Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020591.1 Corchorus olitorius cultivar O-4 contig20624, 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: 8292
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38


Found at i:3676 original size:23 final size:24

Alignment explanation


    Indices: 3650--3695  Score: 85
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       3640 TTTAAAAAAG

                                    
       3650 ATTTA-TTTTTTAAAAGGATTAGT
          1 ATTTATTTTTTTAAAAGGATTAGT

                                   
       3673 ATTTATTTTTTTAAAAGGATTAG
          1 ATTTATTTTTTTAAAAGGATTAG

       3696 GGTATATTGA


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  23    5  0.23
  24   17  0.77

ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52


Consensus pattern (24 bp):   
ATTTATTTTTTTAAAAGGATTAGT

Found at i:3703 original size:24 final size:24

Alignment explanation


    Indices: 3655--3703  Score: 71
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       3645 AAAAGATTTA

                             *  *   
       3655 TTTTTTAAAAGGATTAGTATTTAT
          1 TTTTTTAAAAGGATTAGGATATAT

                              *     
       3679 TTTTTTAAAAGGATTAGGGTATAT
          1 TTTTTTAAAAGGATTAGGATATAT

             
       3703 T
          1 T

       3704 GAAGAATATC


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  24   22  1.00

ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51


Consensus pattern (24 bp):   
TTTTTTAAAAGGATTAGGATATAT

Found at i:4483 original size:14 final size:14

Alignment explanation


    Indices: 4464--4497  Score: 59
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       4454 TTTTATAATT

                          
       4464 ATTTTATTTTTACC
          1 ATTTTATTTTTACC

                         *
       4478 ATTTTATTTTTACT
          1 ATTTTATTTTTACC

                  
       4492 ATTTTA
          1 ATTTTA

       4498 ATTTAAAAGG


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  14   19  1.00

ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68


Consensus pattern (14 bp):   
ATTTTATTTTTACC

Found at i:4545 original size:15 final size:15

Alignment explanation


    Indices: 4525--4555  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       4515 GATTAACCTG

                           
       4525 TTTCTATTTGATAGT
          1 TTTCTATTTGATAGT

                           
       4540 TTTCTATTTGATAGT
          1 TTTCTATTTGATAGT

             
       4555 T
          1 T

       4556 AATGTATTAT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61


Consensus pattern (15 bp):   
TTTCTATTTGATAGT

Found at i:5665 original size:32 final size:32

Alignment explanation


    Indices: 5624--5695  Score: 108
    Period size: 32  Copynumber: 2.2  Consensus size: 32

       5614 TTCAAAGAAC

                         *          *     * 
       5624 ATTTTGTCCTACTTTGTCAAAATTTGAGGGTT
          1 ATTTTGTCCTACTATGTCAAAATTCGAGGGCT

                      *                     
       5656 ATTTTGTCCTTCTATGTCAAAATTCGAGGGCT
          1 ATTTTGTCCTACTATGTCAAAATTCGAGGGCT

                    
       5688 ATTTTGTC
          1 ATTTTGTC

       5696 TATCAATTTG


Statistics
Matches: 36,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  32   36  1.00

ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46


Consensus pattern (32 bp):   
ATTTTGTCCTACTATGTCAAAATTCGAGGGCT
Done.