Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013452.1 Corchorus capsularis cultivar CVL-1 contig13473, 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: 8613
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35


Found at i:1808 original size:13 final size:13

Alignment explanation


    Indices: 1790--1821  Score: 55
    Period size: 13  Copynumber: 2.5  Consensus size: 13

       1780 GGCAAACGAA

                     *   
       1790 AAAATTGGGTGGG
          1 AAAATTGGGAGGG

                         
       1803 AAAATTGGGAGGG
          1 AAAATTGGGAGGG

                  
       1816 AAAATT
          1 AAAATT

       1822 TTTAGTGGCT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   18  1.00

ACGTcount: A:0.41, C:0.00, G:0.38, T:0.22


Consensus pattern (13 bp):   
AAAATTGGGAGGG

Found at i:3808 original size:27 final size:27

Alignment explanation


    Indices: 3776--3836  Score: 95
    Period size: 27  Copynumber: 2.2  Consensus size: 27

       3766 TTGGTCTGTT

                        *              
       3776 TTTGTTGAGCTATATTTGGTGCTGTAA
          1 TTTGTTGAGCTAAATTTGGTGCTGTAA

                                     * 
       3803 TTTGTTGAGCTAAATTTGGTGCTGTTA
          1 TTTGTTGAGCTAAATTTGGTGCTGTAA

                   
       3830 TTGTGTT
          1 TT-TGTT

       3837 TTGGTCTGTT


Statistics
Matches: 31,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  27   27  0.87
  28    4  0.13

ACGTcount: A:0.16, C:0.07, G:0.26, T:0.51


Consensus pattern (27 bp):   
TTTGTTGAGCTAAATTTGGTGCTGTAA

Found at i:8484 original size:28 final size:27

Alignment explanation


    Indices: 8443--8504  Score: 97
    Period size: 28  Copynumber: 2.3  Consensus size: 27

       8433 TCTAAAAATA

                                       
       8443 AAAAATTGAATATTTATAAGAATCCAT
          1 AAAAATTGAATATTTATAAGAATCCAT

                            *        *  
       8470 ACAAAATTGAATATTTTTAAGAATCTAT
          1 A-AAAATTGAATATTTATAAGAATCCAT

                   
       8498 AAAAATT
          1 AAAAATT

       8505 ACAGTAAAAA


Statistics
Matches: 32,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  27    7  0.22
  28   25  0.78

ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35


Consensus pattern (27 bp):   
AAAAATTGAATATTTATAAGAATCCAT
Done.