Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016062.1 Corchorus olitorius cultivar O-4 contig16095, 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: 4365
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.32


Found at i:1831 original size:19 final size:19

Alignment explanation


    Indices: 1807--1846  Score: 62
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       1797 AGAATATTCA

                          *    
       1807 TGTGTGAAATATTCGTATG
          1 TGTGTGAAATATTCATATG

                  *            
       1826 TGTGTGGAATATTCATATG
          1 TGTGTGAAATATTCATATG

              
       1845 TG
          1 TG

       1847 AATGTGTGTG


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.25, C:0.05, G:0.28, T:0.42


Consensus pattern (19 bp):   
TGTGTGAAATATTCATATG

Found at i:1883 original size:47 final size:46

Alignment explanation


    Indices: 1807--1923  Score: 180
    Period size: 47  Copynumber: 2.5  Consensus size: 46

       1797 AGAATATTCA

                                    *                     
       1807 TGTGTGAAATATTCGTATGTGTGTGGAATATTCATATGTGAATGTG
          1 TGTGTGAAATATTCGTATGTGTGTAGAATATTCATATGTGAATGTG

                   *      *                                
       1853 TGTGTGAGATATTTTGTATGTGTGTAGAATATTCATATGTGAATGTG
          1 TGTGTGAAATA-TTCGTATGTGTGTAGAATATTCATATGTGAATGTG

                  *       *         
       1900 TGTGTGGAATATTCATATGTGTGT
          1 TGTGTGAAATATTCGTATGTGTGT

       1924 GTGGTGCAGC


Statistics
Matches: 63,  Mismatches: 7, Indels: 2
        0.88            0.10        0.03

Matches are distributed among these distances:
  46   21  0.33
  47   42  0.67

ACGTcount: A:0.25, C:0.03, G:0.28, T:0.44


Consensus pattern (46 bp):   
TGTGTGAAATATTCGTATGTGTGTAGAATATTCATATGTGAATGTG

Found at i:1926 original size:27 final size:27

Alignment explanation


    Indices: 1824--1920  Score: 120
    Period size: 27  Copynumber: 3.9  Consensus size: 27

       1814 AATATTCGTA

                                       
       1824 TGTGTGTGGAATATTCATATGTGAATG
          1 TGTGTGTGGAATATTCATATGTGAATG

                                        
       1851 TGTGTGT-GAGATATT--T-TGT--A--
          1 TGTGTGTGGA-ATATTCATATGTGAATG

                   *                   
       1871 TGTGTGTAGAATATTCATATGTGAATG
          1 TGTGTGTGGAATATTCATATGTGAATG

                                   
       1898 TGTGTGTGGAATATTCATATGTG
          1 TGTGTGTGGAATATTCATATGTG

       1921 TGTGTGGTGC


Statistics
Matches: 60,  Mismatches: 1, Indels: 18
        0.76            0.01        0.23

Matches are distributed among these distances:
  20   12  0.20
  21    2  0.03
  22    2  0.03
  23    3  0.05
  24    3  0.05
  25    2  0.03
  26    2  0.03
  27   34  0.57

ACGTcount: A:0.25, C:0.03, G:0.29, T:0.43


Consensus pattern (27 bp):   
TGTGTGTGGAATATTCATATGTGAATG
Done.