Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001549.1 Corchorus capsularis cultivar CVL-1 contig01549, 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, 627

Length: 1045
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.28


Found at i:614 original size:27 final size:27

Alignment explanation


    Indices: 583--849  Score: 381
    Period size: 27  Copynumber: 9.4  Consensus size: 27

        573 CGGATCATTT

                                       
        583 ATGATTCGGAGGATGAGCTTCAAGAGA
          1 ATGATTCGGAGGATGAGCTTCAAGAGA

                                       
        610 ATGATTCGGAGGATGAGCTTCAAGAGA
          1 ATGATTCGGAGGATGAGCTTCAAGAGA

                                    *   * 
        637 ATGATTCGGAGGATGAGCTTCAGCGGATCA
          1 ATGATTCGGAGGATGAGCTTCA--AGA-GA

                                          
        667 TTTATGATTCGGAGGATGAGCTTCAAGAGA
          1 ---ATGATTCGGAGGATGAGCTTCAAGAGA

                                       
        697 ATGATTCGGAGGATGAGCTTCAAGAGA
          1 ATGATTCGGAGGATGAGCTTCAAGAGA

                                    *   * 
        724 ATGATTCGGAGGATGAGCTTCAGCGGATCA
          1 ATGATTCGGAGGATGAGCTTCA--AGA-GA

                                          
        754 TTTATGATTCGGAGGATGAGCTTCAAGAGA
          1 ---ATGATTCGGAGGATGAGCTTCAAGAGA

                                        
        784 ATGATTCGGAGGATGAGCTTACAAGAGA
          1 ATGATTCGGAGGATGAGCTT-CAAGAGA

                                       
        812 ATGATTCGGAGGATGAGCTTCAAGAGA
          1 ATGATTCGGAGGATGAGCTTCAAGAGA

                       
        839 ATGATTCGGAG
          1 ATGATTCGGAG

        850 TTCTTGCAGA


Statistics
Matches: 219,  Mismatches: 8, Indels: 26
        0.87            0.03        0.10

Matches are distributed among these distances:
  27  136  0.62
  28   27  0.12
  29    4  0.02
  30    4  0.02
  31    4  0.02
  33   44  0.20

ACGTcount: A:0.31, C:0.12, G:0.33, T:0.24


Consensus pattern (27 bp):   
ATGATTCGGAGGATGAGCTTCAAGAGA

Found at i:703 original size:60 final size:54

Alignment explanation


    Indices: 583--849  Score: 381
    Period size: 60  Copynumber: 4.7  Consensus size: 54

        573 CGGATCATTT

                                                                  
        583 ATGATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTTCAAGAGA
          1 ATGATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTTCAAGAGA

                                    *   *                               
        637 ATGATTCGGAGGATGAGCTTCAGCGGATCATTTATGATTCGGAGGATGAGCTTCAAGAGA
          1 ATGATTCGGAGGATGAGCTTCA--AGA-GA---ATGATTCGGAGGATGAGCTTCAAGAGA

                                                               *   * 
        697 ATGATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTTCAGCGGATCA
          1 ATGATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTTCA--AGA-GA

                                                                      
        754 TTTATGATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTTACAAGAGA
          1 ---ATGATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTT-CAAGAGA

                                                  
        812 ATGATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAG
          1 ATGATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAG

        850 TTCTTGCAGA


Statistics
Matches: 192,  Mismatches: 8, Indels: 25
        0.85            0.04        0.11

Matches are distributed among these distances:
  54   44  0.23
  55   38  0.20
  56    4  0.02
  57    3  0.02
  58    3  0.02
  59    2  0.01
  60   96  0.50
  61    2  0.01

ACGTcount: A:0.31, C:0.12, G:0.33, T:0.24


Consensus pattern (54 bp):   
ATGATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTTCAAGAGA

Found at i:717 original size:87 final size:87

Alignment explanation


    Indices: 571--833  Score: 517
    Period size: 87  Copynumber: 3.0  Consensus size: 87

        561 TTTCGGGGCA

                                                                             
        571 AGCGGATCATTTATGATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTTCAAGAG
          1 AGCGGATCATTTATGATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTTCAAGAG

                                  
        636 AATGATTCGGAGGATGAGCTTC
         66 AATGATTCGGAGGATGAGCTTC

                                                                             
        658 AGCGGATCATTTATGATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTTCAAGAG
          1 AGCGGATCATTTATGATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTTCAAGAG

                                  
        723 AATGATTCGGAGGATGAGCTTC
         66 AATGATTCGGAGGATGAGCTTC

                                                                             
        745 AGCGGATCATTTATGATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTTACAAGA
          1 AGCGGATCATTTATGATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTT-CAAGA

                                   
        810 GAATGATTCGGAGGATGAGCTTC
         65 GAATGATTCGGAGGATGAGCTTC

             
        833 A
          1 A

        834 AGAGAATGAT


Statistics
Matches: 175,  Mismatches: 0, Indels: 1
        0.99            0.00        0.01

Matches are distributed among these distances:
  87  146  0.83
  88   29  0.17

ACGTcount: A:0.30, C:0.13, G:0.32, T:0.25


Consensus pattern (87 bp):   
AGCGGATCATTTATGATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTTCAAGAG
AATGATTCGGAGGATGAGCTTC
Done.