Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011774.1 Corchorus capsularis cultivar CVL-1 contig11795, 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: 28202
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--93  Score: 172
    Period size: 2  Copynumber: 47.5  Consensus size: 2

                                                                          
          1 TC TC TC TC TC TC TC T- TC TC TC TC TC TC TC TC TC T- TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                                                                          
         41 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                            
         83 TC TC TC TC TC T
          1 TC TC TC TC TC T

         94 ATATTTAAAA


Statistics
Matches: 89,  Mismatches: 0, Indels: 4
        0.96            0.00        0.04

Matches are distributed among these distances:
   1    2  0.02
   2   87  0.98

ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52


Consensus pattern (2 bp):   
TC

Found at i:10107 original size:2 final size:2

Alignment explanation


    Indices: 10100--10130  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

      10090 CTTAATTGCG

                                                          
      10100 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T

      10131 AATTCTCCTG


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

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52


Consensus pattern (2 bp):   
TC

Found at i:14081 original size:55 final size:55

Alignment explanation


    Indices: 14003--14115  Score: 183
    Period size: 55  Copynumber: 2.0  Consensus size: 55

      13993 CATTAAGCCC

                         *                                         
      14003 GCGCAATTTAAAAGTCTATTAAAAAGGGCAATATTTTAG-TCTTTTTCAAAGAGA
          1 GCGCAATTTAAAACTCTATTAAAAAGGGCAATATTTTAGTTCTTTTTCAAAGAGA

                                                       *             
      14057 GCGCAATTTAGAAACTCTATTAAAAAGGGCAATATTTTAGTTTTTTTTTCAAAGAGA
          1 GCGCAATTTA-AAACTCTATTAAAAAGGGCAATATTTTAG-TTCTTTTTCAAAGAGA

              
      14114 GC
          1 GC

      14116 AATTCAGTCT


Statistics
Matches: 54,  Mismatches: 2, Indels: 3
        0.92            0.03        0.05

Matches are distributed among these distances:
  54   10  0.19
  55   28  0.52
  57   16  0.30

ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35


Consensus pattern (55 bp):   
GCGCAATTTAAAACTCTATTAAAAAGGGCAATATTTTAGTTCTTTTTCAAAGAGA

Found at i:16778 original size:22 final size:20

Alignment explanation


    Indices: 16729--16783  Score: 56
    Period size: 22  Copynumber: 2.6  Consensus size: 20

      16719 TGGGAAGCCC

                    *           
      16729 CTAAATTGACTTTTAAAAGA
          1 CTAAATTGCCTTTTAAAAGA

               *                  
      16749 CTACATTGCCCTTTTCAAAAGA
          1 CTAAATTG-CCTTTT-AAAAGA

            *            
      16771 TTAAATTGTCCTT
          1 CTAAATTG-CCTT

      16784 CTGGAAGAGA


Statistics
Matches: 28,  Mismatches: 5, Indels: 2
        0.80            0.14        0.06

Matches are distributed among these distances:
  20    7  0.25
  21    5  0.18
  22   16  0.57

ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38


Consensus pattern (20 bp):   
CTAAATTGCCTTTTAAAAGA

Found at i:16875 original size:30 final size:30

Alignment explanation


    Indices: 16834--16903  Score: 97
    Period size: 29  Copynumber: 2.3  Consensus size: 30

      16824 ACAGGTCCTT

                                           
      16834 CTACTTACAAAAAAGGATCAATTTGGTCCCC
          1 CTACTTACAAAAAAGG-TCAATTTGGTCCCC

                         **              *
      16865 CTAC-TACAAAAACTGTCAATTTGGTCCCT
          1 CTACTTACAAAAAAGGTCAATTTGGTCCCC

                      
      16894 CTACTTACAA
          1 CTACTTACAA

      16904 TTTGGTGTCA


Statistics
Matches: 35,  Mismatches: 3, Indels: 3
        0.85            0.07        0.07

Matches are distributed among these distances:
  29   17  0.49
  30   14  0.40
  31    4  0.11

ACGTcount: A:0.34, C:0.27, G:0.10, T:0.29


Consensus pattern (30 bp):   
CTACTTACAAAAAAGGTCAATTTGGTCCCC

Found at i:18585 original size:22 final size:22

Alignment explanation


    Indices: 18540--18585  Score: 67
    Period size: 22  Copynumber: 2.1  Consensus size: 22

      18530 ATTCAATTTG

                               *  
      18540 ATACATATCAATGCATATACAT
          1 ATACATATCAATGCATATAAAT

                                   
      18562 ATACATATCAATGC-TATTAAAT
          1 ATACATATCAATGCATA-TAAAT

              
      18584 AT
          1 AT

      18586 TTACTTCAAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21    2  0.09
  22   20  0.91

ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35


Consensus pattern (22 bp):   
ATACATATCAATGCATATAAAT

Found at i:28139 original size:2 final size:2

Alignment explanation


    Indices: 28132--28164  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      28122 ATGCTAAATT

                                                             
      28132 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      28165 GTCTGTGTGT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.