One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_6nt_m25/peak-motifs_local_words_6nt_m25.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_m25/peak-motifs_local_words_6nt_m25_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: local_words_6nt_m25_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| local_words_6nt_m25_shift0 (local_words_6nt_m25local_words_6nt_m25) |
 |
|
|
; local_words_6nt_m25 (local_words_6nt_m25local_words_6nt_m25); m=0 (reference); ncol1=24; shift=0; ncol=24; msCTGGCAGCTGCCAGCAGCaCms
; Alignment reference
a 14 9 4 5 2 3 1 42 0 1 0 0 1 1 41 3 0 38 0 4 23 5 17 10
c 12 17 37 5 3 2 45 1 0 46 2 0 38 42 0 6 42 2 2 39 9 33 17 14
g 10 18 3 4 40 38 1 3 46 0 1 46 5 2 3 37 2 3 42 3 6 6 5 14
t 11 3 3 33 2 4 0 1 1 0 44 1 3 2 3 1 3 4 3 1 9 3 8 9
|
| MA0500.2_rc_shift3 (MYOG_rc) |
 |
|
|
; local_words_6nt_m25 versus MA0500.2_rc (MYOG_rc); m=1/1; ncol2=12; w=12; offset=3; strand=R; shift=3; score=0.402748; ---sarCAGCTGyts---------
; cor=; Ncor=
a 0 0 0 5310.0 8475.0 7192.0 88.0 21777.0 95.0 169.0 163.0 182.0 1678.0 4692.0 5070.0 0 0 0 0 0 0 0 0 0
c 0 0 0 6369.0 3718.0 2706.0 21985.0 179.0 131.0 21963.0 236.0 101.0 10790.0 5483.0 5596.0 0 0 0 0 0 0 0 0 0
g 0 0 0 5660.0 5497.0 10792.0 102.0 238.0 21964.0 130.0 176.0 21988.0 2730.0 3754.0 6381.0 0 0 0 0 0 0 0 0 0
t 0 0 0 5018.0 4667.0 1667.0 182.0 163.0 167.0 95.0 21782.0 86.0 7159.0 8428.0 5310.0 0 0 0 0 0 0 0 0 0
|