Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g00045.F1

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: 2686
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31


Found at i:1583 original size:42 final size:42

Alignment explanation


    Indices: 1537--1697  Score: 108
    Period size: 42  Copynumber: 3.8  Consensus size: 42

       1527 CTCCCCCTCC

                      *       *        *              
       1537 CTCTCCCCCTTCACCACCTCCACCTCCGCCGCCACCTGTGTA
          1 CTCTCCCCCTCCACCACCACCACCTCCACCGCCACCTGTGTA

                  *        *      *       *        *  
       1579 CTCTCCTCCTCCACCGCCACCATCTCCACCTCCACCTGTTTA
          1 CTCTCCCCCTCCACCACCACCACCTCCACCGCCACCTGTGTA

            *  *  *  *  *           *     *   * *  *  
       1621 TTCACCTCCACCTCCACCACCACCACCACCACCAGCAGTTTA
          1 CTCTCCCCCTCCACCACCACCACCTCCACCGCCACCTGTGTA

                  *  *        *            *    
       1663 CTCTCCACCACCACCACCTCCATCC-CCACCTCCAC
          1 CTCTCCCCCTCCACCACCACCA-CCTCCACCGCCAC

       1698 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:1611 original size:27 final size:26

Alignment explanation


    Indices: 1550--1615  Score: 69
    Period size: 27  Copynumber: 2.5  Consensus size: 26

       1540 TCCCCCTTCA

                          *         * 
       1550 CCACCTCCACCTCCGCCGCCACCTGT
          1 CCACCTCCACCTCCACCGCCACCTCT

            **       *                  
       1576 GTACTCTCCTCCTCCACCGCCACCATCT
          1 CCAC-CTCCACCTCCACCGCCACC-TCT

                        
       1604 CCACCTCCACCT
          1 CCACCTCCACCT

       1616 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:2146 original size:45 final size:44

Alignment explanation


    Indices: 2060--2166  Score: 121
    Period size: 45  Copynumber: 2.5  Consensus size: 44

       2050 ACCGCCGCCA

                                        *               
       2060 CCATCACCATCACCCCCA--CCCCCAATTCATTACAAACCACCT
          1 CCATCACCATCACCCCCACCCCCCCAATCCATTACAAACCACCT

                    *                              **     
       2102 CCATCACCTTCACCCCCACCCCCACCAATCCATTATC-ATTCACCT
          1 CCATCACCATCACCCCCACCCCC-CCAATCCATTA-CAAACCACCT

               *          *     
       2147 CCACCACCATCACCTCCACC
          1 CCATCACCATCACCCCCACC

       2167 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.