Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013819.1 Corchorus capsularis cultivar CVL-1 contig13840, 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: 3707
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33


Found at i:349 original size:27 final size:26

Alignment explanation


    Indices: 287--358  Score: 92
    Period size: 26  Copynumber: 2.7  Consensus size: 26

        277 ATGAATTAAG

                                       
        287 AATGACCAAAATGCCCCCTAGTACAAA
          1 AATGACCAAAATG-CCCCTAGTACAAA

                            * *   *    
        314 AA-GACCAAAATGCCCTTGGATGCAAA
          1 AATGACCAAAATGCCCCTAG-TACAAA

                               
        340 AATGACCAAAATGCCCCTA
          1 AATGACCAAAATGCCCCTA

        359 TACGACTTAA


Statistics
Matches: 38,  Mismatches: 5, Indels: 4
        0.81            0.11        0.09

Matches are distributed among these distances:
  25    5  0.13
  26   17  0.45
  27   16  0.42

ACGTcount: A:0.43, C:0.28, G:0.14, T:0.15


Consensus pattern (26 bp):   
AATGACCAAAATGCCCCTAGTACAAA

Found at i:2898 original size:7 final size:7

Alignment explanation


    Indices: 2886--2917  Score: 55
    Period size: 7  Copynumber: 4.6  Consensus size: 7

       2876 AAATTTCGAA

                   
       2886 AAAAATC
          1 AAAAATC

                   
       2893 AAAAATC
          1 AAAAATC

                   
       2900 AAAAATC
          1 AAAAATC

                *  
       2907 AAAATTC
          1 AAAAATC

                
       2914 AAAA
          1 AAAA

       2918 CAAAATTTCA


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   7   24  1.00

ACGTcount: A:0.72, C:0.12, G:0.00, T:0.16


Consensus pattern (7 bp):   
AAAAATC

Found at i:2927 original size:13 final size:13

Alignment explanation


    Indices: 2887--2924  Score: 51
    Period size: 14  Copynumber: 2.9  Consensus size: 13

       2877 AATTTCGAAA

                      *  
       2887 AAAATCAAAAATC
          1 AAAATCAAAATTC

                          
       2900 AAAAATCAAAATTC
          1 -AAAATCAAAATTC

                        
       2914 AAAA-CAAAATT
          1 AAAATCAAAATT

       2925 TCATTCCAAG


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

Matches are distributed among these distances:
  12    7  0.30
  13    4  0.17
  14   12  0.52

ACGTcount: A:0.68, C:0.13, G:0.00, T:0.18


Consensus pattern (13 bp):   
AAAATCAAAATTC
Done.