Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022190.1 Corchorus olitorius cultivar O-4 contig22223, 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: 20713
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Found at i:2073 original size:22 final size:21

Alignment explanation


    Indices: 2045--2105  Score: 68
    Period size: 22  Copynumber: 2.8  Consensus size: 21

       2035 TGAATATTTT

                            *     
       2045 TATGAAATTTTGATAATTTACA
          1 TATGAAATTTTGATAACTT-CA

                     *           *
       2067 TATGAAATTGTGATAAACTTCG
          1 TATGAAATTTTGAT-AACTTCA

                   *         
       2089 TATGAAACTTTGATAAC
          1 TATGAAATTTTGATAAC

       2106 CTAACTATGA


Statistics
Matches: 33,  Mismatches: 5, Indels: 3
        0.80            0.12        0.07

Matches are distributed among these distances:
  21    3  0.09
  22   26  0.79
  23    4  0.12

ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39


Consensus pattern (21 bp):   
TATGAAATTTTGATAACTTCA

Found at i:2127 original size:44 final size:44

Alignment explanation


    Indices: 2045--2128  Score: 100
    Period size: 44  Copynumber: 1.9  Consensus size: 44

       2035 TGAATATTTT

                   *        * *              *          
       2045 TATGAAATTTTGATAATTTACATATGAAATTGTGATAAACTTCG
          1 TATGAAACTTTGATAACTAACATATGAAATTGTAATAAACTTCG

                                                      
       2089 TATGAAACTTTGATAACCTAAC-TATGAAATAT-TAATAAAC
          1 TATGAAACTTTGATAA-CTAACATATGAAAT-TGTAATAAAC

       2129 CTTTCTATGA


Statistics
Matches: 34,  Mismatches: 4, Indels: 4
        0.81            0.10        0.10

Matches are distributed among these distances:
  44   30  0.88
  45    4  0.12

ACGTcount: A:0.43, C:0.10, G:0.11, T:0.37


Consensus pattern (44 bp):   
TATGAAACTTTGATAACTAACATATGAAATTGTAATAAACTTCG

Found at i:6295 original size:30 final size:30

Alignment explanation


    Indices: 6259--6317  Score: 118
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       6249 AAGCTGCATT

                                          
       6259 TGATCAATGATTTGATCAAATTTGTGGAAA
          1 TGATCAATGATTTGATCAAATTTGTGGAAA

                                         
       6289 TGATCAATGATTTGATCAAATTTGTGGAA
          1 TGATCAATGATTTGATCAAATTTGTGGAA

       6318 CTCATCCATG


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

Matches are distributed among these distances:
  30   29  1.00

ACGTcount: A:0.36, C:0.07, G:0.20, T:0.37


Consensus pattern (30 bp):   
TGATCAATGATTTGATCAAATTTGTGGAAA

Found at i:7721 original size:15 final size:15

Alignment explanation


    Indices: 7696--7749  Score: 63
    Period size: 16  Copynumber: 3.5  Consensus size: 15

       7686 CCTCCTCTAG

                *          
       7696 TTTGGTTTTAGTTTT
          1 TTTGTTTTTAGTTTT

              *             
       7711 TTAGTTTTTAGCTTTT
          1 TTTGTTTTTAG-TTTT

               *            
       7727 TTTTTTTTATAGTTTT
          1 TTTGTTTT-TAGTTTT

                   
       7743 TTTGTTT
          1 TTTGTTT

       7750 CAATTAGGGA


Statistics
Matches: 32,  Mismatches: 5, Indels: 3
        0.80            0.12        0.08

Matches are distributed among these distances:
  15    9  0.28
  16   20  0.62
  17    3  0.09

ACGTcount: A:0.09, C:0.02, G:0.13, T:0.76


Consensus pattern (15 bp):   
TTTGTTTTTAGTTTT

Found at i:20653 original size:15 final size:15

Alignment explanation


    Indices: 20635--20667  Score: 57
    Period size: 15  Copynumber: 2.2  Consensus size: 15

      20625 TAAAAAGATT

                       *   
      20635 AAAAAAAAAACGCAG
          1 AAAAAAAAAACCCAG

                           
      20650 AAAAAAAAAACCCAG
          1 AAAAAAAAAACCCAG

               
      20665 AAA
          1 AAA

      20668 TAGATGGCGG


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.76, C:0.15, G:0.09, T:0.00


Consensus pattern (15 bp):   
AAAAAAAAAACCCAG
Done.