Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010047.1 Corchorus capsularis cultivar CVL-1 contig10068, 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: 11216
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36


Found at i:3629 original size:6 final size:6

Alignment explanation


    Indices: 3615--3645  Score: 53
    Period size: 6  Copynumber: 5.2  Consensus size: 6

       3605 TAAATAGGTC

                *                               
       3615 TCGTCT TCGTGT TCGTGT TCGTGT TCGTGT T
          1 TCGTGT TCGTGT TCGTGT TCGTGT TCGTGT T

       3646 TGGATTTCGT


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.00, C:0.19, G:0.29, T:0.52


Consensus pattern (6 bp):   
TCGTGT

Found at i:4535 original size:2 final size:2

Alignment explanation


    Indices: 4528--4554  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       4518 CTTGTACATA

                                                    
       4528 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 A

       4555 ATAATGCACT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:7157 original size:19 final size:20

Alignment explanation


    Indices: 7117--7158  Score: 59
    Period size: 21  Copynumber: 2.1  Consensus size: 20

       7107 AAAAAATTGC

                        *        
       7117 ATTAGTAGTTTTTTTTAATGA
          1 ATTAGTAGTTTTGTTT-ATGA

                                
       7138 ATTAGTAGTTTTGTTT-TGA
          1 ATTAGTAGTTTTGTTTATGA

              
       7157 AT
          1 AT

       7159 CTTTTGATGT


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  19    5  0.25
  21   15  0.75

ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57


Consensus pattern (20 bp):   
ATTAGTAGTTTTGTTTATGA

Found at i:9776 original size:26 final size:28

Alignment explanation


    Indices: 9723--9776  Score: 76
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       9713 TTACTCAACT

                                **      
       9723 AAAAACTCTATTTTTATTTTTCTGTAAA
          1 AAAAACTCTATTTTTATTTTAATGTAAA

                                        
       9751 AAAAACTCTATTTTTA-TTTAAT-TAAA
          1 AAAAACTCTATTTTTATTTTAATGTAAA

       9777 TCTAATATCC


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  26    4  0.17
  27    4  0.17
  28   16  0.67

ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48


Consensus pattern (28 bp):   
AAAAACTCTATTTTTATTTTAATGTAAA
Done.