One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_7nt_mkv4_m24/peak-motifs_oligos_7nt_mkv4_m24.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_Rep2_motifs50/results/discovered_motifs/oligos_7nt_mkv4_m24/peak-motifs_oligos_7nt_mkv4_m24_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m24_shift2 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv4_m24_shift2 (oligos_7nt_mkv4_m24oligos_7nt_mkv4_m24) |
 |
|
|
; oligos_7nt_mkv4_m24 (oligos_7nt_mkv4_m24oligos_7nt_mkv4_m24); m=0 (reference); ncol1=12; shift=2; ncol=14; --rmTGAGCTAcas
; Alignment reference
a 0 0 43 37 2 5 122 7 3 0 125 13 51 29
c 0 0 21 46 4 0 2 1 102 1 2 85 23 37
g 0 0 40 31 1 120 4 119 2 1 1 12 32 33
t 0 0 25 15 122 4 1 2 22 127 1 19 23 30
|
| MA0793.1_rc_shift0 (POU6F2_rc) |
 |
|
|
; oligos_7nt_mkv4_m24 versus MA0793.1_rc (POU6F2_rc); m=1/2; ncol2=10; w=8; offset=-2; strand=R; shift=0; score=0.42432; wTAATkAGst----
; cor=; Ncor=
a 1278.0 53.0 3297.0 3297.0 21.0 81.0 3297.0 257.0 266.0 546.0 0 0 0 0
c 205.0 22.0 41.0 0.0 0.0 50.0 114.0 219.0 2116.0 582.0 0 0 0 0
g 546.0 27.0 12.0 4.0 75.0 2105.0 64.0 3297.0 1181.0 321.0 0 0 0 0
t 1268.0 3297.0 0.0 0.0 3297.0 1192.0 75.0 239.0 714.0 1848.0 0 0 0 0
|
| MA1542.1_shift6 (OSR1) |
 |
|
|
; oligos_7nt_mkv4_m24 versus MA1542.1 (OSR1); m=2/2; ncol2=10; w=8; offset=4; strand=D; shift=6; score=0.414422; ------yGCTACyG
; cor=; Ncor=
a 0 0 0 0 0 0 1028.0 448.0 0.0 4.0 4890.0 10.0 0.0 62.0
c 0 0 0 0 0 0 1302.0 235.0 4890.0 99.0 83.0 4890.0 2103.0 4.0
g 0 0 0 0 0 0 717.0 4890.0 0.0 0.0 38.0 0.0 5.0 4890.0
t 0 0 0 0 0 0 1843.0 17.0 18.0 4890.0 444.0 0.0 2787.0 24.0
|