Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005988.1 Corchorus capsularis cultivar CVL-1 contig06006, whole genome shotgun sequence

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, 1000

Length: 13850
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29


Found at i:11169 original size:42 final size:42

Alignment explanation


    Indices: 11113--11192  Score: 151
    Period size: 42  Copynumber: 1.9  Consensus size: 42

      11103 AACCGGGATT

                                                      
      11113 TTAGTAGTAAGCGGCGTCCCCTCTTATTTTTTAGTAGGTGGA
          1 TTAGTAGTAAGCGGCGTCCCCTCTTATTTTTTAGTAGGTGGA

                              *                   
      11155 TTAGTAGTAAGCGGCGTCTCCTCTTATTTTTTAGTAGG
          1 TTAGTAGTAAGCGGCGTCCCCTCTTATTTTTTAGTAGG

      11193 ATTTTCCTCC


Statistics
Matches: 37,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  42   37  1.00

ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40


Consensus pattern (42 bp):   
TTAGTAGTAAGCGGCGTCCCCTCTTATTTTTTAGTAGGTGGA

Found at i:11271 original size:24 final size:24

Alignment explanation


    Indices: 11244--11294  Score: 66
    Period size: 24  Copynumber: 2.1  Consensus size: 24

      11234 TCGGCATTTT

                   **         *  *  
      11244 TTTTTATTCTTTTTTCAATTGCTA
          1 TTTTTATGATTTTTTCAACTGATA

                                    
      11268 TTTTTATGATTTTTTCAACTGATA
          1 TTTTTATGATTTTTTCAACTGATA

               
      11292 TTT
          1 TTT

      11295 CGATATGGAA


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.20, C:0.10, G:0.06, T:0.65


Consensus pattern (24 bp):   
TTTTTATGATTTTTTCAACTGATA
Done.