Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2065

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: 12628
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33


Found at i:2975 original size:15 final size:15

Alignment explanation


    Indices: 2955--2995  Score: 73
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       2945 TAGCTTCTTC

                           
       2955 TTTTTTTTTCACGAA
          1 TTTTTTTTTCACGAA

                           
       2970 TTTTTTTTTCACGAA
          1 TTTTTTTTTCACGAA

            *          
       2985 ATTTTTTTTCA
          1 TTTTTTTTTCA

       2996 ACTTGATATC


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  15   25  1.00

ACGTcount: A:0.20, C:0.12, G:0.05, T:0.63


Consensus pattern (15 bp):   
TTTTTTTTTCACGAA

Found at i:3049 original size:12 final size:12

Alignment explanation


    Indices: 3032--3076  Score: 81
    Period size: 12  Copynumber: 3.7  Consensus size: 12

       3022 AAAGGAAACC

                        
       3032 ATTTTTTTTTGA
          1 ATTTTTTTTTGA

                        
       3044 ATTTTTTTTTGA
          1 ATTTTTTTTTGA

                         
       3056 ATTTTTTTTTCGA
          1 ATTTTTTTTT-GA

                    
       3069 ATTTTTTT
          1 ATTTTTTT

       3077 GAAGAAACTA


Statistics
Matches: 32,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  12   22  0.69
  13   10  0.31

ACGTcount: A:0.16, C:0.02, G:0.07, T:0.76


Consensus pattern (12 bp):   
ATTTTTTTTTGA

Found at i:3051 original size:13 final size:13

Alignment explanation


    Indices: 3033--3076  Score: 72
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       3023 AAGGAAACCA

                         
       3033 TTTTTTTTTGAA-
          1 TTTTTTTTTGAAT

                         
       3045 TTTTTTTTTGAAT
          1 TTTTTTTTTGAAT

                    *    
       3058 TTTTTTTTCGAAT
          1 TTTTTTTTTGAAT

                  
       3071 TTTTTT
          1 TTTTTT

       3077 GAAGAAACTA


Statistics
Matches: 30,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  12   12  0.40
  13   18  0.60

ACGTcount: A:0.14, C:0.02, G:0.07, T:0.77


Consensus pattern (13 bp):   
TTTTTTTTTGAAT

Found at i:4101 original size:21 final size:22

Alignment explanation


    Indices: 4057--4102  Score: 67
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       4047 TCACTTGCAA

                           * *    
       4057 TAAACACATTAAAATGAGTTAT
          1 TAAACACATTAAAATCACTTAT

                                  
       4079 TAAACACATTAAAA-CACTTAT
          1 TAAACACATTAAAATCACTTAT

               
       4100 TAA
          1 TAA

       4103 TCATAACACA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  21    8  0.36
  22   14  0.64

ACGTcount: A:0.52, C:0.13, G:0.04, T:0.30


Consensus pattern (22 bp):   
TAAACACATTAAAATCACTTAT
Done.