One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_8nt_mkv5_m36/peak-motifs_oligos_8nt_mkv5_m36.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_m36/peak-motifs_oligos_8nt_mkv5_m36_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: oligos_8nt_mkv5_m36_shift2 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_8nt_mkv5_m36_shift2 (oligos_8nt_mkv5_m36oligos_8nt_mkv5_m36) |
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; oligos_8nt_mkv5_m36 (oligos_8nt_mkv5_m36oligos_8nt_mkv5_m36); m=0 (reference); ncol1=12; shift=2; ncol=14; --msCTGCCACCss
; Alignment reference
a 0 0 96 24 1 2 5 1 0 258 2 0 47 38
c 0 0 88 79 270 25 6 269 265 1 270 267 85 89
g 0 0 51 135 2 12 257 0 7 14 0 5 74 117
t 0 0 38 35 0 234 5 3 1 0 1 1 67 29
|
| MA0739.1_shift4 (Hic1) |
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; oligos_8nt_mkv5_m36 versus MA0739.1 (Hic1); m=1/2; ncol2=9; w=9; offset=2; strand=D; shift=4; score=0.555312; ----rTGCCAaCc-
; cor=; Ncor=
a 0 0 0 0 6337.0 62.0 950.0 50.0 88.0 9008.0 6140.0 1220.0 1610.0 0
c 0 0 0 0 719.0 422.0 588.0 11007.0 11007.0 1999.0 1986.0 11007.0 4822.0 0
g 0 0 0 0 4670.0 73.0 11007.0 121.0 31.0 3.0 2267.0 1629.0 1884.0 0
t 0 0 0 0 666.0 11007.0 183.0 0.0 68.0 317.0 614.0 1488.0 2692.0 0
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| MA0513.1_shift0 (SMAD2::SMAD3::SMAD4) |
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; oligos_8nt_mkv5_m36 versus MA0513.1 (SMAD2::SMAD3::SMAD4); m=2/2; ncol2=13; w=11; offset=-2; strand=D; shift=0; score=0.552693; ctGTCTskCACct-
; cor=; Ncor=
a 166.0 196.0 14.0 33.0 0.0 0.0 106.0 211.0 0.0 765.0 30.0 117.0 110.0 0
c 432.0 75.0 8.0 45.0 899.0 0.0 231.0 125.0 896.0 19.0 736.0 583.0 214.0 0
g 168.0 34.0 877.0 103.0 0.0 0.0 539.0 280.0 3.0 18.0 133.0 47.0 35.0 0
t 133.0 594.0 0.0 718.0 0.0 899.0 23.0 283.0 0.0 97.0 0.0 152.0 540.0 0
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