Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005372.1 Corchorus capsularis cultivar CVL-1 contig05390, 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: 3879
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32


Found at i:478 original size:28 final size:29

Alignment explanation


    Indices: 443--510  Score: 111
    Period size: 29  Copynumber: 2.4  Consensus size: 29

        433 AAAAGATCAT

                      *       *          
        443 TTTAGTCCCTTCATTAT-GAATCTGTCAA
          1 TTTAGTCCCTCCATTATCAAATCTGTCAA

                                         
        471 TTTAGTCCCTCCATTATCAAATCTGTCAA
          1 TTTAGTCCCTCCATTATCAAATCTGTCAA

                       
        500 TTTAGTCCCTC
          1 TTTAGTCCCTC

        511 TACGATTAAA


Statistics
Matches: 37,  Mismatches: 2, Indels: 1
        0.93            0.05        0.03

Matches are distributed among these distances:
  28   16  0.43
  29   21  0.57

ACGTcount: A:0.24, C:0.26, G:0.09, T:0.41


Consensus pattern (29 bp):   
TTTAGTCCCTCCATTATCAAATCTGTCAA

Found at i:1959 original size:31 final size:30

Alignment explanation


    Indices: 1924--2023  Score: 85
    Period size: 31  Copynumber: 3.3  Consensus size: 30

       1914 TCTGTTAATG

                                           
       1924 GAGGGACTAAATTGACCTCTTTTCAATAGTA
          1 GAGGGACTAAATTGA-CTCTTTTCAATAGTA

                  *  *      ***        * *
       1955 GAGGGATTACATTGACAGATTTC-ATAATG
          1 GAGGGACTAAATTGACTCTTTTCAATAGTA

                       *      *            
       1984 GAGGGACTAAAATGATCTTTTTTCAATAGTA
          1 GAGGGACTAAATTGA-CTCTTTTCAATAGTA

            *        
       2015 CAGGGACTA
          1 GAGGGACTA

       2024 GGTTCTTTGA


Statistics
Matches: 51,  Mismatches: 16, Indels: 4
        0.72            0.23        0.06

Matches are distributed among these distances:
  29   16  0.31
  30   10  0.20
  31   25  0.49

ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31


Consensus pattern (30 bp):   
GAGGGACTAAATTGACTCTTTTCAATAGTA

Found at i:3775 original size:2 final size:2

Alignment explanation


    Indices: 3770--3812  Score: 77
    Period size: 2  Copynumber: 21.5  Consensus size: 2

       3760 GTGAGTTGAG

                            *                                             
       3770 AT AT AT AT AT AC 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 AT AT AT AT AT AT

             
       3812 A
          1 A

       3813 GGCTAAAGAG


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Done.