Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020208.1 Corchorus olitorius cultivar O-4 contig20241, 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: 4695
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.34


Found at i:2134 original size:122 final size:127

Alignment explanation


    Indices: 1918--2171  Score: 392
    Period size: 122  Copynumber: 2.0  Consensus size: 127

       1908 ATTTAAGAAA

                                                                             
       1918 TATATTTAAAAAATTCGAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAA
          1 TATATTTAAAAAATTCGAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---A

                                          *     *               *      *     
       1983 TAGCTATAAGGATATTAGATTTAATTAAATTAAAATTGAGTTTTTAGTTGAGTAAAACTGTAAAA
         63 TA-CTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGCAAAACTATAAAA

             
       2048 G
        127 G

                            *                                                
       2049 TATATTTAAAAAATTCTAATATATATAA-TTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-
          1 TATATTTAAAAAATTCGAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAC

                                                                          
       2111 TA-AA-GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGCAAAACTATAAAAG
         66 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGCAAAACTATAAAAG

             
       2171 T
          1 T

       2172 TTAAAAAATG


Statistics
Matches: 118,  Mismatches: 5, Indels: 9
        0.89            0.04        0.07

Matches are distributed among these distances:
 122   53  0.45
 123    2  0.02
 124    2  0.02
 126    2  0.02
 130   32  0.27
 131   27  0.23

ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38


Consensus pattern (127 bp):   
TATATTTAAAAAATTCGAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAC
TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGCAAAACTATAAAAG

Found at i:2868 original size:11 final size:11

Alignment explanation


    Indices: 2852--2878  Score: 54
    Period size: 11  Copynumber: 2.5  Consensus size: 11

       2842 ATCCTGATGT

                       
       2852 AATTAAAACCC
          1 AATTAAAACCC

                       
       2863 AATTAAAACCC
          1 AATTAAAACCC

                 
       2874 AATTA
          1 AATTA

       2879 GTTAATACCT


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

Matches are distributed among these distances:
  11   16  1.00

ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22


Consensus pattern (11 bp):   
AATTAAAACCC

Found at i:3388 original size:19 final size:19

Alignment explanation


    Indices: 3368--3404  Score: 58
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       3358 AATTAATTAT

                               
       3368 TTTA-ATATTAAATTTTTA
          1 TTTATATATTAAATTTTTA

                       *       
       3386 TTTATATATTATATTTTTA
          1 TTTATATATTAAATTTTTA

       3405 CTTAAAAATT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18    4  0.24
  19   13  0.76

ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65


Consensus pattern (19 bp):   
TTTATATATTAAATTTTTA
Done.