# 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_m3/peak-motifs_dyads_m3.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_m3/peak-motifs_dyads_m3_vs_db_FlyFactorSurvey

## One-to-n matrix alignment; reference matrix: dyads_m3_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m3_shift0 (dyads_m3) |  |  |  |
    ; dyads_m3; m=0 (reference); ncol1=14; shift=0; ncol=14; acAyACACACrCac
    ; Alignment reference
    a	1809	388	2704	111	2822	66	2823	59	2741	57	780	115	1573	395
    c	450	1831	99	931	50	2764	26	2769	58	2755	122	2562	346	1815
    g	397	308	87	73	56	48	79	46	91	79	1901	135	632	343
    t	310	439	76	1851	38	88	38	92	76	75	163	154	415	413
CG16778_SANGER_5_FBgn0003715_shift3 (CG16778_SANGER_5_FBgn0003715) |  |  |  |
    ; dyads_m3 versus CG16778_SANGER_5_FBgn0003715; m=1/2; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.42861; ---CACAyAYG---
    ; cor=; Ncor=
    a	0	0	0	0	18	0	20	0	17	0	0	0	0	0
    c	0	0	0	15	1	20	0	9	0	6	1	0	0	0
    g	0	0	0	2	0	0	0	0	3	0	18	0	0	0
    t	0	0	0	1	0	0	0	11	0	14	1	0	0	0
CG5953_SANGER_5_FBgn0032587_shift0 (CG5953_SANGER_5_FBgn0032587) |  |  |  |
    ; dyads_m3 versus CG5953_SANGER_5_FBgn0032587; m=2/2; ncol2=8; w=0; offset=0; strand=D; shift=0; score=0.417603; aCAAACAy------
    ; cor=; Ncor=
    a	10	0	16	16	16	0	16	1	0	0	0	0	0	0
    c	3	16	0	0	0	16	0	5	0	0	0	0	0	0
    g	0	0	0	0	0	0	0	0	0	0	0	0	0	0
    t	3	0	0	0	0	0	0	10	0	0	0	0	0	0