Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006052.1 Corchorus capsularis cultivar CVL-1 contig06070, 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: 4150
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27


Found at i:37 original size:14 final size:14

Alignment explanation


    Indices: 1--41  Score: 64
    Period size: 15  Copynumber: 2.9  Consensus size: 14

                          
          1 GATAATCAGTAAAA
          1 GATAATCAGTAAAA

            *              
         15 TAGTAATCAGTAAAA
          1 GA-TAATCAGTAAAA

                        
         30 GATAATCAGTAA
          1 GATAATCAGTAA

         42 GAGTAAAACA


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

Matches are distributed among these distances:
  14   11  0.46
  15   13  0.54

ACGTcount: A:0.54, C:0.07, G:0.15, T:0.24


Consensus pattern (14 bp):   
GATAATCAGTAAAA

Found at i:64 original size:21 final size:20

Alignment explanation


    Indices: 23--65  Score: 50
    Period size: 21  Copynumber: 2.1  Consensus size: 20

         13 AATAGTAATC

                   *        *   
         23 AGTAAAAGATAATCAGTAAG
          1 AGTAAAACATAATCAGAAAG

                           *     
         43 AGTAAAACAGTAATCGGAAAG
          1 AGTAAAACA-TAATCAGAAAG

              
         64 AG
          1 AG

         66 CAAAGCGATA


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  20    8  0.42
  21   11  0.58

ACGTcount: A:0.53, C:0.07, G:0.23, T:0.16


Consensus pattern (20 bp):   
AGTAAAACATAATCAGAAAG

Found at i:186 original size:29 final size:28

Alignment explanation


    Indices: 161--225  Score: 89
    Period size: 27  Copynumber: 2.4  Consensus size: 28

        151 GTAAAAAGTG

                                        
        161 GTAATAAATAAAAGAGAGTAAGAAAAGA
          1 GTAATAAATAAAAGAGAGTAAGAAAAGA

                 ***                    
        189 GTAATTGGTAAAA-AGAGTAAGAAAAGA
          1 GTAATAAATAAAAGAGAGTAAGAAAAGA

                       
        216 GTAA-AAATAA
          1 GTAATAAATAA

        226 TAAAAGTAGC


Statistics
Matches: 31,  Mismatches: 6, Indels: 2
        0.79            0.15        0.05

Matches are distributed among these distances:
  26    3  0.10
  27   18  0.58
  28   10  0.32

ACGTcount: A:0.62, C:0.00, G:0.22, T:0.17


Consensus pattern (28 bp):   
GTAATAAATAAAAGAGAGTAAGAAAAGA

Done.