# 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.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4.tf -format2 tf -file2 $RSAT/public_html/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey_2016.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.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_vs_db_FlyFactorSurvey

## 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=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_FlyReg_FBgn0013263_rc_shift6 (Trl_FlyReg_FBgn0013263_rc) |  |  |  |
    ; dyads_m4 versus Trl_FlyReg_FBgn0013263_rc; m=1/1; ncol2=10; w=0; offset=6; strand=R; shift=6; score=0.504203; ------raGAGAGmrr-
    ; cor=; Ncor=
    a	0	0	0	0	0	0	19	40	5	56	0	54	4	23	31	36	0
    c	0	0	0	0	0	0	10	11	7	2	0	14	3	30	11	9	0
    g	0	0	0	0	0	0	33	13	54	0	70	0	64	6	23	22	0
    t	0	0	0	0	0	0	9	7	5	13	1	3	0	12	6	4	0