# 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/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/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m4_shift0 (dyads_m4) |  |  |  |
    ; dyads_m4; m=0 (reference); ncol1=13; shift=0; ncol=13; camACACACrCaC
    ; Alignment reference
    a	692	1932	1963	3124	46	3190	60	3155	31	986	38	2067	370
    c	1862	667	1096	52	3156	14	3160	33	3190	50	3147	251	2240
    g	346	403	68	60	25	53	18	45	21	2134	51	608	304
    t	369	267	142	33	42	12	31	36	27	99	33	343	355
twi_shift2 (twi) |  |  |  |
    ; dyads_m4 versus twi; m=1/1; ncol2=8; w=0; offset=2; strand=D; shift=2; score=0.479318; --mACAyaTG---
    ; cor=; Ncor=
    a	0	0	10.6667	12.8	0	16	1.06667	10.6667	0	1.06667	0	0	0
    c	0	0	5.33333	3.2	16	0	7.46667	3.2	3.2	0	0	0	0
    g	0	0	0	0	0	0	1.06667	2.13333	1.06667	13.8667	0	0	0
    t	0	0	0	0	0	0	6.4	0	11.7333	1.06667	0	0	0