# 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.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/oligos_6nt_mkv4_m6/peak-motifs_oligos_6nt_mkv4_m6.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/idmmpmm_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/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/oligos_6nt_mkv4_m6/peak-motifs_oligos_6nt_mkv4_m6_vs_db_IDMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m6_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv4_m6_shift0 (oligos_6nt_mkv4_m6) |  |  |  |
    ; oligos_6nt_mkv4_m6; m=0 (reference); ncol1=12; shift=0; ncol=12; yyCTTATCagym
    ; Alignment reference
    a	258	185	81	30	34	1157	9	27	667	140	266	331
    c	411	359	1020	64	33	44	19	1173	127	207	383	328
    g	231	277	65	39	16	8	37	9	266	679	226	283
    t	339	418	73	1106	1156	30	1174	30	179	213	364	297
srp_rc_shift1 (srp_rc) |  |  |  |
    ; oligos_6nt_mkv4_m6 versus srp_rc; m=1/1; ncol2=9; w=0; offset=1; strand=R; shift=1; score=0.634094; -yvYTATCgm--
    ; cor=; Ncor=
    a	0	0.5625	10.6875	0	0	31.5	0	0	6.75	14.0625	0	0
    c	0	11.8125	14.625	9.5625	0	0	0	36	0	18	0	0
    g	0	6.1875	10.6875	0	0	0	0	0	21.375	2.25	0	0
    t	0	17.4375	0	26.4375	36	4.5	36	0	7.875	1.6875	0	0