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.2026-01-05.125527_2026-01-05.125527_ogDb5d/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.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.2026-01-05.125527_2026-01-05.125527_ogDb5d/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant
One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| positions_6nt_m3_shift0 (positions_6nt_m3) |
 |
|
|
; positions_6nt_m3; m=0 (reference); ncol1=14; shift=0; ncol=14; awAcATATATgTwt
; Alignment reference
a 4863 3175 10539 1420 11163 1114 9757 1021 9453 467 2247 619 4059 3027
c 1852 2994 433 8000 252 922 573 847 709 316 531 607 1970 2456
g 2456 1970 607 531 316 709 847 573 922 252 8000 433 2994 1852
t 3027 4059 619 2247 467 9453 1021 9757 1114 11163 1420 10539 3175 4863
|
| MA0461.3_shift1 (Atoh1) |
 |
|
|
; positions_6nt_m3 versus MA0461.3 (Atoh1); m=1/1; ncol2=8; w=0; offset=1; strand=D; shift=1; score=0.41037; -rmCATATG-----
; cor=; Ncor=
a 0 655.0 523.0 42.0 1027.0 17.0 1027.0 22.0 2.0 0 0 0 0 0
c 0 108.0 334.0 1027.0 20.0 10.0 74.0 4.0 1.0 0 0 0 0 0
g 0 372.0 149.0 8.0 34.0 136.0 0.0 5.0 1027.0 0 0 0 0 0
t 0 59.0 21.0 0.0 0.0 1027.0 0.0 1027.0 31.0 0 0 0 0 0
|