Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007757.1 Corchorus capsularis cultivar CVL-1 contig07778, 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: 6694
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35


Found at i:147 original size:28 final size:28

Alignment explanation


    Indices: 107--163  Score: 78
    Period size: 28  Copynumber: 2.0  Consensus size: 28

         97 TAACATTTAA

                                        
        107 TTTAAAATCTAAAAATTTTTAATAACTT
          1 TTTAAAATCTAAAAATTTTTAATAACTT

                    *    **        *    
        135 TTTAAAATTTAAAGCTTTTTAATCACTT
          1 TTTAAAATCTAAAAATTTTTAATAACTT

             
        163 T
          1 T

        164 AAGTAAGAAA


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  28   25  1.00

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


Consensus pattern (28 bp):   
TTTAAAATCTAAAAATTTTTAATAACTT

Found at i:1666 original size:26 final size:25

Alignment explanation


    Indices: 1637--1689  Score: 61
    Period size: 26  Copynumber: 2.1  Consensus size: 25

       1627 GATTTGTTTC

                 *       *            
       1637 TTTTTTATATGATTTATAAAAATTAA
          1 TTTTTCATATGATAT-TAAAAATTAA

                      *      *       
       1663 TTTTTCATATTATATTACAAATTAA
          1 TTTTTCATATGATATTAAAAATTAA

              
       1688 TT
          1 TT

       1690 AATATGCTAT


Statistics
Matches: 23,  Mismatches: 4, Indels: 1
        0.82            0.14        0.04

Matches are distributed among these distances:
  25   11  0.48
  26   12  0.52

ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55


Consensus pattern (25 bp):   
TTTTTCATATGATATTAAAAATTAA

Found at i:1777 original size:2 final size:2

Alignment explanation


    Indices: 1770--1799  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       1760 ACAATTACTA

                                                        
       1770 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       1800 CACATAAATT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:3258 original size:13 final size:13

Alignment explanation


    Indices: 3240--3264  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       3230 GGAGGCTGAA

                         
       3240 AACAAGTAAAAAT
          1 AACAAGTAAAAAT

                        
       3253 AACAAGTAAAAA
          1 AACAAGTAAAAA

       3265 CAATTCTCAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.72, C:0.08, G:0.08, T:0.12


Consensus pattern (13 bp):   
AACAAGTAAAAAT
Done.