Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2452

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: 13980
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33


Found at i:224 original size:19 final size:19

Alignment explanation


    Indices: 183--225  Score: 52
    Period size: 18  Copynumber: 2.3  Consensus size: 19

        173 AAACTTAACC

                          *    
        183 TATTTTTTAAACAAGTTTA
          1 TATTTTTTAAACAAATTTA

                     **        
        202 -ATTTTTTACTCAAATTTA
          1 TATTTTTTAAACAAATTTA

                  
        220 TATTTT
          1 TATTTT

        226 GAGCTTCTAA


Statistics
Matches: 20,  Mismatches: 3, Indels: 2
        0.80            0.12        0.08

Matches are distributed among these distances:
  18   15  0.75
  19    5  0.25

ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58


Consensus pattern (19 bp):   
TATTTTTTAAACAAATTTA

Found at i:8081 original size:13 final size:13

Alignment explanation


    Indices: 8063--8089  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       8053 AAAGTAATAA

                         
       8063 CTTATATAACAAG
          1 CTTATATAACAAG

                         
       8076 CTTATATAACAAG
          1 CTTATATAACAAG

             
       8089 C
          1 C

       8090 AAAAAAAAAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30


Consensus pattern (13 bp):   
CTTATATAACAAG

Found at i:12730 original size:14 final size:14

Alignment explanation


    Indices: 12706--12746  Score: 64
    Period size: 14  Copynumber: 2.9  Consensus size: 14

      12696 GTTATTAAAT

                           
      12706 TATATTATATATATC
          1 TATA-TATATATATC

                          
      12721 TATATATATATATC
          1 TATATATATATATC

               *        
      12735 TATGTATATATA
          1 TATATATATATA

      12747 CACATGATAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  14   21  0.84
  15    4  0.16

ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51


Consensus pattern (14 bp):   
TATATATATATATC
Done.