Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010547.1 Corchorus capsularis cultivar CVL-1 contig10568, 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: 10388
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:308 original size:2 final size:2

Alignment explanation


    Indices: 301--325  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

        291 AAAATAACAT

                                                 
        301 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

        326 GCAGTGGCGG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:655 original size:2 final size:2

Alignment explanation


    Indices: 648--677  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

        638 AATACAAATA

                                                        
        648 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        678 GATTTGAGTC


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:2044 original size:20 final size:22

Alignment explanation


    Indices: 2018--2067  Score: 77
    Period size: 20  Copynumber: 2.4  Consensus size: 22

       2008 TCGCTTTCTA

                                  
       2018 CATATATAAACGATTAT-AAAT
          1 CATATATAAACGATTATAAAAT

                      *           
       2039 -ATATATAAATGATTATAAAAT
          1 CATATATAAACGATTATAAAAT

                    
       2060 CATATATA
          1 CATATATA

       2068 TTGGCCTATA


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  20   15  0.58
  21    4  0.15
  22    7  0.27

ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36


Consensus pattern (22 bp):   
CATATATAAACGATTATAAAAT

Found at i:7062 original size:20 final size:20

Alignment explanation


    Indices: 7023--7073  Score: 57
    Period size: 20  Copynumber: 2.5  Consensus size: 20

       7013 TGGACTTCTA

                          **    
       7023 CCCCACCACCACCAGGCCAC
          1 CCCCACCACCACCACCCCAC

                   *            
       7043 CCCCACCGCCACCACCCCAC
          1 CCCCACCACCACCACCCCAC

              *        
       7063 GCTCCACCACC
          1 -CCCCACCACC

       7074 TCTCCACCGA


Statistics
Matches: 25,  Mismatches: 5, Indels: 1
        0.81            0.16        0.03

Matches are distributed among these distances:
  20   17  0.68
  21    8  0.32

ACGTcount: A:0.22, C:0.69, G:0.08, T:0.02


Consensus pattern (20 bp):   
CCCCACCACCACCACCCCAC
Done.