# 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.2026-01-25.180830_2026-01-25.180830_qbHDLg/results/discovered_motifs/positions_6-8nt_m4/peak-motifs_positions_6-8nt_m4.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.2026-01-25.180830_2026-01-25.180830_qbHDLg/results/discovered_motifs/positions_6-8nt_m4/peak-motifs_positions_6-8nt_m4_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: positions_6-8nt_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
positions_6-8nt_m4_shift0 (positions_6-8nt_m4) |  |  |  |
    ; positions_6-8nt_m4; m=0 (reference); ncol1=14; shift=0; ncol=14; yaTACATATGTAtr
    ; Alignment reference
    a	996	1897	264	3886	456	3858	281	3905	190	822	186	3770	919	1731
    c	1142	659	321	142	3081	98	195	129	368	155	304	159	1040	645
    g	646	1040	159	304	155	368	129	195	98	3081	142	321	659	1142
    t	1730	918	3770	182	822	190	3909	285	3858	456	3882	264	1896	996
twi_rc_shift4 (twi_rc) |  |  |  |
    ; positions_6-8nt_m4 versus twi_rc; m=1/1; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.413866; ----CAtrTGTk--
    ; cor=; Ncor=
    a	0	0	0	0	1.06667	11.7333	0	6.4	0	0	0	0	0	0
    c	0	0	0	0	13.8667	1.06667	2.13333	1.06667	0	0	0	0	0	0
    g	0	0	0	0	0	3.2	3.2	7.46667	0	16	3.2	5.33333	0	0
    t	0	0	0	0	1.06667	0	10.6667	1.06667	16	0	12.8	10.6667	0	0