One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.125020_2026-01-05.125020_w7RQpp/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt -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/2026/01/05/peak-motifs.2026-01-05.125020_2026-01-05.125020_w7RQpp/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_JASPAR2024_CORE_vertebrates_non-redundant
One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| positions_7nt_m1_shift0 (positions_7nt_m1) |
 |
|
|
; positions_7nt_m1; m=0 (reference); ncol1=24; shift=0; ncol=24; sssCcCCGCCCsCgCCGCCcCsss
; Alignment reference
a 843 1107 410 341 363 289 475 338 304 316 406 335 276 355 243 416 307 311 296 369 454 434 900 878
c 5110 4208 2813 7811 6499 7203 7355 1843 7537 7461 7040 3173 8164 2319 7857 7714 1844 7761 7216 6517 7462 2951 4289 4584
g 2825 3503 5863 1172 2315 1830 1456 7037 1482 1602 1945 5682 1042 6465 1334 1216 6863 1255 1679 2315 1398 5777 3620 3245
t 968 928 660 422 569 424 460 528 423 367 355 556 264 607 312 400 732 419 555 545 432 584 937 1039
|
| MA1961.2_rc_shift2 (PATZ1_rc) |
 |
|
|
; positions_7nt_m1 versus MA1961.2_rc (PATZ1_rc); m=1/1; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.403675; --sCCCCkCCCCs-----------
; cor=; Ncor=
a 0 0 34.0 1.0 1.0 1.0 1.0 155.0 1.0 1.0 1.0 24.0 44.0 0 0 0 0 0 0 0 0 0 0 0
c 0 0 523.0 944.0 964.0 957.0 997.0 1.0 997.0 997.0 727.0 680.0 543.0 0 0 0 0 0 0 0 0 0 0 0
g 0 0 392.0 1.0 34.0 41.0 1.0 489.0 1.0 1.0 78.0 228.0 288.0 0 0 0 0 0 0 0 0 0 0 0
t 0 0 51.0 54.0 1.0 1.0 1.0 355.0 1.0 1.0 195.0 68.0 125.0 0 0 0 0 0 0 0 0 0 0 0
|