One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/06/23/peak-motifs.2025-06-23.130112_2025-06-23.130112_48tvdX/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -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/2025/06/23/peak-motifs.2025-06-23.130112_2025-06-23.130112_48tvdX/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)				; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=24; shift=0; ncol=24; CTGCGCTGCCCTGGAGGTCGAACC ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 c 1 0 0 1 0 1 0 0 1 1 1 0 0 0 0 0 0 0 1 0 0 0 1 1 g 0 0 1 0 1 0 0 1 0 0 0 0 1 1 0 1 1 0 0 1 0 0 0 0 t 0 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)				; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/1; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; CTGCGCTGCCCTGGAGGTCGAACC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 c 1 0 0 1 0 1 0 0 1 1 1 0 0 0 0 0 0 0 1 0 0 0 1 1 g 0 0 1 0 1 0 0 1 0 0 0 0 1 1 0 1 1 0 0 1 0 0 0 0 t 0 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m2_shift0 (oligos_6nt_mkv1_m2)				; oligos_6nt_mkv1_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; yGswGsyCkrr ; Alignment reference a 0 0 0 1 0 0 0 0 0 1 1 c 1 0 1 0 0 1 1 2 0 0 0 g 0 2 1 0 2 1 0 0 1 1 1 t 1 0 0 1 0 0 1 0 1 0 0
oligos_6nt_mkv1_m2_shift0 (oligos_6nt_mkv1_m2)				; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; yGswGsyCkrr ; cor=; Ncor= a 0 0 0 1 0 0 0 0 0 1 1 c 1 0 1 0 0 1 1 2 0 0 0 g 0 2 1 0 2 1 0 0 1 1 1 t 1 0 0 1 0 0 1 0 1 0 0