Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016869.1 Corchorus olitorius cultivar O-4 contig16902, 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: 12192
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33


Found at i:1624 original size:27 final size:28

Alignment explanation


    Indices: 1583--1658  Score: 93
    Period size: 29  Copynumber: 2.7  Consensus size: 28

       1573 ATGTGAACTT

                      *                *
       1583 AAAATGACCAGAATGCCCCTGG-A-CGT
          1 AAAATGACCAAAATGCCCCTGGAATCGG

                                       *  
       1609 ACAAATGACCAAAATGCCCCCTGGAATTGG
          1 A-AAATGACCAAAATG-CCCCTGGAATCGG

                                
       1639 AAAATGACCAAAATGCCCCT
          1 AAAATGACCAAAATGCCCCT

       1659 AGTTGATTCT


Statistics
Matches: 43,  Mismatches: 3, Indels: 6
        0.83            0.06        0.12

Matches are distributed among these distances:
  26    1  0.02
  27   13  0.30
  28   12  0.28
  29   15  0.35
  30    2  0.05

ACGTcount: A:0.38, C:0.28, G:0.18, T:0.16


Consensus pattern (28 bp):   
AAAATGACCAAAATGCCCCTGGAATCGG

Found at i:6816 original size:19 final size:20

Alignment explanation


    Indices: 6785--6822  Score: 69
    Period size: 19  Copynumber: 1.9  Consensus size: 20

       6775 TTTTTGTATG

                                
       6785 ATTTTTATCTTTGGTGGAAC
          1 ATTTTTATCTTTGGTGGAAC

                               
       6805 ATTTTTAT-TTTGGTGGAA
          1 ATTTTTATCTTTGGTGGAA

       6823 TACTACACCC


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  19   10  0.56
  20    8  0.44

ACGTcount: A:0.21, C:0.05, G:0.21, T:0.53


Consensus pattern (20 bp):   
ATTTTTATCTTTGGTGGAAC

Found at i:7208 original size:31 final size:30

Alignment explanation


    Indices: 7137--7209  Score: 83
    Period size: 30  Copynumber: 2.4  Consensus size: 30

       7127 CCGGAAAATC

                 *             *  **      
       7137 CAATTGAGGATATAACGTTTGATGAGGTGA
          1 CAATTAAGGATATAACGTTCGAAAAGGTGA

                 *                       * 
       7167 CAATTCAGGATATAACGTTACGAAAAGGTTA
          1 CAATTAAGGATATAACGTT-CGAAAAGGTGA

                        
       7198 CAATTAAGGATA
          1 CAATTAAGGATA

       7210 ATTTCAGACG


Statistics
Matches: 36,  Mismatches: 6, Indels: 1
        0.84            0.14        0.02

Matches are distributed among these distances:
  30   18  0.50
  31   18  0.50

ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27


Consensus pattern (30 bp):   
CAATTAAGGATATAACGTTCGAAAAGGTGA

Found at i:9567 original size:19 final size:19

Alignment explanation


    Indices: 9545--9595  Score: 59
    Period size: 19  Copynumber: 2.7  Consensus size: 19

       9535 TGGCATAATG

                  *            
       9545 AGAAGATGGAAGAACCTCA
          1 AGAAGAAGGAAGAACCTCA

                     *    *   *
       9564 AGAAGAAGGGAGAAGCTCG
          1 AGAAGAAGGAAGAACCTCA

                          
       9583 AGAAGAA-GAAGAA
          1 AGAAGAAGGAAGAA

       9596 GAAGAAAAAA


Statistics
Matches: 27,  Mismatches: 5, Indels: 1
        0.82            0.15        0.03

Matches are distributed among these distances:
  18    5  0.19
  19   22  0.81

ACGTcount: A:0.51, C:0.10, G:0.33, T:0.06


Consensus pattern (19 bp):   
AGAAGAAGGAAGAACCTCA
Done.