Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002617.1 Corchorus capsularis cultivar CVL-1 contig02625, 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, 621

Length: 1036
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:72 original size:11 final size:11

Alignment explanation


    Indices: 42--101  Score: 63
    Period size: 10  Copynumber: 5.6  Consensus size: 11

         32 TTGATTTAAT

                      *
         42 ATTTAAAT-GG
          1 ATTTAAATAGA

                       
         52 ATTT-AATAGA
          1 ATTTAAATAGA

                       
         62 ATTTAAATAGA
          1 ATTTAAATAGA

                      **
         73 ATTTTAAAT-TT
          1 A-TTTAAATAGA

                       
         84 ATTTAAATAGA
          1 ATTTAAATAGA

                   
         95 ATTTAAA
          1 ATTTAAA

        102 ATTTAATAAA


Statistics
Matches: 41,  Mismatches: 5, Indels: 7
        0.77            0.09        0.13

Matches are distributed among these distances:
   9    3  0.07
  10   16  0.39
  11   15  0.37
  12    7  0.17

ACGTcount: A:0.48, C:0.00, G:0.08, T:0.43


Consensus pattern (11 bp):   
ATTTAAATAGA

Found at i:84 original size:18 final size:19

Alignment explanation


    Indices: 42--107  Score: 55
    Period size: 22  Copynumber: 3.3  Consensus size: 19

         32 TTGATTTAAT

                      *          
         42 ATTTAAAT-GGATTTAATAGA
          1 ATTTAAATAGAATTTAA-A-A

                                 *
         62 ATTTAAATAGAATTTTAAATTT
          1 ATTTAAATAGAA-TTTAAA--A

                               
         84 ATTTAAATAGAATTT-AAA
          1 ATTTAAATAGAATTTAAAA

                  
        102 ATTTAA
          1 ATTTAA

        108 TAAAAATAAA


Statistics
Matches: 39,  Mismatches: 4, Indels: 8
        0.76            0.08        0.16

Matches are distributed among these distances:
  18    6  0.15
  20   10  0.26
  21    6  0.15
  22   17  0.44

ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44


Consensus pattern (19 bp):   
ATTTAAATAGAATTTAAAA

Found at i:87 original size:22 final size:22

Alignment explanation


    Indices: 62--106  Score: 81
    Period size: 22  Copynumber: 2.0  Consensus size: 22

         52 ATTTAATAGA

                           *      
         62 ATTTAAATAGAATTTTAAATTT
          1 ATTTAAATAGAATTTAAAATTT

                                  
         84 ATTTAAATAGAATTTAAAATTT
          1 ATTTAAATAGAATTTAAAATTT

             
        106 A
          1 A

        107 ATAAAAATAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47


Consensus pattern (22 bp):   
ATTTAAATAGAATTTAAAATTT

Found at i:111 original size:21 final size:22

Alignment explanation


    Indices: 65--111  Score: 69
    Period size: 22  Copynumber: 2.2  Consensus size: 22

         55 TAATAGAATT

                        *        *
         65 TAAATAGAATTTTAAATTTATT
          1 TAAATAGAATTTAAAATTTATA

                                  
         87 TAAATAGAATTTAAAATTTA-A
          1 TAAATAGAATTTAAAATTTATA

                
        108 TAAA
          1 TAAA

        112 AATAAAAAAA


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  21    4  0.17
  22   19  0.83

ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43


Consensus pattern (22 bp):   
TAAATAGAATTTAAAATTTATA
Done.