# 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.2026-01-25.181000_2026-01-25.181000_CpuIe4/results/discovered_motifs/oligos_6-8nt_m10/peak-motifs_oligos_6-8nt_m10.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.2026-01-25.181000_2026-01-25.181000_CpuIe4/results/discovered_motifs/oligos_6-8nt_m10/peak-motifs_oligos_6-8nt_m10_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m10_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m10_shift0 (oligos_6-8nt_m10) |  |  |  |
    ; oligos_6-8nt_m10; m=0 (reference); ncol1=10; shift=0; ncol=10; smCAAGGAgm
    ; Alignment reference
    a	257	283	0	1090	1115	0	0	1114	212	318
    c	298	337	1103	1	1	0	0	0	223	316
    g	316	253	1	7	2	1118	1112	3	419	279
    t	247	245	14	20	0	0	6	1	264	205
ttk_rc_shift3 (ttk_rc) |  |  |  |
    ; oligos_6-8nt_m10 versus ttk_rc; m=1/2; ncol2=7; w=0; offset=3; strand=R; shift=3; score=0.568452; ---mAGGAym
    ; cor=; Ncor=
    a	0	0	0	3.375	7.875	0	0	9	0	3.375
    c	0	0	0	5.625	0	0	0	0	5.625	5.625
    g	0	0	0	0	1.125	9	9	0	0	0
    t	0	0	0	0	0	0	0	0	3.375	0
Eip74EF_shift3 (Eip74EF) |  |  |  |
    ; oligos_6-8nt_m10 versus Eip74EF; m=2/2; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.451607; ---mMGGAAk
    ; cor=; Ncor=
    a	0	0	0	3	6	1	0	8	8	1
    c	0	0	0	5	2	0	1	0	0	0
    g	0	0	0	0	0	7	7	0	0	5
    t	0	0	0	0	0	0	0	0	0	2