Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2080

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, 668

Length: 1114
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30


Found at i:15 original size:10 final size:10

Alignment explanation


    Indices: 1--41  Score: 64
    Period size: 10  Copynumber: 3.9  Consensus size: 10

                      
          1 GAAATTTCAT
          1 GAAATTTCAT

                        
         11 GAAATTTCACGT
          1 GAAATTTCA--T

                      
         23 GAAATTTCAT
          1 GAAATTTCAT

                     
         33 GAAATTTCA
          1 GAAATTTCA

         42 CAAGGCCCGA


Statistics
Matches: 29,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
  10   19  0.66
  12   10  0.34

ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37


Consensus pattern (10 bp):   
GAAATTTCAT

Found at i:29 original size:22 final size:22

Alignment explanation


    Indices: 1--42  Score: 84
    Period size: 22  Copynumber: 1.9  Consensus size: 22

                                  
          1 GAAATTTCATGAAATTTCACGT
          1 GAAATTTCATGAAATTTCACGT

                                
         23 GAAATTTCATGAAATTTCAC
          1 GAAATTTCATGAAATTTCAC

         43 AAGGCCCGAA


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

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36


Consensus pattern (22 bp):   
GAAATTTCATGAAATTTCACGT

Found at i:474 original size:14 final size:14

Alignment explanation


    Indices: 457--485  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

        447 TTTTAGCAAA

                          
        457 TGTTTAGCAATGTT
          1 TGTTTAGCAATGTT

                          
        471 TGTTTAGCAATGTT
          1 TGTTTAGCAATGTT

             
        485 T
          1 T

        486 TTACAAATAA


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

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.21, C:0.07, G:0.21, T:0.52


Consensus pattern (14 bp):   
TGTTTAGCAATGTT

Found at i:1059 original size:10 final size:10

Alignment explanation


    Indices: 1046--1093  Score: 87
    Period size: 10  Copynumber: 4.8  Consensus size: 10

       1036 AAGTTTCAAT

                      
       1046 AAATTTCATG
          1 AAATTTCATG

                   *  
       1056 AAATTTCGTG
          1 AAATTTCATG

                      
       1066 AAATTTCATG
          1 AAATTTCATG

                      
       1076 AAATTTCATG
          1 AAATTTCATG

                    
       1086 AAATTTCA
          1 AAATTTCA

       1094 CGCGTGAAAT


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

Matches are distributed among these distances:
  10   36  1.00

ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40


Consensus pattern (10 bp):   
AAATTTCATG

Done.