# 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_m9/peak-motifs_oligos_6-8nt_m9.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_m9/peak-motifs_oligos_6-8nt_m9_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m9_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m9_shift0 (oligos_6-8nt_m9) |  |  |  |
    ; oligos_6-8nt_m9; m=0 (reference); ncol1=10; shift=0; ncol=10; waAATGAAaw
    ; Alignment reference
    a	700	1027	2381	2381	0	0	2381	2381	1101	836
    c	482	452	0	0	0	0	0	0	337	368
    g	529	495	0	0	0	2381	0	0	374	440
    t	670	407	0	0	2381	0	0	0	569	737
en_rc_shift1 (en_rc) |  |  |  |
    ; oligos_6-8nt_m9 versus en_rc; m=1/4; ncol2=8; w=0; offset=1; strand=R; shift=1; score=0.609738; -yAATtAah-
    ; cor=; Ncor=
    a	0	10.125	58.5	57.375	1.125	5.625	51.75	31.5	18	0
    c	0	31.5	3.375	2.25	0	14.625	4.5	11.25	21.375	0
    g	0	1.125	0	1.125	1.125	6.75	6.75	12.375	0	0
    t	0	20.25	1.125	2.25	60.75	36	0	7.875	23.625	0
sd_rc_shift1 (sd_rc) |  |  |  |
    ; oligos_6-8nt_m9 versus sd_rc; m=2/4; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.537557; -mAAwGdAAT
    ; cor=; Ncor=
    a	0	8	16	14	7	0	9	13	15	1
    c	0	7	0	0	0	4	0	3	0	1
    g	0	4	0	1	2	14	5	0	3	1
    t	0	0	3	4	10	1	5	3	1	16
zen_shift2 (zen) |  |  |  |
    ; oligos_6-8nt_m9 versus zen; m=3/4; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.484903; --AATwAA--
    ; cor=; Ncor=
    a	0	0	11.9167	11.9167	0	8.66667	13	13	0	0
    c	0	0	0.541667	0	1.08333	0	0	0	0	0
    g	0	0	0	0	0	0	0	0	0	0
    t	0	0	0.541667	1.08333	11.9167	4.33333	0	0	0	0
ap_shift2 (ap) |  |  |  |
    ; oligos_6-8nt_m9 versus ap; m=4/4; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.422116; --AAThAt--
    ; cor=; Ncor=
    a	0	0	14	14	0	5	13	2	0	0
    c	0	0	0	0	1	4	0	1	0	0
    g	0	0	0	0	1	1	1	3	0	0
    t	0	0	0	0	12	4	0	8	0	0