One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/oligos_6nt_mkv4_m11/peak-motifs_oligos_6nt_mkv4_m11.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/oligos_6nt_mkv4_m11/peak-motifs_oligos_6nt_mkv4_m11_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m11_shift2 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv4_m11_shift2 (oligos_6nt_mkv4_m11oligos_6nt_mkv4_m11) |
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; oligos_6nt_mkv4_m11 (oligos_6nt_mkv4_m11oligos_6nt_mkv4_m11); m=0 (reference); ncol1=12; shift=2; ncol=14; --ssGCGGAGCGss
; Alignment reference
a 0 0 919 744 134 37 22 68 4369 93 39 369 770 989
c 0 0 1967 2233 436 5797 213 234 884 180 5740 799 2098 1742
g 0 0 2498 2375 5272 118 5750 5640 595 5670 185 4368 2351 2539
t 0 0 617 649 159 49 16 59 153 58 37 465 782 731
|
| MA1513.1_rc_shift0 (KLF15_rc) |
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; oligos_6nt_mkv4_m11 versus MA1513.1_rc (KLF15_rc); m=1/1; ncol2=11; w=9; offset=-2; strand=R; shift=0; score=0.458253; sgGGGCGGGgs---
; cor=; Ncor=
a 2165.0 1602.0 3.0 1.0 11.0 0.0 0.0 3.0 9.0 1809.0 1744.0 0 0 0
c 3124.0 1934.0 100.0 359.0 2.0 11369.0 1.0 333.0 86.0 2117.0 5538.0 0 0 0
g 5013.0 6267.0 11254.0 10954.0 11345.0 0.0 11368.0 10940.0 11234.0 6506.0 2903.0 0 0 0
t 1067.0 1566.0 12.0 55.0 11.0 0.0 0.0 93.0 40.0 937.0 1184.0 0 0 0
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