# 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_m8/peak-motifs_oligos_6nt_mkv2_m8.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_m8/peak-motifs_oligos_6nt_mkv2_m8_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m8_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m8_shift0 (oligos_6nt_mkv2_m8) |  |  |  |
    ; oligos_6nt_mkv2_m8; m=0 (reference); ncol1=11; shift=0; ncol=11; rrAACGAGAac
    ; Alignment reference
    a	25	24	64	76	3	3	77	2	71	31	18
    c	12	14	5	4	74	1	2	5	5	18	26
    g	31	26	5	0	4	76	3	72	1	17	19
    t	15	19	9	3	2	3	1	4	6	17	20
MA0508.4_rc_shift5 (PRDM1_rc) |  |  |  |
    ; oligos_6nt_mkv2_m8 versus MA0508.4_rc (PRDM1_rc); m=1/2; ncol2=7; w=0; offset=5; strand=R; shift=5; score=0.418357; -----GAGAAA
    ; cor=; Ncor=
    a	0	0	0	0	0	660.0	49466.0	432.0	52619.0	50943.0	52905.0
    c	0	0	0	0	0	290.0	1390.0	207.0	561.0	1011.0	826.0
    g	0	0	0	0	0	52821.0	1076.0	53465.0	488.0	1346.0	467.0
    t	0	0	0	0	0	1710.0	3549.0	1377.0	1813.0	2181.0	1283.0
MA0877.4_rc_shift0 (BARHL1_rc) |  |  |  |
    ; oligos_6nt_mkv2_m8 versus MA0877.4_rc (BARHL1_rc); m=2/2; ncol2=6; w=0; offset=0; strand=R; shift=0; score=0.41423; TAAACG-----
    ; cor=; Ncor=
    a	125.0	3960.0	3960.0	3960.0	46.0	26.0	0	0	0	0	0
    c	26.0	0.0	0.0	33.0	3960.0	3.0	0	0	0	0	0
    g	16.0	9.0	4.0	223.0	34.0	3960.0	0	0	0	0	0
    t	3960.0	96.0	0.0	281.0	833.0	202.0	0	0	0	0	0