# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/oligos_6-8nt_m2/peak-motifs_oligos_6-8nt_m2.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/2026/01/25/peak-motifs.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/oligos_6-8nt_m2/peak-motifs_oligos_6-8nt_m2_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2) |  |  |  |
    ; oligos_6-8nt_m2; m=0 (reference); ncol1=10; shift=0; ncol=10; atAGATACww
    ; Alignment reference
    a	1041	447	2425	0	2382	0	2537	17	987	715
    c	427	578	80	52	35	1	25	2256	411	627
    g	614	435	50	2021	86	46	0	86	412	500
    t	487	1109	14	496	66	2522	7	210	759	727
br-Z1_shift3 (br-Z1) |  |  |  |
    ; oligos_6-8nt_m2 versus br-Z1; m=1/1; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.459406; ---raTaCwA
    ; cor=; Ncor=
    a	0	0	0	10.5882	11.6471	2.11765	11.6471	3.17647	9.52941	15.8824
    c	0	0	0	0	0	0	3.17647	12.7059	1.05882	2.11765
    g	0	0	0	7.41176	3.17647	1.05882	3.17647	2.11765	0	0
    t	0	0	0	0	3.17647	14.8235	0	0	7.41176	0