Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017135.1 Corchorus olitorius cultivar O-4 contig17168, 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: 18911
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31


Found at i:300 original size:13 final size:12

Alignment explanation


    Indices: 282--311  Score: 51
    Period size: 13  Copynumber: 2.4  Consensus size: 12

        272 AATAATGTTA

                         
        282 ATTATATTATATT
          1 ATTATATTATA-T

                        
        295 ATTATATTATAT
          1 ATTATATTATAT

                 
        307 ATTAT
          1 ATTAT

        312 CAATAAATTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12    6  0.35
  13   11  0.65

ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60


Consensus pattern (12 bp):   
ATTATATTATAT

Found at i:485 original size:16 final size:15

Alignment explanation


    Indices: 466--538  Score: 65
    Period size: 16  Copynumber: 4.6  Consensus size: 15

        456 GACCCGACCT

                      *     
        466 GAACCCAACATAACCC
          1 GAACCCAA-AAAACCC

                            
        482 GAACCCGAAAAAACCC
          1 GAACCC-AAAAAACCC

                     **     
        498 GAACCCAACTTAACCC
          1 GAACCCAA-AAAACCC

              *             
        514 GAGCCCGAAAAAACCC
          1 GAACCC-AAAAAACCC

               *     
        530 GAATCCAAA
          1 GAACCCAAA

        539 GTCCCCGAAC


Statistics
Matches: 46,  Mismatches: 8, Indels: 7
        0.75            0.13        0.11

Matches are distributed among these distances:
  15    5  0.11
  16   37  0.80
  17    4  0.09

ACGTcount: A:0.45, C:0.38, G:0.11, T:0.05


Consensus pattern (15 bp):   
GAACCCAAAAAACCC

Found at i:488 original size:32 final size:32

Alignment explanation


    Indices: 466--537  Score: 117
    Period size: 32  Copynumber: 2.2  Consensus size: 32

        456 GACCCGACCT

                                            
        466 GAACCCAACATAACCCGAACCCGAAAAAACCC
          1 GAACCCAACATAACCCGAACCCGAAAAAACCC

                     *        *             
        498 GAACCCAACTTAACCCGAGCCCGAAAAAACCC
          1 GAACCCAACATAACCCGAACCCGAAAAAACCC

               *    
        530 GAATCCAA
          1 GAACCCAA

        538 AGTCCCCGAA


Statistics
Matches: 37,  Mismatches: 3, Indels: 0
        0.93            0.08        0.00

Matches are distributed among these distances:
  32   37  1.00

ACGTcount: A:0.44, C:0.39, G:0.11, T:0.06


Consensus pattern (32 bp):   
GAACCCAACATAACCCGAACCCGAAAAAACCC

Found at i:13137 original size:42 final size:42

Alignment explanation


    Indices: 13078--13163  Score: 154
    Period size: 42  Copynumber: 2.0  Consensus size: 42

      13068 AAGTTCCTCC

                     *                                
      13078 AAAACAAGAGGTTGGGATCAGGAAAATTTGATTCTGATGGTG
          1 AAAACAAGAAGTTGGGATCAGGAAAATTTGATTCTGATGGTG

                                          *           
      13120 AAAACAAGAAGTTGGGATCAGGAAAATTTGGTTCTGATGGTG
          1 AAAACAAGAAGTTGGGATCAGGAAAATTTGATTCTGATGGTG

              
      13162 AA
          1 AA

      13164 GAAGCCGGTG


Statistics
Matches: 42,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  42   42  1.00

ACGTcount: A:0.37, C:0.07, G:0.30, T:0.26


Consensus pattern (42 bp):   
AAAACAAGAAGTTGGGATCAGGAAAATTTGATTCTGATGGTG
Done.