Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014549.1 Corchorus capsularis cultivar CVL-1 contig14570, 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: 15030
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32


Found at i:133 original size:2 final size:2

Alignment explanation


    Indices: 126--164  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

        116 AGGGTTACTA

                                                                      
        126 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

        165 CGAGATTTTC


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:6058 original size:60 final size:60

Alignment explanation


    Indices: 5971--6128  Score: 192
    Period size: 60  Copynumber: 2.6  Consensus size: 60

       5961 ATTGTTCAAT

                  *                                 *                 *   
       5971 TAAGGGTCTAATGTT-TACCAAAAATGCTCAAATAAGGGCTCAATCTTTTAATTTGGCTAAA
          1 TAAGGGCCTAATGTTATA--AAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGCCAAA

                                                *   **                * 
       6032 TAAGGGCCTAATGTTATAAAAAATGCTCAAATAAGGACCCGGTCTTTTAATTTGGCCACA
          1 TAAGGGCCTAATGTTATAAAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGCCAAA

                       *     **     *            
       6092 TAAGGGCCTAACGTTATCGAAAATACTCAAATAAGGG
          1 TAAGGGCCTAATGTTATAAAAAATGCTCAAATAAGGG

       6129 TCTAACGTTA


Statistics
Matches: 84,  Mismatches: 12, Indels: 3
        0.85            0.12        0.03

Matches are distributed among these distances:
  60   68  0.81
  61   14  0.17
  62    2  0.02

ACGTcount: A:0.37, C:0.16, G:0.18, T:0.28


Consensus pattern (60 bp):   
TAAGGGCCTAATGTTATAAAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGCCAAA

Found at i:6134 original size:31 final size:31

Alignment explanation


    Indices: 6091--6162  Score: 117
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       6081 ATTTGGCCAC

                                           
       6091 ATAAGGGCCTAACGTTATCGAAAATACTCAA
          1 ATAAGGGCCTAACGTTATCGAAAATACTCAA

                   *                 *     
       6122 ATAAGGGTCTAACGTTATCGAAAATGCTCAA
          1 ATAAGGGCCTAACGTTATCGAAAATACTCAA

                *     
       6153 ATAAAGGCCT
          1 ATAAGGGCCT

       6163 GGTGGCAGTT


Statistics
Matches: 37,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  31   37  1.00

ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24


Consensus pattern (31 bp):   
ATAAGGGCCTAACGTTATCGAAAATACTCAA

Found at i:7482 original size:1 final size:1

Alignment explanation


    Indices: 7476--7514  Score: 78
    Period size: 1  Copynumber: 39.0  Consensus size: 1

       7466 TCATTCATTT

                                                   
       7476 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

       7515 CCCAACTCTT


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   38  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Done.