Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g02555.N1

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, 932

Length: 1554
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28


Found at i:53 original size:6 final size:6

Alignment explanation


    Indices: 38--71  Score: 52
    Period size: 6  Copynumber: 5.8  Consensus size: 6

         28 TTTGGATACC

                 *                                  
         38 AAAAAA AAAAAG AAAAA- AAAAAG AAAAAG AAAAA
          1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA

         72 CATATCGGAC


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
   5    5  0.19
   6   21  0.81

ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00


Consensus pattern (6 bp):   
AAAAAG

Found at i:55 original size:11 final size:11

Alignment explanation


    Indices: 39--71  Score: 57
    Period size: 11  Copynumber: 2.9  Consensus size: 11

         29 TTGGATACCA

                       
         39 AAAAAAAAAAG
          1 AAAAAAAAAAG

                       
         50 AAAAAAAAAAG
          1 AAAAAAAAAAG

                       
         61 AAAAAGAAAAA
          1 AAAAA-AAAAA

         72 CATATCGGAC


Statistics
Matches: 21,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  11   16  0.76
  12    5  0.24

ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00


Consensus pattern (11 bp):   
AAAAAAAAAAG

Found at i:64 original size:17 final size:16

Alignment explanation


    Indices: 38--71  Score: 59
    Period size: 17  Copynumber: 2.1  Consensus size: 16

         28 TTTGGATACC

                            
         38 AAAAAAAAAAAGAAAA
          1 AAAAAAAAAAAGAAAA

                             
         54 AAAAAAGAAAAAGAAAA
          1 AAAAAA-AAAAAGAAAA

             
         71 A
          1 A

         72 CATATCGGAC


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16    6  0.35
  17   11  0.65

ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00


Consensus pattern (16 bp):   
AAAAAAAAAAAGAAAA

Found at i:1349 original size:42 final size:42

Alignment explanation


    Indices: 1290--1372  Score: 157
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       1280 ACTGTAACGT

                                        *             
       1290 AGTAGACGGTACGGAGCTTTCGAACCCATTTTCAGCTGTTGC
          1 AGTAGACGGTACGGAGCTTTCGAACCCACTTTCAGCTGTTGC

                                                     
       1332 AGTAGACGGTACGGAGCTTTCGAACCCACTTTCAGCTGTTG
          1 AGTAGACGGTACGGAGCTTTCGAACCCACTTTCAGCTGTTG

       1373 AGGAGTTGAT


Statistics
Matches: 40,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  42   40  1.00

ACGTcount: A:0.22, C:0.24, G:0.27, T:0.28


Consensus pattern (42 bp):   
AGTAGACGGTACGGAGCTTTCGAACCCACTTTCAGCTGTTGC
Done.