Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_33041

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: 1845
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.26


Found at i:1512 original size:96 final size:96

Alignment explanation


    Indices: 1275--1517  Score: 369
    Period size: 96  Copynumber: 2.5  Consensus size: 96

       1265 AGCCCCTTAA

                            *           *                **         **       
       1275 GCCAAAACCACCGAAAGAAGAGGAATCAGCTGTAACAAGGGAACGACCTCCACCACTTAAATTGC
          1 GCCAAAACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCCACCACCAAAATTGC

                       *                   
       1340 CACCGCCAGTTGTTAAGCCCCCGAAACCAGT
         66 CACCGCCAGTTATTAAGCCCCCGAAACCAGT

             *     *  *                                                      
       1371 GTCAAAATCATCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCCACCACCAAAATTGC
          1 GCCAAAACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCCACCACCAAAATTGC

                                    *      
       1436 CACCGCCAGTTATTAAGCCCCCGACACCAGT
         66 CACCGCCAGTTATTAAGCCCCCGAAACCAGT

               *                           *                   
       1467 GCCGAAACCACCGAAACAAGAGGAATCACCTATAACAAGGGAACGGTCTCC
          1 GCCAAAACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCC

       1518 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:1567 original size:78 final size:78

Alignment explanation


    Indices: 1438--1595  Score: 271
    Period size: 78  Copynumber: 2.0  Consensus size: 78

       1428 AAAATTGCCA

                                           **                                
       1438 CCGCCAGTTATTAAGCCCCCGACACCAGTGCCGAAACCACCGAAACAAGAGGAATCACCTATAAC
          1 CCGCCAGTTATTAAGCCCCCGACACCAGTGCAAAAACCACCGAAACAAGAGGAATCACCTATAAC

                         
       1503 AAGGGAACGGTCT
         66 AAGGGAACGGTCT

                                 *        *                             *    
       1516 CCGCCAGTTATTAAGCCCCCGCCACCAGTGGAAAAACCACCGAAACAAGAGGAATCACCTGTAAC
          1 CCGCCAGTTATTAAGCCCCCGACACCAGTGCAAAAACCACCGAAACAAGAGGAATCACCTATAAC

                         
       1581 AAGGGAACGGTCT
         66 AAGGGAACGGTCT

              
       1594 CC
          1 CC

       1596 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:1660 original size:21 final size:21

Alignment explanation


    Indices: 1634--1724  Score: 92
    Period size: 21  Copynumber: 4.2  Consensus size: 21

       1624 AAGCCCCCGA

                                 
       1634 CACCACCAGTCCACTCTCCAC
          1 CACCACCAGTCCACTCTCCAC

                                    
       1655 CACCACCTCCAGTCCACTCTCCAC
          1 CACCA---CCAGTCCACTCTCCAC

             *     *  *        * 
       1679 CTCCACCTGTTCACTCTCCTC
          1 CACCACCAGTCCACTCTCCAC

                      *  *     * 
       1700 CACCACCAGTGCATTCTCCTC
          1 CACCACCAGTCCACTCTCCAC

                
       1721 CACC
          1 CACC

       1725 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:1686 original size:24 final size:24

Alignment explanation


    Indices: 1634--1706  Score: 89
    Period size: 24  Copynumber: 3.2  Consensus size: 24

       1624 AAGCCCCCGA

                *                   
       1634 CACCACCAGTCCACTCTCCACCAC
          1 CACCTCCAGTCCACTCTCCACCAC

                                  * 
       1658 CACCTCCAGTCCACTCTCCACCTC
          1 CACCTCCAGTCCACTCTCCACCAC

                      *        *    
       1682 CACCT---GTTCACTCTCCTCCAC
          1 CACCTCCAGTCCACTCTCCACCAC

                
       1703 CACC
          1 CACC

       1707 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.