Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015004.1 Corchorus olitorius cultivar O-4 contig15037, 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: 28361
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:8919 original size:2 final size:2

Alignment explanation


    Indices: 8912--8942  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       8902 AAAGATAAAG

                                                          
       8912 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       8943 GATTTGAGAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:10990 original size:30 final size:30

Alignment explanation


    Indices: 10956--11017  Score: 115
    Period size: 30  Copynumber: 2.1  Consensus size: 30

      10946 ATTTTTATCT

                                          
      10956 TGACTTTCCTCTTATACCCTCAAATTTTAA
          1 TGACTTTCCTCTTATACCCTCAAATTTTAA

                   *                      
      10986 TGACTTTTCTCTTATACCCTCAAATTTTAA
          1 TGACTTTCCTCTTATACCCTCAAATTTTAA

              
      11016 TG
          1 TG

      11018 GCTTATTAAC


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   31  1.00

ACGTcount: A:0.26, C:0.24, G:0.05, T:0.45


Consensus pattern (30 bp):   
TGACTTTCCTCTTATACCCTCAAATTTTAA

Found at i:13130 original size:32 final size:34

Alignment explanation


    Indices: 13084--13150  Score: 102
    Period size: 32  Copynumber: 2.0  Consensus size: 34

      13074 TTCTGAGAGG

                     *                    *   
      13084 TCAGATTGAGGAAGCAATT-A-AAGCAGAAGAAA
          1 TCAGATTGAAGAAGCAATTAATAAGCAGAAAAAA

                                              
      13116 TCAGATTGAAGAAGCAATTAATAAGCAGAAAAAA
          1 TCAGATTGAAGAAGCAATTAATAAGCAGAAAAAA

             
      13150 T
          1 T

      13151 GGGGTGGACG


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  32   18  0.58
  33    1  0.03
  34   12  0.39

ACGTcount: A:0.52, C:0.09, G:0.21, T:0.18


Consensus pattern (34 bp):   
TCAGATTGAAGAAGCAATTAATAAGCAGAAAAAA

Found at i:24939 original size:48 final size:48

Alignment explanation


    Indices: 24864--24993  Score: 149
    Period size: 49  Copynumber: 2.7  Consensus size: 48

      24854 GAGCGTGCCA

                     *   *         *                  *      
      24864 ATCAATTTTATC-CAAAAATTGATAAAAAGTGCAA-TGAAAATTAAAAG
          1 ATCAATTTTGTCTTAAAAATTGAGAAAAAGTGCAAGT-AAAAATAAAAG

                                                             
      24911 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
          1 ATCAATTTTGTCTTAAAAATTGAGAAAAAG-TGCAAGTAAAAATAAAAG

            * *                        *       
      24960 TTAAATTTTGT-TGTAAAAATTGAGAATAAGTGCA
          1 ATCAATTTTGTCT-TAAAAATTGAGAAAAAGTGCA

      24994 GGAAATGTAA


Statistics
Matches: 72,  Mismatches: 7, Indels: 7
        0.84            0.08        0.08

Matches are distributed among these distances:
  47   11  0.15
  48   20  0.28
  49   40  0.56
  50    1  0.01

ACGTcount: A:0.50, C:0.06, G:0.14, T:0.30


Consensus pattern (48 bp):   
ATCAATTTTGTCTTAAAAATTGAGAAAAAGTGCAAGTAAAAATAAAAG

Done.