Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold652

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: 13363
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:655 original size:21 final size:19

Alignment explanation


    Indices: 606--655  Score: 55
    Period size: 19  Copynumber: 2.5  Consensus size: 19

        596 TAAAATTTAC

                  *           *
        606 AAATATAATTTTTTTTATT
          1 AAATATTATTTTTTTTATA

               *                 
        625 AAAGATTATTTTTATTTAATA
          1 AAATATTATTTTT-TTT-ATA

                      
        646 AAATATTATT
          1 AAATATTATT

        656 GACATATTTT


Statistics
Matches: 25,  Mismatches: 4, Indels: 2
        0.81            0.13        0.06

Matches are distributed among these distances:
  19   11  0.44
  20    3  0.12
  21   11  0.44

ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56


Consensus pattern (19 bp):   
AAATATTATTTTTTTTATA

Found at i:1894 original size:3 final size:3

Alignment explanation


    Indices: 1886--1919  Score: 59
    Period size: 3  Copynumber: 11.3  Consensus size: 3

       1876 TTCCATCCCT

                                              *          
       1886 TTC TTC TTC TTC TTC TTC TTC TTC TTT TTC TTC T
          1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T

       1920 CCTCCTCCTT


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   3   29  1.00

ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71


Consensus pattern (3 bp):   
TTC

Found at i:5919 original size:11 final size:11

Alignment explanation


    Indices: 5905--5930  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       5895 ATTTTTTTAA

                       
       5905 TTTTAAAATAC
          1 TTTTAAAATAC

                       
       5916 TTTTAAAATAC
          1 TTTTAAAATAC

                
       5927 TTTT
          1 TTTT

       5931 TTTAAGCCGG


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54


Consensus pattern (11 bp):   
TTTTAAAATAC

Found at i:12014 original size:11 final size:11

Alignment explanation


    Indices: 11993--12025  Score: 59
    Period size: 11  Copynumber: 3.1  Consensus size: 11

      11983 CTCTTTTAAC

                       
      11993 TTTCTTT-TTT
          1 TTTCTTTATTT

                       
      12003 TTTCTTTATTT
          1 TTTCTTTATTT

                       
      12014 TTTCTTTATTT
          1 TTTCTTTATTT

             
      12025 T
          1 T

      12026 CCATTCTATT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  10    7  0.32
  11   15  0.68

ACGTcount: A:0.06, C:0.09, G:0.00, T:0.85


Consensus pattern (11 bp):   
TTTCTTTATTT
Done.