# 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_m2/peak-motifs_dyads_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/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m2_shift0 (dyads_m2) |  |  |  |
    ; dyads_m2; m=0 (reference); ncol1=17; shift=0; ncol=17; GaGAGAGAGAGAGAGaG
    ; Alignment reference
    a	1146	5072	674	6098	581	6400	516	6520	527	6554	534	6417	568	6169	757	5112	1251
    c	601	904	326	610	226	569	166	521	148	520	134	571	200	633	274	1020	526
    g	5388	771	6362	387	6628	275	6791	285	6812	285	6823	311	6662	380	6323	751	5329
    t	505	893	278	545	205	396	167	314	153	281	149	341	210	458	286	757	534
Trl_rc_shift3 (Trl_rc) |  |  |  |
    ; dyads_m2 versus Trl_rc; m=1/1; ncol2=13; w=0; offset=3; strand=R; shift=3; score=0.641698; ---agaGaGAGmrmaA-
    ; cor=; Ncor=
    a	0	0	0	42	17	46	7	50	11	62	0	40	26	30	41	57	0
    c	0	0	0	14	9	6	1	9	8	11	5	27	10	24	13	0	0
    g	0	0	0	3	47	16	56	12	56	0	72	3	41	19	8	10	0
    t	0	0	0	18	4	9	13	6	2	4	0	7	0	4	15	10	0