Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021971.1 Corchorus olitorius cultivar O-4 contig22004, 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: 7607
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31


Found at i:660 original size:10 final size:10

Alignment explanation


    Indices: 639--676  Score: 67
    Period size: 10  Copynumber: 3.7  Consensus size: 10

        629 TCCATTGATA

                       
        639 TATAGATATAT
          1 TATAGAT-TAT

                      
        650 TATAGATTAT
          1 TATAGATTAT

                      
        660 TATAGATTAT
          1 TATAGATTAT

                   
        670 TATAGAT
          1 TATAGAT

        677 ATAAGAATAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  10   20  0.74
  11    7  0.26

ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47


Consensus pattern (10 bp):   
TATAGATTAT

Found at i:687 original size:17 final size:18

Alignment explanation


    Indices: 635--690  Score: 69
    Period size: 20  Copynumber: 3.0  Consensus size: 18

        625 TAAGTCCATT

                               
        635 GATATATAGATATATTATA
          1 GATATATAGA-ATATTATA

                        *       
        654 GATTATTATAGATTATTATA
          1 GA-TA-TATAGAATATTATA

                              
        674 GATATA-AGAATATTATA
          1 GATATATAGAATATTATA

        691 AGAAAATTCC


Statistics
Matches: 33,  Mismatches: 2, Indels: 6
        0.80            0.05        0.15

Matches are distributed among these distances:
  17   10  0.30
  18    2  0.06
  19    4  0.12
  20   11  0.33
  21    6  0.18

ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43


Consensus pattern (18 bp):   
GATATATAGAATATTATA

Found at i:2915 original size:15 final size:15

Alignment explanation


    Indices: 2897--2927  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       2887 TTTAAGTTTC

                           
       2897 AGGGACTTAATTGAA
          1 AGGGACTTAATTGAA

                *          
       2912 AGGGGCTTAATTGAA
          1 AGGGACTTAATTGAA

             
       2927 A
          1 A

       2928 AGAAAATAAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.39, C:0.06, G:0.29, T:0.26


Consensus pattern (15 bp):   
AGGGACTTAATTGAA
Done.