# 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_m8/peak-motifs_oligos_6nt_mkv4_m8.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/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/oligos_6nt_mkv4_m8/peak-motifs_oligos_6nt_mkv4_m8_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m8_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv4_m8_shift0 (oligos_6nt_mkv4_m8) |  |  |  |
    ; oligos_6nt_mkv4_m8; m=0 (reference); ncol1=10; shift=0; ncol=10; mrCAAAACam
    ; Alignment reference
    a	588	575	0	1505	1527	1517	1531	0	700	535
    c	401	285	1520	0	0	0	0	1533	288	428
    g	275	408	0	3	0	1	0	0	317	327
    t	269	265	13	25	6	15	2	0	228	243
pan_shift0 (pan) |  |  |  |
    ; oligos_6nt_mkv4_m8 versus pan; m=1/1; ncol2=6; w=0; offset=0; strand=D; shift=0; score=0.527626; WtCAAA----
    ; cor=; Ncor=
    a	18.72	5.2	3.12	20.8	23.92	23.92	0	0	0	0
    c	0	4.16	20.8	0	1.04	0	0	0	0	0
    g	0	0	1.04	0	0	0	0	0	0	0
    t	7.28	16.64	1.04	5.2	1.04	2.08	0	0	0	0