Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012747.1 Corchorus capsularis cultivar CVL-1 contig12768, 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, 712

Length: 1188
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27


Found at i:101 original size:37 final size:34

Alignment explanation


    Indices: 1--103  Score: 100
    Period size: 34  Copynumber: 2.9  Consensus size: 34

                *         *                    
          1 AAATAGTAAAGAGTGAAGAG-AAGTCAGTAAAGAA
          1 AAATGGTAAAGAGTAAAGAGTAA-TCAGTAAAGAA

            *      *                            
         35 GAATGGTGAAGAGTAAAGAGTAATCCAGTAAAGAAA
          1 AAATGGTAAAGAGTAAAGAGTAAT-CAGTAAAG-AA

                               * *           
         71 AAAGTGGTAAAGAGTAAAATATTAATCAGTAAA
          1 AAA-TGGTAAAGAGT-AAAGAGTAATCAGTAAA

        104 AAGGTAATGG


Statistics
Matches: 56,  Mismatches: 8, Indels: 7
        0.79            0.11        0.10

Matches are distributed among these distances:
  34   17  0.30
  35   10  0.18
  36    4  0.07
  37   17  0.30
  38    8  0.14

ACGTcount: A:0.53, C:0.04, G:0.24, T:0.18


Consensus pattern (34 bp):   
AAATGGTAAAGAGTAAAGAGTAATCAGTAAAGAA

Found at i:188 original size:21 final size:21

Alignment explanation


    Indices: 128--194  Score: 64
    Period size: 21  Copynumber: 3.1  Consensus size: 21

        118 CAGCAAAGAA

                  *      *        
        128 TAAAATGGTAACTAGTAATCAG
          1 TAAAATAGTAA-TGGTAATCAG

              *        *  *       
        150 TACAA-AGTAAAGAATAATCAG
          1 TAAAATAGTAATG-GTAATCAG

                                 
        171 TAAAATAGTAATGGTAATCAG
          1 TAAAATAGTAATGGTAATCAG

               
        192 TAA
          1 TAA

        195 TTCAGTAAAG


Statistics
Matches: 35,  Mismatches: 8, Indels: 5
        0.73            0.17        0.10

Matches are distributed among these distances:
  21   25  0.71
  22   10  0.29

ACGTcount: A:0.51, C:0.07, G:0.16, T:0.25


Consensus pattern (21 bp):   
TAAAATAGTAATGGTAATCAG
Done.