Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022791.1 Corchorus olitorius cultivar O-4 contig22824, 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: 34688
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:17700 original size:19 final size:19

Alignment explanation


    Indices: 17650--17700  Score: 61
    Period size: 19  Copynumber: 2.7  Consensus size: 19

      17640 CATAAGATTT

                               
      17650 TTAATAA-TAATTATTCAA
          1 TTAATAATTAATTATTCAA

              *              *  
      17668 TAAAATAATT-ATTATTTAA
          1 T-TAATAATTAATTATTCAA

                          
      17687 TTAATAATTAATTA
          1 TTAATAATTAATTA

      17701 ATTTCAGCCT


Statistics
Matches: 27,  Mismatches: 3, Indels: 5
        0.77            0.09        0.14

Matches are distributed among these distances:
  18    8  0.30
  19   18  0.67
  20    1  0.04

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47


Consensus pattern (19 bp):   
TTAATAATTAATTATTCAA

Found at i:22320 original size:68 final size:67

Alignment explanation


    Indices: 22196--22330  Score: 252
    Period size: 68  Copynumber: 2.0  Consensus size: 67

      22186 CTTACGTGTC

                                                                             
      22196 ATATTAGTACACTATTACAAATTAAGAGAATATGGAAATTTACCCACTGCAAGGGTAAAACAGGA
          1 ATATTAGTACACTATTACAAATTAAGAGAATATGGAAATTTACCCACTGCAAGGGTAAAACAGGA

              
      22261 AT
         66 AT

                                                *                            
      22263 ATATTAGTACACTATTACAAATTAAGAGTAATATGGTAATTTACCCACTGCAAGGGTAAAACAGG
          1 ATATTAGTACACTATTACAAATTAAGAG-AATATGGAAATTTACCCACTGCAAGGGTAAAACAGG

               
      22328 AAT
         65 AAT

      22331 TTATGCTTCT


Statistics
Matches: 66,  Mismatches: 1, Indels: 1
        0.97            0.01        0.01

Matches are distributed among these distances:
  67   28  0.42
  68   38  0.58

ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27


Consensus pattern (67 bp):   
ATATTAGTACACTATTACAAATTAAGAGAATATGGAAATTTACCCACTGCAAGGGTAAAACAGGA
AT

Found at i:22642 original size:24 final size:24

Alignment explanation


    Indices: 22615--22670  Score: 96
    Period size: 24  Copynumber: 2.4  Consensus size: 24

      22605 AGCCAGGCCG

                                    
      22615 CTGGGCCTGCGCTGGCCCGCGCGC
          1 CTGGGCCTGCGCTGGCCCGCGCGC

                                 *  
      22639 CTGGGCCTGCGCTGGCCCGCGTGC
          1 CTGGGCCTGCGCTGGCCCGCGCGC

                     
      22663 CT-GGCCTG
          1 CTGGGCCTG

      22671 GCATGCCTGG


Statistics
Matches: 31,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  23    6  0.19
  24   25  0.81

ACGTcount: A:0.00, C:0.43, G:0.41, T:0.16


Consensus pattern (24 bp):   
CTGGGCCTGCGCTGGCCCGCGCGC
Done.