Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022398.1 Corchorus olitorius cultivar O-4 contig22431, 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: 23052
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:22559 original size:20 final size:20

Alignment explanation


    Indices: 22534--22572  Score: 78
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      22524 TTGGCTACTA

                                
      22534 CACATGTTATTCACTAGGGG
          1 CACATGTTATTCACTAGGGG

                               
      22554 CACATGTTATTCACTAGGG
          1 CACATGTTATTCACTAGGG

      22573 TCATTTACAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31


Consensus pattern (20 bp):   
CACATGTTATTCACTAGGGG

Found at i:22725 original size:26 final size:25

Alignment explanation


    Indices: 22643--22890  Score: 390
    Period size: 25  Copynumber: 9.8  Consensus size: 25

      22633 TCACGTCAAA

                             *       
      22643 TAGTT-CATATTCAGTATGGACATG
          1 TAGTTGCATATTCAGTAGGGACATG

                                       
      22667 TAGTTGCATATTCAGTAGGGACACATG
          1 TAGTTGCATATTCAGTAGGG--ACATG

                                      
      22694 TAGTTGCATATTCAGTAGGGGACATG
          1 TAGTTGCATATTCAGTA-GGGACATG

                                      
      22720 TAGTTGCATATTCAGTAGGGGACATG
          1 TAGTTGCATATTCAGTA-GGGACATG

                                *    
      22746 TAGTTGCATATTCAGTAGGGTCATG
          1 TAGTTGCATATTCAGTAGGGACATG

                                      
      22771 TAGTTGCATATTCAGTAGGGGACATG
          1 TAGTTGCATATTCAGTA-GGGACATG

                                *    
      22797 TAGTTGCATATTCAGTAGGGTCATG
          1 TAGTTGCATATTCAGTAGGGACATG

                 *              *    
      22822 TAGTTACATATTCAGTAGGGTCATG
          1 TAGTTGCATATTCAGTAGGGACATG

                                *    
      22847 TAGTTGCATATTCAGTAGGGTCATG
          1 TAGTTGCATATTCAGTAGGGACATG

                               
      22872 TAGTTGCATATTCAGTAGG
          1 TAGTTGCATATTCAGTAGG

      22891 TCTATCGTTA


Statistics
Matches: 213,  Mismatches: 6, Indels: 9
        0.93            0.03        0.04

Matches are distributed among these distances:
  24    5  0.02
  25  111  0.52
  26   72  0.34
  27   22  0.10
  28    3  0.01

ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34


Consensus pattern (25 bp):   
TAGTTGCATATTCAGTAGGGACATG

Found at i:22792 original size:51 final size:51

Alignment explanation


    Indices: 22643--22890  Score: 410
    Period size: 51  Copynumber: 4.9  Consensus size: 51

      22633 TCACGTCAAA

                             *  *                         *     
      22643 TAGTT-CATATTCAGTATGGACATGTAGTTGCATATTCAGTAGGGACACATG
          1 TAGTTGCATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGG-GACATG

                                 *                              
      22694 TAGTTGCATATTCAGTAGGGGACATGTAGTTGCATATTCAGTAGGGGACATG
          1 TAGTTGCATATTCAGTA-GGGTCATGTAGTTGCATATTCAGTAGGGGACATG

                                                               
      22746 TAGTTGCATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGGGACATG
          1 TAGTTGCATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGGGACATG

                                          *               *    
      22797 TAGTTGCATATTCAGTAGGGTCATGTAGTTACATATTCAGTA-GGGTCATG
          1 TAGTTGCATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGGGACATG

                                                        
      22847 TAGTTGCATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGG
          1 TAGTTGCATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGG

      22891 TCTATCGTTA


Statistics
Matches: 188,  Mismatches: 6, Indels: 6
        0.94            0.03        0.03

Matches are distributed among these distances:
  50   48  0.26
  51   80  0.43
  52   33  0.18
  53   27  0.14

ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34


Consensus pattern (51 bp):   
TAGTTGCATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGGGACATG

Found at i:22922 original size:31 final size:31

Alignment explanation


    Indices: 22887--23052  Score: 316
    Period size: 31  Copynumber: 5.4  Consensus size: 31

      22877 GCATATTCAG

                  *                        
      22887 TAGGTCTATCGTTATTGCATATAGTTCATTT
          1 TAGGTCCATCGTTATTGCATATAGTTCATTT

                                           
      22918 TAGGTCCATCGTTATTGCATATAGTTCATTT
          1 TAGGTCCATCGTTATTGCATATAGTTCATTT

                                           
      22949 TAGGTCCATCGTTATTGCATATAGTTCATTT
          1 TAGGTCCATCGTTATTGCATATAGTTCATTT

                                           
      22980 TAGGTCCATCGTTATTGCATATAGTTCATTT
          1 TAGGTCCATCGTTATTGCATATAGTTCATTT

                                           
      23011 TAGGTCCATCGTTATTGCATATAGTTCATTT
          1 TAGGTCCATCGTTATTGCATATAGTTCATTT

                        
      23042 TAGG-CCATCGT
          1 TAGGTCCATCGT


Statistics
Matches: 134,  Mismatches: 1, Indels: 1
        0.99            0.01        0.01

Matches are distributed among these distances:
  30    7  0.05
  31  127  0.95

ACGTcount: A:0.22, C:0.16, G:0.17, T:0.45


Consensus pattern (31 bp):   
TAGGTCCATCGTTATTGCATATAGTTCATTT

Done.