# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.044641_2025-04-28.044641_ntYsd5/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4.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/2025/04/28/peak-motifs.2025-04-28.044641_2025-04-28.044641_ntYsd5/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m4_shift0 (dyads_m4) |  |  |  |
    ; dyads_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; wdwAAAATAtwd
    ; Alignment reference
    a	27	21	23	63	66	63	67	0	66	16	21	17
    c	15	12	11	1	0	0	0	0	0	12	15	7
    g	2	17	6	2	0	0	0	1	1	5	13	20
    t	23	17	27	1	1	4	0	66	0	34	18	23
hb_shift0 (hb) |  |  |  |
    ; dyads_m4 versus hb; m=1/2; ncol2=9; w=0; offset=0; strand=D; shift=0; score=0.526125; mayAAAAAa---
    ; cor=; Ncor=
    a	30.2913	47.4563	1.00971	96.932	101.981	104	97.9417	102.99	68.6602	0	0	0
    c	49.4757	16.1553	29.2816	1.00971	1.00971	0	1.00971	1.00971	8.07767	0	0	0
    g	21.2039	17.165	11.1068	4.03883	0	0	4.03883	0	12.1165	0	0	0
    t	3.02913	23.2233	62.6019	2.01942	1.00971	0	1.00971	0	15.1456	0	0	0
br-Z3_rc_shift3 (br-Z3_rc) |  |  |  |
    ; dyads_m4 versus br-Z3_rc; m=2/2; ncol2=11; w=0; offset=3; strand=R; shift=3; score=0.459766; ---AwAMTAdWd
    ; cor=; Ncor=
    a	0	0	0	14	8	13	4	1	13	5	4	5
    c	0	0	0	0	0	1	11	1	1	0	0	0
    g	0	0	0	1	0	2	0	1	0	6	0	4
    t	0	0	0	1	8	0	1	13	2	5	12	7