Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_16399

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 360

Length: 600
ACGTcount: A:0.27, C:0.16, G:0.35, T:0.21


Found at i:302 original size:36 final size:35

Alignment explanation


    Indices: 254--344  Score: 121
    Period size: 36  Copynumber: 2.5  Consensus size: 35

        244 GTTGGTCGTG

                   *           *                
        254 GGGGAGGTGGAGGTGGTGGCGGC-GGGGGTGGAGGT
          1 GGGGAGGAGGAGGTGGTGGAGGCGGGGGGTGG-GGT

                             *                   
        289 GGAGGAGGAGGAGGTGGCGGAGGCGGGGGGTGGGGAT
          1 GG-GGAGGAGGAGGTGGTGGAGGCGGGGGGTGGGG-T

                               
        326 GGGGAGGAGGAGGTGGTGG
          1 GGGGAGGAGGAGGTGGTGG

        345 TTGGTATAAA


Statistics
Matches: 49,  Mismatches: 4, Indels: 5
        0.84            0.07        0.09

Matches are distributed among these distances:
  35    2  0.04
  36   36  0.73
  37   11  0.22

ACGTcount: A:0.13, C:0.04, G:0.71, T:0.11


Consensus pattern (35 bp):   
GGGGAGGAGGAGGTGGTGGAGGCGGGGGGTGGGGT

Found at i:304 original size:21 final size:21

Alignment explanation


    Indices: 256--305  Score: 64
    Period size: 21  Copynumber: 2.4  Consensus size: 21

        246 TGGTCGTGGG

                          *  *  *
        256 GGAGGTGGAGGTGGTGGCGGC
          1 GGAGGTGGAGGTGGAGGAGGA

              *                  
        277 GGGGGTGGAGGTGGAGGAGGA
          1 GGAGGTGGAGGTGGAGGAGGA

                    
        298 GGAGGTGG
          1 GGAGGTGG

        306 CGGAGGCGGG


Statistics
Matches: 24,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.14, C:0.04, G:0.70, T:0.12


Consensus pattern (21 bp):   
GGAGGTGGAGGTGGAGGAGGA
Done.