Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1328

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: 4647
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.36


Found at i:4072 original size:21 final size:21

Alignment explanation


    Indices: 4043--4095  Score: 74
    Period size: 20  Copynumber: 2.6  Consensus size: 21

       4033 TTACAAGCAA

                *                 
       4043 GTATTGATACAATT-TCCTCAT
          1 GTATCGATACAATTGTCC-CAT

                                 
       4064 GTATCGATAC-ATTGTCCCAT
          1 GTATCGATACAATTGTCCCAT

                        
       4084 GTATCGATACAA
          1 GTATCGATACAA

       4096 ATAGTGATAG


Statistics
Matches: 29,  Mismatches: 1, Indels: 4
        0.85            0.03        0.12

Matches are distributed among these distances:
  20   16  0.55
  21   13  0.45

ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36


Consensus pattern (21 bp):   
GTATCGATACAATTGTCCCAT

Found at i:4171 original size:19 final size:19

Alignment explanation


    Indices: 4123--4175  Score: 61
    Period size: 19  Copynumber: 2.7  Consensus size: 19

       4113 ACTGCCATCT

                           *  **
       4123 CATGTATCGATACAATTGTC
          1 CATGTATCGATAC-AGTGAA

               *               
       4143 CATTTATCGATACAGTGAA
          1 CATGTATCGATACAGTGAA

                          
       4162 CATGTATCGATACA
          1 CATGTATCGATACA

       4176 ATGTATCGAT


Statistics
Matches: 28,  Mismatches: 5, Indels: 1
        0.82            0.15        0.03

Matches are distributed among these distances:
  19   16  0.57
  20   12  0.43

ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32


Consensus pattern (19 bp):   
CATGTATCGATACAGTGAA

Found at i:4181 original size:13 final size:13

Alignment explanation


    Indices: 4163--4189  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       4153 TACAGTGAAC

                         
       4163 ATGTATCGATACA
          1 ATGTATCGATACA

                         
       4176 ATGTATCGATACA
          1 ATGTATCGATACA

             
       4189 A
          1 A

       4190 AAGCATAATG


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:0.41, C:0.15, G:0.15, T:0.30


Consensus pattern (13 bp):   
ATGTATCGATACA
Done.