# 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.2026-01-25.184326_2026-01-25.184326_ptOhrJ/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.2026-01-25.184326_2026-01-25.184326_ptOhrJ/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=13; shift=0; ncol=13; rgaGAGcGAGAgr
    ; Alignment reference
    a	187	100	341	11	483	23	129	13	478	36	377	93	195
    c	113	94	71	7	9	11	347	7	14	29	64	87	123
    g	141	280	74	497	21	479	30	496	28	423	54	268	145
    t	85	52	40	11	13	13	20	10	6	38	31	78	63
Trl_rc_shift0 (Trl_rc) |  |  |  |
    ; oligos_6-8nt_m4 versus Trl_rc; m=1/1; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.746623; agaGaGAGmrmaA
    ; cor=; Ncor=
    a	42	17	46	7	50	11	62	0	40	26	30	41	57
    c	14	9	6	1	9	8	11	5	27	10	24	13	0
    g	3	47	16	56	12	56	0	72	3	41	19	8	10
    t	18	4	9	13	6	2	4	0	7	0	4	15	10