# 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.2026-04-21.024047_2026-04-21.024047_gRzMOf/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.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.2026-04-21.024047_2026-04-21.024047_gRzMOf/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_JASPAR2024_CORE_nematodes_non-redundant

## One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift3 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
positions_6nt_m2_shift3 (positions_6nt_m2) |  |  |  |
    ; positions_6nt_m2; m=0 (reference); ncol1=10; shift=3; ncol=13; ---wrTTCAAAaw
    ; Alignment reference
    a	0	0	0	44	46	0	0	0	142	142	142	94	58
    c	0	0	0	30	24	0	0	142	0	0	0	15	13
    g	0	0	0	8	40	0	0	0	0	0	0	7	23
    t	0	0	0	60	32	142	142	0	0	0	0	26	48
MA1450.2_shift0 (lin-54) |  |  |  |
    ; positions_6nt_m2 versus MA1450.2 (lin-54); m=1/1; ncol2=13; w=-3; offset=-3; strand=D; shift=0; score=0.640499; ggaAATTCAAATw
    ; cor=; Ncor=
    a	445.0	543.0	1740.0	2616.0	2709.0	23.0	14.0	66.0	2771.0	2901.0	2820.0	327.0	814.0
    c	351.0	393.0	174.0	93.0	16.0	27.0	11.0	2612.0	51.0	14.0	13.0	158.0	159.0
    g	1823.0	1744.0	554.0	109.0	98.0	5.0	23.0	19.0	109.0	11.0	17.0	29.0	338.0
    t	328.0	267.0	479.0	129.0	124.0	2892.0	2899.0	250.0	16.0	21.0	97.0	2433.0	1636.0