One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184256_2025-05-16.184256_DOHBqC/results/discovered_motifs/oligos_6nt_mkv1_m1/peak-motifs_oligos_6nt_mkv1_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/2025/05/16/peak-motifs.2025-05-16.184256_2025-05-16.184256_DOHBqC/results/discovered_motifs/oligos_6nt_mkv1_m1/peak-motifs_oligos_6nt_mkv1_m1_vs_db_JASPAR2024_CORE_vertebrates_non-redundant
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1) |
 |
|
|
; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=13; shift=0; ncol=13; mAGCCAGCCAGCC
; Alignment reference
a 32 59 1 1 1 63 1 0 0 62 1 2 3
c 33 0 8 62 63 1 8 65 63 0 0 58 58
g 0 5 56 1 0 0 56 0 1 3 64 4 3
t 0 1 0 1 1 1 0 0 1 0 0 1 1
|
| MA2341.1_shift2 (FEZF2) |
 |
|
|
; oligos_6nt_mkv1_m1 versus MA2341.1 (FEZF2); m=1/1; ncol2=8; w=0; offset=2; strand=D; shift=2; score=0.432688; --CCCAGCCT---
; cor=; Ncor=
a 0 0 17.0 5.0 4.0 231.0 6.0 8.0 7.0 14.0 0 0 0
c 0 0 202.0 206.0 258.0 15.0 8.0 224.0 247.0 10.0 0 0 0
g 0 0 10.0 9.0 0.0 14.0 251.0 28.0 2.0 8.0 0 0 0
t 0 0 36.0 45.0 3.0 5.0 0.0 5.0 9.0 233.0 0 0 0
|