Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold807

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: 30610
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33


Found at i:1623 original size:33 final size:34

Alignment explanation


    Indices: 1585--1653  Score: 104
    Period size: 33  Copynumber: 2.1  Consensus size: 34

       1575 GTTTATTAAA

                   *                          
       1585 TTTAGTTTAGCTCAAATAAGTGTTAG-AAATAAT
          1 TTTAGTTCAGCTCAAATAAGTGTTAGTAAATAAT

                        *                *    
       1618 TTTAGTTCAGCTTAAATAAGTGTTAGTAATTAAT
          1 TTTAGTTCAGCTCAAATAAGTGTTAGTAAATAAT

              
       1652 TT
          1 TT

       1654 GTTTAAATCT


Statistics
Matches: 32,  Mismatches: 3, Indels: 1
        0.89            0.08        0.03

Matches are distributed among these distances:
  33   24  0.75
  34    8  0.25

ACGTcount: A:0.36, C:0.06, G:0.14, T:0.43


Consensus pattern (34 bp):   
TTTAGTTCAGCTCAAATAAGTGTTAGTAAATAAT

Found at i:6459 original size:5 final size:6

Alignment explanation


    Indices: 6430--6474  Score: 54
    Period size: 6  Copynumber: 7.5  Consensus size: 6

       6420 AAAGGAAGAC

                        * *                       *   *         
       6430 AGAAAA AGAAAT CGAAAA AGAAAA AGAAAA AGAGAA TGAAAA AGA
          1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGA

       6475 GTGAAAAGAG


Statistics
Matches: 31,  Mismatches: 8, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
   6   31  1.00

ACGTcount: A:0.73, C:0.02, G:0.20, T:0.04


Consensus pattern (6 bp):   
AGAAAA

Found at i:8284 original size:33 final size:34

Alignment explanation


    Indices: 8247--8318  Score: 101
    Period size: 33  Copynumber: 2.1  Consensus size: 34

       8237 GAGTTAGTTT

                                              
       8247 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
          1 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA

                 *       *    * *             
       8280 ATTAATTTTAGTTTAGCTTATATAAGTGTTAGTA
          1 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA

                 
       8314 ATTAA
          1 ATTAA

       8319 TTTGTTTAAA


Statistics
Matches: 34,  Mismatches: 4, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  33   28  0.82
  34    6  0.18

ACGTcount: A:0.38, C:0.06, G:0.14, T:0.43


Consensus pattern (34 bp):   
ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA

Found at i:17102 original size:11 final size:10

Alignment explanation


    Indices: 17072--17101  Score: 60
    Period size: 10  Copynumber: 3.0  Consensus size: 10

      17062 AGTAGTTTCT

                      
      17072 TCAAAAAAAA
          1 TCAAAAAAAA

                      
      17082 TCAAAAAAAA
          1 TCAAAAAAAA

                      
      17092 TCAAAAAAAA
          1 TCAAAAAAAA

      17102 AAATTTGGTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   20  1.00

ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10


Consensus pattern (10 bp):   
TCAAAAAAAA

Found at i:17166 original size:15 final size:15

Alignment explanation


    Indices: 17146--17198  Score: 88
    Period size: 15  Copynumber: 3.4  Consensus size: 15

      17136 TATCAAGTTG

                           
      17146 AAAAAAAATTCGTGA
          1 AAAAAAAATTCGTGA

                           
      17161 AAAAAAAATTCGTGA
          1 AAAAAAAATTCGTGA

                             
      17176 AAAAAAAATTTTCGTGA
          1 AAAAAAAA--TTCGTGA

                  
      17193 AAAAAA
          1 AAAAAA

      17199 GAAGAAGCTA


Statistics
Matches: 36,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
  15   23  0.64
  17   13  0.36

ACGTcount: A:0.62, C:0.06, G:0.11, T:0.21


Consensus pattern (15 bp):   
AAAAAAAATTCGTGA

Found at i:17168 original size:17 final size:17

Alignment explanation


    Indices: 17146--17198  Score: 74
    Period size: 17  Copynumber: 3.2  Consensus size: 17

      17136 TATCAAGTTG

                             
      17146 AAAAAAAATTCGTG--A
          1 AAAAAAAATTCGTGAAA

                             
      17161 AAAAAAAATTCGTGAAA
          1 AAAAAAAATTCGTGAAA

                  **         
      17178 AAAAAATTTTCGTGAAA
          1 AAAAAAAATTCGTGAAA

                
      17195 AAAA
          1 AAAA

      17199 GAAGAAGCTA


Statistics
Matches: 34,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
  15   14  0.41
  17   20  0.59

ACGTcount: A:0.62, C:0.06, G:0.11, T:0.21


Consensus pattern (17 bp):   
AAAAAAAATTCGTGAAA
Done.