# 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_m2/peak-motifs_dyads_m2.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_m2/peak-motifs_dyads_m2_vs_db_FlyFactorSurvey

## 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=20; shift=0; ncol=20; camACACACACACACACaca
    ; Alignment reference
    a	965	3377	1678	5060	154	5244	90	5341	63	3968	63	5368	41	5276	41	5210	128	3152	571	2859
    c	3349	891	3227	170	5234	40	5358	28	5333	80	5322	14	5384	26	5404	78	5174	357	3514	760
    g	544	801	227	203	44	204	40	104	50	1298	40	110	29	170	32	141	100	729	639	1111
    t	688	477	414	113	114	58	58	73	100	200	121	54	92	74	69	117	144	1308	822	816
klu_SANGER_10_FBgn0013469_rc_shift5 (klu_SANGER_10_FBgn0013469_rc) |  |  |  |
    ; dyads_m2 versus klu_SANGER_10_FBgn0013469_rc; m=1/1; ncol2=11; w=0; offset=5; strand=R; shift=5; score=0.420483; -----mCACCCmCrCa----
    ; cor=; Ncor=
    a	0	0	0	0	0	7	0	18	0	0	0	13	0	9	0	12	0	0	0	0
    c	0	0	0	0	0	11	20	0	20	20	19	7	20	0	16	2	0	0	0	0
    g	0	0	0	0	0	2	0	0	0	0	0	0	0	10	0	2	0	0	0	0
    t	0	0	0	0	0	0	0	2	0	0	1	0	0	1	3	2	0	0	0	0