Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013340.1 Corchorus olitorius cultivar O-4 contig13373, 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: 22611
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32


Found at i:532 original size:28 final size:28

Alignment explanation


    Indices: 501--598  Score: 196
    Period size: 28  Copynumber: 3.5  Consensus size: 28

        491 AGTGCACTCG

                                        
        501 AAATGACCAAAATGCCCCTGGAGATGAA
          1 AAATGACCAAAATGCCCCTGGAGATGAA

                                        
        529 AAATGACCAAAATGCCCCTGGAGATGAA
          1 AAATGACCAAAATGCCCCTGGAGATGAA

                                        
        557 AAATGACCAAAATGCCCCTGGAGATGAA
          1 AAATGACCAAAATGCCCCTGGAGATGAA

                          
        585 AAATGACCAAAATG
          1 AAATGACCAAAATG

        599 AGAAGTAAAT


Statistics
Matches: 70,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   70  1.00

ACGTcount: A:0.45, C:0.20, G:0.20, T:0.14


Consensus pattern (28 bp):   
AAATGACCAAAATGCCCCTGGAGATGAA

Found at i:3889 original size:18 final size:18

Alignment explanation


    Indices: 3856--3907  Score: 77
    Period size: 18  Copynumber: 2.9  Consensus size: 18

       3846 AAAAAAGTGG

                    *  *      
       3856 AGAGCACATGACGCCATA
          1 AGAGCACACGATGCCATA

                 *            
       3874 AGAGCGCACGATGCCATA
          1 AGAGCACACGATGCCATA

                            
       3892 AGAGCACACGATGCCA
          1 AGAGCACACGATGCCA

       3908 CGCTTTGGGC


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   30  1.00

ACGTcount: A:0.37, C:0.29, G:0.25, T:0.10


Consensus pattern (18 bp):   
AGAGCACACGATGCCATA

Found at i:19635 original size:15 final size:15

Alignment explanation


    Indices: 19605--19646  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      19595 TTATTTTGCT

                            
      19605 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
      19621 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

                       
      19636 TTGTTTTCTGT
          1 TTGTTTTCTGT

      19647 CAACCTCTGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA
Done.