Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015642.1 Corchorus olitorius cultivar O-4 contig15675, 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: 22961
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:1513 original size:27 final size:27

Alignment explanation


    Indices: 1472--1560  Score: 115
    Period size: 27  Copynumber: 3.3  Consensus size: 27

       1462 AAAGTGCTTA

                    * *      *     * * 
       1472 AAATGACCGAGATGCCCTTGAACGTAC
          1 AAATGACCAAAATGCCCCTGAACATGC

                                *      
       1499 AAATGACCAAAATGCCCCTGGACATGC
          1 AAATGACCAAAATGCCCCTGAACATGC

                   *                   
       1526 AAATGACTAAAATGCCCCTGAACATGC
          1 AAATGACCAAAATGCCCCTGAACATGC

                    
       1553 AAATGACC
          1 AAATGACC

       1561 CCAAAATTCC


Statistics
Matches: 53,  Mismatches: 9, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  27   53  1.00

ACGTcount: A:0.38, C:0.27, G:0.18, T:0.17


Consensus pattern (27 bp):   
AAATGACCAAAATGCCCCTGAACATGC

Found at i:8148 original size:38 final size:38

Alignment explanation


    Indices: 8097--8174  Score: 138
    Period size: 38  Copynumber: 2.1  Consensus size: 38

       8087 ATGAGGATTT

                                                  
       8097 TCAAGAAGGATTTTCATTTGAATAGTGATATTTCAAAA
          1 TCAAGAAGGATTTTCATTTGAATAGTGATATTTCAAAA

                                         *   *    
       8135 TCAAGAAGGATTTTCATTTGAATAGTGATTTTTTAAAA
          1 TCAAGAAGGATTTTCATTTGAATAGTGATATTTCAAAA

              
       8173 TC
          1 TC

       8175 TAAAAATACA


Statistics
Matches: 38,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  38   38  1.00

ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40


Consensus pattern (38 bp):   
TCAAGAAGGATTTTCATTTGAATAGTGATATTTCAAAA

Found at i:8164 original size:18 final size:18

Alignment explanation


    Indices: 8105--8166  Score: 54
    Period size: 18  Copynumber: 3.3  Consensus size: 18

       8095 TTTCAAGAAG

                              
       8105 GATTTTCATTTGAATAGT
          1 GATTTTCATTTGAATAGT

                      ** *   *   
       8123 GATATTTCAAAATCAAGAAG-
          1 GAT-TTTC-ATTTGAA-TAGT

                              
       8143 GATTTTCATTTGAATAGT
          1 GATTTTCATTTGAATAGT

                  
       8161 GATTTT
          1 GATTTT

       8167 TTAAAATCTA


Statistics
Matches: 32,  Mismatches: 8, Indels: 8
        0.67            0.17        0.17

Matches are distributed among these distances:
  17    2  0.06
  18   13  0.41
  19    8  0.25
  20    7  0.22
  21    2  0.06

ACGTcount: A:0.34, C:0.06, G:0.16, T:0.44


Consensus pattern (18 bp):   
GATTTTCATTTGAATAGT

Found at i:10240 original size:22 final size:22

Alignment explanation


    Indices: 10215--10291  Score: 102
    Period size: 22  Copynumber: 3.5  Consensus size: 22

      10205 TATTTTTATG

                                 *
      10215 AAATTTTGATAACTACCCTATT
          1 AAATTTTGATAACTACCCTATA

                             *   *
      10237 AAATTTTGATAACTACCATATG
          1 AAATTTTGATAACTACCCTATA

                        *         
      10259 AAATTTTGATAATTA-CCTATA
          1 AAATTTTGATAACTACCCTATA

                 *      
      10280 AAATTGTGATAA
          1 AAATTTTGATAA

      10292 ATTCCATAAG


Statistics
Matches: 49,  Mismatches: 6, Indels: 1
        0.88            0.11        0.02

Matches are distributed among these distances:
  21   15  0.31
  22   34  0.69

ACGTcount: A:0.42, C:0.12, G:0.08, T:0.39


Consensus pattern (22 bp):   
AAATTTTGATAACTACCCTATA

Found at i:10299 original size:43 final size:44

Alignment explanation


    Indices: 10211--10314  Score: 129
    Period size: 43  Copynumber: 2.4  Consensus size: 44

      10201 TGAATATTTT

                                     *     *      *     
      10211 TATGAAATTTTGATAACTACCCTATTAAATTTTGATAACTACCA
          1 TATGAAATTTTGATAACTACCCTATAAAATTGTGATAAATACCA

                            *                       *   
      10255 TATGAAATTTTGATAATTA-CCTATAAAATTGTGATAAATTCCA
          1 TATGAAATTTTGATAACTACCCTATAAAATTGTGATAAATACCA

              *    * *       
      10298 TAAGAAACTCTGATAAC
          1 TATGAAATTTTGATAAC

      10315 CTAACAATGA


Statistics
Matches: 51,  Mismatches: 9, Indels: 1
        0.84            0.15        0.02

Matches are distributed among these distances:
  43   33  0.65
  44   18  0.35

ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37


Consensus pattern (44 bp):   
TATGAAATTTTGATAACTACCCTATAAAATTGTGATAAATACCA

Found at i:14785 original size:60 final size:61

Alignment explanation


    Indices: 14689--14813  Score: 171
    Period size: 60  Copynumber: 2.0  Consensus size: 61

      14679 TAGCCGGCTG

                                                              *        *   
      14689 TCAACCCAATCAATCGTTCCCAATTGAGCTTCCATGGTGCCCAACTCCCATTCCAAATTTGGC
          1 TCAACCCAATCAA-C-TTCCCAATTGAGCTTCCATGGTGCCCAACTCCCAATCCAAATTGGGC

                             *  *                *                *      
      14752 TCAACCCAATCAA-TTCTCATTTGAGCTTCCATGGTGGCCAACTCCCAATCCAACTTGGGC
          1 TCAACCCAATCAACTTCCCAATTGAGCTTCCATGGTGCCCAACTCCCAATCCAAATTGGGC

              
      14812 TC
          1 TC

      14814 CGATTGGTTA


Statistics
Matches: 56,  Mismatches: 6, Indels: 3
        0.86            0.09        0.05

Matches are distributed among these distances:
  60   43  0.77
  63   13  0.23

ACGTcount: A:0.25, C:0.34, G:0.14, T:0.27


Consensus pattern (61 bp):   
TCAACCCAATCAACTTCCCAATTGAGCTTCCATGGTGCCCAACTCCCAATCCAAATTGGGC
Done.