Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005675.1 Corchorus capsularis cultivar CVL-1 contig05693, 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: 2327
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:661 original size:15 final size:16

Alignment explanation


    Indices: 641--674  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

        631 GATTGCTTTC

                         *  
        641 TTAGTTA-ATTTACTT
          1 TTAGTTAGATTTAATT

                            
        656 TTAGTTAGATTTAATT
          1 TTAGTTAGATTTAATT

               
        672 TTA
          1 TTA

        675 ATTCTTCTTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    7  0.41
  16   10  0.59

ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59


Consensus pattern (16 bp):   
TTAGTTAGATTTAATT

Found at i:2053 original size:6 final size:6

Alignment explanation


    Indices: 2044--2076  Score: 66
    Period size: 6  Copynumber: 5.5  Consensus size: 6

       2034 AAAAGCAAGC

                                                  
       2044 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
          1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA

       2077 GCAGATTATA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   27  1.00

ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30


Consensus pattern (6 bp):   
AAATCT

Found at i:2088 original size:12 final size:13

Alignment explanation


    Indices: 2073--2117  Score: 74
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       2063 AATCTAAATC

                         
       2073 TAAAGCAGATT-A
          1 TAAAGCAGATTAA

                   *     
       2085 TAAAGCAAATTAA
          1 TAAAGCAGATTAA

                         
       2098 TAAAGCAGATTAA
          1 TAAAGCAGATTAA

                   
       2111 TAAAGCA
          1 TAAAGCA

       2118 AACAATAATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  12   10  0.33
  13   20  0.67

ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22


Consensus pattern (13 bp):   
TAAAGCAGATTAA

Found at i:2124 original size:25 final size:25

Alignment explanation


    Indices: 2073--2125  Score: 81
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       2063 AATCTAAATC

                                  *  
       2073 TAAAGCAGATTATAAAGCAAATTAA
          1 TAAAGCAGATTATAAAGCAAATCAA

                                      
       2098 TAAAGCAGATTAATAAAGCAAA-CAA
          1 TAAAGCAGATT-ATAAAGCAAATCAA

               
       2123 TAA
          1 TAA

       2126 TTATAAAGCA


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  25   16  0.62
  26   10  0.38

ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21


Consensus pattern (25 bp):   
TAAAGCAGATTATAAAGCAAATCAA
Done.