Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006598.1 Corchorus olitorius cultivar O-4 contig06623, 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, 700

Length: 1167
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30


Found at i:793 original size:2 final size:2

Alignment explanation


    Indices: 786--826  Score: 68
    Period size: 2  Copynumber: 21.5  Consensus size: 2

        776 AGGAAAACAA

                                                                          
        786 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT -T AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

             
        826 A
          1 A

        827 AGAGTAGAAA


Statistics
Matches: 37,  Mismatches: 0, Indels: 4
        0.90            0.00        0.10

Matches are distributed among these distances:
   1    2  0.05
   2   35  0.95

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
AT

Found at i:809 original size:15 final size:14

Alignment explanation


    Indices: 786--826  Score: 68
    Period size: 13  Copynumber: 3.1  Consensus size: 14

        776 AGGAAAACAA

                          
        786 ATATATATATATAT
          1 ATATATATATATAT

                          
        800 ATAT-TATATATAT
          1 ATATATATATATAT

                          
        813 ATATATAT-TATAT
          1 ATATATATATATAT

             
        826 A
          1 A

        827 AGAGTAGAAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  13   19  0.73
  14    7  0.27

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (14 bp):   
ATATATATATATAT

Found at i:809 original size:17 final size:17

Alignment explanation


    Indices: 787--826  Score: 80
    Period size: 17  Copynumber: 2.4  Consensus size: 17

        777 GGAAAACAAA

                             
        787 TATATATATATATATAT
          1 TATATATATATATATAT

                             
        804 TATATATATATATATAT
          1 TATATATATATATATAT

                  
        821 TATATA
          1 TATATA

        827 AGAGTAGAAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   23  1.00

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (17 bp):   
TATATATATATATATAT
Done.