Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2357

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: 20883
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31


Found at i:780 original size:29 final size:29

Alignment explanation


    Indices: 734--803  Score: 115
    Period size: 29  Copynumber: 2.4  Consensus size: 29

        724 CTAACATAAC

                         *             * 
        734 AAGCACTAAGTGTGCGAGTTTGATTATGT
          1 AAGCACTAAGTGTCCGAGTTTGATTATAT

                                         
        763 AAGCACTAAGTGTCCGAGTTTGATTATAT
          1 AAGCACTAAGTGTCCGAGTTTGATTATAT

                         
        792 AA-CACTAAGTGT
          1 AAGCACTAAGTGT

        804 GCGGACTTAC


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  28   10  0.26
  29   29  0.74

ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33


Consensus pattern (29 bp):   
AAGCACTAAGTGTCCGAGTTTGATTATAT

Found at i:8693 original size:28 final size:28

Alignment explanation


    Indices: 8627--8783  Score: 215
    Period size: 29  Copynumber: 5.5  Consensus size: 28

       8617 CATGAGATTG

                          *     *   **   
       8627 GCACTAAGTGTGCGGGTTTAAATTGCATA
          1 GCACTAAGTGTGCGAGTTT-GATTATATA

                         *              
       8656 GCACTAAGTGTGCAAGTTTGATTATATA
          1 GCACTAAGTGTGCGAGTTTGATTATATA

                                     *   
       8684 GCACTAAGTGTGCGAGTTTGATTATGTAA
          1 GCACTAAGTGTGCGAGTTTGATTATAT-A

                                     *   
       8713 GCACTAAGTGTGCGAGTTTGATTATGTAA
          1 GCACTAAGTGTGCGAGTTTGATTATAT-A

                                        
       8742 GCACTAAGTGTGCGAGTTTGATTATATA
          1 GCACTAAGTGTGCGAGTTTGATTATATA

            *             
       8770 ACACTAAGTGTGCG
          1 GCACTAAGTGTGCG

       8784 GACTTACTAT


Statistics
Matches: 118,  Mismatches: 9, Indels: 3
        0.91            0.07        0.02

Matches are distributed among these distances:
  28   45  0.38
  29   73  0.62

ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33


Consensus pattern (28 bp):   
GCACTAAGTGTGCGAGTTTGATTATATA

Found at i:8716 original size:57 final size:58

Alignment explanation


    Indices: 8627--8782  Score: 219
    Period size: 57  Copynumber: 2.7  Consensus size: 58

       8617 CATGAGATTG

                          *    * *    *                                
       8627 GCACTAAGTGTGCGGGTTTAAAT-TGCATAGCACTAAGTGTGCAAGTTTGATTATAT-A
          1 GCACTAAGTGTGCGAGTTTGATTATGTA-AGCACTAAGTGTGCAAGTTTGATTATATAA

                                                      *           *   
       8684 GCACTAAGTGTGCGAGTTTGATTATGTAAGCACTAAGTGTGCGAGTTTGATTATGTAA
          1 GCACTAAGTGTGCGAGTTTGATTATGTAAGCACTAAGTGTGCAAGTTTGATTATATAA

                                     *                
       8742 GCACTAAGTGTGCGAGTTTGATTATATAA-CACTAAGTGTGC
          1 GCACTAAGTGTGCGAGTTTGATTATGTAAGCACTAAGTGTGC

       8783 GGACTTACTA


Statistics
Matches: 90,  Mismatches: 7, Indels: 4
        0.89            0.07        0.04

Matches are distributed among these distances:
  57   58  0.64
  58   32  0.36

ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33


Consensus pattern (58 bp):   
GCACTAAGTGTGCGAGTTTGATTATGTAAGCACTAAGTGTGCAAGTTTGATTATATAA

Found at i:13256 original size:17 final size:19

Alignment explanation


    Indices: 13216--13258  Score: 63
    Period size: 19  Copynumber: 2.4  Consensus size: 19

      13206 GACTTAATGA

                           *   
      13216 AAATTAAAAATTGAGTTGC
          1 AAATTAAAAATTGAGATGC

                               
      13235 AAATTAAAAATTG-GAT-C
          1 AAATTAAAAATTGAGATGC

                   
      13252 AAATTAA
          1 AAATTAA

      13259 CCCTTTTATT


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  17    8  0.35
  18    2  0.09
  19   13  0.57

ACGTcount: A:0.53, C:0.05, G:0.12, T:0.30


Consensus pattern (19 bp):   
AAATTAAAAATTGAGATGC
Done.