Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003156.1 Corchorus capsularis cultivar CVL-1 contig03164, 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, 623

Length: 1039
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29


Found at i:122 original size:21 final size:22

Alignment explanation


    Indices: 84--136  Score: 81
    Period size: 22  Copynumber: 2.4  Consensus size: 22

         74 TCAGTAATTC

                         *        
         84 AAAAAGTAAAATGGTAATCAGT
          1 AAAAAGTAAAATGATAATCAGT

                                  
        106 AAAAAGTAAAA-GATAATCAGT
          1 AAAAAGTAAAATGATAATCAGT

                      
        127 AAAATAGTAA
          1 AAAA-AGTAA

        137 TCAGTAAAAG


Statistics
Matches: 29,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  21   13  0.45
  22   16  0.55

ACGTcount: A:0.60, C:0.04, G:0.15, T:0.21


Consensus pattern (22 bp):   
AAAAAGTAAAATGATAATCAGT

Found at i:139 original size:15 final size:14

Alignment explanation


    Indices: 110--157  Score: 78
    Period size: 14  Copynumber: 3.4  Consensus size: 14

        100 ATCAGTAAAA

                          
        110 AGTAAAAGATAATC
          1 AGTAAAAGATAATC

                   *       
        124 AGTAAAATAGTAATC
          1 AGTAAAAGA-TAATC

                          
        139 AGTAAAAGATAATC
          1 AGTAAAAGATAATC

                 
        153 AGTAA
          1 AGTAA

        158 GAGTAAAACA


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

Matches are distributed among these distances:
  14   18  0.58
  15   13  0.42

ACGTcount: A:0.56, C:0.06, G:0.15, T:0.23


Consensus pattern (14 bp):   
AGTAAAAGATAATC

Found at i:157 original size:21 final size:20

Alignment explanation


    Indices: 132--205  Score: 51
    Period size: 21  Copynumber: 3.5  Consensus size: 20

        122 TCAGTAAAAT

                                 
        132 AGTAATCAGTAAAAGATAATC
          1 AGTAA-CAGTAAAAGATAATC

                 *       *       
        153 AGTAAGAGTAAAACAGTAATC
          1 AGTAACAGTAAAAGA-TAATC

            *    *  *             
        174 GGTAAGAGCAAAAGCGATAAT-
          1 AGTAACAGTAAAA--GATAATC

                       
        195 AGTAATCAGTA
          1 AGTAA-CAGTA

        206 GAGAGTAAAA


Statistics
Matches: 41,  Mismatches: 8, Indels: 7
        0.73            0.14        0.12

Matches are distributed among these distances:
  20    8  0.20
  21   25  0.61
  22    7  0.17
  23    1  0.02

ACGTcount: A:0.50, C:0.09, G:0.20, T:0.20


Consensus pattern (20 bp):   
AGTAACAGTAAAAGATAATC

Found at i:303 original size:29 final size:28

Alignment explanation


    Indices: 278--342  Score: 89
    Period size: 27  Copynumber: 2.4  Consensus size: 28

        268 GTAAAAAGTG

                                        
        278 GTAATAAATAAAAGAGAGTAAGAAAAGA
          1 GTAATAAATAAAAGAGAGTAAGAAAAGA

                 ***                    
        306 GTAATTGGTAAAA-AGAGTAAGAAAAGA
          1 GTAATAAATAAAAGAGAGTAAGAAAAGA

                       
        333 GTAA-AAATAA
          1 GTAATAAATAA

        343 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.