# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184256_2025-05-16.184256_DOHBqC/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_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/2025/05/16/peak-motifs.2025-05-16.184256_2025-05-16.184256_DOHBqC/results/discovered_motifs/oligos_7nt_mkv1_m2/peak-motifs_oligos_7nt_mkv1_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift0 ; 2 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; drCAGAGAGrv
    ; Alignment reference
    a	2	2	0	7	0	7	0	7	0	3	2
    c	0	1	7	0	0	0	0	0	0	1	2
    g	3	3	0	0	7	0	7	0	6	2	2
    t	2	1	0	0	0	0	0	0	1	1	1
MA1731.2_rc_shift2 (ZNF768_rc) |  |  |  |
    ; oligos_7nt_mkv1_m2 versus MA1731.2_rc (ZNF768_rc); m=1/1; ncol2=9; w=0; offset=2; strand=R; shift=2; score=0.772426; --CAGAGAgGs
    ; cor=; Ncor=
    a	0	0	1.0	987.0	1.0	945.0	20.0	917.0	123.0	141.0	43.0
    c	0	0	973.0	11.0	11.0	43.0	29.0	11.0	179.0	62.0	268.0
    g	0	0	25.0	1.0	987.0	6.0	950.0	39.0	655.0	768.0	478.0
    t	0	0	1.0	1.0	1.0	6.0	1.0	34.0	43.0	29.0	211.0