# 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_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2.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_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_vs_db_ArabidopsisPBM

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift0 ; 3 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=12; shift=0; ncol=12; waACGsCGTtwa
    ; Alignment reference
    a	11	12	23	0	1	2	1	1	1	2	11	10
    c	3	5	1	25	0	14	23	0	1	5	0	4
    g	1	5	0	0	24	7	1	23	0	3	1	6
    t	10	3	1	0	0	2	0	1	23	15	13	5
7240_MYB52_ArabidopsisPBM_20140210__rc_shift4 (7240_MYB52_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; oligos_7nt_mkv2_m2 versus 7240_MYB52_ArabidopsisPBM_20140210__rc; m=1/2; ncol2=10; w=0; offset=4; strand=R; shift=4; score=0.418947; ----wCCGTTAg
    ; cor=; Ncor=
    a	0	0	0	0	27	6	7	3	2	3	75	14
    c	0	0	0	0	9	79	79	3	1	4	4	10
    g	0	0	0	0	18	2	5	92	10	1	11	52
    t	0	0	0	0	46	13	9	2	87	92	10	24
7218_DOF5.7_2_ArabidopsisPBM_20140210__shift4 (7218_DOF5.7_2_ArabidopsisPBM_20140210_) |  |  |  |
    ; oligos_7nt_mkv2_m2 versus 7218_DOF5.7_2_ArabidopsisPBM_20140210_; m=2/2; ncol2=10; w=0; offset=4; strand=D; shift=4; score=0.406268; ----awCGTTAA
    ; cor=; Ncor=
    a	0	0	0	0	44	47	2	2	2	1	88	87
    c	0	0	0	0	8	15	94	0	0	1	3	5
    g	0	0	0	0	24	13	2	94	2	2	3	3
    t	0	0	0	0	24	25	2	4	96	96	6	5