Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023098.1 Corchorus olitorius cultivar O-4 contig23131, 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: 6291
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34


Found at i:2024 original size:33 final size:33

Alignment explanation


    Indices: 1987--2067  Score: 101
    Period size: 33  Copynumber: 2.5  Consensus size: 33

       1977 CTGTTCTAGA

                   *       *                  
       1987 TGTTGTTAGTGATGATACTAAAACTAATTTGA-G
          1 TGTTGTTTGTGATGACACTAAAACT-ATTTGAGG

                                  *  *   *   
       2020 TGTTGTTTGTGATGACACTAAATCTGTTTTAGG
          1 TGTTGTTTGTGATGACACTAAAACTATTTGAGG

                           
       2053 TGTTGTTTGTGATGA
          1 TGTTGTTTGTGATGA

       2068 AACAAATTCT


Statistics
Matches: 42,  Mismatches: 5, Indels: 2
        0.86            0.10        0.04

Matches are distributed among these distances:
  32    4  0.10
  33   38  0.90

ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44


Consensus pattern (33 bp):   
TGTTGTTTGTGATGACACTAAAACTATTTGAGG

Found at i:2079 original size:33 final size:32

Alignment explanation


    Indices: 2014--2108  Score: 102
    Period size: 33  Copynumber: 2.8  Consensus size: 32

       2004 CTAAAACTAA

                                 *            
       2014 TTTGAGTGTTGTTTGTGATGACACTAAA-TCTGT
          1 TTTG-GTGTTGTTTGTGATGAAAC-AAATTCTGT

                                             
       2047 TTTAGGTGTTGTTTGTGATGAAACAAATTCTGT
          1 TTT-GGTGTTGTTTGTGATGAAACAAATTCTGT

                    * **                 
       2080 TTTGGATGCTAATTGTGATGAAAACAAAT
          1 TTTGG-TGTTGTTTGTGATG-AAACAAAT

       2109 CTCTTGAAAA


Statistics
Matches: 54,  Mismatches: 4, Indels: 7
        0.83            0.06        0.11

Matches are distributed among these distances:
  32    5  0.09
  33   40  0.74
  34    9  0.17

ACGTcount: A:0.27, C:0.07, G:0.23, T:0.42


Consensus pattern (32 bp):   
TTTGGTGTTGTTTGTGATGAAACAAATTCTGT

Found at i:4075 original size:20 final size:21

Alignment explanation


    Indices: 4052--4094  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       4042 ATCTTGAAGA

                                 
       4052 ATTTAAAG-CCATCGGAGATC
          1 ATTTAAAGCCCATCGGAGATC

                *        *       
       4072 ATTTGAAGCCCATTGGAGATC
          1 ATTTAAAGCCCATCGGAGATC

              
       4093 AT
          1 AT

       4095 CAACAAAGGA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20    7  0.35
  21   13  0.65

ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28


Consensus pattern (21 bp):   
ATTTAAAGCCCATCGGAGATC

Done.