One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_8nt_mkv5_m16/peak-motifs_oligos_8nt_mkv5_m16.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_8nt_mkv5_m16/peak-motifs_oligos_8nt_mkv5_m16_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: oligos_8nt_mkv5_m16_shift2 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_8nt_mkv5_m16_shift2 (oligos_8nt_mkv5_m16oligos_8nt_mkv5_m16) |
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; oligos_8nt_mkv5_m16 (oligos_8nt_mkv5_m16oligos_8nt_mkv5_m16); m=0 (reference); ncol1=12; shift=2; ncol=14; --vsCACAGGCAsc
; Alignment reference
a 0 0 55 31 1 169 0 163 1 0 2 167 16 38
c 0 0 45 66 164 0 170 1 9 0 169 0 46 77
g 0 0 45 46 2 3 0 8 161 172 1 5 73 38
t 0 0 27 29 5 0 2 0 1 0 0 0 37 19
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| MA0002.2_rc_shift0 (RUNX1_rc) |
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; oligos_8nt_mkv5_m16 versus MA0002.2_rc (RUNX1_rc); m=1/1; ncol2=11; w=9; offset=-2; strand=R; shift=0; score=0.481034; waaCCACAram---
; cor=; Ncor=
a 1053.0 1325.0 1339.0 93.0 13.0 1716.0 53.0 1936.0 656.0 814.0 521.0 0 0 0
c 289.0 81.0 251.0 1848.0 1987.0 70.0 1872.0 7.0 149.0 467.0 696.0 0 0 0
g 158.0 463.0 400.0 42.0 0.0 127.0 75.0 0.0 1072.0 485.0 496.0 0 0 0
t 500.0 131.0 10.0 17.0 0.0 87.0 0.0 57.0 123.0 234.0 287.0 0 0 0
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