Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008917.1 Corchorus capsularis cultivar CVL-1 contig08938, 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: 69524
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34


Found at i:21253 original size:4 final size:4

Alignment explanation


    Indices: 21244--21276  Score: 66
    Period size: 4  Copynumber: 8.2  Consensus size: 4

      21234 CGGTCAAGCC

                                                     
      21244 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A
          1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A

      21277 GTCTCGGTGT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   29  1.00

ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00


Consensus pattern (4 bp):   
AAAG

Found at i:22663 original size:2 final size:2

Alignment explanation


    Indices: 22658--22693  Score: 56
    Period size: 2  Copynumber: 18.5  Consensus size: 2

      22648 AATTTTCTTC

                                              *                    
      22658 AT AT AT AT AT AT AT AT AT A- AT AA 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 A

      22694 GTTAAATTAA


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   30  0.97

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (2 bp):   
AT

Found at i:23461 original size:24 final size:25

Alignment explanation


    Indices: 23434--23484  Score: 86
    Period size: 24  Copynumber: 2.1  Consensus size: 25

      23424 CTCAAAATTG

                                     
      23434 AAGATAAGTACAAAAA-GGAAAAAA
          1 AAGATAAGTACAAAAAGGGAAAAAA

                               *     
      23458 AAGATAAGTACAAAAAGGGGAAAAA
          1 AAGATAAGTACAAAAAGGGAAAAAA

              
      23483 AA
          1 AA

      23485 TCCAGAAAGG


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  24   16  0.64
  25    9  0.36

ACGTcount: A:0.69, C:0.04, G:0.20, T:0.08


Consensus pattern (25 bp):   
AAGATAAGTACAAAAAGGGAAAAAA

Found at i:28704 original size:113 final size:113

Alignment explanation


    Indices: 28530--28733  Score: 354
    Period size: 113  Copynumber: 1.8  Consensus size: 113

      28520 ATAATGAGCA

                                          *                       *          
      28530 ACGAGAAAAATTATAAAGCTAATTTCAGCATAATTTCGATTAGGGATGGCAAAATCCGCTTTGCC
          1 ACGAGAAAAATTATAAAGCTAATTTCAGCAGAATTTCGATTAGGGATGGCAAAACCCGCTTTGCC

                                                            
      28595 CCGCCATTCCCGCCCTGTCCCACCCCGTTTTGTTTGGGCGGGGCGGTT
         66 CCGCCATTCCCGCCCTGTCCCACCCCGTTTTGTTTGGGCGGGGCGGTT

                        *     *         *                                    
      28643 ACGAGAAAAATTGTAAAGTTAATTTCAGTAGAATTTCGATTAGGGATGGCAAAACCCGCTTTGCC
          1 ACGAGAAAAATTATAAAGCTAATTTCAGCAGAATTTCGATTAGGGATGGCAAAACCCGCTTTGCC

                                 *    
      28708 CCGCCATTCCCGCCCTGTCCCGCCCC
         66 CCGCCATTCCCGCCCTGTCCCACCCC

      28734 ATTCGGCCCC


Statistics
Matches: 85,  Mismatches: 6, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
 113   85  1.00

ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26


Consensus pattern (113 bp):   
ACGAGAAAAATTATAAAGCTAATTTCAGCAGAATTTCGATTAGGGATGGCAAAACCCGCTTTGCC
CCGCCATTCCCGCCCTGTCCCACCCCGTTTTGTTTGGGCGGGGCGGTT

Found at i:33148 original size:13 final size:14

Alignment explanation


    Indices: 33121--33150  Score: 53
    Period size: 13  Copynumber: 2.2  Consensus size: 14

      33111 TTATTGACAG

                          
      33121 AAAACATGAAAATC
          1 AAAACATGAAAATC

                          
      33135 AAAACATG-AAATC
          1 AAAACATGAAAATC

               
      33148 AAA
          1 AAA

      33151 GGCAAAAAAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    8  0.50
  14    8  0.50

ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13


Consensus pattern (14 bp):   
AAAACATGAAAATC

Found at i:65896 original size:11 final size:11

Alignment explanation


    Indices: 65880--65909  Score: 60
    Period size: 11  Copynumber: 2.7  Consensus size: 11

      65870 GCTAAATCAA

                       
      65880 ACAACAAATTC
          1 ACAACAAATTC

                       
      65891 ACAACAAATTC
          1 ACAACAAATTC

                    
      65902 ACAACAAA
          1 ACAACAAA

      65910 AATTAAGATT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   19  1.00

ACGTcount: A:0.60, C:0.27, G:0.00, T:0.13


Consensus pattern (11 bp):   
ACAACAAATTC

Found at i:66067 original size:22 final size:21

Alignment explanation


    Indices: 66041--66081  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      66031 TAATTATAGA

                                  
      66041 AAAAGGAAGAAATTTTACAAAC
          1 AAAAGG-AGAAATTTTACAAAC

                  * *          
      66063 AAAAGGGGGAATTTTACAA
          1 AAAAGGAGAAATTTTACAA

      66082 CAAGTGCTCA


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21   11  0.65
  22    6  0.35

ACGTcount: A:0.54, C:0.07, G:0.20, T:0.20


Consensus pattern (21 bp):   
AAAAGGAGAAATTTTACAAAC
Done.