# 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_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_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/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv4_m3_shift0 (oligos_6nt_mkv4_m3) |  |  |  |
    ; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; mrCTGTCAaamg
    ; Alignment reference
    a	526	362	41	28	74	16	39	1314	942	891	393	301
    c	353	229	1319	34	50	45	1321	36	139	210	434	341
    g	252	522	20	27	1237	28	21	34	168	140	278	427
    t	281	299	32	1323	51	1323	31	28	163	171	307	343
gt_shift4 (gt) |  |  |  |
    ; oligos_6nt_mkv4_m3 versus gt; m=1/1; ncol2=7; w=0; offset=4; strand=D; shift=4; score=0.427456; ----GTmAwAW-
    ; cor=; Ncor=
    a	0	0	0	0	0	1	5	8	3	8	6	0
    c	0	0	0	0	1	1	3	0	0	0	0	0
    g	0	0	0	0	7	0	0	0	0	0	0	0
    t	0	0	0	0	0	6	0	0	5	0	2	0