compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5_vs_db_footprintDB-plants Program version 1.118 Quick mode Input files file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5.tf Output files alignments_1ton $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5_vs_db_footprintDB-plants_alignments_1ton.tab alignments_1ton_html $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5_vs_db_footprintDB-plants_alignments_1ton.html match_table_html $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5_vs_db_footprintDB-plants.html match_table_txt $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5_vs_db_footprintDB-plants.tab prefix $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5_vs_db_footprintDB-plants html_index $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5_vs_db_footprintDB-plants_index.html Matrices file1 1 matrices $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5.tf file1 1 12 43 file2 2958 matrices $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf file2 1 8 5 file2 2 8 3 file2 3 8 5 file2 4 8 1 file2 5 8 2 file2 6 8 2 file2 7 8 6 file2 8 8 2 file2 9 8 8 file2 10 8 1 file2 11 8 4 ... 2948 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 w1 Width of the first matrix 8 w2 Width of the second matrix 9 w Alignment length (number of overlapping columns between matrix 1 and matrix 2, as a function of the offset) 10 W Total alignment length (overlapping + non-overlapping columns). W = w1 + w2 - w 11 Wr Relative alignment length (overlap divided by the total alignemnt length). Wr = w/W 12 wr1 Alignment length relative to the width of the first matrix. wr1 = w/w1 13 wr2 Alignment length relative to the width of the second matrix. wr2 = w/w2 14 strand "strand", i.e. orientation of matrix 2 relative to matrix 1 (D=direct; R=reverse) 15 offset shift of the second matrix relative to the first matrix (negative:left; positive: right)
| id1 | id2 | name1 | name2 | cor | Ncor | w1 | w2 | w | W | Wr | wr1 | wr2 | strand | offset |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| oligos_8nt_mkv2_m5 | ChCUC1-chipseq/EEAD0152/EEADannot | oligos_8nt_mkv2_m5 | ChCUC1-chipseq:EEAD0152:EEADannot | 0.827 | 0.551 | 12 | 8 | 8 | 12 | 0.6667 | 0.6667 | 1.0000 | R | 0 |
| oligos_8nt_mkv2_m5 | TF3A.DAP/M0328/AthalianaCistrome | oligos_8nt_mkv2_m5 | TF3A.DAP:M0328:AthalianaCistrome | 0.781 | 0.493 | 12 | 19 | 12 | 19 | 0.6316 | 1.0000 | 0.6316 | R | -1 |
| oligos_8nt_mkv2_m5 | AT3G57600/MA1242.1/JASPAR | oligos_8nt_mkv2_m5 | AT3G57600:MA1242.1:JASPAR | 0.708 | 0.455 | 12 | 11 | 9 | 14 | 0.6429 | 0.7500 | 0.8182 | R | -2 |
| oligos_8nt_mkv2_m5 | 3XHMGBOX1.ampDAP/M0425/AthalianaCistrome | oligos_8nt_mkv2_m5 | 3XHMGBOX1.ampDAP:M0425:AthalianaCistrome | 0.768 | 0.452 | 12 | 15 | 10 | 17 | 0.5882 | 0.8333 | 0.6667 | R | -5 |
| oligos_8nt_mkv2_m5 | ONAC127/UN0429.2/JASPAR | oligos_8nt_mkv2_m5 | ONAC127:UN0429.2:JASPAR | 0.721 | 0.421 | 12 | 7 | 7 | 12 | 0.5833 | 0.5833 | 1.0000 | D | 3 |
| oligos_8nt_mkv2_m5 | LBD13/MA2021.2/JASPAR | oligos_8nt_mkv2_m5 | LBD13:MA2021.2:JASPAR | 0.748 | 0.403 | 12 | 8 | 7 | 13 | 0.5385 | 0.5833 | 0.8750 | R | -1 |
Host name rsat Job started 2025-05-21.034016 Job done 2025-05-21.034017 Seconds 1.26 user 1.26 system 0.05 cuser 0.22 ; csystem 0.04