Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014871.1 Corchorus olitorius cultivar O-4 contig14904, 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: 33535
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31


Found at i:4091 original size:22 final size:22

Alignment explanation


    Indices: 4066--4109  Score: 88
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       4056 ATCTTTAAGA

                                  
       4066 ATATACTTTTAAGAGTAAATTT
          1 ATATACTTTTAAGAGTAAATTT

                                  
       4088 ATATACTTTTAAGAGTAAATTT
          1 ATATACTTTTAAGAGTAAATTT

       4110 TATTATTTAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45


Consensus pattern (22 bp):   
ATATACTTTTAAGAGTAAATTT

Found at i:7690 original size:32 final size:31

Alignment explanation


    Indices: 7653--7727  Score: 87
    Period size: 32  Copynumber: 2.4  Consensus size: 31

       7643 CCTGCACTAG

                                *           
       7653 GGATAAATTGTCCCAAATTTTAAAAGTTAAAA
          1 GGATAAATTGTCCCAAATTTGAAAA-TTAAAA

                     *  **             *   
       7685 GGATAAATTTTCTTAAATTTGAAAATTTAAA
          1 GGATAAATTGTCCCAAATTTGAAAATTAAAA

               *        
       7716 GGACAAATTGTC
          1 GGATAAATTGTC

       7728 ACGATATGAA


Statistics
Matches: 36,  Mismatches: 7, Indels: 1
        0.82            0.16        0.02

Matches are distributed among these distances:
  31   15  0.42
  32   21  0.58

ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35


Consensus pattern (31 bp):   
GGATAAATTGTCCCAAATTTGAAAATTAAAA

Found at i:12654 original size:23 final size:23

Alignment explanation


    Indices: 12600--12654  Score: 62
    Period size: 23  Copynumber: 2.4  Consensus size: 23

      12590 GAAATCCAAG

                         *         
      12600 AAAATAG-AAGATTAAACGAAAT
          1 AAAATAGAAAGATAAAACGAAAT

                                     
      12622 AAAAGT-GAAAGATAAAAC-AAATT
          1 AAAA-TAGAAAGATAAAACGAAA-T

                      
      12645 AAAATAGAAA
          1 AAAATAGAAA

      12655 TTAAAGTATT


Statistics
Matches: 28,  Mismatches: 1, Indels: 7
        0.78            0.03        0.19

Matches are distributed among these distances:
  22    9  0.32
  23   19  0.68

ACGTcount: A:0.67, C:0.04, G:0.13, T:0.16


Consensus pattern (23 bp):   
AAAATAGAAAGATAAAACGAAAT

Found at i:12659 original size:22 final size:22

Alignment explanation


    Indices: 12600--12659  Score: 54
    Period size: 22  Copynumber: 2.7  Consensus size: 22

      12590 GAAATCCAAG

                                   
      12600 AAAATAGAAGATT-AAACGAAAT
          1 AAAATAGAA-ATTAAAACGAAAT

                        *            
      12622 AAAAGT-GAAAGATAAAAC-AAATT
          1 AAAA-TAGAAA-TTAAAACGAAA-T

                           
      12645 AAAATAGAAATTAAA
          1 AAAATAGAAATTAAA

      12660 GTATTCCCCG


Statistics
Matches: 31,  Mismatches: 2, Indels: 10
        0.72            0.05        0.23

Matches are distributed among these distances:
  21    1  0.03
  22   16  0.52
  23   14  0.45

ACGTcount: A:0.67, C:0.03, G:0.12, T:0.18


Consensus pattern (22 bp):   
AAAATAGAAATTAAAACGAAAT

Found at i:27150 original size:52 final size:51

Alignment explanation


    Indices: 27006--27151  Score: 163
    Period size: 52  Copynumber: 2.9  Consensus size: 51

      26996 AGATTGACTC

                                *         * *                  
      27006 AACTGGTAAGGTGCATACTCATTGGACCGTGATGTCTCA--T-ATGAGATT
          1 AACTGGTAAGGTGCATACTCTTTGGACCGTAAAGTCTCATCTCATGAGATT

                         *         *   *     *                  
      27054 AACTGGTAAGGTGTATACTCTTTTGACTGTAAAATCTCAGTCTCATGAGATT
          1 AACTGGTAAGGTGCATACTCTTTGGACCGTAAAGTCTCA-TCTCATGAGATT

            *    *                            *           
      27106 GACTGATAAGGTGCATACTCTTTGGACCGTAAAGCCTCATTCTCAT
          1 AACTGGTAAGGTGCATACTCTTTGGACCGTAAAGTCTCA-TCTCAT

      27152 ATGAGATTTG


Statistics
Matches: 79,  Mismatches: 15, Indels: 4
        0.81            0.15        0.04

Matches are distributed among these distances:
  48   32  0.41
  51    1  0.01
  52   46  0.58

ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33


Consensus pattern (51 bp):   
AACTGGTAAGGTGCATACTCTTTGGACCGTAAAGTCTCATCTCATGAGATT
Done.