# 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_m6/peak-motifs_dyads_m6.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_m6/peak-motifs_dyads_m6_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: dyads_m6_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m6_shift0 (dyads_m6) |  |  |  |
    ; dyads_m6; m=0 (reference); ncol1=13; shift=0; ncol=13; camACACACAyac
    ; Alignment reference
    a	641	1787	1910	2920	40	2982	31	2973	30	2915	148	1847	393
    c	1706	619	936	41	2945	17	2942	28	2937	41	987	432	1939
    g	346	362	48	33	15	30	21	19	24	30	98	415	351
    t	345	270	144	44	38	9	44	18	47	52	1805	344	355
twi_shift4 (twi) |  |  |  |
    ; dyads_m6 versus twi; m=1/1; ncol2=8; w=0; offset=4; strand=D; shift=4; score=0.440078; ----mACAyaTG-
    ; cor=; Ncor=
    a	0	0	0	0	10.6667	12.8	0	16	1.06667	10.6667	0	1.06667	0
    c	0	0	0	0	5.33333	3.2	16	0	7.46667	3.2	3.2	0	0
    g	0	0	0	0	0	0	0	0	1.06667	2.13333	1.06667	13.8667	0
    t	0	0	0	0	0	0	0	0	6.4	0	11.7333	1.06667	0