Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003884.1 Corchorus capsularis cultivar CVL-1 contig03892, 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: 2060
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.28


Found at i:768 original size:21 final size:21

Alignment explanation


    Indices: 724--769  Score: 58
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        714 GTCCCCATCC

                            *    
        724 AAATAAAAATAAAAAATAAAA
          1 AAATAAAAATAAAAAAGAAAA

                                   
        745 AAATAAAAA-AAAAGAAGAAGAA
          1 AAATAAAAATAAAA-AAGAA-AA

               
        767 AAA
          1 AAA

        770 GCACTCGGGG


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  20    4  0.18
  21   13  0.59
  22    5  0.23

ACGTcount: A:0.85, C:0.00, G:0.07, T:0.09


Consensus pattern (21 bp):   
AAATAAAAATAAAAAAGAAAA

Found at i:1585 original size:6 final size:6

Alignment explanation


    Indices: 1576--1608  Score: 66
    Period size: 6  Copynumber: 5.5  Consensus size: 6

       1566 AAAGCAAAGC

                                                  
       1576 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
          1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA

       1609 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:1620 original size:12 final size:13

Alignment explanation


    Indices: 1605--1649  Score: 74
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       1595 AATCTAAATC

                         
       1605 TAAAGCAGATT-A
          1 TAAAGCAGATTAA

                   *     
       1617 TAAAGCAAATTAA
          1 TAAAGCAGATTAA

                         
       1630 TAAAGCAGATTAA
          1 TAAAGCAGATTAA

                   
       1643 TAAAGCA
          1 TAAAGCA

       1650 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:1656 original size:25 final size:25

Alignment explanation


    Indices: 1605--1657  Score: 81
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       1595 AATCTAAATC

                                  *  
       1605 TAAAGCAGATTATAAAGCAAATTAA
          1 TAAAGCAGATTATAAAGCAAATCAA

                                      
       1630 TAAAGCAGATTAATAAAGCAAA-CAA
          1 TAAAGCAGATT-ATAAAGCAAATCAA

               
       1655 TAA
          1 TAA

       1658 TTAAAAAGCA


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.