Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012000.1 Corchorus olitorius cultivar O-4 contig12033, 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: 10455
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:988 original size:66 final size:66

Alignment explanation


    Indices: 911--1037  Score: 184
    Period size: 66  Copynumber: 1.9  Consensus size: 66

        901 AGTAATTCTG

                          *        *                        *                
        911 AACCTAATTTGAGTGTTGTTTG-TATTGACACGAAATCTGTTTTAGATGTTGTTAGTGATGATAC
          1 AACCTAATTTGAGTATTGTTTGCGA-TGACACGAAATCTGTTTTAGATATTGTTAGTGATGATAC

              
        975 TA
         65 TA

                                           *             *       *       
        977 AACCTAATTTGAGTATTGTTTGCGATGACACTAAATCTGTTTTAGGTATTGTTTGTGATGA
          1 AACCTAATTTGAGTATTGTTTGCGATGACACGAAATCTGTTTTAGATATTGTTAGTGATGA

       1038 AACAAATTCT


Statistics
Matches: 54,  Mismatches: 6, Indels: 2
        0.87            0.10        0.03

Matches are distributed among these distances:
  66   53  0.98
  67    1  0.02

ACGTcount: A:0.27, C:0.09, G:0.21, T:0.43


Consensus pattern (66 bp):   
AACCTAATTTGAGTATTGTTTGCGATGACACGAAATCTGTTTTAGATATTGTTAGTGATGATACT
A

Found at i:1004 original size:33 final size:33

Alignment explanation


    Indices: 967--1037  Score: 81
    Period size: 33  Copynumber: 2.2  Consensus size: 33

        957 TGTTGTTAGT

                 *                            
        967 GATGATACTAAACCTAATTTGA-GTATTGTTTGC
          1 GATGACACTAAACCT-ATTTGAGGTATTGTTTGC

                        *  *   *            *
       1000 GATGACACTAAATCTGTTTTAGGTATTGTTTGT
          1 GATGACACTAAACCTATTTGAGGTATTGTTTGC

                 
       1033 GATGA
          1 GATGA

       1038 AACAAATTCT


Statistics
Matches: 32,  Mismatches: 5, Indels: 2
        0.82            0.13        0.05

Matches are distributed among these distances:
  32    4  0.12
  33   28  0.88

ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41


Consensus pattern (33 bp):   
GATGACACTAAACCTATTTGAGGTATTGTTTGC

Found at i:1049 original size:33 final size:32

Alignment explanation


    Indices: 984--1078  Score: 93
    Period size: 33  Copynumber: 2.8  Consensus size: 32

        974 CTAAACCTAA

                           *     *            
        984 TTTGAGTATTGTTTGCGATGACACTAAA-TCTGT
          1 TTTG-GTATTGTTTGTGATGAAAC-AAATTCTGT

                                             
       1017 TTTAGGTATTGTTTGTGATGAAACAAATTCTGT
          1 TTT-GGTATTGTTTGTGATGAAACAAATTCTGT

                   *  **                 
       1050 TTTGGATGTTAATTGTGATGAAAACAAAT
          1 TTTGG-TATTGTTTGTGATG-AAACAAAT

       1079 CTATTTGGGT


Statistics
Matches: 53,  Mismatches: 5, Indels: 7
        0.82            0.08        0.11

Matches are distributed among these distances:
  32    5  0.09
  33   39  0.74
  34    9  0.17

ACGTcount: A:0.29, C:0.07, G:0.21, T:0.42


Consensus pattern (32 bp):   
TTTGGTATTGTTTGTGATGAAACAAATTCTGT
Done.