Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g02742.F3

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: 2052
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27


Found at i:1019 original size:12 final size:12

Alignment explanation


    Indices: 1002--1031  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

        992 ATCAGGAACG

                        
       1002 ACGCCAATGCCA
          1 ACGCCAATGCCA

                       *
       1014 ACGCCAATGCCT
          1 ACGCCAATGCCA

                  
       1026 ACGCCA
          1 ACGCCA

       1032 TATTTCCCGG


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

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.30, C:0.43, G:0.17, T:0.10


Consensus pattern (12 bp):   
ACGCCAATGCCA

Found at i:1516 original size:27 final size:26

Alignment explanation


    Indices: 1475--1530  Score: 76
    Period size: 27  Copynumber: 2.1  Consensus size: 26

       1465 CCCGAAACGG

                      *                
       1475 GTCGAGCCTGTCAGGTAGGCACGACTA
          1 GTCGAGCCTGACAGGTAGGCACGA-TA

                *               *     
       1502 GTCGTGCCTGACAGGTAGGCGCGATA
          1 GTCGAGCCTGACAGGTAGGCACGATA

               
       1528 GTC
          1 GTC

       1531 CCACCTACTG


Statistics
Matches: 26,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  26    5  0.19
  27   21  0.81

ACGTcount: A:0.20, C:0.25, G:0.36, T:0.20


Consensus pattern (26 bp):   
GTCGAGCCTGACAGGTAGGCACGATA

Found at i:1577 original size:27 final size:27

Alignment explanation


    Indices: 1539--1599  Score: 113
    Period size: 27  Copynumber: 2.3  Consensus size: 27

       1529 TCCCACCTAC

                                       
       1539 TGCTGCTGCTACCGCTCCACCTGCTGA
          1 TGCTGCTGCTACCGCTCCACCTGCTGA

                          *            
       1566 TGCTGCTGCTACCGTTCCACCTGCTGA
          1 TGCTGCTGCTACCGCTCCACCTGCTGA

                   
       1593 TGCTGCT
          1 TGCTGCT

       1600 ACCGTTGCTT


Statistics
Matches: 33,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  27   33  1.00

ACGTcount: A:0.10, C:0.38, G:0.23, T:0.30


Consensus pattern (27 bp):   
TGCTGCTGCTACCGCTCCACCTGCTGA

Found at i:1615 original size:24 final size:24

Alignment explanation


    Indices: 1531--1605  Score: 96
    Period size: 27  Copynumber: 3.0  Consensus size: 24

       1521 CGCGATAGTC

                  *   *           * 
       1531 CCACCTACTGCTGCTGCTACCGCT
          1 CCACCTGCTGATGCTGCTACCGTT

                                       
       1555 CCACCTGCTGATGCTGCTGCTACCGTT
          1 CCACCTGCTGA---TGCTGCTACCGTT

                                    
       1582 CCACCTGCTGATGCTGCTACCGTT
          1 CCACCTGCTGATGCTGCTACCGTT

       1606 GCTTTTGCTG


Statistics
Matches: 45,  Mismatches: 3, Indels: 6
        0.83            0.06        0.11

Matches are distributed among these distances:
  24   22  0.49
  27   23  0.51

ACGTcount: A:0.12, C:0.40, G:0.20, T:0.28


Consensus pattern (24 bp):   
CCACCTGCTGATGCTGCTACCGTT

Found at i:1766 original size:3 final size:3

Alignment explanation


    Indices: 1758--1795  Score: 58
    Period size: 3  Copynumber: 12.3  Consensus size: 3

       1748 AAGGAGAAAG

                                                  *           
       1758 AGA AGA AGA AGGA AGA AGA AGA AGA AGA ATA AGA AGA A
          1 AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA A

       1796 AAAAGGGTAA


Statistics
Matches: 32,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
   3   29  0.91
   4    3  0.09

ACGTcount: A:0.66, C:0.00, G:0.32, T:0.03


Consensus pattern (3 bp):   
AGA

Found at i:1774 original size:19 final size:18

Alignment explanation


    Indices: 1748--1786  Score: 53
    Period size: 19  Copynumber: 2.1  Consensus size: 18

       1738 AAAGGAGAGA

                               
       1748 AAGGAGAA-AGAGAAGAAG
          1 AAGGAGAAGA-AGAAGAAG

                               
       1766 AAGGAAGAAGAAGAAGAAG
          1 AAGG-AGAAGAAGAAGAAG

              
       1785 AA
          1 AA

       1787 TAAGAAGAAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  18    4  0.21
  19   14  0.74
  20    1  0.05

ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00


Consensus pattern (18 bp):   
AAGGAGAAGAAGAAGAAG

Found at i:1962 original size:18 final size:19

Alignment explanation


    Indices: 1927--1963  Score: 58
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       1917 TATAAATTAT

                 *             
       1927 TAGTTTTTTGTATTTGTTA
          1 TAGTTATTTGTATTTGTTA

                               
       1946 TAGTTATTTGT-TTTGTTA
          1 TAGTTATTTGTATTTGTTA

       1964 ATAATTTATG


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18    7  0.41
  19   10  0.59

ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68


Consensus pattern (19 bp):   
TAGTTATTTGTATTTGTTA
Done.