Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g00082.N4

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: 3098
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32


Found at i:1573 original size:42 final size:42

Alignment explanation


    Indices: 1527--1689  Score: 112
    Period size: 42  Copynumber: 3.9  Consensus size: 42

       1517 ACCGCCAGTA

                        *       *        *            
       1527 TACTCTCCCCCTTCACCACCTCCACCTCCGCCGCCACCTGTG
          1 TACTCTCCCCCTCCACCACCACCACCTCCACCGCCACCTGTG

                    *        *      *       *        *
       1569 TACTCTCCTCCTCCACCGCCACCATCTCCACCTCCACCTGTT
          1 TACTCTCCCCCTCCACCACCACCACCTCCACCGCCACCTGTG

              *  *  *  *  *           *     *   * *  *
       1611 TATTCACCTCCACCTCCACCACCACCACCACCACCAGCAGTT
          1 TACTCTCCCCCTCCACCACCACCACCTCCACCGCCACCTGTG

                    *  *        *            *    
       1653 TACTCTCCACCACCACCACCTCCATCC-CCACCTCCAC
          1 TACTCTCCCCCTCCACCACCACCA-CCTCCACCGCCAC

       1690 TATCACCCCC


Statistics
Matches: 95,  Mismatches: 25, Indels: 2
        0.78            0.20        0.02

Matches are distributed among these distances:
  42   93  0.98
  43    2  0.02

ACGTcount: A:0.18, C:0.56, G:0.05, T:0.20


Consensus pattern (42 bp):   
TACTCTCCCCCTCCACCACCACCACCTCCACCGCCACCTGTG

Found at i:1603 original size:27 final size:26

Alignment explanation


    Indices: 1542--1607  Score: 69
    Period size: 27  Copynumber: 2.5  Consensus size: 26

       1532 TCCCCCTTCA

                          *         * 
       1542 CCACCTCCACCTCCGCCGCCACCTGT
          1 CCACCTCCACCTCCACCGCCACCTCT

            **       *                  
       1568 GTACTCTCCTCCTCCACCGCCACCATCT
          1 CCAC-CTCCACCTCCACCGCCACC-TCT

                        
       1596 CCACCTCCACCT
          1 CCACCTCCACCT

       1608 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:2137 original size:45 final size:44

Alignment explanation


    Indices: 2051--2157  Score: 121
    Period size: 45  Copynumber: 2.5  Consensus size: 44

       2041 ACCGCCGCCA

                                        *               
       2051 CCATCACCATCACCCCCA--CCCCCAATTCATTACAAACCACCT
          1 CCATCACCATCACCCCCACCCCCCCAATCCATTACAAACCACCT

                    *                              **     
       2093 CCATCACCTTCACCCCCACCCCCACCAATCCATTATC-ATTCACCT
          1 CCATCACCATCACCCCCACCCCC-CCAATCCATTA-CAAACCACCT

               *          *     
       2138 CCACCACCATCACCTCCACC
          1 CCATCACCATCACCCCCACC

       2158 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.