Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009807.1 Corchorus capsularis cultivar CVL-1 contig09828, 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: 2607
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34


Found at i:1757 original size:16 final size:17

Alignment explanation


    Indices: 1723--1817  Score: 101
    Period size: 16  Copynumber: 5.8  Consensus size: 17

       1713 TCGGGCCATT

                              
       1723 TTCGGGTTCGGGCTTGAA
          1 TTCGGGTTCGGG-TTGAA

                             
       1741 -TCGGGTTCGGGTTGAA
          1 TTCGGGTTCGGGTTGAA

              *      *       
       1757 TTTGGG-TCAGGTT-AA
          1 TTCGGGTTCGGGTTGAA

                 *           
       1772 TTCGGTTTCGGGTTGAA
          1 TTCGGGTTCGGGTTGAA

              *      *       
       1789 TTTGGG-TCAGGTT-AA
          1 TTCGGGTTCGGGTTGAA

                          
       1804 TTCGGGTTCGGGTT
          1 TTCGGGTTCGGGTT

       1818 CAGTTTGGGT


Statistics
Matches: 63,  Mismatches: 10, Indels: 10
        0.76            0.12        0.12

Matches are distributed among these distances:
  15   13  0.21
  16   29  0.46
  17   21  0.33

ACGTcount: A:0.13, C:0.12, G:0.38, T:0.38


Consensus pattern (17 bp):   
TTCGGGTTCGGGTTGAA

Found at i:1787 original size:32 final size:32

Alignment explanation


    Indices: 1741--1827  Score: 147
    Period size: 32  Copynumber: 2.7  Consensus size: 32

       1731 CGGGCTTGAA

                                            
       1741 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
          1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT

                *                           
       1773 TCGGTTTCGGGTTGAATTTGGGTCAGGTTAAT
          1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT

                         * *       
       1805 TCGGGTTCGGGTTCAGTTTGGGT
          1 TCGGGTTCGGGTTGAATTTGGGT

       1828 TTTGGCCAGA


Statistics
Matches: 51,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  32   51  1.00

ACGTcount: A:0.13, C:0.10, G:0.38, T:0.39


Consensus pattern (32 bp):   
TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT

Found at i:1997 original size:16 final size:15

Alignment explanation


    Indices: 1973--2058  Score: 82
    Period size: 16  Copynumber: 5.5  Consensus size: 15

       1963 AATTTTCGGA

                           
       1973 TCGGGTTTTTCGGGT
          1 TCGGGTTTTTCGGGT

             *        *     
       1988 TTGAGGTTTTCCGGGT
          1 TCG-GGTTTTTCGGGT

                            
       2004 TCGGGTTTTTTCGGGT
          1 TCGGG-TTTTTCGGGT

             *   *      *   
       2020 TTGAGCTTTTTCAGGT
          1 TCG-GGTTTTTCGGGT

                            
       2036 TCGGGTTTTTTCGGGT
          1 TCGGG-TTTTTCGGGT

              *    
       2052 TCAGGTT
          1 TCGGGTT

       2059 CAGGCGGATT


Statistics
Matches: 56,  Mismatches: 11, Indels: 8
        0.75            0.15        0.11

Matches are distributed among these distances:
  15    7  0.12
  16   48  0.86
  17    1  0.02

ACGTcount: A:0.05, C:0.13, G:0.35, T:0.48


Consensus pattern (15 bp):   
TCGGGTTTTTCGGGT

Found at i:2019 original size:32 final size:32

Alignment explanation


    Indices: 1973--2052  Score: 126
    Period size: 32  Copynumber: 2.5  Consensus size: 32

       1963 AATTTTCGGA

                                 *      *   
       1973 TCGGG-TTTTTCGGGTTTGAGGTTTTCCGGGT
          1 TCGGGTTTTTTCGGGTTTGAGCTTTTCCAGGT

                                      *     
       2004 TCGGGTTTTTTCGGGTTTGAGCTTTTTCAGGT
          1 TCGGGTTTTTTCGGGTTTGAGCTTTTCCAGGT

                             
       2036 TCGGGTTTTTTCGGGTT
          1 TCGGGTTTTTTCGGGTT

       2053 CAGGTTCAGG


Statistics
Matches: 45,  Mismatches: 3, Indels: 1
        0.92            0.06        0.02

Matches are distributed among these distances:
  31    5  0.11
  32   40  0.89

ACGTcount: A:0.04, C:0.12, G:0.35, T:0.49


Consensus pattern (32 bp):   
TCGGGTTTTTTCGGGTTTGAGCTTTTCCAGGT

Found at i:2499 original size:2 final size:2

Alignment explanation


    Indices: 2492--2530  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       2482 GTATCAAATA

                                                                      
       2492 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       2531 ATGCCAATTT


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:2592 original size:15 final size:15

Alignment explanation


    Indices: 2574--2605  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       2564 AGAGATGGAC

                           
       2574 TAAAGAATATAGGCT
          1 TAAAGAATATAGGCT

                           
       2589 TAAAGAATATAGGCT
          1 TAAAGAATATAGGCT

              
       2604 TA
          1 TA

       2606 CT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28


Consensus pattern (15 bp):   
TAAAGAATATAGGCT
Done.