# 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.2026-01-25.202113_2026-01-25.202113_GYd2gc/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_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/2026/01/25/peak-motifs.2026-01-25.202113_2026-01-25.202113_GYd2gc/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv3_m3_shift1 (oligos_6nt_mkv3_m3) |  |  |  |
    ; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -gaGAGCGAGag
    ; Alignment reference
    a	0	90	185	8	405	23	99	8	424	37	204	80
    c	0	90	102	9	10	6	320	15	6	20	107	74
    g	0	232	99	437	20	422	21	434	18	391	76	241
    t	0	50	76	8	27	11	22	5	14	14	75	67
Trl_rc_shift0 (Trl_rc) |  |  |  |
    ; oligos_6nt_mkv3_m3 versus Trl_rc; m=1/2; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.641769; agaGaGAGmrma
    ; cor=; Ncor=
    a	42	17	46	7	50	11	62	0	40	26	30	41
    c	14	9	6	1	9	8	11	5	27	10	24	13
    g	3	47	16	56	12	56	0	72	3	41	19	8
    t	18	4	9	13	6	2	4	0	7	0	4	15
z_shift2 (z) |  |  |  |
    ; oligos_6nt_mkv3_m3 versus z; m=2/2; ncol2=6; w=0; offset=1; strand=D; shift=2; score=0.447867; --TGAGtG----
    ; cor=; Ncor=
    a	0	0	2.04878	0	42	0	7.17073	1.02439	0	0	0	0
    c	0	0	7.17073	0	0	0	10.2439	5.12195	0	0	0	0
    g	0	0	3.07317	42	0	42	0	30.7317	0	0	0	0
    t	0	0	29.7073	0	0	0	24.5854	5.12195	0	0	0	0