Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_09807

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: 2034
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.18


Found at i:1490 original size:54 final size:54

Alignment explanation


    Indices: 1426--1799  Score: 466
    Period size: 54  Copynumber: 6.9  Consensus size: 54

       1416 TGAAAACAAT

                    *            *   *   *     **                *
       1426 AACAATGAAAATGCGGGTCAGGACGGGAAGAATGCCACTCAGAGTAACACTGAC
          1 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCTCAGAGTAACACTGAG

                    *    *         *                    *         
       1480 AACAATGAAAATGTGGGTCAGAATGAGAACAATGCTGCTCAGAGCAACACTGAG
          1 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCTCAGAGTAACACTGAG

                    *              *    *      **       *         
       1534 AACAATGAAAATGCGGGTCAGAATGAGAGCAATGCAACTCAGAGCAACACTGAG
          1 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCTCAGAGTAACACTGAG

                                         *                   *     
       1588 AACAATGAGAATGCGGGTCAGAACGAGAAAAATGCTGCTCCA-AGTAACGCTGAG
          1 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCT-CAGAGTAACACTGAG

                         *                     *                   
       1642 AACAATGAGAATGTGGGTCAGAACGAGAACAATGCCGCTCCA-AGTAACACTGAG
          1 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCT-CAGAGTAACACTGAG

                                                    *         *  *
       1696 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCTCCGAGTAACACCGAC
          1 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCTCAGAGTAACACTGAG

                          *                              *     
       1750 AACAATGAGAATGCAGGTCAGAACGAGAACAATGC-GACTCAGAGCAACAC
          1 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTG-CTCAGAGTAACAC

       1800 CGACGAAAAC


Statistics
Matches: 284,  Mismatches: 33, Indels: 6
        0.88            0.10        0.02

Matches are distributed among these distances:
  53    2  0.01
  54  280  0.99
  55    2  0.01

ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14


Consensus pattern (54 bp):   
AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCTCAGAGTAACACTGAG

Found at i:1560 original size:27 final size:27

Alignment explanation


    Indices: 1530--1621  Score: 73
    Period size: 27  Copynumber: 3.4  Consensus size: 27

       1520 AGAGCAACAC

                                       
       1530 TGAGAACAATGAAAATGCGGGTCAGAA
          1 TGAGAACAATGAAAATGCGGGTCAGAA

                 *     *  *     *        
       1557 TGAGAGCAATGCAACT-CAGAG-CA-ACA
          1 TGAGAACAATGAAAATGC-GGGTCAGA-A

                         *              
       1583 CTGAGAACAATGAGAATGCGGGTCAGAA
          1 -TGAGAACAATGAAAATGCGGGTCAGAA

            *     *    
       1611 CGAGAAAAATG
          1 TGAGAACAATG

       1622 CTGCTCCAAG


Statistics
Matches: 48,  Mismatches: 11, Indels: 12
        0.68            0.15        0.17

Matches are distributed among these distances:
  25    1  0.02
  26    4  0.08
  27   38  0.79
  28    4  0.08
  29    1  0.02

ACGTcount: A:0.43, C:0.15, G:0.28, T:0.13


Consensus pattern (27 bp):   
TGAGAACAATGAAAATGCGGGTCAGAA

Found at i:1723 original size:27 final size:27

Alignment explanation


    Indices: 1639--1783  Score: 91
    Period size: 27  Copynumber: 5.4  Consensus size: 27

       1629 AAGTAACGCT

                            *          
       1639 GAGAACAATGAGAATGTGGGTCAGAAC
          1 GAGAACAATGAGAATGCGGGTCAGAAC

                       *  * * **         
       1666 GAGAACAATGCCG-CTCCAAGT-A-ACAC
          1 GAGAACAATG-AGAATGCGGGTCAGA-AC

                                        
       1692 TGAGAACAATGAGAATGCGGGTCAGAAC
          1 -GAGAACAATGAGAATGCGGGTCAGAAC

                       *  * *  *  * * * 
       1720 GAGAACAATGCTG-CTCCGAGTAACACC
          1 GAGAACAATG-AGAATGCGGGTCAGAAC

              *              *         
       1747 GACAACAATGAGAATGCAGGTCAGAAC
          1 GAGAACAATGAGAATGCGGGTCAGAAC

                      
       1774 GAGAACAATG
          1 GAGAACAATG

       1784 CGACTCAGAG


Statistics
Matches: 82,  Mismatches: 28, Indels: 16
        0.65            0.22        0.13

Matches are distributed among these distances:
  25    1  0.01
  26    5  0.06
  27   70  0.85
  28    5  0.06
  29    1  0.01

ACGTcount: A:0.40, C:0.20, G:0.27, T:0.13


Consensus pattern (27 bp):   
GAGAACAATGAGAATGCGGGTCAGAAC

Done.