Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g01941.F2

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: 5481
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:1358 original size:33 final size:33

Alignment explanation


    Indices: 1321--1399  Score: 140
    Period size: 33  Copynumber: 2.4  Consensus size: 33

       1311 CTCTGTTTCA

                      *                      
       1321 GGTTGCTGGATAGGAGCTGGAATGTGAGTGTTT
          1 GGTTGCTGGACAGGAGCTGGAATGTGAGTGTTT

                            *                
       1354 GGTTGCTGGACAGGAGTTGGAATGTGAGTGTTT
          1 GGTTGCTGGACAGGAGCTGGAATGTGAGTGTTT

                         
       1387 GGTTGCTGGACAG
          1 GGTTGCTGGACAG

       1400 TAGATAGAAT


Statistics
Matches: 44,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  33   44  1.00

ACGTcount: A:0.18, C:0.08, G:0.43, T:0.32


Consensus pattern (33 bp):   
GGTTGCTGGACAGGAGCTGGAATGTGAGTGTTT

Found at i:1410 original size:33 final size:33

Alignment explanation


    Indices: 1321--1411  Score: 137
    Period size: 33  Copynumber: 2.8  Consensus size: 33

       1311 CTCTGTTTCA

                      *     *                
       1321 GGTTGCTGGATAGGAGCTGGAATGTGAGTGTTT
          1 GGTTGCTGGACAGGAGATGGAATGTGAGTGTTT

                            *                
       1354 GGTTGCTGGACAGGAGTTGGAATGTGAGTGTTT
          1 GGTTGCTGGACAGGAGATGGAATGTGAGTGTTT

                         *    *      
       1387 GGTTGCTGGACAGTAGATAGAATGT
          1 GGTTGCTGGACAGGAGATGGAATGT

       1412 CAAGAAGAAA


Statistics
Matches: 53,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  33   53  1.00

ACGTcount: A:0.21, C:0.07, G:0.41, T:0.32


Consensus pattern (33 bp):   
GGTTGCTGGACAGGAGATGGAATGTGAGTGTTT

Found at i:4063 original size:16 final size:16

Alignment explanation


    Indices: 4026--4064  Score: 53
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       4016 AAACTAAAGG

                       *    
       4026 GAGAAGAGAAATATCA
          1 GAGAAGAGAAAAATCA

                            
       4042 GAGAAGAGAAAAAT-A
          1 GAGAAGAGAAAAATCA

                    
       4057 GAGGAAGA
          1 GA-GAAGA

       4065 AGACAAGAGT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  15    3  0.14
  16   18  0.86

ACGTcount: A:0.59, C:0.03, G:0.31, T:0.08


Consensus pattern (16 bp):   
GAGAAGAGAAAAATCA
Done.