One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep3_motifs50/results/discovered_motifs/oligos_8nt_mkv2_m21/peak-motifs_oligos_8nt_mkv2_m21.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_m21/peak-motifs_oligos_8nt_mkv2_m21_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m21_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_8nt_mkv2_m21_shift0 (oligos_8nt_mkv2_m21oligos_8nt_mkv2_m21) |
 |
|
|
; oligos_8nt_mkv2_m21 (oligos_8nt_mkv2_m21oligos_8nt_mkv2_m21); m=0 (reference); ncol1=12; shift=0; ncol=14; yTGTAGAACAkw--
; Alignment reference
a 1 0 0 0 32 0 32 32 0 32 2 14 0 0
c 16 0 0 0 0 1 0 0 30 0 0 1 0 0
g 4 1 32 0 0 31 0 0 0 0 10 1 0 0
t 11 31 0 32 0 0 0 0 2 0 20 16 0 0
|
| MA0868.2_shift4 (SOX8) |
 |
|
|
; oligos_8nt_mkv2_m21 versus MA0868.2 (SOX8); m=1/1; ncol2=10; w=8; offset=4; strand=D; shift=4; score=0.416451; ----agAACAATrg
; cor=; Ncor=
a 0 0 0 0 1827.0 740.0 1827.0 1827.0 3.0 1827.0 1827.0 273.0 1356.0 300.0
c 0 0 0 0 1124.0 414.0 151.0 0.0 1827.0 0.0 43.0 36.0 208.0 421.0
g 0 0 0 0 854.0 1827.0 263.0 0.0 35.0 0.0 0.0 20.0 1827.0 912.0
t 0 0 0 0 724.0 571.0 222.0 45.0 70.0 16.0 36.0 1827.0 287.0 193.0
|