Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000342.1 Corchorus capsularis cultivar CVL-1 contig00342, 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: 4630
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33


Found at i:795 original size:2 final size:2

Alignment explanation


    Indices: 788--827  Score: 64
    Period size: 2  Copynumber: 20.5  Consensus size: 2

        778 CAAACGCCGT

                        *                                                
        788 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

        828 TCATATAAAA


Statistics
Matches: 35,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   34  0.97

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:1913 original size:90 final size:90

Alignment explanation


    Indices: 1757--1939  Score: 287
    Period size: 90  Copynumber: 2.0  Consensus size: 90

       1747 CTTTGCTGCT

                                                        *                    
       1757 GAGCTTTTAAGTGATATTGTTAAGAGTTTAGACAAGGATCATCAGCAGGTTCTTCGAAACAGACT
          1 GAGCTTTTAAGTGATATTGTTAAGAGTTTAGACAAGGATCATCAACAGGTTCTTCGAAACAGACT

                          *          
       1822 CTTCTTTTAAGTGATACATGGTCAA
         66 CTTCTTTTAAGTGAGACATGGTCAA

                                                            *       *     *  
       1847 GAGCTTTTAAGTGATA-TGATTAAGAGTTTAGACAAGGATCATCAACATGTTCTTCTAAACATAC
          1 GAGCTTTTAAGTGATATTG-TTAAGAGTTTAGACAAGGATCATCAACAGGTTCTTCGAAACAGAC

                             *     *  
       1911 TCTTCTTTTAAGTGAGATATGGTTAA
         65 TCTTCTTTTAAGTGAGACATGGTCAA

               
       1937 GAG
          1 GAG

       1940 TTTAGTTGTC


Statistics
Matches: 85,  Mismatches: 7, Indels: 2
        0.90            0.07        0.02

Matches are distributed among these distances:
  89    2  0.02
  90   83  0.98

ACGTcount: A:0.32, C:0.13, G:0.20, T:0.34


Consensus pattern (90 bp):   
GAGCTTTTAAGTGATATTGTTAAGAGTTTAGACAAGGATCATCAACAGGTTCTTCGAAACAGACT
CTTCTTTTAAGTGAGACATGGTCAA

Found at i:4094 original size:35 final size:36

Alignment explanation


    Indices: 4020--4116  Score: 133
    Period size: 35  Copynumber: 2.6  Consensus size: 36

       4010 ATAGTTTGAT

                      *                       *    
       4020 ATTGGGTTTCAGCTCAAAATCTTTTTAATAGTTTTAGAC
          1 ATTGGGTTTCGGCTCAAAATC---TTAATAGTTTAAGAC

                     *                          
       4059 ATTGGGTTTGGGCTCAAAATCTT-ATAGTTTAAGAC
          1 ATTGGGTTTCGGCTCAAAATCTTAATAGTTTAAGAC

                                   
       4094 ATTGGGTTTCGGCTCAAAATCTT
          1 ATTGGGTTTCGGCTCAAAATCTT

       4117 TTTGATACAT


Statistics
Matches: 54,  Mismatches: 4, Indels: 4
        0.87            0.06        0.06

Matches are distributed among these distances:
  35   33  0.61
  36    2  0.04
  39   19  0.35

ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40


Consensus pattern (36 bp):   
ATTGGGTTTCGGCTCAAAATCTTAATAGTTTAAGAC
Done.