# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/04/21/peak-motifs.2026-04-21.014834_2026-04-21.014834_X2uSrl/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_nematodes_non-redundant_pfms_transfac.txt -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/2026/04/21/peak-motifs.2026-04-21.014834_2026-04-21.014834_X2uSrl/results/discovered_vs_db/peak-motifs_motifs_vs_db_JASPAR2024_CORE_nematodes_non-redundant.tab

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift3 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m1_shift3 (oligos_6nt_mkv2_m1) |  |  |  |
    ; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=10; shift=3; ncol=13; ---hwATACTAaw
    ; Alignment reference
    a	0	0	0	24	37	76	0	76	0	0	76	44	38
    c	0	0	0	21	11	0	0	0	76	0	0	6	1
    g	0	0	0	3	4	0	0	0	0	0	0	12	9
    t	0	0	0	28	24	0	76	0	0	76	0	14	28
MA2183.1_shift0 (nhr-33) |  |  |  |
    ; oligos_6nt_mkv2_m1 versus MA2183.1 (nhr-33); m=1/1; ncol2=13; w=-3; offset=-3; strand=D; shift=0; score=0.589805; wsTACAwACTAsw
    ; cor=; Ncor=
    a	27.0	0.0	0.0	90.0	0.0	100.0	38.0	100.0	0.0	3.0	93.0	8.0	32.0
    c	0.0	35.0	13.0	2.0	92.0	0.0	5.0	0.0	93.0	3.0	0.0	35.0	8.0
    g	6.0	53.0	0.0	2.0	5.0	0.0	0.0	0.0	6.0	0.0	0.0	51.0	5.0
    t	66.0	11.0	86.0	5.0	2.0	0.0	56.0	0.0	0.0	93.0	6.0	5.0	54.0