Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: evm.model.Ga12G0180

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: 2415
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27


Found at i:1462 original size:71 final size:72

Alignment explanation


    Indices: 1345--1496  Score: 234
    Period size: 71  Copynumber: 2.1  Consensus size: 72

       1335 TGGCTTTCAT

                           *                                   *          *  
       1345 TCTTCGGGTTCTACATTGGGTAATGGGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA
          1 TCTTCGGGTTCTACAGTGGGTAATGGGCTCTTCGGAAGCAGTAGCAGCTCTCACCCTAGTCTCAA

                   
       1410 TAGCAGC
         66 TAGCAGC

                         *     *            *              *                 
       1417 TCTTCGGGTTCTATAGTGGTTAAT-GGCTCTTTGGAAGCAGTAGCAGGTCTCACCCTAGTCTCAA
          1 TCTTCGGGTTCTACAGTGGGTAATGGGCTCTTCGGAAGCAGTAGCAGCTCTCACCCTAGTCTCAA

                   
       1481 TAGCAGC
         66 TAGCAGC

                     
       1488 TCTTCGGGT
          1 TCTTCGGGT

       1497 CAGTAGCAGC


Statistics
Matches: 73,  Mismatches: 7, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
  71   52  0.71
  72   21  0.29

ACGTcount: A:0.20, C:0.23, G:0.26, T:0.31


Consensus pattern (72 bp):   
TCTTCGGGTTCTACAGTGGGTAATGGGCTCTTCGGAAGCAGTAGCAGCTCTCACCCTAGTCTCAA
TAGCAGC

Found at i:1546 original size:24 final size:24

Alignment explanation


    Indices: 1503--1548  Score: 74
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       1493 GGGTCAGTAG

                          **        
       1503 CAGCTCTTACCCTAGTCTGAATAA
          1 CAGCTCTTACCCTACCCTGAATAA

                                  
       1527 CAGCTCTTACCCTACCCTGAAT
          1 CAGCTCTTACCCTACCCTGAAT

       1549 CCTGGTTACA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  24   20  1.00

ACGTcount: A:0.26, C:0.35, G:0.11, T:0.28


Consensus pattern (24 bp):   
CAGCTCTTACCCTACCCTGAATAA

Found at i:2242 original size:6 final size:6

Alignment explanation


    Indices: 2227--2290  Score: 74
    Period size: 6  Copynumber: 10.7  Consensus size: 6

       2217 GACTGCCCCA

                 *                                  *      *      *
       2227 GCTCCT GCTCCC GCTCCC GCTCCC GCTCCC GCTCCT GCTCCA GCTCCT
          1 GCTCCC GCTCCC GCTCCC GCTCCC GCTCCC GCTCCC GCTCCC GCTCCC

                 *      *     
       2275 GCTCCT GCTCCA GCTC
          1 GCTCCC GCTCCC GCTC

       2291 TGGCTGTATA


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

Matches are distributed among these distances:
   6   53  1.00

ACGTcount: A:0.03, C:0.56, G:0.17, T:0.23


Consensus pattern (6 bp):   
GCTCCC

Found at i:2254 original size:18 final size:18

Alignment explanation


    Indices: 2227--2290  Score: 92
    Period size: 18  Copynumber: 3.6  Consensus size: 18

       2217 GACTGCCCCA

                 *           *
       2227 GCTCCTGCTCCCGCTCCC
          1 GCTCCAGCTCCCGCTCCT

                 *            
       2245 GCTCCCGCTCCCGCTCCT
          1 GCTCCAGCTCCCGCTCCT

                       *      
       2263 GCTCCAGCTCCTGCTCCT
          1 GCTCCAGCTCCCGCTCCT

                      
       2281 GCTCCAGCTC
          1 GCTCCAGCTC

       2291 TGGCTGTATA


Statistics
Matches: 42,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  18   42  1.00

ACGTcount: A:0.03, C:0.56, G:0.17, T:0.23


Consensus pattern (18 bp):   
GCTCCAGCTCCCGCTCCT
Done.