Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010416.1 Corchorus capsularis cultivar CVL-1 contig10437, 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: 8520
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30


Found at i:234 original size:21 final size:22

Alignment explanation


    Indices: 192--237  Score: 58
    Period size: 21  Copynumber: 2.1  Consensus size: 22

        182 AAAAATTATA

                            **    
        192 AAAAGAGGGAGCGGTATTTAGC
          1 AAAAGAGGGAGCGGTAAATAGC

                 *                
        214 AAAAGGGGGA-CGGTAAATAGC
          1 AAAAGAGGGAGCGGTAAATAGC

               
        235 AAA
          1 AAA

        238 CCCCATTTAA


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  21   12  0.57
  22    9  0.43

ACGTcount: A:0.43, C:0.09, G:0.35, T:0.13


Consensus pattern (22 bp):   
AAAAGAGGGAGCGGTAAATAGC

Found at i:1790 original size:21 final size:22

Alignment explanation


    Indices: 1760--1800  Score: 66
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       1750 TAAAAGTGTA

                                  
       1760 AAAAAGGGGGACGGTATTTAAC
          1 AAAAAGGGGGACGGTATTTAAC

                           *    
       1782 AAAAAGGGGG-CGGTGTTTA
          1 AAAAAGGGGGACGGTATTTA

       1801 GCCCACAATA


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

Matches are distributed among these distances:
  21    8  0.44
  22   10  0.56

ACGTcount: A:0.37, C:0.07, G:0.37, T:0.20


Consensus pattern (22 bp):   
AAAAAGGGGGACGGTATTTAAC

Found at i:8032 original size:3 final size:3

Alignment explanation


    Indices: 8024--8061  Score: 76
    Period size: 3  Copynumber: 12.7  Consensus size: 3

       8014 TACATAACAA

                                                              
       8024 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT

       8062 AAGTATTCTA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   35  1.00

ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66


Consensus pattern (3 bp):   
ATT

Done.