Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_06412

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, 707

Length: 1179
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31


Found at i:111 original size:3 final size:3

Alignment explanation


    Indices: 105--174  Score: 54
    Period size: 3  Copynumber: 23.3  Consensus size: 3

         95 GTTCCCTTCT

                                  *   *   **                            
        105 TCC TCC TCC TCC TCC TCG TCG TGGT TCC -CC TCC TCC TCC TCC TCC
          1 TCC TCC TCC TCC TCC TCC TCC T-CC TCC TCC TCC TCC TCC TCC TCC

               *             *                
        150 TCGT TCC -CC TCC CCC TCC TCC TCC T
          1 TC-C TCC TCC TCC TCC TCC TCC TCC T

        175 TTCGTTGCTG


Statistics
Matches: 54,  Mismatches: 9, Indels: 8
        0.76            0.13        0.11

Matches are distributed among these distances:
   2    4  0.07
   3   47  0.87
   4    3  0.06

ACGTcount: A:0.00, C:0.60, G:0.07, T:0.33


Consensus pattern (3 bp):   
TCC

Found at i:136 original size:24 final size:24

Alignment explanation


    Indices: 106--174  Score: 93
    Period size: 24  Copynumber: 2.8  Consensus size: 24

         96 TTCCCTTCTT

                                 *     
        106 CCTCCTCCTCCTCCTCGTCGTGGTTCC
          1 CCTCCTCCTCCTCCTC--C-TCGTTCC

                                    
        133 CCTCCTCCTCCTCCTCCTCGTTCC
          1 CCTCCTCCTCCTCCTCCTCGTTCC

                 *            
        157 CCTCCCCCTCCTCCTCCT
          1 CCTCCTCCTCCTCCTCCT

        175 TTCGTTGCTG


Statistics
Matches: 40,  Mismatches: 2, Indels: 3
        0.89            0.04        0.07

Matches are distributed among these distances:
  24   23  0.57
  25    1  0.03
  27   16  0.40

ACGTcount: A:0.00, C:0.61, G:0.07, T:0.32


Consensus pattern (24 bp):   
CCTCCTCCTCCTCCTCCTCGTTCC

Found at i:165 original size:30 final size:30

Alignment explanation


    Indices: 105--174  Score: 88
    Period size: 30  Copynumber: 2.3  Consensus size: 30

         95 GTTCCCTTCT

                                 *** *    
        105 TCCTCCTCCTCCTCCTCGTCGTGGTTCCCC
          1 TCCTCCTCCTCCTCCTCGTCGCCCTCCCCC

                                           
        135 TCCTCCTCCTCCTCCTCGTTC-CCCTCCCCC
          1 TCCTCCTCCTCCTCCTCG-TCGCCCTCCCCC

                      
        165 TCCTCCTCCT
          1 TCCTCCTCCT

        175 TTCGTTGCTG


Statistics
Matches: 35,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  30   33  0.94
  31    2  0.06

ACGTcount: A:0.00, C:0.60, G:0.07, T:0.33


Consensus pattern (30 bp):   
TCCTCCTCCTCCTCCTCGTCGCCCTCCCCC

Found at i:264 original size:48 final size:48

Alignment explanation


    Indices: 158--266  Score: 112
    Period size: 48  Copynumber: 2.3  Consensus size: 48

        148 CCTCGTTCCC

                              *   *                  *      *
        158 CTCC-CCCTCCTCCTCCTTTCGTTGCTGATGGCCCAAATACGGTCGTTT
          1 CTCCTCCC-CCTCCTCCTGTCGGTGCTGATGGCCCAAATACCGTCGTTG

             *** *                            *      *      
        206 CGAATGCCCCTCCTCCTGTCGGTGCTGATGGCCCGAATACCTTCGTTG
          1 CTCCTCCCCCTCCTCCTGTCGGTGCTGATGGCCCAAATACCGTCGTTG

                         
        254 CTCCTCCCCCTCC
          1 CTCCTCCCCCTCC

        267 AGCGGCTCGA


Statistics
Matches: 46,  Mismatches: 14, Indels: 2
        0.74            0.23        0.03

Matches are distributed among these distances:
  48   44  0.96
  49    2  0.04

ACGTcount: A:0.10, C:0.42, G:0.18, T:0.29


Consensus pattern (48 bp):   
CTCCTCCCCCTCCTCCTGTCGGTGCTGATGGCCCAAATACCGTCGTTG
Done.