Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019637.1 Corchorus olitorius cultivar O-4 contig19670, 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: 10375
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34


Found at i:3766 original size:91 final size:91

Alignment explanation


    Indices: 3603--3776  Score: 276
    Period size: 91  Copynumber: 1.9  Consensus size: 91

       3593 TTCACGAGAG

                                *            *         *   *               * 
       3603 ATTATTAGGTGGACCGGGTTTACCACGTCATCCGTGGTCCCGATCAATAAGATTTCGACAAATCA
          1 ATTATTAGGTGGACCGGGTTCACCACGTCATCCATGGTCCCGACCAACAAGATTTCGACAAATAA

                                      
       3668 GAGTTTTTCCTACAATTTCTAGAGCA
         66 GAGTTTTTCCTACAATTTCTAGAGCA

                                                                   *     *   
       3694 ATTATTAGGTGGACCGGGTTCACCACGTCATCCATGGTCCCGACCAACAAGATTTTGACAAGTAA
          1 ATTATTAGGTGGACCGGGTTCACCACGTCATCCATGGTCCCGACCAACAAGATTTCGACAAATAA

              *               
       3759 GATTTTTTCCTACAATTT
         66 GAGTTTTTCCTACAATTT

       3777 TTAAAACACT


Statistics
Matches: 75,  Mismatches: 8, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  91   75  1.00

ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31


Consensus pattern (91 bp):   
ATTATTAGGTGGACCGGGTTCACCACGTCATCCATGGTCCCGACCAACAAGATTTCGACAAATAA
GAGTTTTTCCTACAATTTCTAGAGCA

Found at i:9569 original size:25 final size:26

Alignment explanation


    Indices: 9545--9592  Score: 73
    Period size: 26  Copynumber: 1.9  Consensus size: 26

       9535 TTAATGTTTA

                                      
       9545 AATT-TTATTTT-TATTAAAAAATTT
          1 AATTATTATTTTATATTAAAAAATTT

                          *         
       9569 AATTATTATTTTATTTTAAAAAAT
          1 AATTATTATTTTATATTAAAAAAT

       9593 AAATATGGGC


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  24    4  0.19
  25    7  0.33
  26   10  0.48

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (26 bp):   
AATTATTATTTTATATTAAAAAATTT

Found at i:9580 original size:24 final size:25

Alignment explanation


    Indices: 9545--9592  Score: 64
    Period size: 24  Copynumber: 1.9  Consensus size: 25

       9535 TTAATGTTTA

                                     
       9545 AATTTTATTTTTA-TTAAAAAATTT
          1 AATTTTATTTTTATTTAAAAAATTT

                                     
       9569 AATTATTA-TTTTATTTTAAAAAAT
          1 AATT-TTATTTTTA-TTTAAAAAAT

       9593 AAATATGGGC


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  24    9  0.43
  25    3  0.14
  26    9  0.43

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (25 bp):   
AATTTTATTTTTATTTAAAAAATTT
Done.