Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1782

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: 25471
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:7377 original size:17 final size:17

Alignment explanation


    Indices: 7352--7405  Score: 63
    Period size: 17  Copynumber: 3.2  Consensus size: 17

       7342 TCTCTTTTCA

                *            
       7352 TTCTCTTTTTTTGAATT
          1 TTCTTTTTTTTTGAATT

                        * *  
       7369 TTCTTTTTTTTTCATTT
          1 TTCTTTTTTTTTGAATT

                   *     *   
       7386 TTCTTTTCTTTTGTATT
          1 TTCTTTTTTTTTGAATT

               
       7403 TTC
          1 TTC

       7406 GCTCTTTTCT


Statistics
Matches: 30,  Mismatches: 7, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  17   30  1.00

ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76


Consensus pattern (17 bp):   
TTCTTTTTTTTTGAATT

Found at i:18055 original size:22 final size:22

Alignment explanation


    Indices: 18027--18070  Score: 79
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      18017 TTTTGAACCA

                                  
      18027 TTACCATTTCGTACCAAATCCC
          1 TTACCATTTCGTACCAAATCCC

                             *    
      18049 TTACCATTTCGTACCAATTCCC
          1 TTACCATTTCGTACCAAATCCC

      18071 AAATACCAAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34


Consensus pattern (22 bp):   
TTACCATTTCGTACCAAATCCC

Found at i:20684 original size:20 final size:20

Alignment explanation


    Indices: 20659--20701  Score: 59
    Period size: 20  Copynumber: 2.1  Consensus size: 20

      20649 AAAAGAAAAG

                                
      20659 AAAGAAGAGAGATTGAGAGA
          1 AAAGAAGAGAGATTGAGAGA

                  **       *    
      20679 AAAGAATCGAGATTGTGAGA
          1 AAAGAAGAGAGATTGAGAGA

               
      20699 AAA
          1 AAA

      20702 ACAAGAGAAA


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.53, C:0.02, G:0.30, T:0.14


Consensus pattern (20 bp):   
AAAGAAGAGAGATTGAGAGA
Done.