One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/04/21/peak-motifs.2026-04-21.015247_2026-04-21.015247_DTyOML/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/2026/04/21/peak-motifs.2026-04-21.015247_2026-04-21.015247_DTyOML/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift2 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=11; shift=2; ncol=13; --vwAAAATTCwr ; Alignment reference a 0 0 22 27 81 75 78 79 0 11 4 23 24 c 0 0 24 14 1 0 1 2 0 0 78 2 12 g 0 0 22 6 0 0 0 1 1 0 0 17 37 t 0 0 14 35 0 7 3 0 81 71 0 40 9
positions_6nt_m1_shift2 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --vwAAAATTCwr ; cor=; Ncor= a 0 0 22 27 81 75 78 79 0 11 4 23 24 c 0 0 24 14 1 0 1 2 0 0 78 2 12 g 0 0 22 6 0 0 0 1 1 0 0 17 37 t 0 0 14 35 0 7 3 0 81 71 0 40 9
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m1 versus positions_6nt_m2; m=2/2; ncol2=10; w=-2; offset=-2; strand=D; shift=0; score=0.466699; twAAAAAAww--- ; cor=; Ncor= a 115 130 507 507 507 507 507 507 130 182 0 0 0 c 104 118 0 0 0 0 0 0 60 108 0 0 0 g 119 105 0 0 0 0 0 0 56 46 0 0 0 t 169 154 0 0 0 0 0 0 261 171 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=10; shift=0; ncol=10; twAAAAAAww ; Alignment reference a 115 130 507 507 507 507 507 507 130 182 c 104 118 0 0 0 0 0 0 60 108 g 119 105 0 0 0 0 0 0 56 46 t 169 154 0 0 0 0 0 0 261 171
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; twAAAAAAww ; cor=; Ncor= a 115 130 507 507 507 507 507 507 130 182 c 104 118 0 0 0 0 0 0 60 108 g 119 105 0 0 0 0 0 0 56 46 t 169 154 0 0 0 0 0 0 261 171
positions_6nt_m1_shift2 (positions_6nt_m1)				; positions_6nt_m2 versus positions_6nt_m1; m=2/2; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.466699; --vwAAAATT ; cor=; Ncor= a 0 0 22 27 81 75 78 79 0 11 c 0 0 24 14 1 0 1 2 0 0 g 0 0 22 6 0 0 0 1 1 0 t 0 0 14 35 0 7 3 0 81 71