# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/results/discovered_motifs/oligos_6nt_mkv1_m4/peak-motifs_oligos_6nt_mkv1_m4.tf -format2 tf -file2 $RSAT/public_html/motif_databases/ArabidopsisPBM/ArabidopsisPBM_2015-11-06.tf -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/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/results/discovered_motifs/oligos_6nt_mkv1_m4/peak-motifs_oligos_6nt_mkv1_m4_vs_db_ArabidopsisPBM

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m4_shift3 ; 6 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv1_m4_shift3 (oligos_6nt_mkv1_m4) |  |  |  |
    ; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=10; shift=3; ncol=13; ---sgAGGTAGwm
    ; Alignment reference
    a	0	0	0	3	3	16	0	0	0	18	0	6	5
    c	0	0	0	7	4	0	0	2	0	0	1	3	5
    g	0	0	0	5	7	0	17	16	0	0	16	4	4
    t	0	0	0	3	4	2	1	0	18	0	1	5	4
7265_STY1_2_ArabidopsisPBM_20140210__rc_shift2 (7265_STY1_2_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; oligos_6nt_mkv1_m4 versus 7265_STY1_2_ArabidopsisPBM_20140210__rc; m=1/5; ncol2=10; w=-1; offset=-1; strand=R; shift=2; score=0.578813; --rCTAGCTAGt-
    ; cor=; Ncor=
    a	0	0	31	3	5	91	2	2	5	91	3	16	0
    c	0	0	8	89	1	0	1	95	4	3	5	20	0
    g	0	0	50	5	3	4	95	1	0	1	89	23	0
    t	0	0	11	3	91	5	2	2	91	5	3	41	0
7237_MYB111_2_ArabidopsisPBM_20140210__shift5 (7237_MYB111_2_ArabidopsisPBM_20140210_) |  |  |  |
    ; oligos_6nt_mkv1_m4 versus 7237_MYB111_2_ArabidopsisPBM_20140210_; m=2/5; ncol2=10; w=0; offset=2; strand=D; shift=5; score=0.526712; -----aGGTwGKT
    ; cor=; Ncor=
    a	0	0	0	0	0	57	6	1	0	59	2	0	2
    c	0	0	0	0	0	10	0	0	0	1	0	1	1
    g	0	0	0	0	0	11	93	85	1	3	98	73	0
    t	0	0	0	0	0	22	1	14	99	37	0	26	97
7236_MYB111_ArabidopsisPBM_20140210__shift1 (7236_MYB111_ArabidopsisPBM_20140210_) |  |  |  |
    ; oligos_6nt_mkv1_m4 versus 7236_MYB111_ArabidopsisPBM_20140210_; m=3/5; ncol2=10; w=-2; offset=-2; strand=D; shift=1; score=0.506784; -dGkTAGGTrs--
    ; cor=; Ncor=
    a	0	28	23	0	0	87	2	1	1	53	7	0	0
    c	0	10	0	0	2	1	0	1	0	3	32	0	0
    g	0	28	76	64	0	1	98	85	0	39	46	0	0
    t	0	34	1	36	98	11	0	13	99	5	15	0	0
7238_MYB46_ArabidopsisPBM_20140210__shift1 (7238_MYB46_ArabidopsisPBM_20140210_) |  |  |  |
    ; oligos_6nt_mkv1_m4 versus 7238_MYB46_ArabidopsisPBM_20140210_; m=4/5; ncol2=10; w=-2; offset=-2; strand=D; shift=1; score=0.499562; -aGkTAGGTrr--
    ; cor=; Ncor=
    a	0	42	8	0	1	84	0	0	0	58	26	0	0
    c	0	16	0	0	1	3	0	0	4	2	22	0	0
    g	0	22	91	39	0	1	100	91	0	36	37	0	0
    t	0	20	1	61	98	12	0	9	96	4	15	0	0
7242_MYB55_ArabidopsisPBM_20140210__rc_shift0 (7242_MYB55_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; oligos_6nt_mkv1_m4 versus 7242_MYB55_ArabidopsisPBM_20140210__rc; m=5/5; ncol2=10; w=-3; offset=-3; strand=R; shift=0; score=0.407551; bCGKTAGGTr---
    ; cor=; Ncor=
    a	17	7	4	0	0	70	1	0	0	48	0	0	0
    c	30	76	0	0	2	2	0	0	2	5	0	0	0
    g	28	5	96	73	0	5	99	95	0	36	0	0	0
    t	25	12	0	27	98	23	0	5	98	11	0	0	0