# 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_m4/peak-motifs_oligos_6-8nt_m4.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_m4/peak-motifs_oligos_6-8nt_m4_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m4_shift0 (oligos_6-8nt_m4) |  |  |  |
    ; oligos_6-8nt_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; cvCACTCACccw
    ; Alignment reference
    a	116	153	37	516	8	44	7	512	11	93	146	166
    c	270	157	494	19	574	31	550	11	554	345	226	145
    g	74	151	29	20	4	15	7	22	13	38	103	116
    t	134	133	34	39	8	504	30	49	16	118	119	167
z_rc_shift2 (z_rc) |  |  |  |
    ; oligos_6-8nt_m4 versus z_rc; m=1/1; ncol2=6; w=0; offset=2; strand=R; shift=2; score=0.480791; --CaCTCA----
    ; cor=; Ncor=
    a	0	0	5.12195	24.5854	0	0	0	29.7073	0	0	0	0
    c	0	0	30.7317	0	42	0	42	3.07317	0	0	0	0
    g	0	0	5.12195	10.2439	0	0	0	7.17073	0	0	0	0
    t	0	0	1.02439	7.17073	0	42	0	2.04878	0	0	0	0