# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.180941_2026-01-25.180941_K9UVGH/results/discovered_motifs/oligos_6-8nt_m3/peak-motifs_oligos_6-8nt_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.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/2026/01/25/peak-motifs.2026-01-25.180941_2026-01-25.180941_K9UVGH/results/discovered_motifs/oligos_6-8nt_m3/peak-motifs_oligos_6-8nt_m3_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3) |  |  |  |
    ; oligos_6-8nt_m3; m=0 (reference); ncol1=14; shift=0; ncol=14; wygaATCGATtcgw
    ; Alignment reference
    a	150	135	100	346	500	15	17	13	517	41	114	79	141	169
    c	131	157	107	66	18	18	525	10	18	7	42	283	129	120
    g	119	130	283	42	7	18	12	527	18	15	67	107	160	129
    t	167	145	77	113	42	516	13	17	14	504	344	98	137	149
Dref_shift2 (Dref) |  |  |  |
    ; oligos_6-8nt_m3 versus Dref; m=1/1; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.508009; --aTAwCGATAr--
    ; cor=; Ncor=
    a	0	0	6.66667	1.11111	7.77778	3.33333	0	1.11111	10	0	7.77778	3.33333	0	0
    c	0	0	1.11111	0	1.11111	0	10	0	0	0	1.11111	0	0	0
    g	0	0	0	1.11111	0	0	0	8.88889	0	0	1.11111	6.66667	0	0
    t	0	0	2.22222	7.77778	1.11111	6.66667	0	0	0	10	0	0	0	0