Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007257.1 Corchorus capsularis cultivar CVL-1 contig07278, 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: 18108
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:544 original size:33 final size:33

Alignment explanation


    Indices: 507--615  Score: 130
    Period size: 33  Copynumber: 3.3  Consensus size: 33

        497 TATTTTTATT

                    *                        
        507 GCAAACAATACTCAAATTAGGTTTAGTATCATC
          1 GCAAACAACACTCAAATTAGGTTTAGTATCATC

                             **  *      *    *
        540 GCAAACAACA-TCTAAAACAGATTTAGTGTCATT
          1 GCAAACAACACTC-AAATTAGGTTTAGTATCATC

              *         *                    
        573 GCTAACAACACTAAAATTAGGTTTAGTATCATC
          1 GCAAACAACACTCAAATTAGGTTTAGTATCATC

                      
        606 GCAAACAACA
          1 GCAAACAACA

        616 TCTAAAACAC


Statistics
Matches: 60,  Mismatches: 14, Indels: 4
        0.77            0.18        0.05

Matches are distributed among these distances:
  32    2  0.03
  33   57  0.95
  34    1  0.02

ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27


Consensus pattern (33 bp):   
GCAAACAACACTCAAATTAGGTTTAGTATCATC

Found at i:564 original size:66 final size:66

Alignment explanation


    Indices: 482--624  Score: 223
    Period size: 66  Copynumber: 2.2  Consensus size: 66

        472 TTACAATTAG

                *            * * *           *   *                           
        482 CATCCAAAACAGATTTATTTTTATTGCAAACAATACTCAAATTAGGTTTAGTATCATCGCAAACA
          1 CATCTAAAACAGATTTAGTGTCATTGCAAACAACACTAAAATTAGGTTTAGTATCATCGCAAACA

             
        547 A
         66 A

                                       *                                     
        548 CATCTAAAACAGATTTAGTGTCATTGCTAACAACACTAAAATTAGGTTTAGTATCATCGCAAACA
          1 CATCTAAAACAGATTTAGTGTCATTGCAAACAACACTAAAATTAGGTTTAGTATCATCGCAAACA

             
        613 A
         66 A

                       
        614 CATCTAAAACA
          1 CATCTAAAACA

        625 CTTTTTTCAA


Statistics
Matches: 70,  Mismatches: 7, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  66   70  1.00

ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29


Consensus pattern (66 bp):   
CATCTAAAACAGATTTAGTGTCATTGCAAACAACACTAAAATTAGGTTTAGTATCATCGCAAACA
A

Found at i:5210 original size:18 final size:19

Alignment explanation


    Indices: 5187--5224  Score: 60
    Period size: 18  Copynumber: 2.1  Consensus size: 19

       5177 GTGCATGGGC

                      *        
       5187 TGCATGGAG-GCATGGAGA
          1 TGCATGGAGACCATGGAGA

                               
       5205 TGCATGGAGACCATGGAGA
          1 TGCATGGAGACCATGGAGA

             
       5224 T
          1 T

       5225 AACGATGGAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18    9  0.50
  19    9  0.50

ACGTcount: A:0.29, C:0.13, G:0.39, T:0.18


Consensus pattern (19 bp):   
TGCATGGAGACCATGGAGA

Found at i:6714 original size:10 final size:10

Alignment explanation


    Indices: 6699--6723  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

       6689 TCATTTTCCT

                      
       6699 ATGCTTTTGA
          1 ATGCTTTTGA

                      
       6709 ATGCTTTTGA
          1 ATGCTTTTGA

                 
       6719 ATGCT
          1 ATGCT

       6724 AGATTTTGCC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.20, C:0.12, G:0.20, T:0.48


Consensus pattern (10 bp):   
ATGCTTTTGA
Done.