Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014294.1 Corchorus olitorius cultivar O-4 contig14327, 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: 16360
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:4043 original size:17 final size:17

Alignment explanation


    Indices: 4009--4044  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       3999 TTCCTATGAT

                       *     
       4009 GTGTTCTTACATGATTG
          1 GTGTTCTTACACGATTG

                         *   
       4026 GTGTTCTTACACGGTTG
          1 GTGTTCTTACACGATTG

              
       4043 GT
          1 GT

       4045 CTAGTCCCAC


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.14, C:0.14, G:0.28, T:0.44


Consensus pattern (17 bp):   
GTGTTCTTACACGATTG

Found at i:4528 original size:18 final size:18

Alignment explanation


    Indices: 4505--4540  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       4495 GAATGTTTTC

                              
       4505 ATGAATAAAATAGATTGG
          1 ATGAATAAAATAGATTGG

                              
       4523 ATGAATAAAATAGATTGG
          1 ATGAATAAAATAGATTGG

       4541 TTAGATTAAC


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.50, C:0.00, G:0.22, T:0.28


Consensus pattern (18 bp):   
ATGAATAAAATAGATTGG

Found at i:12787 original size:6 final size:6

Alignment explanation


    Indices: 12776--12804  Score: 58
    Period size: 6  Copynumber: 4.8  Consensus size: 6

      12766 GGATATATTC

                                             
      12776 ATACAA ATACAA ATACAA ATACAA ATACA
          1 ATACAA ATACAA ATACAA ATACAA ATACA

      12805 CATCAATGTA


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

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17


Consensus pattern (6 bp):   
ATACAA

Found at i:13698 original size:2 final size:2

Alignment explanation


    Indices: 13691--13724  Score: 59
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      13681 TTTAGGTACA

                                                      *       
      13691 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      13725 GAATAATGTG


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:14138 original size:2 final size:2

Alignment explanation


    Indices: 14086--14127  Score: 50
    Period size: 2  Copynumber: 21.5  Consensus size: 2

      14076 ATAAAGTACT

                     *                                       * *          
      14086 TA TA TA AA TA TA -A TA TA TA TA TA TA TA TA TA TG CA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

             
      14127 T
          1 T

      14128 GATCCATATA


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

Matches are distributed among these distances:
   1    1  0.03
   2   32  0.97

ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45


Consensus pattern (2 bp):   
TA

Found at i:14655 original size:28 final size:28

Alignment explanation


    Indices: 14623--14678  Score: 112
    Period size: 28  Copynumber: 2.0  Consensus size: 28

      14613 GAAAGTGAAA

                                        
      14623 GCAGAAAAATTAGAGTAATTCTATTTGT
          1 GCAGAAAAATTAGAGTAATTCTATTTGT

                                        
      14651 GCAGAAAAATTAGAGTAATTCTATTTGT
          1 GCAGAAAAATTAGAGTAATTCTATTTGT

      14679 CCGCCTAATT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   28  1.00

ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36


Consensus pattern (28 bp):   
GCAGAAAAATTAGAGTAATTCTATTTGT
Done.