Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021460.1 Corchorus olitorius cultivar O-4 contig21493, 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: 12201
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36


Found at i:371 original size:24 final size:24

Alignment explanation


    Indices: 339--388  Score: 73
    Period size: 24  Copynumber: 2.1  Consensus size: 24

        329 TAATAGATAG

                             *      
        339 AATTCCGTTTTTGATTCTATTGCA
          1 AATTCCGTTTTTGATTCCATTGCA

                *             *     
        363 AATTTCGTTTTTGATTCCGTTGCA
          1 AATTCCGTTTTTGATTCCATTGCA

              
        387 AA
          1 AA

        389 GTACTCAGAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.22, C:0.16, G:0.14, T:0.48


Consensus pattern (24 bp):   
AATTCCGTTTTTGATTCCATTGCA

Found at i:2180 original size:25 final size:26

Alignment explanation


    Indices: 2150--2198  Score: 82
    Period size: 25  Copynumber: 1.9  Consensus size: 26

       2140 TGTAGTTTGA

                                      
       2150 TATGTTTAGTAGTTTT-AGTTTTTAG
          1 TATGTTTAGTAGTTTTAAGTTTTTAG

                   *                
       2175 TATGTTTTGTAGTTTTAAGTTTTT
          1 TATGTTTAGTAGTTTTAAGTTTTT

       2199 TTTTTTCCTG


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

Matches are distributed among these distances:
  25   15  0.68
  26    7  0.32

ACGTcount: A:0.18, C:0.00, G:0.18, T:0.63


Consensus pattern (26 bp):   
TATGTTTAGTAGTTTTAAGTTTTTAG

Found at i:3589 original size:178 final size:178

Alignment explanation


    Indices: 3320--3657  Score: 484
    Period size: 178  Copynumber: 1.9  Consensus size: 178

       3310 CCGATTAAGG

                                                     *       *               
       3320 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAATTTTCATGCAGGACTCGAAAACTA
          1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA

            *                  *                     *        *        *     
       3385 CATTTAATGTTTCAAGTATCAAAAATGCTTCCGAAA-AATTTGTTGTTTCGGTTAACGGGAATAG
         66 AATTTAATGTTTCAAGTATAAAAAATGCTT-CGAAAGAATTAGTTGTTTCAGTTAACGGAAATAG

             *                *                               
       3449 ATGGTCCACTAAATATTATATAACTTT-TGCTCCAGATGTCTGATTGAGA
        130 ACGGTCCACTAAATATTACATAA-TTTGTGCTCCAGATGTCTGATTGAGA

                          *  *    *                                 *        
       3498 TGATTCAAGTGTCTCTTCAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGACTTGAAAACTA
          1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA

                                            *                                
       3563 AATTTAATG-TTCAAGGTATAAAAAATGCTTCTAAAGAATTAGTTGTTTCAGTTAACGGAAATAG
         66 AATTTAATGTTTCAA-GTATAAAAAATGCTTCGAAAGAATTAGTTGTTTCAGTTAACGGAAATAG

                  *   *                    
       3627 ACGGTCTACTTAATATTACATAATTTGTGCT
        130 ACGGTCCACTAAATATTACATAATTTGTGCT

       3658 TCTGGTGGAA


Statistics
Matches: 141,  Mismatches: 16, Indels: 6
        0.87            0.10        0.04

Matches are distributed among these distances:
 177   12  0.09
 178  129  0.91

ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36


Consensus pattern (178 bp):   
TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
AATTTAATGTTTCAAGTATAAAAAATGCTTCGAAAGAATTAGTTGTTTCAGTTAACGGAAATAGA
CGGTCCACTAAATATTACATAATTTGTGCTCCAGATGTCTGATTGAGA

Found at i:4200 original size:51 final size:51

Alignment explanation


    Indices: 4135--4237  Score: 197
    Period size: 51  Copynumber: 2.0  Consensus size: 51

       4125 TGATGTAGTC

                                                               
       4135 AAATTAAACCGTGCGTGTTGACAATTGGGCATTTATTTTAAGTAGAGAGAG
          1 AAATTAAACCGTGCGTGTTGACAATTGGGCATTTATTTTAAGTAGAGAGAG

                     *                                         
       4186 AAATTAAACTGTGCGTGTTGACAATTGGGCATTTATTTTAAGTAGAGAGAG
          1 AAATTAAACCGTGCGTGTTGACAATTGGGCATTTATTTTAAGTAGAGAGAG

             
       4237 A
          1 A

       4238 GAAATTATTA


Statistics
Matches: 51,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  51   51  1.00

ACGTcount: A:0.34, C:0.09, G:0.25, T:0.32


Consensus pattern (51 bp):   
AAATTAAACCGTGCGTGTTGACAATTGGGCATTTATTTTAAGTAGAGAGAG

Done.