Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013065.1 Corchorus capsularis cultivar CVL-1 contig13086, 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: 13007
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33


Found at i:3821 original size:70 final size:69

Alignment explanation


    Indices: 3705--3844  Score: 271
    Period size: 70  Copynumber: 2.0  Consensus size: 69

       3695 AGATCATGAA

                                                                             
       3705 TTGAGTATTTAACCAAAAAGTAAGTACGAAATGGTCACCCAACTTGTTATTTGGTCGCACTACCC
          1 TTGAGTATTTAACCAAAAAGTAAGTACGAAATGGTCACCCAACTTGTTATTTGGTCGCACTACCC

                
       3770 AACT
         66 AACT

                                                                             
       3774 TTGAGTATTTAACCAAAAAGTAAGGTACGAAATGGTCACCCAACTTGTTATTTGGTCGCACTACC
          1 TTGAGTATTTAACCAAAAAGTAA-GTACGAAATGGTCACCCAACTTGTTATTTGGTCGCACTACC

                 
       3839 CAACT
         65 CAACT

             
       3844 T
          1 T

       3845 CGATTTAAAA


Statistics
Matches: 70,  Mismatches: 0, Indels: 1
        0.99            0.00        0.01

Matches are distributed among these distances:
  69   23  0.33
  70   47  0.67

ACGTcount: A:0.33, C:0.21, G:0.16, T:0.29


Consensus pattern (69 bp):   
TTGAGTATTTAACCAAAAAGTAAGTACGAAATGGTCACCCAACTTGTTATTTGGTCGCACTACCC
AACT

Found at i:4321 original size:40 final size:40

Alignment explanation


    Indices: 4263--4343  Score: 119
    Period size: 40  Copynumber: 2.0  Consensus size: 40

       4253 TTTATAACTA

                                   *                
       4263 GGGGCTAAACCTGAATTTAAATTCTTACCTTAATTATTAG
          1 GGGGCTAAACCTGAATTTAAATTATTACCTTAATTATTAG

                                 *     *             
       4303 GGGGCTAAACCT-AGATTTAATTTATTTCCTTAATTATTAG
          1 GGGGCTAAACCTGA-ATTTAAATTATTACCTTAATTATTAG

             
       4343 G
          1 G

       4344 AGGGATAAGT


Statistics
Matches: 37,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  39    1  0.03
  40   36  0.97

ACGTcount: A:0.31, C:0.14, G:0.16, T:0.40


Consensus pattern (40 bp):   
GGGGCTAAACCTGAATTTAAATTATTACCTTAATTATTAG

Found at i:7051 original size:12 final size:12

Alignment explanation


    Indices: 7016--7051  Score: 54
    Period size: 12  Copynumber: 2.9  Consensus size: 12

       7006 CAAAATAAAG

                         
       7016 TTTTGTTTTTTTC
          1 TTTT-TTTTTTTC

                 *      
       7029 TTTTTCTTTTTC
          1 TTTTTTTTTTTC

                       
       7041 TTTTTTTTTTT
          1 TTTTTTTTTTT

       7052 TGATGTAACG


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  12   17  0.81
  13    4  0.19

ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89


Consensus pattern (12 bp):   
TTTTTTTTTTTC

Found at i:7930 original size:2 final size:2

Alignment explanation


    Indices: 7923--7957  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       7913 TAACAACCAA

                                                                
       7923 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 A

       7958 ACAACAGAAT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:12859 original size:2 final size:2

Alignment explanation


    Indices: 12852--12886  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      12842 TAACAACCAA

                                                                
      12852 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 A

      12887 ACAACAGAAT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

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


Consensus pattern (2 bp):   
AT

Done.