Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020348.1 Corchorus olitorius cultivar O-4 contig20381, 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: 30150
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:5671 original size:2 final size:2

Alignment explanation


    Indices: 5664--5695  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       5654 ACCAATCGAA

                                                           
       5664 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       5696 TTAAATACAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:10873 original size:31 final size:31

Alignment explanation


    Indices: 10835--10910  Score: 116
    Period size: 31  Copynumber: 2.5  Consensus size: 31

      10825 CAAGTTGACA

                          *                
      10835 AATTTGAGACTAAATCTTTCAAAATTTGCTC
          1 AATTTGAGACTAAACCTTTCAAAATTTGCTC

                    *   *                  
      10866 AATTTGAGCCTATACCTTTCAAAATTTGCTC
          1 AATTTGAGACTAAACCTTTCAAAATTTGCTC

                    *     
      10897 AATTTGAGTCTAAA
          1 AATTTGAGACTAAA

      10911 AAATAATTTA


Statistics
Matches: 40,  Mismatches: 5, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  31   40  1.00

ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38


Consensus pattern (31 bp):   
AATTTGAGACTAAACCTTTCAAAATTTGCTC

Found at i:14035 original size:21 final size:21

Alignment explanation


    Indices: 14011--14054  Score: 72
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      14001 AAAGTATATC

                 *               
      14011 TTTTTGTGG-AAAAAAATTAT
          1 TTTTTATGGAAAAAAAATTAT

                                 
      14031 TTTTTATGGAAAAAAAATTAT
          1 TTTTTATGGAAAAAAAATTAT

               
      14052 TTT
          1 TTT

      14055 AAATAAACCT


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  20    8  0.36
  21   14  0.64

ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48


Consensus pattern (21 bp):   
TTTTTATGGAAAAAAAATTAT

Found at i:22098 original size:41 final size:41

Alignment explanation


    Indices: 22023--22100  Score: 113
    Period size: 41  Copynumber: 1.9  Consensus size: 41

      22013 ATGACTTTCT

                                         *           
      22023 TTTCTTAACTAAATTTTCTTAAAAACACTTATAAAATTCCA
          1 TTTCTTAACTAAATTTTCTTAAAAACACTCATAAAATTCCA

                      *             *             
      22064 TTTCTTAACTGAATTTTCTTAAAGGA-ACTCATAAAAT
          1 TTTCTTAACTAAATTTTCTTAAA-AACACTCATAAAAT

      22101 AAAACAGACG


Statistics
Matches: 33,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  41   32  0.97
  42    1  0.03

ACGTcount: A:0.40, C:0.15, G:0.04, T:0.41


Consensus pattern (41 bp):   
TTTCTTAACTAAATTTTCTTAAAAACACTCATAAAATTCCA
Done.