Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga14g01971.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: 2405
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29


Found at i:1653 original size:45 final size:41

Alignment explanation


    Indices: 1538--1700  Score: 112
    Period size: 42  Copynumber: 3.8  Consensus size: 41

       1528 CTCCCCCTCC

                  *   *       *        *  *     *  *  
       1538 CCCTCCCCCTTCACCACCTCCACCTCCGCCGCCACCTGTGTA
          1 CCCTCCACCTCCACCACCACCACC-CCACCTCCACCAGTTTA

             *     *       *        *           *     
       1580 CTCTCC-TCTCCACCGCCACCATCTCCACCTCCACCTGTTTA
          1 CCCTCCACCTCCACCACCACCA-CCCCACCTCCACCAGTTTA

                                             *           
       1621 TTCACCTCCACCTCCACCACCACCACCACCACCACCACCAGTTTA
          1 --C-CCTCCACCTCCACCACCACCACC-CCACCTCCACCAGTTTA

             *       *        *                
       1666 CTCTCCACCACCACCACCTCCATCCCCACCTCCAC
          1 CCCTCCACCTCCACCACCACCA-CCCCACCTCCAC

       1701 TATCACCCCG


Statistics
Matches: 95,  Mismatches: 19, Indels: 14
        0.74            0.15        0.11

Matches are distributed among these distances:
  41   25  0.26
  42   33  0.35
  43    4  0.04
  44    5  0.05
  45   28  0.29

ACGTcount: A:0.18, C:0.58, G:0.04, T:0.19


Consensus pattern (41 bp):   
CCCTCCACCTCCACCACCACCACCCCACCTCCACCAGTTTA

Found at i:1680 original size:3 final size:3

Alignment explanation


    Indices: 1623--1660  Score: 58
    Period size: 3  Copynumber: 12.7  Consensus size: 3

       1613 CCTGTTTATT

                 *       *                                    
       1623 CAC CTC CAC CTC CAC CAC CAC CAC CAC CAC CAC CAC CA
          1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA

       1661 GTTTACTCTC


Statistics
Matches: 31,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   3   31  1.00

ACGTcount: A:0.29, C:0.66, G:0.00, T:0.05


Consensus pattern (3 bp):   
CAC

Found at i:2148 original size:45 final size:44

Alignment explanation


    Indices: 2062--2168  Score: 121
    Period size: 45  Copynumber: 2.5  Consensus size: 44

       2052 ACCGCCGCCA

                                        *               
       2062 CCATCACCATCACCCCCA--CCCCCAATTCATTACAAACCACCT
          1 CCATCACCATCACCCCCACCCCCCCAATCCATTACAAACCACCT

                    *                              **     
       2104 CCATCACCTTCACCCCCACCCCCACCAATCCATTATC-ATTCACCT
          1 CCATCACCATCACCCCCACCCCC-CCAATCCATTA-CAAACCACCT

               *          *     
       2149 CCACCACCATCACCTCCACC
          1 CCATCACCATCACCCCCACC

       2169 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.