# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/02/26/peak-motifs.2026-02-26.135827_2026-02-26.135827_NiTe41/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1.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/2026/02/26/peak-motifs.2026-02-26.135827_2026-02-26.135827_NiTe41/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_vs_db_ArabidopsisPBM

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1) |  |  |  |
    ; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=13; shift=0; ncol=13; ytcACCAACCCmm
    ; Alignment reference
    a	9	11	11	46	0	0	44	45	11	1	11	19	18
    c	14	6	27	1	50	47	1	2	38	42	34	18	17
    g	4	7	5	0	0	1	1	2	1	0	4	5	7
    t	23	26	7	3	0	2	4	1	0	7	1	8	8
7237_MYB111_2_ArabidopsisPBM_20140210__rc_shift1 (7237_MYB111_2_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; oligos_6nt_mkv2_m1 versus 7237_MYB111_2_ArabidopsisPBM_20140210__rc; m=1/5; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.613959; -cYAMCwACCt--
    ; cor=; Ncor=
    a	0	13	0	97	26	0	37	99	14	1	22	0	0
    c	0	58	68	0	73	98	3	1	85	93	11	0	0
    g	0	13	2	1	1	0	1	0	0	0	10	0	0
    t	0	16	30	2	0	2	59	0	1	6	57	0	0
7242_MYB55_ArabidopsisPBM_20140210__shift2 (7242_MYB55_ArabidopsisPBM_20140210_) |  |  |  |
    ; oligos_6nt_mkv2_m1 versus 7242_MYB55_ArabidopsisPBM_20140210_; m=2/5; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.601847; --yACCTAMCGv-
    ; cor=; Ncor=
    a	0	0	11	98	5	0	23	98	27	0	12	25	0
    c	0	0	36	0	95	99	5	0	73	96	5	28	0
    g	0	0	5	2	0	0	2	2	0	0	76	30	0
    t	0	0	48	0	0	1	70	0	0	4	7	17	0
7236_MYB111_ArabidopsisPBM_20140210__rc_shift1 (7236_MYB111_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; oligos_6nt_mkv2_m1 versus 7236_MYB111_ArabidopsisPBM_20140210__rc; m=3/5; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.578132; -syACCTAmCh--
    ; cor=; Ncor=
    a	0	15	5	99	13	0	11	98	36	1	34	0	0
    c	0	46	39	0	85	98	1	0	64	76	28	0	0
    g	0	32	3	0	1	0	1	2	0	0	10	0	0
    t	0	7	53	1	1	2	87	0	0	23	28	0	0
7238_MYB46_ArabidopsisPBM_20140210__rc_shift1 (7238_MYB46_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; oligos_6nt_mkv2_m1 versus 7238_MYB46_ArabidopsisPBM_20140210__rc; m=4/5; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.569328; -yyACCTAmCt--
    ; cor=; Ncor=
    a	0	15	4	96	9	0	12	98	61	1	20	0	0
    c	0	37	36	0	91	100	1	0	39	91	22	0	0
    g	0	22	2	4	0	0	3	1	0	0	16	0	0
    t	0	26	58	0	0	0	84	1	0	8	42	0	0
7243_MYB55_2_ArabidopsisPBM_20140210__rc_shift4 (7243_MYB55_2_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; oligos_6nt_mkv2_m1 versus 7243_MYB55_2_ArabidopsisPBM_20140210__rc; m=5/5; ncol2=10; w=0; offset=4; strand=R; shift=4; score=0.459937; ----cCAmCCAMC
    ; cor=; Ncor=
    a	0	0	0	0	13	2	96	54	1	17	91	28	2
    c	0	0	0	0	62	83	2	44	98	69	0	70	89
    g	0	0	0	0	11	5	0	1	0	3	8	1	1
    t	0	0	0	0	14	10	2	1	1	11	1	1	8