# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep3_motifs50/results/discovered_motifs/oligos_8nt_mkv2_m9/peak-motifs_oligos_8nt_mkv2_m9.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_8nt_mkv2_m9/peak-motifs_oligos_8nt_mkv2_m9_vs_db_jaspar_core_nonredundant_vertebrates

## One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m9_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_8nt_mkv2_m9_shift0 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9) |  |  |  |
    ; oligos_8nt_mkv2_m9 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9); m=0 (reference); ncol1=12; shift=0; ncol=12; ayGTTTTTCAsK
    ; Alignment reference
    a	51	4	20	1	2	1	0	3	0	95	8	1
    c	7	52	1	0	0	1	2	0	94	1	29	3
    g	19	5	77	0	1	0	0	0	0	0	47	27
    t	23	39	2	99	97	98	98	97	6	4	16	69
MA0606.1_shift2 (NFAT5) |  |  |  |
    ; oligos_8nt_mkv2_m9 versus MA0606.1 (NFAT5); m=1/2; ncol2=10; w=10; offset=2; strand=D; shift=2; score=0.593243; --atTTTCCAyw
    ; cor=; Ncor=
    a	0	0	371.0	176.0	0.0	0.0	89.0	0.0	0.0	831.0	124.0	268.0
    c	0	0	210.0	88.0	0.0	0.0	84.0	915.0	826.0	84.0	287.0	163.0
    g	0	0	210.0	88.0	0.0	0.0	0.0	0.0	85.0	0.0	41.0	248.0
    t	0	0	210.0	649.0	1000.0	1000.0	827.0	85.0	89.0	85.0	548.0	322.0
MA0152.1_shift3 (NFATC2) |  |  |  |
    ; oligos_8nt_mkv2_m9 versus MA0152.1 (NFATC2); m=2/2; ncol2=7; w=7; offset=3; strand=D; shift=3; score=0.446461; ---TTTTCCA--
    ; cor=; Ncor=
    a	0	0	0	3.0	1.0	1.0	0.0	1.0	0.0	18.0	0	0
    c	0	0	0	1.0	2.0	1.0	0.0	25.0	26.0	3.0	0	0
    g	0	0	0	2.0	2.0	0.0	0.0	0.0	0.0	1.0	0	0
    t	0	0	0	20.0	21.0	24.0	26.0	0.0	0.0	4.0	0	0