# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep3_motifs50/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_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_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6_vs_db_jaspar_core_nonredundant_vertebrates

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m6_shift3 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m6_shift3 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6) |  |  |  |
    ; oligos_6nt_mkv2_m6 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6); m=0 (reference); ncol1=11; shift=3; ncol=14; ---ssCCGCCGGGs
    ; Alignment reference
    a	0	0	0	3	2	1	0	0	0	0	0	2	2	4
    c	0	0	0	11	13	21	25	1	23	22	3	3	4	10
    g	0	0	0	10	9	3	1	25	3	4	23	20	18	11
    t	0	0	0	2	2	1	0	0	0	0	0	1	2	1
MA1513.1_shift2 (KLF15) |  |  |  |
    ; oligos_6nt_mkv2_m6 versus MA1513.1 (KLF15); m=1/2; ncol2=11; w=10; offset=-1; strand=D; shift=2; score=0.586589; --scCCCGCCCcs-
    ; cor=; Ncor=
    a	0	0	1184.0	937.0	40.0	93.0	0.0	0.0	11.0	55.0	12.0	1566.0	1067.0	0
    c	0	0	2903.0	6506.0	11234.0	10940.0	11368.0	0.0	11345.0	10954.0	11254.0	6267.0	5013.0	0
    g	0	0	5538.0	2117.0	86.0	333.0	1.0	11369.0	2.0	359.0	100.0	1934.0	3124.0	0
    t	0	0	1744.0	1809.0	9.0	3.0	0.0	0.0	11.0	1.0	3.0	1602.0	2165.0	0
MA1122.1_rc_shift0 (TFDP1_rc) |  |  |  |
    ; oligos_6nt_mkv2_m6 versus MA1122.1_rc (TFDP1_rc); m=2/2; ncol2=11; w=8; offset=-3; strand=R; shift=0; score=0.411274; ssTTCCCGCsc---
    ; cor=; Ncor=
    a	374.0	247.0	55.0	30.0	29.0	26.0	7.0	71.0	26.0	120.0	328.0	0	0	0
    c	648.0	648.0	137.0	98.0	1919.0	1865.0	1932.0	22.0	1862.0	940.0	777.0	0	0	0
    g	604.0	647.0	170.0	24.0	32.0	80.0	54.0	1886.0	71.0	684.0	491.0	0	0	0
    t	381.0	465.0	1645.0	1855.0	27.0	36.0	14.0	28.0	48.0	263.0	411.0	0	0	0