Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018260.1 Corchorus olitorius cultivar O-4 contig18293, 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: 11440
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31


Found at i:111 original size:1 final size:1

Alignment explanation


    Indices: 105--146  Score: 75
    Period size: 1  Copynumber: 42.0  Consensus size: 1

         95 GAAATAAGAG

                                                 *    
        105 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

        147 GAAAGAAGAA


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   1   39  1.00

ACGTcount: A:0.98, C:0.00, G:0.02, T:0.00


Consensus pattern (1 bp):   
A

Found at i:151 original size:9 final size:8

Alignment explanation


    Indices: 103--173  Score: 65
    Period size: 8  Copynumber: 8.6  Consensus size: 8

         93 CGGAAATAAG

                    
        103 AGAAAAAA
          1 AGAAAAAA

                    
        111 A-AAAAAA
          1 AGAAAAAA

                    
        118 A-AAAAAA
          1 AGAAAAAA

             *      
        125 AAAAAAAA
          1 AGAAAAAA

             *      
        133 AAAAAAAA
          1 AGAAAAAA

                     
        141 AGAAAAGAA
          1 AGAAAA-AA

                   * 
        150 AGAAGAAGA
          1 AGAA-AAAA

                      
        159 AGAAGAAGAA
          1 AGAA-AA-AA

                 
        169 AGAAA
          1 AGAAA

        174 TGCATCACAT


Statistics
Matches: 56,  Mismatches: 3, Indels: 7
        0.85            0.05        0.11

Matches are distributed among these distances:
   7   14  0.25
   8   20  0.36
   9   15  0.27
  10    7  0.12

ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00


Consensus pattern (8 bp):   
AGAAAAAA

Found at i:3054 original size:205 final size:205

Alignment explanation


    Indices: 2702--3112  Score: 822
    Period size: 205  Copynumber: 2.0  Consensus size: 205

       2692 TAAAGATTAC

                                                                             
       2702 TTATGTTTTAGATTTGTGATGAGCATCTTTGTAAGAATAAGTCGAATTTCTAAACTATTTAAAAA
          1 TTATGTTTTAGATTTGTGATGAGCATCTTTGTAAGAATAAGTCGAATTTCTAAACTATTTAAAAA

                                                                             
       2767 CATATTTATCTTTGAACTTGTCTGGTGCAGTTGTGTAGGCTATTTTTTACAGCCAGATTCTCATT
         66 CATATTTATCTTTGAACTTGTCTGGTGCAGTTGTGTAGGCTATTTTTTACAGCCAGATTCTCATT

                                                                             
       2832 ACAGATGATGAGAGTGTGCTTTTTTTATTGGGTCTTTTTCCTAAGTGTTCATCCAGATTATGCAA
        131 ACAGATGATGAGAGTGTGCTTTTTTTATTGGGTCTTTTTCCTAAGTGTTCATCCAGATTATGCAA

                      
       2897 CTGCAAGGAG
        196 CTGCAAGGAG

                                                                             
       2907 TTATGTTTTAGATTTGTGATGAGCATCTTTGTAAGAATAAGTCGAATTTCTAAACTATTTAAAAA
          1 TTATGTTTTAGATTTGTGATGAGCATCTTTGTAAGAATAAGTCGAATTTCTAAACTATTTAAAAA

                                                                             
       2972 CATATTTATCTTTGAACTTGTCTGGTGCAGTTGTGTAGGCTATTTTTTACAGCCAGATTCTCATT
         66 CATATTTATCTTTGAACTTGTCTGGTGCAGTTGTGTAGGCTATTTTTTACAGCCAGATTCTCATT

                                                                             
       3037 ACAGATGATGAGAGTGTGCTTTTTTTATTGGGTCTTTTTCCTAAGTGTTCATCCAGATTATGCAA
        131 ACAGATGATGAGAGTGTGCTTTTTTTATTGGGTCTTTTTCCTAAGTGTTCATCCAGATTATGCAA

                      
       3102 CTGCAAGGAG
        196 CTGCAAGGAG

             
       3112 T
          1 T

       3113 CGCATGACCC


Statistics
Matches: 206,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
 205  206  1.00

ACGTcount: A:0.26, C:0.13, G:0.19, T:0.41


Consensus pattern (205 bp):   
TTATGTTTTAGATTTGTGATGAGCATCTTTGTAAGAATAAGTCGAATTTCTAAACTATTTAAAAA
CATATTTATCTTTGAACTTGTCTGGTGCAGTTGTGTAGGCTATTTTTTACAGCCAGATTCTCATT
ACAGATGATGAGAGTGTGCTTTTTTTATTGGGTCTTTTTCCTAAGTGTTCATCCAGATTATGCAA
CTGCAAGGAG

Found at i:7844 original size:4 final size:4

Alignment explanation


    Indices: 7830--7865  Score: 63
    Period size: 4  Copynumber: 8.8  Consensus size: 4

       7820 TTATTCATAA

                                                        
       7830 AAAT AAAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
          1 AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA

       7866 GGAAAGAAAA


Statistics
Matches: 31,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
   4   27  0.87
   5    4  0.13

ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22


Consensus pattern (4 bp):   
AAAT

Found at i:8330 original size:7 final size:6

Alignment explanation


    Indices: 8295--8329  Score: 52
    Period size: 6  Copynumber: 5.8  Consensus size: 6

       8285 TTAATTACTT

                 *     *                            
       8295 AAAAAC AAAAGG AAAAAG AAAAAG AAAAAG AAAAA
          1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA

       8330 AACTAGCTCG


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
   6   26  1.00

ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00


Consensus pattern (6 bp):   
AAAAAG
Done.