# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1.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/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1) |  |  |  |
    ; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; maAACACAAmm
    ; Alignment reference
    a	623	573	1802	1747	96	1720	81	1680	1767	555	640
    c	544	437	1	22	1609	67	1586	57	20	518	599
    g	384	449	28	54	61	58	114	51	39	350	326
    t	329	421	49	57	114	35	99	92	54	457	315
eve_shift4 (eve) |  |  |  |
    ; oligos_7nt_mkv5_m1 versus eve; m=1/1; ncol2=8; w=0; offset=4; strand=D; shift=4; score=0.42504; ----mACaaTw
    ; cor=; Ncor=
    a	0	0	0	0	8	18	1	13	13	0	9
    c	0	0	0	0	9	0	16	3	0	1	1
    g	0	0	0	0	3	2	0	4	3	0	1
    t	0	0	0	0	0	0	3	0	4	19	9