Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019750.1 Corchorus olitorius cultivar O-4 contig19783, 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: 22618
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32


Found at i:320 original size:2 final size:2

Alignment explanation


    Indices: 313--343  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

        303 CTAGCGCTGA

                                                          
        313 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

        344 GACACACACA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:1052 original size:20 final size:20

Alignment explanation


    Indices: 1016--1054  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       1006 CGACTCGAGA

                       *        
       1016 AAAATTCGAGTTCAGCTCGG
          1 AAAATTCGAGTCCAGCTCGG

                                
       1036 AAAATTCGAG-CCGAGCTCG
          1 AAAATTCGAGTCC-AGCTCG

       1055 ATCGAGCTCG


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19    1  0.06
  20   16  0.94

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


Consensus pattern (20 bp):   
AAAATTCGAGTCCAGCTCGG

Found at i:3305 original size:21 final size:21

Alignment explanation


    Indices: 3279--3412  Score: 191
    Period size: 21  Copynumber: 6.4  Consensus size: 21

       3269 TGCTAGAAGT

                                  
       3279 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                  
       3300 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                *
       3321 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
       3342 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
       3363 TCATTGGAGAAGGTTCCAAGA
          1 TCATTGGAGAAGGTTCCAAGC

            *              *     
       3384 ACATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
       3405 TCATTGGA
          1 TCATTGGA

       3413 ATTGCCTAAG


Statistics
Matches: 106,  Mismatches: 6, Indels: 2
        0.93            0.05        0.02

Matches are distributed among these distances:
  20    2  0.02
  21  104  0.98

ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Found at i:12918 original size:42 final size:42

Alignment explanation


    Indices: 12859--12939  Score: 153
    Period size: 42  Copynumber: 1.9  Consensus size: 42

      12849 GCTAAGTCTT

                                                      
      12859 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
          1 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA

                                        *          
      12901 GAAAATTCTTTGTAAATTAAGAAATACTTAACTCAAATC
          1 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC

      12940 CTGATCCTTA


Statistics
Matches: 38,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  42   38  1.00

ACGTcount: A:0.47, C:0.14, G:0.07, T:0.32


Consensus pattern (42 bp):   
GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA

Found at i:13108 original size:56 final size:57

Alignment explanation


    Indices: 13005--13119  Score: 187
    Period size: 56  Copynumber: 2.0  Consensus size: 57

      12995 TTTATTTTGT

                                         *     *      *              
      13005 AGAATAATTAAGTAGAGATAGAGGGGATATGATTTTTTATAACATTTATTGTGTGAA
          1 AGAATAATTAAGTAGAGATAGAGGGGATAAGATTTATTATAAAATTTATTGTGTGAA

                      *                                              
      13062 AGAATAATTATGTAGAGATAG-GGGGATAAGATTTATTATAAAATTTATTGTGTGAA
          1 AGAATAATTAAGTAGAGATAGAGGGGATAAGATTTATTATAAAATTTATTGTGTGAA

              
      13118 AG
          1 AG

      13120 GAAACGAATA


Statistics
Matches: 54,  Mismatches: 4, Indels: 1
        0.92            0.07        0.02

Matches are distributed among these distances:
  56   34  0.63
  57   20  0.37

ACGTcount: A:0.40, C:0.01, G:0.23, T:0.36


Consensus pattern (57 bp):   
AGAATAATTAAGTAGAGATAGAGGGGATAAGATTTATTATAAAATTTATTGTGTGAA
Done.