Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000847.1 Corchorus capsularis cultivar CVL-1 contig00847, 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: 2793
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35


Found at i:82 original size:26 final size:26

Alignment explanation


    Indices: 53--119  Score: 93
    Period size: 26  Copynumber: 2.6  Consensus size: 26

         43 TACTTAGTTT

                                      
         53 ATTAGTTTATGTTTAATTAGTATCTA
          1 ATTAGTTTATGTTTAATTAGTATCTA

                                    *  
         79 ATTAGTTTAT-TATTAATTAGTATTTA
          1 ATTAGTTTATGT-TTAATTAGTATCTA

                       *    
        105 ATTAG-TTATGATTAA
          1 ATTAGTTTATGTTTAA

        120 AATGAAGGAA


Statistics
Matches: 37,  Mismatches: 2, Indels: 5
        0.84            0.05        0.11

Matches are distributed among these distances:
  25    9  0.24
  26   28  0.76

ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54


Consensus pattern (26 bp):   
ATTAGTTTATGTTTAATTAGTATCTA

Found at i:167 original size:24 final size:25

Alignment explanation


    Indices: 128--187  Score: 97
    Period size: 25  Copynumber: 2.5  Consensus size: 25

        118 AAAATGAAGG

                              *      
        128 AAAATGAA-TTTGAAG-ATTTGTTA
          1 AAAATGAAGTTTGAAGAAGTTGTTA

                                     
        151 AAAATGAAGTTTGAAGAAGTTGTTA
          1 AAAATGAAGTTTGAAGAAGTTGTTA

                        
        176 AAAATGAAGTTT
          1 AAAATGAAGTTT

        188 AGGGTTTGAA


Statistics
Matches: 34,  Mismatches: 1, Indels: 2
        0.92            0.03        0.05

Matches are distributed among these distances:
  23    8  0.24
  24    7  0.21
  25   19  0.56

ACGTcount: A:0.45, C:0.00, G:0.20, T:0.35


Consensus pattern (25 bp):   
AAAATGAAGTTTGAAGAAGTTGTTA

Found at i:1469 original size:19 final size:20

Alignment explanation


    Indices: 1432--1469  Score: 51
    Period size: 19  Copynumber: 1.9  Consensus size: 20

       1422 GTTAGTTGTC

                          *     
       1432 ATTTATTTCTTTGGGAACAA
          1 ATTTATTTCTTTGGAAACAA

                         *     
       1452 ATTTATTT-TTTGTAAACA
          1 ATTTATTTCTTTGGAAACA

       1470 TTGTTGTTCT


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  19    8  0.50
  20    8  0.50

ACGTcount: A:0.32, C:0.08, G:0.11, T:0.50


Consensus pattern (20 bp):   
ATTTATTTCTTTGGAAACAA
Done.