Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g01337.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: 2193
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28


Found at i:1532 original size:96 final size:96

Alignment explanation


    Indices: 1295--1537  Score: 369
    Period size: 96  Copynumber: 2.5  Consensus size: 96

       1285 AGCCCCTTAA

                            *           *                **         **       
       1295 GCCAAAACCACCGAAAGAAGAGGAATCAGCTGTAACAAGGGAACGACCTCCACCACTTAAATTGC
          1 GCCAAAACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCCACCACCAAAATTGC

                       *                   
       1360 CACCGCCAGTTGTTAAGCCCCCGAAACCAGT
         66 CACCGCCAGTTATTAAGCCCCCGAAACCAGT

             *     *  *                                                      
       1391 GTCAAAATCATCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCCACCACCAAAATTGC
          1 GCCAAAACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCCACCACCAAAATTGC

                                    *      
       1456 CACCGCCAGTTATTAAGCCCCCGACACCAGT
         66 CACCGCCAGTTATTAAGCCCCCGAAACCAGT

               *                           *                   
       1487 GCCGAAACCACCGAAACAAGAGGAATCACCTATAACAAGGGAACGGTCTCC
          1 GCCAAAACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCC

       1538 GCCAGTTATT


Statistics
Matches: 131,  Mismatches: 16, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  96  131  1.00

ACGTcount: A:0.36, C:0.31, G:0.19, T:0.14


Consensus pattern (96 bp):   
GCCAAAACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCCACCACCAAAATTGC
CACCGCCAGTTATTAAGCCCCCGAAACCAGT

Found at i:1587 original size:78 final size:78

Alignment explanation


    Indices: 1458--1615  Score: 271
    Period size: 78  Copynumber: 2.0  Consensus size: 78

       1448 AAAATTGCCA

                                           **                                
       1458 CCGCCAGTTATTAAGCCCCCGACACCAGTGCCGAAACCACCGAAACAAGAGGAATCACCTATAAC
          1 CCGCCAGTTATTAAGCCCCCGACACCAGTGCAAAAACCACCGAAACAAGAGGAATCACCTATAAC

                         
       1523 AAGGGAACGGTCT
         66 AAGGGAACGGTCT

                                 *        *                             *    
       1536 CCGCCAGTTATTAAGCCCCCGCCACCAGTGGAAAAACCACCGAAACAAGAGGAATCACCTGTAAC
          1 CCGCCAGTTATTAAGCCCCCGACACCAGTGCAAAAACCACCGAAACAAGAGGAATCACCTATAAC

                         
       1601 AAGGGAACGGTCT
         66 AAGGGAACGGTCT

              
       1614 CC
          1 CC

       1616 ACCACCAAAA


Statistics
Matches: 75,  Mismatches: 5, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  78   75  1.00

ACGTcount: A:0.34, C:0.32, G:0.21, T:0.13


Consensus pattern (78 bp):   
CCGCCAGTTATTAAGCCCCCGACACCAGTGCAAAAACCACCGAAACAAGAGGAATCACCTATAAC
AAGGGAACGGTCT

Found at i:1680 original size:21 final size:21

Alignment explanation


    Indices: 1654--1744  Score: 92
    Period size: 21  Copynumber: 4.2  Consensus size: 21

       1644 AAGCCCCCGA

                                 
       1654 CACCACCAGTCCACTCTCCAC
          1 CACCACCAGTCCACTCTCCAC

                                    
       1675 CACCACCTCCAGTCCACTCTCCAC
          1 CACCA---CCAGTCCACTCTCCAC

             *     *  *        * 
       1699 CTCCACCTGTTCACTCTCCTC
          1 CACCACCAGTCCACTCTCCAC

                      *  *     * 
       1720 CACCACCAGTGCATTCTCCTC
          1 CACCACCAGTCCACTCTCCAC

                
       1741 CACC
          1 CACC

       1745 TCTTTCTCCT


Statistics
Matches: 59,  Mismatches: 8, Indels: 6
        0.81            0.11        0.08

Matches are distributed among these distances:
  21   39  0.66
  24   20  0.34

ACGTcount: A:0.19, C:0.55, G:0.05, T:0.21


Consensus pattern (21 bp):   
CACCACCAGTCCACTCTCCAC

Found at i:1706 original size:24 final size:24

Alignment explanation


    Indices: 1654--1726  Score: 89
    Period size: 24  Copynumber: 3.2  Consensus size: 24

       1644 AAGCCCCCGA

                *                   
       1654 CACCACCAGTCCACTCTCCACCAC
          1 CACCTCCAGTCCACTCTCCACCAC

                                  * 
       1678 CACCTCCAGTCCACTCTCCACCTC
          1 CACCTCCAGTCCACTCTCCACCAC

                      *        *    
       1702 CACCT---GTTCACTCTCCTCCAC
          1 CACCTCCAGTCCACTCTCCACCAC

                
       1723 CACC
          1 CACC

       1727 AGTGCATTCT


Statistics
Matches: 44,  Mismatches: 5, Indels: 3
        0.85            0.10        0.06

Matches are distributed among these distances:
  21   17  0.39
  24   27  0.61

ACGTcount: A:0.19, C:0.58, G:0.04, T:0.19


Consensus pattern (24 bp):   
CACCTCCAGTCCACTCTCCACCAC
Done.