# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep3_motifs50/results/discovered_motifs/oligos_7nt_mkv2_m6/peak-motifs_oligos_7nt_mkv2_m6.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2020/nonredundant/JASPAR2020_CORE_vertebrates_non-redundant_pfms.tf -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 Myogenin_Rep3_motifs50/results/discovered_motifs/oligos_7nt_mkv2_m6/peak-motifs_oligos_7nt_mkv2_m6_vs_db_jaspar_core_nonredundant_vertebrates

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m6_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m6_shift0 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6) |  |  |  |
    ; oligos_7nt_mkv2_m6 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6); m=0 (reference); ncol1=11; shift=0; ncol=11; msTGAAAAAyr
    ; Alignment reference
    a	78	23	0	1	138	138	138	124	139	6	38
    c	58	59	0	0	0	0	0	0	0	59	4
    g	1	41	0	138	1	1	0	0	0	16	93
    t	2	16	139	0	0	0	1	15	0	58	4
MA0606.1_rc_shift0 (NFAT5_rc) |  |  |  |
    ; oligos_7nt_mkv2_m6 versus MA0606.1_rc (NFAT5_rc); m=1/2; ncol2=10; w=10; offset=0; strand=R; shift=0; score=0.671421; wrTGGAAAat-
    ; cor=; Ncor=
    a	322.0	548.0	85.0	89.0	85.0	827.0	1000.0	1000.0	649.0	210.0	0
    c	248.0	41.0	0.0	85.0	0.0	0.0	0.0	0.0	88.0	210.0	0
    g	163.0	287.0	84.0	826.0	915.0	84.0	0.0	0.0	88.0	210.0	0
    t	268.0	124.0	831.0	0.0	0.0	89.0	0.0	0.0	176.0	371.0	0
MA0152.1_rc_shift2 (NFATC2_rc) |  |  |  |
    ; oligos_7nt_mkv2_m6 versus MA0152.1_rc (NFATC2_rc); m=2/2; ncol2=7; w=7; offset=2; strand=R; shift=2; score=0.486673; --TGGAAAA--
    ; cor=; Ncor=
    a	0	0	4.0	0.0	0.0	26.0	24.0	21.0	20.0	0	0
    c	0	0	1.0	0.0	0.0	0.0	0.0	2.0	2.0	0	0
    g	0	0	3.0	26.0	25.0	0.0	1.0	2.0	1.0	0	0
    t	0	0	18.0	0.0	1.0	0.0	1.0	1.0	3.0	0	0