Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g01842.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: 4335
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.26


Found at i:1458 original size:27 final size:27

Alignment explanation


    Indices: 1427--1493  Score: 116
    Period size: 27  Copynumber: 2.5  Consensus size: 27

       1417 TTGGTGCCAA

                                *      
       1427 AGGCGGCACCAGTGTTGCCTTTGGCAG
          1 AGGCGGCACCAGTGTTGCCTCTGGCAG

                      *                
       1454 AGGCGGCACCGGTGTTGCCTCTGGCAG
          1 AGGCGGCACCAGTGTTGCCTCTGGCAG

                         
       1481 AGGCGGCACCAGT
          1 AGGCGGCACCAGT

       1494 TGTGTGGGTC


Statistics
Matches: 37,  Mismatches: 3, Indels: 0
        0.93            0.08        0.00

Matches are distributed among these distances:
  27   37  1.00

ACGTcount: A:0.15, C:0.28, G:0.39, T:0.18


Consensus pattern (27 bp):   
AGGCGGCACCAGTGTTGCCTCTGGCAG

Found at i:1628 original size:15 final size:15

Alignment explanation


    Indices: 1571--1633  Score: 56
    Period size: 15  Copynumber: 3.9  Consensus size: 15

       1561 ATTCAGCAGT

                           *
       1571 AAGGAGAAGAAAATAA
          1 AAGGAGAAGAAAA-AG

                         *  
       1587 AAGGA-AAGAAAGGAG
          1 AAGGAGAAGAAA-AAG

                              
       1602 AAGAGAAGGAAGAAAAAG
          1 AAG-G-A-GAAGAAAAAG

                          
       1620 AAGGAGAAGAAAAA
          1 AAGGAGAAGAAAAA

       1634 AAGAAGATTG


Statistics
Matches: 39,  Mismatches: 3, Indels: 11
        0.74            0.06        0.21

Matches are distributed among these distances:
  15   19  0.49
  16    7  0.18
  17    2  0.05
  18    5  0.13
  19    6  0.15

ACGTcount: A:0.67, C:0.00, G:0.32, T:0.02


Consensus pattern (15 bp):   
AAGGAGAAGAAAAAG
Done.