Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009597.1 Corchorus capsularis cultivar CVL-1 contig09618, 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: 23942
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35


Found at i:641 original size:19 final size:19

Alignment explanation


    Indices: 613--650  Score: 51
    Period size: 19  Copynumber: 2.0  Consensus size: 19

        603 AATCTCTTTT

                                
        613 TAGCTAAAAAGT-AAAAAGC
          1 TAGCTAAAAA-TCAAAAAGC

                 *             
        632 TAGCTCAAAATCAAAAAGC
          1 TAGCTAAAAATCAAAAAGC

        651 AATAGCAACA


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

Matches are distributed among these distances:
  18    1  0.06
  19   16  0.94

ACGTcount: A:0.55, C:0.16, G:0.13, T:0.16


Consensus pattern (19 bp):   
TAGCTAAAAATCAAAAAGC

Found at i:8183 original size:6 final size:6

Alignment explanation


    Indices: 8174--8203  Score: 51
    Period size: 6  Copynumber: 5.0  Consensus size: 6

       8164 ATCCAATAAA

                             *                
       8174 TAATCT TAATCT TAACCT TAATCT TAATCT
          1 TAATCT TAATCT TAATCT TAATCT TAATCT

       8204 CATATATACT


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   6   22  1.00

ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47


Consensus pattern (6 bp):   
TAATCT

Found at i:10183 original size:25 final size:27

Alignment explanation


    Indices: 10131--10183  Score: 74
    Period size: 27  Copynumber: 2.0  Consensus size: 27

      10121 TTACTCAACT

                                **     
      10131 AAAAACTCTATTTTTATTTTTCTGTAA
          1 AAAAACTCTATTTTTATTTTAATGTAA

                                       
      10158 AAAAACTCTATTTTTA-TTTAAT-TAA
          1 AAAAACTCTATTTTTATTTTAATGTAA

             
      10183 A
          1 A

      10184 TCTAATATCC


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  25    4  0.17
  26    4  0.17
  27   16  0.67

ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49


Consensus pattern (27 bp):   
AAAAACTCTATTTTTATTTTAATGTAA

Found at i:12851 original size:19 final size:20

Alignment explanation


    Indices: 12827--12867  Score: 57
    Period size: 19  Copynumber: 2.1  Consensus size: 20

      12817 TTATAGTGAA

                                
      12827 TTACTAAATACCG-CCCCTT
          1 TTACTAAATACCGCCCCCTT

                  **            
      12846 TTACTAGCTACCGCCCCCTT
          1 TTACTAAATACCGCCCCCTT

              
      12866 TT
          1 TT

      12868 GGACTATTTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  19   11  0.58
  20    8  0.42

ACGTcount: A:0.20, C:0.39, G:0.07, T:0.34


Consensus pattern (20 bp):   
TTACTAAATACCGCCCCCTT

Found at i:13272 original size:26 final size:26

Alignment explanation


    Indices: 13232--13295  Score: 119
    Period size: 26  Copynumber: 2.5  Consensus size: 26

      13222 AAAAAGAACA

                      *               
      13232 GCGGGTCGCGCCACCCGATCGCGCGC
          1 GCGGGTCGCGACACCCGATCGCGCGC

                                      
      13258 GCGGGTCGCGACACCCGATCGCGCGC
          1 GCGGGTCGCGACACCCGATCGCGCGC

                        
      13284 GCGGGTCGCGAC
          1 GCGGGTCGCGAC

      13296 TTGGACCGTG


Statistics
Matches: 37,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  26   37  1.00

ACGTcount: A:0.09, C:0.42, G:0.41, T:0.08


Consensus pattern (26 bp):   
GCGGGTCGCGACACCCGATCGCGCGC
Done.