# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.174600_2025-05-16.174600_au3zWU/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/2025/05/16/peak-motifs.2025-05-16.174600_2025-05-16.174600_au3zWU/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2) |  |  |  |
    ; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; mwAAACAAAwh
    ; Alignment reference
    a	9	17	31	30	29	0	32	34	30	14	10
    c	14	3	0	1	2	34	2	0	4	3	13
    g	7	5	0	1	1	0	0	0	0	3	2
    t	4	9	3	2	2	0	0	0	0	14	9
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2) |  |  |  |
    ; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; mwAAACAAAwh
    ; cor=; Ncor=
    a	9	17	31	30	29	0	32	34	30	14	10
    c	14	3	0	1	2	34	2	0	4	3	13
    g	7	5	0	1	1	0	0	0	0	3	2
    t	4	9	3	2	2	0	0	0	0	14	9

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1) |  |  |  |
    ; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; mtCCCAGCAas
    ; Alignment reference
    a	17	8	5	1	0	40	1	0	44	19	8
    c	13	8	40	40	41	2	1	41	0	8	12
    g	8	7	0	1	0	1	41	2	0	8	17
    t	7	22	0	3	4	2	2	2	1	10	8
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1) |  |  |  |
    ; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; mtCCCAGCAas
    ; cor=; Ncor=
    a	17	8	5	1	0	40	1	0	44	19	8
    c	13	8	40	40	41	2	1	41	0	8	12
    g	8	7	0	1	0	1	41	2	0	8	17
    t	7	22	0	3	4	2	2	2	1	10	8

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3) |  |  |  |
    ; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; myAGCCAATww
    ; Alignment reference
    a	11	4	26	1	2	2	25	26	4	9	8
    c	7	8	1	1	22	24	0	1	0	5	6
    g	3	4	0	25	1	0	1	0	0	5	3
    t	6	11	0	0	2	1	1	0	23	8	10
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3) |  |  |  |
    ; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; myAGCCAATww
    ; cor=; Ncor=
    a	11	4	26	1	2	2	25	26	4	9	8
    c	7	8	1	1	22	24	0	1	0	5	6
    g	3	4	0	25	1	0	1	0	0	5	3
    t	6	11	0	0	2	1	1	0	23	8	10