# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/oligos_7nt_mkv1_m2/peak-motifs_oligos_7nt_mkv1_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_plants_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/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/oligos_7nt_mkv1_m2/peak-motifs_oligos_7nt_mkv1_m2_vs_db_JASPAR2024_CORE_plants_non-redundant

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2) |  |  |  |
    ; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; bhATGGCYCww
    ; Alignment reference
    a	1	2	8	0	0	0	1	0	0	3	2
    c	2	2	0	0	1	0	7	2	7	1	1
    g	3	1	0	0	7	7	0	0	1	1	0
    t	2	3	0	8	0	1	0	6	0	3	5
MA1794.2_shift3 (NLP7) |  |  |  |
    ; oligos_7nt_mkv1_m2 versus MA1794.2 (NLP7); m=1/2; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.540025; ---TGrCyyTT
    ; cor=; Ncor=
    a	0	0	0	10.0	66.0	329.0	0.0	0.0	18.0	10.0	39.0
    c	0	0	0	182.0	0.0	175.0	1000.0	444.0	390.0	81.0	15.0
    g	0	0	0	2.0	934.0	339.0	0.0	40.0	22.0	0.0	0.0
    t	0	0	0	807.0	0.0	156.0	0.0	516.0	570.0	909.0	946.0
MA1414.2_rc_shift3 (E2FA_rc) |  |  |  |
    ; oligos_7nt_mkv1_m2 versus MA1414.2_rc (E2FA_rc); m=2/2; ncol2=6; w=0; offset=3; strand=R; shift=3; score=0.427624; ---TGGCGC--
    ; cor=; Ncor=
    a	0	0	0	52.0	73.0	11.0	19.0	33.0	11.0	0	0
    c	0	0	0	21.0	1.0	18.0	1391.0	22.0	1355.0	0	0
    g	0	0	0	10.0	1376.0	1415.0	6.0	1375.0	62.0	0	0
    t	0	0	0	1368.0	1.0	7.0	35.0	21.0	23.0	0	0