Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005324.1 Corchorus capsularis cultivar CVL-1 contig05342, 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: 10160
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38


Found at i:3763 original size:35 final size:30

Alignment explanation


    Indices: 3698--3756  Score: 109
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       3688 TTTTAAAAGT

                                          
       3698 CTTTCTTTTTTCCCTTTTAATTTAAGAAAA
          1 CTTTCTTTTTTCCCTTTTAATTTAAGAAAA

                         *               
       3728 CTTTCTTTTTTCCTTTTTAATTTAAGAAA
          1 CTTTCTTTTTTCCCTTTTAATTTAAGAAA

       3757 TTAAAACAAA


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   28  1.00

ACGTcount: A:0.25, C:0.15, G:0.03, T:0.56


Consensus pattern (30 bp):   
CTTTCTTTTTTCCCTTTTAATTTAAGAAAA

Found at i:6742 original size:22 final size:22

Alignment explanation


    Indices: 6689--6733  Score: 81
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       6679 TTATTTTTAT

                   *              
       6689 TAAATTTTAAATTCTATTTAAA
          1 TAAATTTAAAATTCTATTTAAA

                                  
       6711 TAAATTTAAAATTCTATTTAAA
          1 TAAATTTAAAATTCTATTTAAA

             
       6733 T
          1 T

       6734 TCTATTAAAT


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49


Consensus pattern (22 bp):   
TAAATTTAAAATTCTATTTAAA

Found at i:6743 original size:10 final size:11

Alignment explanation


    Indices: 6694--6753  Score: 63
    Period size: 11  Copynumber: 5.6  Consensus size: 11

       6684 TTTATTAAAT

                       
       6694 TTTAAATTCTA
          1 TTTAAATTCTA

                    ** 
       6705 TTTAAA-TAAA
          1 TTTAAATTCTA

                        
       6715 TTTAAAATTCTA
          1 TTT-AAATTCTA

                       
       6727 TTTAAATTCTA
          1 TTTAAATTCTA

                     * 
       6738 -TTAAA-TCCA
          1 TTTAAATTCTA

                   
       6747 TTTAAAT
          1 TTTAAAT

       6754 ATTAAATAAA


Statistics
Matches: 40,  Mismatches: 5, Indels: 8
        0.75            0.09        0.15

Matches are distributed among these distances:
   9    3  0.08
  10   15  0.38
  11   17  0.43
  12    5  0.12

ACGTcount: A:0.43, C:0.08, G:0.00, T:0.48


Consensus pattern (11 bp):   
TTTAAATTCTA

Found at i:9985 original size:35 final size:31

Alignment explanation


    Indices: 9919--9978  Score: 104
    Period size: 30  Copynumber: 2.0  Consensus size: 31

       9909 TTTTAAAAGT

                                           
       9919 CTTTCTTTTTTTCCCTTTTAATTTAAGAAAA
          1 CTTTCTTTTTTTCCCTTTTAATTTAAGAAAA

                          *               
       9950 CTTTC-TTTTTTCCTTTTTAATTTAAGAAA
          1 CTTTCTTTTTTTCCCTTTTAATTTAAGAAA

       9979 TTAAAACAAA


Statistics
Matches: 28,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  30   23  0.82
  31    5  0.18

ACGTcount: A:0.25, C:0.15, G:0.03, T:0.57


Consensus pattern (31 bp):   
CTTTCTTTTTTTCCCTTTTAATTTAAGAAAA
Done.