Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_D_gene_10003317

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: 5992
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30


Found at i:1734 original size:11 final size:11

Alignment explanation


    Indices: 1720--1750  Score: 53
    Period size: 11  Copynumber: 2.7  Consensus size: 11

       1710 TGAAAATTTG

                       
       1720 AAATTCAAATA
          1 AAATTCAAATA

                       
       1731 AAATTCAAATA
          1 AAATTCAAATA

                     
       1742 AAATATCAA
          1 AAAT-TCAA

       1751 TTTAAAGCAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  11   15  0.79
  12    4  0.21

ACGTcount: A:0.65, C:0.10, G:0.00, T:0.26


Consensus pattern (11 bp):   
AAATTCAAATA

Found at i:1740 original size:24 final size:23

Alignment explanation


    Indices: 1673--1740  Score: 57
    Period size: 24  Copynumber: 2.9  Consensus size: 23

       1663 ATATAAATAA

                         *  *      
       1673 AAATTCAAATAAACTTTAA-TTG
          1 AAATTCAAATAAAATTAAATTTG

                   *   *     *       
       1695 AAAGTTCCAATTAAATGAAAATTTG
          1 AAA-TTCAAATAAAAT-TAAATTTG

                                 
       1720 AAATTCAAATAAAATTCAAAT
          1 AAATTCAAATAAAATT-AAAT

       1741 AAAATATCAA


Statistics
Matches: 34,  Mismatches: 8, Indels: 6
        0.71            0.17        0.12

Matches are distributed among these distances:
  22    3  0.09
  23    9  0.26
  24   16  0.47
  25    6  0.18

ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32


Consensus pattern (23 bp):   
AAATTCAAATAAAATTAAATTTG

Found at i:1802 original size:35 final size:35

Alignment explanation


    Indices: 1762--1870  Score: 114
    Period size: 35  Copynumber: 3.1  Consensus size: 35

       1752 TTAAAGCAAT

                  *                            
       1762 ATTTATCAAATTACAATTTAAATATATGAATAAAA
          1 ATTTATAAAATTACAATTTAAATATATGAATAAAA

                       *  *            *         *
       1797 ATTTATAATAAATATAATTTAAATA-AAGAA-AGCAAT
          1 ATTTATAA-AATTACAATTTAAATATATGAATA--AAA

                  *                    *       
       1833 ATTTATTAAATTACAATTTAAATATATAAATAAAA
          1 ATTTATAAAATTACAATTTAAATATATGAATAAAA

               
       1868 ATT
          1 ATT

       1871 CAAATAAAAT


Statistics
Matches: 58,  Mismatches: 11, Indels: 10
        0.73            0.14        0.13

Matches are distributed among these distances:
  34    1  0.02
  35   30  0.52
  36   26  0.45
  37    1  0.02

ACGTcount: A:0.56, C:0.04, G:0.03, T:0.38


Consensus pattern (35 bp):   
ATTTATAAAATTACAATTTAAATATATGAATAAAA

Found at i:1817 original size:36 final size:37

Alignment explanation


    Indices: 1769--1878  Score: 115
    Period size: 36  Copynumber: 3.1  Consensus size: 37

       1759 AATATTTATC

                                                 
       1769 AAATTACAATTTAAATATATGAATAAAAATTTATAAT
          1 AAATTACAATTTAAATATATGAATAAAAATTTATAAT

                  *            *         *         
       1806 AAA-TATAATTTAAATA-AAGAA-AGCAATATTTAT--T
          1 AAATTACAATTTAAATATATGAATA--AAAATTTATAAT

                                *          *     
       1840 AAATTACAATTTAAATATATAAATAAAAATTCA-AAT
          1 AAATTACAATTTAAATATATGAATAAAAATTTATAAT

               
       1876 AAA
          1 AAA

       1879 ATTTAATTAA


Statistics
Matches: 58,  Mismatches: 8, Indels: 15
        0.72            0.10        0.19

Matches are distributed among these distances:
  34    5  0.09
  35   22  0.38
  36   27  0.47
  37    4  0.07

ACGTcount: A:0.59, C:0.04, G:0.03, T:0.35


Consensus pattern (37 bp):   
AAATTACAATTTAAATATATGAATAAAAATTTATAAT

Found at i:4887 original size:3 final size:3

Alignment explanation


    Indices: 4881--4927  Score: 76
    Period size: 3  Copynumber: 15.7  Consensus size: 3

       4871 TATGGTCTTA

                      *               *                                   
       4881 TAT TAT TAA TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TA
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA

       4928 AATAAAGTAA


Statistics
Matches: 40,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   3   40  1.00

ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62


Consensus pattern (3 bp):   
TAT

Done.