Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g02457.F1

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: 4454
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28


Found at i:29 original size:2 final size:2

Alignment explanation


    Indices: 16--50  Score: 52
    Period size: 2  Copynumber: 17.5  Consensus size: 2

          6 CATTGCTACG

                      *                             *           
         16 TC TC TC TT TC TC TC TC TC TC TC TC TC TT TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T

         51 TTCTAGTTGG


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

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57


Consensus pattern (2 bp):   
TC

Found at i:29 original size:8 final size:8

Alignment explanation


    Indices: 16--54  Score: 50
    Period size: 8  Copynumber: 5.4  Consensus size: 8

          6 CATTGCTACG

                    
         16 TCTCTCTT
          1 TCTCTCTT

                    
         24 TCTCTC--
          1 TCTCTCTT

                    
         30 TCTCTC--
          1 TCTCTCTT

                    
         36 TCTCTCTT
          1 TCTCTCTT

                    
         44 TCTCTCTT
          1 TCTCTCTT

               
         52 TCT
          1 TCT

         55 AGTTGGCTTG


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

Matches are distributed among these distances:
   6   12  0.41
   8   17  0.59

ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59


Consensus pattern (8 bp):   
TCTCTCTT

Found at i:31 original size:10 final size:10

Alignment explanation


    Indices: 16--50  Score: 61
    Period size: 10  Copynumber: 3.5  Consensus size: 10

          6 CATTGCTACG

                      
         16 TCTCTCTTTC
          1 TCTCTCTTTC

                   *  
         26 TCTCTCTCTC
          1 TCTCTCTTTC

                      
         36 TCTCTCTTTC
          1 TCTCTCTTTC

                 
         46 TCTCT
          1 TCTCT

         51 TTCTAGTTGG


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  10   23  1.00

ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57


Consensus pattern (10 bp):   
TCTCTCTTTC

Found at i:4127 original size:74 final size:74

Alignment explanation


    Indices: 4034--4181  Score: 235
    Period size: 74  Copynumber: 2.0  Consensus size: 74

       4024 TGTTGAGAAA

                  *                       *                        *         
       4034 GGTAGACACGATACATTGATGAATACT-ACTGATGGGGCTTATGCTTCCTTGGTGGCACTTCACT
          1 GGTAGAAACGATACATTGATGAATA-TAACCGATGGGGCTTATGCTTCCTTGGTGACACTTCACT

                      
       4098 TGACATCTTC
         65 TGACATCTTC

                        * *                                                  
       4108 GGTAGAAACGATGCGTTGATGAATATAACCGATGGGGCTTATGCTTCCTTGGTGACACTTCACTT
          1 GGTAGAAACGATACATTGATGAATATAACCGATGGGGCTTATGCTTCCTTGGTGACACTTCACTT

                     
       4173 GACATCTTC
         66 GACATCTTC

       4182 AACACAAGGC


Statistics
Matches: 68,  Mismatches: 5, Indels: 2
        0.91            0.07        0.03

Matches are distributed among these distances:
  73    1  0.01
  74   67  0.99

ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32


Consensus pattern (74 bp):   
GGTAGAAACGATACATTGATGAATATAACCGATGGGGCTTATGCTTCCTTGGTGACACTTCACTT
GACATCTTC
Done.