# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.174416_2025-05-16.174416_Ix0OVW/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.2025-05-16.174416_2025-05-16.174416_Ix0OVW/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1) |  |  |  |
    ; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=11; shift=1; ncol=12; -crCCTCAGCct
    ; Alignment reference
    a	0	9	12	5	2	0	0	34	2	3	7	6
    c	0	11	4	31	35	2	33	3	0	31	14	9
    g	0	8	12	0	0	3	1	0	35	1	7	8
    t	0	9	9	1	0	32	3	0	0	2	9	14
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1) |  |  |  |
    ; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=1; score=      1; -crCCTCAGCct
    ; cor=; Ncor=
    a	0	9	12	5	2	0	0	34	2	3	7	6
    c	0	11	4	31	35	2	33	3	0	31	14	9
    g	0	8	12	0	0	3	1	0	35	1	7	8
    t	0	9	9	1	0	32	3	0	0	2	9	14
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc) |  |  |  |
    ; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1_rc; m=2/2; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.735941; hdGCCTCAGsy-
    ; cor=; Ncor=
    a	7	7	2	0	2	0	0	24	1	5	5	0
    c	10	2	0	28	25	1	27	2	1	10	11	0
    g	3	8	26	0	0	2	0	2	26	9	5	0
    t	8	11	0	0	1	25	1	0	0	4	7	0

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1) |  |  |  |
    ; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=11; shift=1; ncol=12; -rsCTGAGGChd
    ; Alignment reference
    a	0	7	4	0	0	1	25	1	0	0	11	8
    c	0	5	9	26	2	0	2	0	0	26	8	3
    g	0	11	10	1	2	27	1	25	28	0	2	10
    t	0	5	5	1	24	0	0	2	0	2	7	7
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1) |  |  |  |
    ; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=1; score=      1; -rsCTGAGGChd
    ; cor=; Ncor=
    a	0	7	4	0	0	1	25	1	0	0	11	8
    c	0	5	9	26	2	0	2	0	0	26	8	3
    g	0	11	10	1	2	27	1	25	28	0	2	10
    t	0	5	5	1	24	0	0	2	0	2	7	7
oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc) |  |  |  |
    ; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1_rc; m=2/2; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.735941; agGCTGAGGyg-
    ; cor=; Ncor=
    a	14	9	2	0	0	3	32	0	1	9	9	0
    c	8	7	1	35	0	1	3	0	0	12	8	0
    g	9	14	31	0	3	33	2	35	31	4	11	0
    t	6	7	3	2	34	0	0	2	5	12	9	0

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2) |  |  |  |
    ; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; dvCAGATGGkd
    ; Alignment reference
    a	12	13	8	42	3	43	0	1	2	11	13
    c	11	15	33	1	2	0	2	1	2	7	7
    g	12	12	4	2	41	0	0	43	41	12	13
    t	12	7	2	2	1	4	45	2	2	17	14
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2) |  |  |  |
    ; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; dvCAGATGGkd
    ; cor=; Ncor=
    a	12	13	8	42	3	43	0	1	2	11	13
    c	11	15	33	1	2	0	2	1	2	7	7
    g	12	12	4	2	41	0	0	43	41	12	13
    t	12	7	2	2	1	4	45	2	2	17	14