TandemRep-P
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
    
>EXAMPLE SEQ
Masked regions:
p1:  81       p2: 120       l: 40        chain(+) [Tandem Repeat]
p1: 191       p2: 208       l: 18        chain(+) [Tandem Repeat]
    p1: - left position of the Tandem Repeat
    p2: - right position of the Tandem Repeat
    l: - length of the Tandem Repeat
    chain(+) - chain direction
  • Output sequence, masked lett. replaced with X
    
>EXAMPLE SEQ
ASFDPHEKQLIGDLWHKVDVAHCGGEALSRMLIVYPWKRRYFENFGDISNAQAIMHNEKVQAHGKKVLASFGEAVCHLDG
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXIRAHFANLSKLHCEKLHVDPENFKLLGDIIIIVLAAHYPK
DFGLECHAAYQKLVRQVAAALAAEYHIGDLXXXXXXXXXXXXXXXXXX
  • Output sequence, masked lett. are in upper case
    
>EXAMPLE SEQ
asfdphekqligdlwhkvdvahcggealsrmlivypwkrryfenfgdisnaqaimhnekvqahgkkvlasfgeavchldg
EKEKEKEKEKEKEKEKEKEKEEKEKEKEKEKEKEKEKEKEirahfanlsklhceklhvdpenfkllgdiiiivlaahypk
dfglechaayqklvrqvaaalaaeyhigdlEKPEKPEKPEKPEKPEKP
  • Output repeats during calculation (regions may overlap)
    
>seq:1  beg:81  len:40
EKEKEKEKEKEKEKEKEKEKEEKEKEKEKEKEKEKEKEKE
>seq:1  beg:191  len:18
EKPEKPEKPEKPEKPEKP
    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.