | 6 | 4.2000 | 4 |
| cluster_5 | AtHB32.DAP_M0856_AthalianaCistrome | cluster_5 | AtHB32.DAP:M0856:AthalianaCistrome | 0.700 | 0.539 | 3.456 | 0.880 | 0.89040 | 12 | 11 | 10 | 13 | 0.7692 | 0.8333 | 0.9091 | D | 2 | ..ATACGTATww | wwwCGhATwW. | 6 | 3 | 3 | 4 | 5 | 4.2000 | 5 |
| cluster_5 | ARR11_MA0946.1_JASPAR | cluster_5 | ARR11:MA0946.1:JASPAR | 0.815 | 0.439 | 2.644 | 0.897 | 0.87870 | 12 | 8 | 7 | 13 | 0.5385 | 0.5833 | 0.8750 | R | 5 | .....CGTATww | CGTATCT. | 3 | 6 | 6 | 5 | 3 | 4.6000 | 6 |
Host name rsat Job started 2026-01-09.163848 Job done 2026-01-09.163900 Seconds 10.65 user 10.65 system 0.31 cuser 0.93 ; csystem 0.28