compare-matrices -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/09/15/compare-matrices_2025-09-15.163721_GCEzmB/compare-matrices_query_matrices.transfac -file2 $RSAT/public_html/motif_databases/ArabidopsisPBM/ArabidopsisPBM_2015-11-06.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/2025/09/15/compare-matrices_2025-09-15.163721_GCEzmB/compare-matrices.tab Program version 1.118 Slow mode Input files file2 $RSAT/public_html/motif_databases/ArabidopsisPBM/ArabidopsisPBM_2015-11-06.tf file1 $RSAT/public_html/tmp/www-data/2025/09/15/compare-matrices_2025-09-15.163721_GCEzmB/compare-matrices_query_matrices.transfac Output files html_index $RSAT/public_html/tmp/www-data/2025/09/15/compare-matrices_2025-09-15.163721_GCEzmB/compare-matrices_index.html alignments_1ton $RSAT/public_html/tmp/www-data/2025/09/15/compare-matrices_2025-09-15.163721_GCEzmB/compare-matrices_alignments_1ton.tab alignments_1ton_html $RSAT/public_html/tmp/www-data/2025/09/15/compare-matrices_2025-09-15.163721_GCEzmB/compare-matrices_alignments_1ton.html prefix $RSAT/public_html/tmp/www-data/2025/09/15/compare-matrices_2025-09-15.163721_GCEzmB/compare-matrices match_table_txt $RSAT/public_html/tmp/www-data/2025/09/15/compare-matrices_2025-09-15.163721_GCEzmB/compare-matrices.tab match_table_html $RSAT/public_html/tmp/www-data/2025/09/15/compare-matrices_2025-09-15.163721_GCEzmB/compare-matrices.html Matrices file1 13 matrices $RSAT/public_html/tmp/www-data/2025/09/15/compare-matrices_2025-09-15.163721_GCEzmB/compare-matrices_query_matrices.transfac file1 1 14 497 wdGcAGAGAGAcww file1 2 17 544 dwtGAAGAAGArGArra file1 3 11 412 hdCCGGCGAww file1 4 12 394 daAGCAGCAGmw file1 5 13 105 wwTGAGCTTCCww file1 6 11 3312 waACCACAAww file1 7 12 422 wwTGAGCTGAww file1 8 10 951 waAGAAAGww file1 9 10 1043 wwCAAAAGww file1 10 10 263 waAGGACAwd file1 11 11 2159 wwTCTGAGAww ... 3 more matrices file2 108 matrices $RSAT/public_html/motif_databases/ArabidopsisPBM/ArabidopsisPBM_2015-11-06.tf file2 1 10 100 wAAwwwwTTw file2 2 10 100 rwwAWWTwwT file2 3 10 100 wAwwwwwwTw file2 4 10 100 wAATATATTw file2 5 10 100 hAATTAAwTa file2 6 10 100 tAwwWWwwTa file2 7 10 100 dAwTTAAwTw file2 8 10 100 aAwwWWwwTw file2 9 10 100 waWwWwAwTw file2 10 10 100 tayACGcmAy file2 11 10 100 wACACGTAAy ... 98 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| tcp4_c1_m11_assembly_11 | 7207_At4g35610_ArabidopsisPBM_20140210_ | assembly_11 | 7207_At4g35610_ArabidopsisPBM_20140210_ | 0.795 | 0.662 | 2.898 | 0.920 | 0.91064 | 12 | 10 | 10 | 12 | 0.8333 | 0.8333 | 1.0000 | D | 1 | .wTGAGCTGAw. | rkCAGCTGmm | 1 | 1 | 5 | 1 | 1 | 1.8000 | 1 |
| tcp4_c1_m5_assembly_5 | 7203_ATERF1_2_ArabidopsisPBM_20140210_ | assembly_5 | 7203_ATERF1_2_ArabidopsisPBM_20140210_ | 0.737 | 0.553 | 3.906 | 0.887 | 0.88777 | 11 | 10 | 9 | 12 | 0.7500 | 0.8182 | 0.9000 | D | -1 | hdCCGGCGA.. | .tGCCGGCar | 3 | 3 | 4 | 2 | 2 | 2.8000 | 2 |
| tcp4_c1_m16_assembly_16 | 7217_DOF5.7_ArabidopsisPBM_20140210_ | assembly_16 | 7217_DOF5.7_ArabidopsisPBM_20140210_ | 0.738 | 0.492 | 3.989 | 0.869 | 0.87188 | 10 | 10 | 8 | 12 | 0.6667 | 0.8000 | 0.8000 | D | 2 | ..CAAAAGww | raAAArrk.. | 2 | 4 | 2 | 4 | 3 | 3.0000 | 3 |
| tcp4_c1_m14_assembly_14 | 7211_DAG2_ArabidopsisPBM_20140210_ | assembly_14 | 7211_DAG2_ArabidopsisPBM_20140210_ | 0.703 | 0.575 | 6.857 | 0.860 | 0.87514 | 10 | 10 | 9 | 11 | 0.8182 | 0.9000 | 0.9000 | D | 1 | .aAGAAAGww | sAwAARGTg. | 5 | 2 | 1 | 3 | 5 | 3.2000 | 4 |
| tcp4_c1_m14_assembly_14 | 7217_DOF5.7_ArabidopsisPBM_20140210_ | assembly_14 | 7217_DOF5.7_ArabidopsisPBM_20140210_ | 0.730 | 0.487 | 3.975 | 0.864 | 0.86979 | 10 | 10 | 8 | 12 | 0.6667 | 0.8000 | 0.8000 | D | 2 | ..AGAAAGww | raAAArrk.. | 4 | 5 | 3 | 5 | 4 | 4.2000 | 5 |
Host name rsat Job started 2025-09-15.163721 Job done 2025-09-15.163725 Seconds 2.75 user 2.75 system 0.12 cuser 1.15 ; csystem 0.21