Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007379.1 Corchorus capsularis cultivar CVL-1 contig07400, 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: 12361
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32


Found at i:1585 original size:48 final size:48

Alignment explanation


    Indices: 1528--1621  Score: 152
    Period size: 48  Copynumber: 2.0  Consensus size: 48

       1518 TATTTACTTT

                      *                   *        *        
       1528 TCTTTTAATTTTAGCTCTATATAATAATTAGATCTATTTTTGTGTAAG
          1 TCTTTTAATTATAGCTCTATATAATAATTACATCTATTTATGTGTAAG

                            *                             
       1576 TCTTTTAATTATAGCTTTATATAATAATTACATCTATTTATGTGTA
          1 TCTTTTAATTATAGCTCTATATAATAATTACATCTATTTATGTGTA

       1622 GGGCATACAA


Statistics
Matches: 42,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  48   42  1.00

ACGTcount: A:0.31, C:0.09, G:0.09, T:0.52


Consensus pattern (48 bp):   
TCTTTTAATTATAGCTCTATATAATAATTACATCTATTTATGTGTAAG

Found at i:3345 original size:63 final size:63

Alignment explanation


    Indices: 3267--3398  Score: 255
    Period size: 63  Copynumber: 2.1  Consensus size: 63

       3257 TCGTGATAGT

                                                                           
       3267 GCGGTGTTTCAAGATTAGAAAATGAAGCAAAGGGCAAAAGCGTAAAAAAGCGTAAAAAATGGA
          1 GCGGTGTTTCAAGATTAGAAAATGAAGCAAAGGGCAAAAGCGTAAAAAAGCGTAAAAAATGGA

                                                                          *
       3330 GCGGTGTTTCAAGATTAGAAAATGAAGCAAAGGGCAAAAGCGTAAAAAAGCGTAAAAAATGGG
          1 GCGGTGTTTCAAGATTAGAAAATGAAGCAAAGGGCAAAAGCGTAAAAAAGCGTAAAAAATGGA

                  
       3393 GCGGTG
          1 GCGGTG

       3399 AATAGCAAAA


Statistics
Matches: 68,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  63   68  1.00

ACGTcount: A:0.45, C:0.10, G:0.30, T:0.16


Consensus pattern (63 bp):   
GCGGTGTTTCAAGATTAGAAAATGAAGCAAAGGGCAAAAGCGTAAAAAAGCGTAAAAAATGGA

Found at i:5109 original size:15 final size:16

Alignment explanation


    Indices: 5091--5128  Score: 60
    Period size: 15  Copynumber: 2.4  Consensus size: 16

       5081 ATAAATTGAG

                            
       5091 TTCGGGTTAATTC-AA
          1 TTCGGGTTAATTCGAA

                          * 
       5106 TTCGGGTTAATTCGGA
          1 TTCGGGTTAATTCGAA

                   
       5122 TTCGGGT
          1 TTCGGGT

       5129 CACTTACACA


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  15   13  0.62
  16    8  0.38

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


Consensus pattern (16 bp):   
TTCGGGTTAATTCGAA

Found at i:7503 original size:19 final size:19

Alignment explanation


    Indices: 7479--7531  Score: 79
    Period size: 21  Copynumber: 2.7  Consensus size: 19

       7469 ATGAACAGGA

                               
       7479 AAACAAAGAGAGAGAGGGG
          1 AAACAAAGAGAGAGAGGGG

                            *    
       7498 AAACAAACAGAGAGAGGGGGG
          1 AAAC-AA-AGAGAGAGAGGGG

                         
       7519 AAACAAAGAGAGA
          1 AAACAAAGAGAGA

       7532 TGAGAAATGA


Statistics
Matches: 31,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  19   11  0.35
  20    4  0.13
  21   16  0.52

ACGTcount: A:0.55, C:0.08, G:0.38, T:0.00


Consensus pattern (19 bp):   
AAACAAAGAGAGAGAGGGG

Found at i:10798 original size:23 final size:24

Alignment explanation


    Indices: 10772--10822  Score: 68
    Period size: 24  Copynumber: 2.2  Consensus size: 24

      10762 AAAACAAGTT

                      *             
      10772 GTGAAAGCTTGA-TAAAAAACATG
          1 GTGAAAGCTTAATTAAAAAACATG

                           **       
      10795 GTGAAAGCTTAATTATCAAACATG
          1 GTGAAAGCTTAATTAAAAAACATG

                
      10819 GTGA
          1 GTGA

      10823 CTGAAGAAGT


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  23   11  0.46
  24   13  0.54

ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25


Consensus pattern (24 bp):   
GTGAAAGCTTAATTAAAAAACATG

Found at i:12109 original size:109 final size:110

Alignment explanation


    Indices: 11958--12254  Score: 454
    Period size: 109  Copynumber: 2.6  Consensus size: 110

      11948 TAAATTAAAA

                         **           *                                      
      11958 TGGTAAAAATAAAAAAGATTATATAAAATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGT
          1 TGGTAAAAATAAAGTA-ATTATA-AAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGT

                                                            
      12022 AGAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAA-TTTTT
         63 AGAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTTT

                                                                             
      12069 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
          1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA

                                        *                
      12134 ATAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAATTTTTT
         66 ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTTT

                                                             *            *  
      12179 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
          1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTA

                       
      12244 GTAGAATAAAA
         61 GTAGAATAAAA

      12255 CTATAATAGT


Statistics
Matches: 173,  Mismatches: 6, Indels: 10
        0.92            0.03        0.05

Matches are distributed among these distances:
 109   78  0.45
 110   50  0.29
 111   16  0.09
 112    1  0.01
 115   28  0.16

ACGTcount: A:0.49, C:0.02, G:0.11, T:0.37


Consensus pattern (110 bp):   
TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTTT
Done.