One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep3_motifs50/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6.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_Rep3_motifs50/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m6_shift3 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv2_m6_shift3 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6) |
 |
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; oligos_6nt_mkv2_m6 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6); m=0 (reference); ncol1=11; shift=3; ncol=14; ---ssCCGCCGGGs
; Alignment reference
a 0 0 0 3 2 1 0 0 0 0 0 2 2 4
c 0 0 0 11 13 21 25 1 23 22 3 3 4 10
g 0 0 0 10 9 3 1 25 3 4 23 20 18 11
t 0 0 0 2 2 1 0 0 0 0 0 1 2 1
|
| MA1513.1_shift2 (KLF15) |
 |
|
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; oligos_6nt_mkv2_m6 versus MA1513.1 (KLF15); m=1/2; ncol2=11; w=10; offset=-1; strand=D; shift=2; score=0.586589; --scCCCGCCCcs-
; cor=; Ncor=
a 0 0 1184.0 937.0 40.0 93.0 0.0 0.0 11.0 55.0 12.0 1566.0 1067.0 0
c 0 0 2903.0 6506.0 11234.0 10940.0 11368.0 0.0 11345.0 10954.0 11254.0 6267.0 5013.0 0
g 0 0 5538.0 2117.0 86.0 333.0 1.0 11369.0 2.0 359.0 100.0 1934.0 3124.0 0
t 0 0 1744.0 1809.0 9.0 3.0 0.0 0.0 11.0 1.0 3.0 1602.0 2165.0 0
|
| MA1122.1_rc_shift0 (TFDP1_rc) |
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; oligos_6nt_mkv2_m6 versus MA1122.1_rc (TFDP1_rc); m=2/2; ncol2=11; w=8; offset=-3; strand=R; shift=0; score=0.411274; ssTTCCCGCsc---
; cor=; Ncor=
a 374.0 247.0 55.0 30.0 29.0 26.0 7.0 71.0 26.0 120.0 328.0 0 0 0
c 648.0 648.0 137.0 98.0 1919.0 1865.0 1932.0 22.0 1862.0 940.0 777.0 0 0 0
g 604.0 647.0 170.0 24.0 32.0 80.0 54.0 1886.0 71.0 684.0 491.0 0 0 0
t 381.0 465.0 1645.0 1855.0 27.0 36.0 14.0 28.0 48.0 263.0 411.0 0 0 0
|