TandemRep

Input
  Sequences set   Source file with nucleotide sequences in multiFASTA format Maximum file size is 1 GB
  Base   Select one of the configuration files:
Normal - default configuration
Sensistive - more sensitive configuration resulting in higher masking percent
Rough - more roung configuration resulting in lower masking percent
Output
  Result   Name of the output file
FormatResult presentation mode examples:
  • Output list of tandem repeat regions
    
>c20
Masked regions:
p1:  96       p2: 127      l: 31        chain(+) [Tandem Repeat]
p1: 240       p2: 262      l: 22        chain(+) [Tandem Repeat]
p1: 277       p2: 322      l: 45        chain(+) [Tandem Repeat]
    p1: - start position of the tandem region
    p2: - end position of the tandem region
    l: - length of the tandem region
    chain(+) - chain direction
  • Output sequence, masked lett. replaced with N
    
>c20
CGGTGGCGGCAGCCGGCTCAAGCCCGGGCCGCAGCTGCCTGGCCGCGGGGGCCGCCGAGCAGCGGGAGGGCCTTTGGGGG
GCGGGGCGGCGGCGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTGCTGGAAGTGCGCCTGGTCGAGACCCCGGGG
CGGGAGCTGTGGAGGATGGTCCCGGCGGGACGGGCCGCTCGGGGACAAGCGGAGCGCGCCCAAGGGCCGTCGGGCGAGGG
NNNNNNNNNNNNNNNNNNNNNNTCCCCGACACCGTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NTGAGGAAGGTGAAGAGGAGACGGTGGCGTCGGGGGAGGAGTCGCTGGGCTTTCTGTCCAGGCTGCCCCCTGGCCCGGCC
  • Output sequence, masked lett. are in upper case
    
>c20
cggtggcggcagccggctcaagcccgggccgcagctgcctggccgcgggggccgccgagcagcgggagggcctttggggg
gcggggcggcggcgccCGAGGACGACGATGAAGACGACGACGAGGAGctgctggaagtgcgcctggtcgagaccccgggg
cgggagctgtggaggatggtcccggcgggacgggccgctcggggacaagcggagcgcgcccaagggccgtcgggcgaggg
GGCGGCCGCCGCCGCCGCCGCCtccccgacaccgtcGGAGGACGAGGAGCCGGAGGAAGAGGAGGAGGAGGCGGCAGCGG
Ctgaggaaggtgaagaggagacggtggcgtcgggggaggagtcgctgggctttctgtccaggctgccccctggcccggcc
  • Output repeats during calculation (regions may overlap)
    
>seq:1  beg:96  len:31
CGAGGACGACGATGAAGACGACGACGAGGAG
>seq:1  beg:240  len:22
GGCGGCCGCCGCCGCCGCCGCC
>seq:1  beg:277  len:45
GGAGGACGAGGAGCCGGAGGAAGAGGAGGAGGAGGCGGCAGCGGC
    seq:1 - sequence number in input file
    beg: - start position of the Tandem Repeat
    len: - length of the Tandem Repeat
Options
  Minimal length   Lowest acceptable tandem region length
  Maximum diplet distance   Maximum acceptable difference in diplet composition between two windows in the tested region (from 0 to 200)
  Maximum unit size   Maximum acceptable tandem unit size
  Smith-Waterman identity   Minimum allowed identity in Smith-Waterman algorithm for repeated units
  Strict extending   Extend tandem with more strict conditions for shorter units and low monoplet complexity regions.