One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_6nt_m28/peak-motifs_local_words_6nt_m28.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_Rep1_motifs50/results/discovered_motifs/local_words_6nt_m28/peak-motifs_local_words_6nt_m28_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: local_words_6nt_m28_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| local_words_6nt_m28_shift0 (local_words_6nt_m28local_words_6nt_m28) |
 |
|
|
; local_words_6nt_m28 (local_words_6nt_m28local_words_6nt_m28); m=0 (reference); ncol1=24; shift=0; ncol=24; scwGCTGCasCTGCAGCTGTCayc
; Alignment reference
a 9 13 25 4 2 6 2 4 32 2 1 3 1 1 50 0 2 1 0 0 3 35 5 8
c 16 24 6 1 49 4 4 40 8 32 52 1 3 50 2 4 52 0 1 1 47 10 20 30
g 18 11 9 45 1 3 46 5 6 16 0 2 50 2 0 50 0 1 52 3 3 5 13 5
t 11 6 14 4 2 41 2 5 8 4 1 48 0 1 2 0 0 52 1 50 1 4 16 11
|
| MA0499.2_shift10 (MYOD1) |
 |
|
|
; local_words_6nt_m28 versus MA0499.2 (MYOD1); m=1/1; ncol2=13; w=13; offset=10; strand=D; shift=10; score=0.43671; ----------cwgCACCTGTymy-
; cor=; Ncor=
a 0 0 0 0 0 0 0 0 0 0 7175.0 9462.0 4549.0 349.0 32281.0 463.0 534.0 241.0 208.0 402.0 1808.0 9462.0 5687.0 0
c 0 0 0 0 0 0 0 0 0 0 11279.0 7103.0 5622.0 33328.0 583.0 25275.0 32504.0 563.0 386.0 2555.0 19052.0 10485.0 11760.0 0
g 0 0 0 0 0 0 0 0 0 0 8118.0 8444.0 21884.0 354.0 849.0 7336.0 932.0 366.0 33468.0 1699.0 4440.0 6202.0 7495.0 0
t 0 0 0 0 0 0 0 0 0 0 7728.0 9291.0 2245.0 269.0 587.0 1226.0 330.0 33130.0 238.0 29644.0 9000.0 8151.0 9358.0 0
|