# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.142119_2026-03-30.142119_XX18DY/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/2026/03/30/peak-motifs.2026-03-30.142119_2026-03-30.142119_XX18DY/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_test_vs_ctrl_m1_shift0 (dyads_test_vs_ctrl_m1) |  |  |  |
    ; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; twCTTtwAAAwt
    ; Alignment reference
    a	11	12	0	0	0	11	21	47	47	47	20	10
    c	4	9	47	0	0	7	2	0	0	0	10	7
    g	10	9	0	0	0	8	10	0	0	0	5	9
    t	22	17	0	47	47	21	14	0	0	0	12	21
dyads_test_vs_ctrl_m1_shift0 (dyads_test_vs_ctrl_m1) |  |  |  |
    ; dyads_test_vs_ctrl_m1 versus dyads_test_vs_ctrl_m1; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; twCTTtwAAAwt
    ; cor=; Ncor=
    a	11	12	0	0	0	11	21	47	47	47	20	10
    c	4	9	47	0	0	7	2	0	0	0	10	7
    g	10	9	0	0	0	8	10	0	0	0	5	9
    t	22	17	0	47	47	21	14	0	0	0	12	21

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1) |  |  |  |
    ; oligos_6-8nt_m1; m=0 (reference); ncol1=10; shift=0; ncol=10; awAGTAGGww
    ; Alignment reference
    a	13	12	20	0	3	24	0	0	8	10
    c	3	1	3	0	1	2	0	1	3	6
    g	5	6	1	26	1	0	26	25	4	2
    t	5	7	2	0	21	0	0	0	11	8
oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1) |  |  |  |
    ; oligos_6-8nt_m1 versus oligos_6-8nt_m1; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score=      1; awAGTAGGww
    ; cor=; Ncor=
    a	13	12	20	0	3	24	0	0	8	10
    c	3	1	3	0	1	2	0	1	3	6
    g	5	6	1	26	1	0	26	25	4	2
    t	5	7	2	0	21	0	0	0	11	8