# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.044641_2025-04-28.044641_ntYsd5/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2.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/2025/04/28/peak-motifs.2025-04-28.044641_2025-04-28.044641_ntYsd5/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2) |  |  |  |
    ; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=20; shift=0; ncol=20; hdmyatCGATAsTATCGayr
    ; Alignment reference
    a	22	19	19	14	32	6	0	2	62	0	61	1	1	59	2	2	3	35	14	22
    c	18	10	24	22	10	11	63	0	0	1	0	25	3	2	3	59	1	13	16	9
    g	6	18	10	9	12	7	0	60	1	3	1	35	0	1	1	0	59	10	12	18
    t	18	17	11	19	10	40	1	2	1	60	2	3	60	2	58	3	1	6	22	15
Dref_shift2 (Dref) |  |  |  |
    ; oligos_6nt_mkv2_m2 versus Dref; m=1/1; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.436093; --aTAwCGATAr--------
    ; cor=; Ncor=
    a	0	0	6.66667	1.11111	7.77778	3.33333	0	1.11111	10	0	7.77778	3.33333	0	0	0	0	0	0	0	0
    c	0	0	1.11111	0	1.11111	0	10	0	0	0	1.11111	0	0	0	0	0	0	0	0	0
    g	0	0	0	1.11111	0	0	0	8.88889	0	0	1.11111	6.66667	0	0	0	0	0	0	0	0
    t	0	0	2.22222	7.77778	1.11111	6.66667	0	0	0	10	0	0	0	0	0	0	0	0	0	0