# 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/dyads_m4/peak-motifs_dyads_m4.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/dyads_m4/peak-motifs_dyads_m4_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m4_shift0 (dyads_m4) |  |  |  |
    ; dyads_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; gyCGCCGCCGmc
    ; Alignment reference
    a	53	36	8	6	8	10	2	12	6	16	59	47
    c	43	80	198	4	208	204	2	198	208	7	98	80
    g	83	57	10	222	10	2	228	8	4	201	32	52
    t	56	62	19	3	9	19	3	17	17	11	46	56
brk_shift0 (brk) |  |  |  |
    ; dyads_m4 versus brk; m=1/2; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.477766; rGCGCCr-----
    ; cor=; Ncor=
    a	4.4	2.2	0	0	0	0	5.5	0	0	0	0	0
    c	0	0	9.9	0	11	11	0	0	0	0	0	0
    g	6.6	8.8	0	9.9	0	0	5.5	0	0	0	0	0
    t	0	0	1.1	1.1	0	0	0	0	0	0	0	0
Med_shift3 (Med) |  |  |  |
    ; dyads_m4 versus Med; m=2/2; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.460207; ---sCmssCsmm
    ; cor=; Ncor=
    a	0	0	0	1	0	5	0	0	0	0	3	4
    c	0	0	0	2	8	3	3	4	7	3	5	4
    g	0	0	0	5	0	0	4	4	1	5	0	0
    t	0	0	0	0	0	0	1	0	0	0	0	0