# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m29/peak-motifs_dyads_m29.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/dyads_m29/peak-motifs_dyads_m29_vs_db_jaspar_core_nonredundant_vertebrates

## One-to-n matrix alignment; reference matrix: dyads_m29_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m29_shift2 (dyads_m29dyads_m29) |  |  |  |
    ; dyads_m29 (dyads_m29dyads_m29); m=0 (reference); ncol1=12; shift=2; ncol=14; --AmTGArAAAyry
    ; Alignment reference
    a	0	0	139	98	0	2	163	55	163	162	163	14	104	6
    c	0	0	4	43	9	0	0	0	0	0	0	103	6	87
    g	0	0	14	19	0	160	0	108	0	0	0	0	48	5
    t	0	0	6	3	154	1	0	0	0	1	0	46	5	65
MA1549.1_shift0 (POU6F1(var.2)) |  |  |  |
    ; dyads_m29 versus MA1549.1 (POU6F1(var.2)); m=1/2; ncol2=10; w=8; offset=-2; strand=D; shift=0; score=0.42953; rTAATGAGst----
    ; cor=; Ncor=
    a	2756.0	164.0	6413.0	6413.0	0.0	67.0	6413.0	314.0	1972.0	1577.0	0	0	0	0
    c	416.0	273.0	179.0	0.0	0.0	206.0	96.0	851.0	3065.0	1238.0	0	0	0	0
    g	1930.0	10.0	255.0	0.0	298.0	5799.0	0.0	6413.0	3348.0	1534.0	0	0	0	0
    t	1312.0	6413.0	0.0	0.0	6413.0	615.0	411.0	1855.0	1462.0	2064.0	0	0	0	0
MA0033.2_shift6 (FOXL1) |  |  |  |
    ; dyads_m29 versus MA0033.2 (FOXL1); m=2/2; ncol2=7; w=7; offset=4; strand=D; shift=6; score=0.40889; ------rTAAACA-
    ; cor=; Ncor=
    a	0	0	0	0	0	0	2102.0	10.0	4780.0	4780.0	4780.0	0.0	4780.0	0
    c	0	0	0	0	0	0	13.0	416.0	628.0	38.0	82.0	3723.0	54.0	0
    g	0	0	0	0	0	0	2678.0	0.0	57.0	0.0	50.0	0.0	0.0	0
    t	0	0	0	0	0	0	140.0	4780.0	0.0	15.0	0.0	1057.0	17.0	0