Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_10334

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: 2216
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28


Found at i:1401 original size:42 final size:42

Alignment explanation


    Indices: 1355--1515  Score: 108
    Period size: 42  Copynumber: 3.8  Consensus size: 42

       1345 CTCCCCCTCC

                      *       *        *              
       1355 CTCTCCCCCTTCACCACCTCCACCTCCGCCGCCACCTGTGTA
          1 CTCTCCCCCTCCACCACCACCACCTCCACCGCCACCTGTGTA

                  *        *      *       *        *  
       1397 CTCTCCTCCTCCACCGCCACCATCTCCACCTCCACCTGTTTA
          1 CTCTCCCCCTCCACCACCACCACCTCCACCGCCACCTGTGTA

            *  *  *  *  *           *     *   * *  *  
       1439 TTCACCTCCACCTCCACCACCACCACCACCACCAGCAGTTTA
          1 CTCTCCCCCTCCACCACCACCACCTCCACCGCCACCTGTGTA

                  *  *        *            *    
       1481 CTCTCCACCACCACCACCTCCATCC-CCACCTCCAC
          1 CTCTCCCCCTCCACCACCACCA-CCTCCACCGCCAC

       1516 TATCACCCCC


Statistics
Matches: 93,  Mismatches: 25, Indels: 2
        0.77            0.21        0.02

Matches are distributed among these distances:
  42   91  0.98
  43    2  0.02

ACGTcount: A:0.18, C:0.57, G:0.05, T:0.20


Consensus pattern (42 bp):   
CTCTCCCCCTCCACCACCACCACCTCCACCGCCACCTGTGTA

Found at i:1429 original size:27 final size:26

Alignment explanation


    Indices: 1368--1433  Score: 69
    Period size: 27  Copynumber: 2.5  Consensus size: 26

       1358 TCCCCCTTCA

                          *         * 
       1368 CCACCTCCACCTCCGCCGCCACCTGT
          1 CCACCTCCACCTCCACCGCCACCTCT

            **       *                  
       1394 GTACTCTCCTCCTCCACCGCCACCATCT
          1 CCAC-CTCCACCTCCACCGCCACC-TCT

                        
       1422 CCACCTCCACCT
          1 CCACCTCCACCT

       1434 GTTTATTCAC


Statistics
Matches: 30,  Mismatches: 8, Indels: 3
        0.73            0.20        0.07

Matches are distributed among these distances:
  26    2  0.07
  27   24  0.80
  28    4  0.13

ACGTcount: A:0.14, C:0.59, G:0.08, T:0.20


Consensus pattern (26 bp):   
CCACCTCCACCTCCACCGCCACCTCT

Found at i:1920 original size:156 final size:156

Alignment explanation


    Indices: 1773--2098  Score: 634
    Period size: 156  Copynumber: 2.1  Consensus size: 156

       1763 ATACTTATCT

                                                                             
       1773 CCACCACCACCACCTCCTGTTTATTCCCCACCTCCTCCATGTATTGAGCCACCTCCACCACCACC
          1 CCACCACCACCACCTCCTGTTTATTCCCCACCTCCTCCATGTATTGAGCCACCTCCACCACCACC

                                                                             
       1838 ACCACCATGTGTAGAGTACACGCCATCACCGCCGCCACCATCACCATCACCCCCACCCCCAATTC
         66 ACCACCATGTGTAGAGTACACGCCATCACCGCCGCCACCATCACCATCACCCCCACCCCCAATTC

                                      
       1903 ATTACAAACCACCTCCATCACCTTCA
        131 ATTACAAACCACCTCCATCACCTTCA

                                                                             
       1929 CCACCACCACCACCTCCTGTTTATTCCCCACCTCCTCCATGTATTGAGCCACCTCCACCACCACC
          1 CCACCACCACCACCTCCTGTTTATTCCCCACCTCCTCCATGTATTGAGCCACCTCCACCACCACC

                                                                             
       1994 ACCACCATGTGTAGAGTACACGCCATCACCGCCGCCACCATCACCATCACCCCCACCCCCAATTC
         66 ACCACCATGTGTAGAGTACACGCCATCACCGCCGCCACCATCACCATCACCCCCACCCCCAATTC

                                      
       2059 ATTACAAACCACCTCCATCACCTTCA
        131 ATTACAAACCACCTCCATCACCTTCA

              *     *     
       2085 CCCCCACCCCCACC
          1 CCACCACCACCACC

       2099 AATCCATTAT


Statistics
Matches: 168,  Mismatches: 2, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 156  168  1.00

ACGTcount: A:0.25, C:0.51, G:0.07, T:0.18


Consensus pattern (156 bp):   
CCACCACCACCACCTCCTGTTTATTCCCCACCTCCTCCATGTATTGAGCCACCTCCACCACCACC
ACCACCATGTGTAGAGTACACGCCATCACCGCCGCCACCATCACCATCACCCCCACCCCCAATTC
ATTACAAACCACCTCCATCACCTTCA

Found at i:2117 original size:45 final size:44

Alignment explanation


    Indices: 2031--2137  Score: 121
    Period size: 45  Copynumber: 2.5  Consensus size: 44

       2021 ACCGCCGCCA

                                        *               
       2031 CCATCACCATCACCCCCA--CCCCCAATTCATTACAAACCACCT
          1 CCATCACCATCACCCCCACCCCCCCAATCCATTACAAACCACCT

                    *                              **     
       2073 CCATCACCTTCACCCCCACCCCCACCAATCCATTATC-ATTCACCT
          1 CCATCACCATCACCCCCACCCCC-CCAATCCATTA-CAAACCACCT

               *          *     
       2118 CCACCACCATCACCTCCACC
          1 CCATCACCATCACCCCCACC

       2138 GGCTCCCGTA


Statistics
Matches: 54,  Mismatches: 7, Indels: 5
        0.82            0.11        0.08

Matches are distributed among these distances:
  42   17  0.31
  44    3  0.06
  45   33  0.61
  46    1  0.02

ACGTcount: A:0.27, C:0.55, G:0.00, T:0.18


Consensus pattern (44 bp):   
CCATCACCATCACCCCCACCCCCCCAATCCATTACAAACCACCT

Done.