Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023686.1 Corchorus olitorius cultivar O-4 contig23719, 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: 11276
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31


Found at i:3968 original size:24 final size:23

Alignment explanation


    Indices: 3932--3976  Score: 54
    Period size: 24  Copynumber: 1.9  Consensus size: 23

       3922 AGGCCTGGCG

                 *                  
       3932 AGGCCTGGAGCGGCCCAAGCGCCC
          1 AGGCCAGGAGCGGCCC-AGCGCCC

                    *    *       
       3956 AGGCCAGGCGCGGGCCAGCGC
          1 AGGCCAGGAGCGGCCCAGCGC

       3977 ATGGCCCAGC


Statistics
Matches: 18,  Mismatches: 3, Indels: 1
        0.82            0.14        0.05

Matches are distributed among these distances:
  23    5  0.28
  24   13  0.72

ACGTcount: A:0.16, C:0.40, G:0.42, T:0.02


Consensus pattern (23 bp):   
AGGCCAGGAGCGGCCCAGCGCCC

Found at i:3985 original size:23 final size:23

Alignment explanation


    Indices: 3966--4034  Score: 129
    Period size: 23  Copynumber: 3.0  Consensus size: 23

       3956 AGGCCAGGCG

                                    
       3966 CGGGCCAGCGCATGGCCCAGCGCA
          1 CGGGCCAGC-CATGGCCCAGCGCA

                                   
       3990 CGGGCCAGCCATGGCCCAGCGCA
          1 CGGGCCAGCCATGGCCCAGCGCA

                                  
       4013 CGGGCCAGCCATGGCCCAGCGC
          1 CGGGCCAGCCATGGCCCAGCGC

       4035 CCAAGCTTGG


Statistics
Matches: 45,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  23   36  0.80
  24    9  0.20

ACGTcount: A:0.16, C:0.43, G:0.36, T:0.04


Consensus pattern (23 bp):   
CGGGCCAGCCATGGCCCAGCGCA

Found at i:3987 original size:12 final size:12

Alignment explanation


    Indices: 3970--4034  Score: 80
    Period size: 12  Copynumber: 5.6  Consensus size: 12

       3960 CAGGCGCGGG

                        
       3970 CCAGCGCATGGC
          1 CCAGCGCATGGC

                    *  *
       3982 CCAGCGCACGGG
          1 CCAGCGCATGGC

                        
       3994 CCAGC-CATGGC
          1 CCAGCGCATGGC

                    *  *
       4005 CCAGCGCACGGG
          1 CCAGCGCATGGC

                        
       4017 CCAGC-CATGGC
          1 CCAGCGCATGGC

                   
       4028 CCAGCGC
          1 CCAGCGC

       4035 CCAAGCTTGG


Statistics
Matches: 43,  Mismatches: 8, Indels: 4
        0.78            0.15        0.07

Matches are distributed among these distances:
  11   18  0.42
  12   25  0.58

ACGTcount: A:0.17, C:0.45, G:0.34, T:0.05


Consensus pattern (12 bp):   
CCAGCGCATGGC

Found at i:4982 original size:27 final size:27

Alignment explanation


    Indices: 4926--4985  Score: 68
    Period size: 27  Copynumber: 2.2  Consensus size: 27

       4916 TGAGTATCCT

                         *     * *      
       4926 AATTGATGATTTTGCCCCTGATTGATAA
          1 AATT-ATGATTTTACCCCTAAATGATAA

                                        
       4954 AATTATGATTTTACCCCTAACATGA-AA
          1 AATTATGATTTTACCCCTAA-ATGATAA

                 
       4981 AATTA
          1 AATTA

       4986 CCGTTTTGCC


Statistics
Matches: 28,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  27   21  0.75
  28    7  0.25

ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37


Consensus pattern (27 bp):   
AATTATGATTTTACCCCTAAATGATAA

Found at i:6383 original size:15 final size:15

Alignment explanation


    Indices: 6363--6400  Score: 67
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       6353 GAGCCTTGGT

                        *  
       6363 GCACGTGACCGGTTG
          1 GCACGTGACCGGCTG

                           
       6378 GCACGTGACCGGCTG
          1 GCACGTGACCGGCTG

                    
       6393 GCACGTGA
          1 GCACGTGA

       6401 TTCGAGGTAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  15   22  1.00

ACGTcount: A:0.16, C:0.29, G:0.39, T:0.16


Consensus pattern (15 bp):   
GCACGTGACCGGCTG

Found at i:11183 original size:27 final size:27

Alignment explanation


    Indices: 11127--11186  Score: 68
    Period size: 27  Copynumber: 2.2  Consensus size: 27

      11117 TGAGTATCCT

                         *     * *      
      11127 AATTGATGATTTTGCCCCTGATTGATAA
          1 AATT-ATGATTTTACCCCTAAATGATAA

                                        
      11155 AATTATGATTTTACCCCTAACATGA-AA
          1 AATTATGATTTTACCCCTAA-ATGATAA

                 
      11182 AATTA
          1 AATTA

      11187 CCGTTTTGCC


Statistics
Matches: 28,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  27   21  0.75
  28    7  0.25

ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37


Consensus pattern (27 bp):   
AATTATGATTTTACCCCTAAATGATAA
Done.