Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014116.1 Corchorus capsularis cultivar CVL-1 contig14137, 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: 8453
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30


Found at i:3143 original size:31 final size:33

Alignment explanation


    Indices: 3083--3143  Score: 81
    Period size: 31  Copynumber: 1.9  Consensus size: 33

       3073 GTCGACTTGT

                                    *        
       3083 GTCGACTTGCTTCCTCTAATCGACTTTGCTCTA
          1 GTCGACTTGCTTCCTCTAATCGACCTTGCTCTA

                                * *       
       3116 GTCGACTT-C-TCCTCTAATTGGCCTTGCT
          1 GTCGACTTGCTTCCTCTAATCGACCTTGCT

       3144 TCTCAAAAAT


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  31   16  0.64
  32    1  0.04
  33    8  0.32

ACGTcount: A:0.13, C:0.31, G:0.16, T:0.39


Consensus pattern (33 bp):   
GTCGACTTGCTTCCTCTAATCGACCTTGCTCTA

Found at i:5640 original size:12 final size:13

Alignment explanation


    Indices: 5625--5669  Score: 74
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       5615 AATCTAAATC

                         
       5625 TAAAGCAGATT-A
          1 TAAAGCAGATTAA

                   *     
       5637 TAAAGCAAATTAA
          1 TAAAGCAGATTAA

                         
       5650 TAAAGCAGATTAA
          1 TAAAGCAGATTAA

                   
       5663 TAAAGCA
          1 TAAAGCA

       5670 AACAATAATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  12   10  0.33
  13   20  0.67

ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22


Consensus pattern (13 bp):   
TAAAGCAGATTAA

Found at i:5676 original size:25 final size:25

Alignment explanation


    Indices: 5625--5677  Score: 81
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       5615 AATCTAAATC

                                  *  
       5625 TAAAGCAGATTATAAAGCAAATTAA
          1 TAAAGCAGATTATAAAGCAAATCAA

                                      
       5650 TAAAGCAGATTAATAAAGCAAA-CAA
          1 TAAAGCAGATT-ATAAAGCAAATCAA

               
       5675 TAA
          1 TAA

       5678 TTAAAAAGCA


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  25   16  0.62
  26   10  0.38

ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21


Consensus pattern (25 bp):   
TAAAGCAGATTATAAAGCAAATCAA
Done.