# 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/positions_6-8nt_m5/peak-motifs_positions_6-8nt_m5.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/positions_6-8nt_m5/peak-motifs_positions_6-8nt_m5_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: positions_6-8nt_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
positions_6-8nt_m5_shift0 (positions_6-8nt_m5) |  |  |  |
    ; positions_6-8nt_m5; m=0 (reference); ncol1=10; shift=0; ncol=10; acACACACac
    ; Alignment reference
    a	3234	818	5808	0	5705	0	5739	0	3405	906
    c	764	3452	0	5651	34	5616	19	5751	585	3242
    g	1164	365	0	1	0	5	0	10	898	737
    t	646	1173	0	156	69	187	50	47	920	923
twi_shift3 (twi) |  |  |  |
    ; positions_6-8nt_m5 versus twi; m=1/1; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.462983; ---mACAyaT
    ; cor=; Ncor=
    a	0	0	0	10.6667	12.8	0	16	1.06667	10.6667	0
    c	0	0	0	5.33333	3.2	16	0	7.46667	3.2	3.2
    g	0	0	0	0	0	0	0	1.06667	2.13333	1.06667
    t	0	0	0	0	0	0	0	6.4	0	11.7333