# 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.2026-03-19.135315_2026-03-19.135315_TQdT35/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4.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.2026-03-19.135315_2026-03-19.135315_TQdT35/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4) |  |  |  |
    ; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; ryAGTCTACgsc
    ; Alignment reference
    a	68	42	237	3	18	5	11	245	7	29	61	61
    c	62	83	10	12	14	243	7	7	224	41	77	84
    g	95	53	11	241	9	12	14	7	24	148	71	54
    t	40	87	7	9	224	5	233	6	10	47	56	66
MA1602.2_shift2 (ZSCAN29) |  |  |  |
    ; oligos_6nt_mkv3_m4 versus MA1602.2 (ZSCAN29); m=1/1; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.59728; --yGTCTACrCr
    ; cor=; Ncor=
    a	0	0	68.0	20.0	0.0	4.0	0.0	989.0	4.0	647.0	0.0	306.0
    c	0	0	497.0	0.0	16.0	993.0	48.0	4.0	838.0	0.0	961.0	207.0
    g	0	0	124.0	977.0	4.0	0.0	0.0	0.0	0.0	350.0	24.0	310.0
    t	0	0	310.0	0.0	977.0	0.0	949.0	4.0	155.0	0.0	12.0	175.0