# 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.2026-04-21.015247_2026-04-21.015247_DTyOML/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_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.2026-04-21.015247_2026-04-21.015247_DTyOML/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_vs_db_JASPAR2024_CORE_nematodes_non-redundant

## One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
positions_6nt_m1_shift0 (positions_6nt_m1) |  |  |  |
    ; positions_6nt_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; vwAAAATTCwr
    ; Alignment reference
    a	22	27	81	75	78	79	0	11	4	23	24
    c	24	14	1	0	1	2	0	0	78	2	12
    g	22	6	0	0	0	1	1	0	0	17	37
    t	14	35	0	7	3	0	81	71	0	40	9
MA2179.1_rc_shift2 (ceh-10_rc) |  |  |  |
    ; positions_6nt_m1 versus MA2179.1_rc (ceh-10_rc); m=1/1; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.500354; --AwAATTwdm
    ; cor=; Ncor=
    a	0	0	75.0	47.0	85.0	91.0	8.0	0.0	64.0	25.0	36.0
    c	0	0	0.0	0.0	0.0	0.0	0.0	8.0	0.0	7.0	50.0
    g	0	0	8.0	0.0	7.0	8.0	0.0	0.0	0.0	39.0	0.0
    t	0	0	16.0	52.0	7.0	0.0	91.0	91.0	35.0	28.0	13.0