# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/03/19/peak-motifs.2026-03-19.135349_2026-03-19.135349_WDqUmM/results/discovered_motifs/oligos_6nt_mkv2_m5/peak-motifs_oligos_6nt_mkv2_m5.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_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/2026/03/19/peak-motifs.2026-03-19.135349_2026-03-19.135349_WDqUmM/results/discovered_motifs/oligos_6nt_mkv2_m5/peak-motifs_oligos_6nt_mkv2_m5_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift1 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5) |  |  |  |
    ; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=10; shift=1; ncol=11; -ssGCTAGCss
    ; Alignment reference
    a	0	7	10	0	0	0	49	1	0	8	10
    c	0	17	15	0	48	0	0	0	49	17	15
    g	0	15	16	49	0	0	0	47	0	14	16
    t	0	10	8	0	1	49	0	1	0	10	8
MA1973.2_rc_shift0 (ZKSCAN3_rc) |  |  |  |
    ; oligos_6nt_mkv2_m5 versus MA1973.2_rc (ZKSCAN3_rc); m=1/1; ncol2=14; w=-1; offset=-1; strand=R; shift=0; score=0.557679; tGGGCTAGCCT
    ; cor=; Ncor=
    a	34.0	15.0	16.0	2.0	13.0	2.0	200.0	18.0	2.0	2.0	1.0
    c	16.0	2.0	1.0	4.0	188.0	8.0	2.0	4.0	203.0	201.0	19.0
    g	24.0	192.0	193.0	168.0	6.0	3.0	6.0	183.0	5.0	1.0	2.0
    t	136.0	1.0	0.0	36.0	3.0	197.0	2.0	5.0	0.0	6.0	188.0