# 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_m1/peak-motifs_oligos_7nt_mkv2_m1.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_m1/peak-motifs_oligos_7nt_mkv2_m1_vs_db_JASPAR2024_CORE_nematodes_non-redundant

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1) |  |  |  |
    ; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; bmGCAAGACdr
    ; Alignment reference
    a	2	43	0	19	115	116	0	132	3	51	64
    c	38	48	0	113	0	0	16	0	113	2	20
    g	56	17	116	0	1	16	111	0	16	41	48
    t	36	24	16	0	16	0	5	0	0	38	0
MA0925.2_rc_shift3 (sma-4_rc) |  |  |  |
    ; oligos_7nt_mkv2_m1 versus MA0925.2_rc (sma-4_rc); m=1/1; ncol2=7; w=0; offset=3; strand=R; shift=3; score=0.477602; ---CCAGACA-
    ; cor=; Ncor=
    a	0	0	0	110.0	0.0	1000.0	0.0	917.0	83.0	901.0	0
    c	0	0	0	836.0	785.0	0.0	0.0	0.0	917.0	33.0	0
    g	0	0	0	27.0	0.0	0.0	1000.0	0.0	0.0	33.0	0
    t	0	0	0	27.0	215.0	0.0	0.0	83.0	0.0	33.0	0