# 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.2026-04-21.022353_2026-04-21.022353_CcghX5/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4.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.2026-04-21.022353_2026-04-21.022353_CcghX5/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4_vs_db_JASPAR2024_CORE_nematodes_non-redundant

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4) |  |  |  |
    ; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; TCTGGCTTCAym
    ; Alignment reference
    a	11	1	0	0	0	0	0	0	0	48	0	28
    c	0	44	0	0	0	57	11	0	59	9	31	19
    g	0	13	0	59	59	0	0	0	0	0	1	0
    t	48	1	59	0	0	2	48	59	0	2	27	12
MA0260.1_rc_shift3 (che-1_rc) |  |  |  |
    ; oligos_7nt_mkv2_m4 versus MA0260.1_rc (che-1_rc); m=1/1; ncol2=6; w=0; offset=3; strand=R; shift=3; score=0.455367; ---SGyTTC---
    ; cor=; Ncor=
    a	0	0	0	0.0	0.0	0.0	0.0	0.0	0.0	0	0	0
    c	0	0	0	11.0	0.0	18.0	0.0	0.0	37.0	0	0	0
    g	0	0	0	26.0	37.0	0.0	0.0	0.0	0.0	0	0	0
    t	0	0	0	0.0	0.0	19.0	37.0	37.0	0.0	0	0	0