Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023688.1 Corchorus olitorius cultivar O-4 contig23721, 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: 5592
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36


Found at i:1592 original size:36 final size:35

Alignment explanation


    Indices: 1516--1643  Score: 179
    Period size: 36  Copynumber: 3.6  Consensus size: 35

       1506 GGCCTGCCTG

                       *                 *     
       1516 GCGCGGCCCAAACG-CTAGGCCAGGCGCCAGGCCA
          1 GCGCGGCCCAAGCGCCTAGGCCAGGCGCCGGGCCA

                                                
       1550 GCGCGGCCCAAGCGCCTAGGCCAGGCGCGCGGGCCA
          1 GCGCGGCCCAAGCGCCTAGGCCAGGCGC-CGGGCCA

                                         *      
       1586 GCGCGGCCCAAGCGCCTAGGCCAGGCGCATGGGCCA
          1 GCGCGGCCCAAGCGCCTAGGCCAGGCGC-CGGGCCA

                                   
       1622 GCGCATGGCCC-AGCGCCTAGGC
          1 GCGC--GGCCCAAGCGCCTAGGC

       1644 TAAGCTTGGG


Statistics
Matches: 86,  Mismatches: 4, Indels: 5
        0.91            0.04        0.05

Matches are distributed among these distances:
  34   13  0.15
  35   13  0.15
  36   44  0.51
  37   11  0.13
  38    5  0.06

ACGTcount: A:0.16, C:0.41, G:0.38, T:0.05


Consensus pattern (35 bp):   
GCGCGGCCCAAGCGCCTAGGCCAGGCGCCGGGCCA

Found at i:1627 original size:12 final size:12

Alignment explanation


    Indices: 1604--1637  Score: 50
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       1594 CAAGCGCCTA

                         
       1604 GGCCAGGCGCATG
          1 GGCCA-GCGCATG

                        
       1617 GGCCAGCGCATG
          1 GGCCAGCGCATG

             *       
       1629 GCCCAGCGC
          1 GGCCAGCGC

       1638 CTAGGCTAAG


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  12   15  0.75
  13    5  0.25

ACGTcount: A:0.15, C:0.38, G:0.41, T:0.06


Consensus pattern (12 bp):   
GGCCAGCGCATG

Found at i:1690 original size:6 final size:6

Alignment explanation


    Indices: 1675--1713  Score: 71
    Period size: 6  Copynumber: 6.7  Consensus size: 6

       1665 GCAGAAATTT

                                                          
       1675 AAAA-A AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
          1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAA

       1714 AGAAGAAATG


Statistics
Matches: 33,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
   5    4  0.12
   6   29  0.88

ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13


Consensus pattern (6 bp):   
AAAATA

Done.