# 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_m9/peak-motifs_oligos_6-8nt_m9.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_m9/peak-motifs_oligos_6-8nt_m9_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m9_shift1 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m9_shift1 (oligos_6-8nt_m9) |  |  |  |
    ; oligos_6-8nt_m9; m=0 (reference); ncol1=14; shift=1; ncol=15; -awAAACAACAAAma
    ; Alignment reference
    a	0	150	129	275	318	329	26	327	321	38	323	323	275	130	125
    c	0	58	64	53	18	16	286	15	14	282	14	19	37	93	66
    g	0	84	70	25	14	9	20	12	17	13	19	16	19	65	88
    t	0	79	108	18	21	17	39	17	19	38	15	13	40	83	92
hb_shift0 (hb) |  |  |  |
    ; oligos_6-8nt_m9 versus hb; m=1/1; ncol2=9; w=-1; offset=-1; strand=D; shift=0; score=0.400658; mayAAAAAa------
    ; cor=; Ncor=
    a	30.2913	47.4563	1.00971	96.932	101.981	104	97.9417	102.99	68.6602	0	0	0	0	0	0
    c	49.4757	16.1553	29.2816	1.00971	1.00971	0	1.00971	1.00971	8.07767	0	0	0	0	0	0
    g	21.2039	17.165	11.1068	4.03883	0	0	4.03883	0	12.1165	0	0	0	0	0	0
    t	3.02913	23.2233	62.6019	2.01942	1.00971	0	1.00971	0	15.1456	0	0	0	0	0	0