# 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_m9/peak-motifs_dyads_m9.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DrosophilaTFs/DrosophilaTFs_2015-11-06.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_m9/peak-motifs_dyads_m9_vs_db_DrosophilaTFs

## One-to-n matrix alignment; reference matrix: dyads_m9_shift1 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m9_shift1 (dyads_m9) |  |  |  |
    ; dyads_m9; m=0 (reference); ncol1=13; shift=1; ncol=14; -acATACACACmca
    ; Alignment reference
    a	0	1425	347	2251	103	2337	38	2277	26	2263	37	767	520	1082
    c	0	426	1452	85	532	46	2255	72	2298	85	2267	1376	1114	522
    g	0	318	252	52	45	26	51	36	34	26	65	149	430	440
    t	0	266	384	47	1755	26	91	50	77	61	66	143	371	391
4935_Cf2_DrosophilaTF_1.1__rc_shift0 (4935_Cf2_DrosophilaTF_1.1__rc) |  |  |  |
    ; dyads_m9 versus 4935_Cf2_DrosophilaTF_1.1__rc; m=1/1; ncol2=9; w=-1; offset=-1; strand=R; shift=0; score=0.405587; yAyATATAy-----
    ; cor=; Ncor=
    a	5	83	5	95	0	88	0	94	1	0	0	0	0	0
    c	26	2	41	0	4	4	6	0	51	0	0	0	0	0
    g	6	13	3	4	2	8	0	6	15	0	0	0	0	0
    t	63	2	51	1	94	0	94	0	33	0	0	0	0	0