# 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_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.2026-04-21.015247_2026-04-21.015247_DTyOML/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_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
positions_6nt_m2_shift0 (positions_6nt_m2) |  |  |  |
    ; positions_6nt_m2; m=0 (reference); ncol1=10; shift=0; ncol=10; twAAAAAAww
    ; Alignment reference
    a	115	130	507	507	507	507	507	507	130	182
    c	104	118	0	0	0	0	0	0	60	108
    g	119	105	0	0	0	0	0	0	56	46
    t	169	154	0	0	0	0	0	0	261	171
MA1440.1_shift1 (fkh-9) |  |  |  |
    ; positions_6nt_m2 versus MA1440.1 (fkh-9); m=1/2; ncol2=8; w=0; offset=1; strand=D; shift=1; score=0.595686; -aAwAACAw-
    ; cor=; Ncor=
    a	0	527.0	809.0	655.0	983.0	999.0	47.0	968.0	574.0	0
    c	0	236.0	16.0	93.0	15.0	0.0	780.0	0.0	75.0	0
    g	0	236.0	0.0	0.0	0.0	0.0	0.0	0.0	75.0	0
    t	0	0.0	174.0	250.0	0.0	0.0	171.0	31.0	274.0	0
MA2173.1_shift4 (mef-2) |  |  |  |
    ; positions_6nt_m2 versus MA2173.1 (mef-2); m=2/2; ncol2=7; w=0; offset=4; strand=D; shift=4; score=0.475956; ----AAAATA
    ; cor=; Ncor=
    a	0	0	0	0	422.0	517.0	501.0	516.0	9.0	514.0
    c	0	0	0	0	26.0	9.0	15.0	11.0	7.0	12.0
    g	0	0	0	0	80.0	27.0	26.0	8.0	12.0	19.0
    t	0	0	0	0	30.0	5.0	16.0	23.0	530.0	13.0