Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008339.1 Corchorus olitorius cultivar O-4 contig08366, 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, 636

Length: 1061
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28


Found at i:495 original size:38 final size:38

Alignment explanation


    Indices: 437--518  Score: 110
    Period size: 38  Copynumber: 2.1  Consensus size: 38

        427 GGCCTGCCTG

                           *                       
        437 GCGCTGGCCCAAGCGTGCCAGGCCAAGCACGCTGGGCCA
          1 GCGC-GGCCCAAGCGCGCCAGGCCAAGCACGCTGGGCCA

                      *          *  *  *          
        476 GCGCGGCCCAGGCGCGCCAGGGCAGGCGCGCTGGGCCA
          1 GCGCGGCCCAAGCGCGCCAGGCCAAGCACGCTGGGCCA

                 
        514 GCGCG
          1 GCGCG

        519 CGGCCCAGCT


Statistics
Matches: 38,  Mismatches: 5, Indels: 1
        0.86            0.11        0.02

Matches are distributed among these distances:
  38   34  0.89
  39    4  0.11

ACGTcount: A:0.13, C:0.39, G:0.43, T:0.05


Consensus pattern (38 bp):   
GCGCGGCCCAAGCGCGCCAGGCCAAGCACGCTGGGCCA

Found at i:641 original size:4 final size:4

Alignment explanation


    Indices: 632--669  Score: 58
    Period size: 4  Copynumber: 9.0  Consensus size: 4

        622 CCTGGACCAA

                                                          
        632 AAAT AAAT AAAT AAAT AAAT AAAT AAAAT AAAAT AAAT
          1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT -AAAT AAAT

        670 TAGGTAAAAT


Statistics
Matches: 33,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   4   24  0.73
   5    9  0.27

ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24


Consensus pattern (4 bp):   
AAAT

Found at i:792 original size:27 final size:26

Alignment explanation


    Indices: 738--798  Score: 68
    Period size: 27  Copynumber: 2.3  Consensus size: 26

        728 GACCATTTTG

                               *   *  
        738 CCCTTAGATGTTAAATCACTAAATTA
          1 CCCTTAGATGTTAAATCACGAAACTA

                    *        *         
        764 CCCTTAAGTTGTTAAATTACGAAACTA
          1 CCCTT-AGATGTTAAATCACGAAACTA

               *    
        791 CCCATAGA
          1 CCCTTAGA

        799 AGAGAAATTT


Statistics
Matches: 28,  Mismatches: 6, Indels: 2
        0.78            0.17        0.06

Matches are distributed among these distances:
  26    7  0.25
  27   21  0.75

ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31


Consensus pattern (26 bp):   
CCCTTAGATGTTAAATCACGAAACTA
Done.