Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g00082.N1

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: 3194
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32


Found at i:1614 original size:27 final size:26

Alignment explanation


    Indices: 1553--1618  Score: 69
    Period size: 27  Copynumber: 2.5  Consensus size: 26

       1543 TCCCCCTTCA

                          *         * 
       1553 CCACCTCCACCTCCGCCGCCACCTGT
          1 CCACCTCCACCTCCACCGCCACCTCT

            **       *                  
       1579 GTACTCTCCTCCTCCACCGCCACCATCT
          1 CCAC-CTCCACCTCCACCGCCACC-TCT

                        
       1607 CCACCTCCACCT
          1 CCACCTCCACCT

       1619 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:1632 original size:42 final size:42

Alignment explanation


    Indices: 1571--1703  Score: 131
    Period size: 42  Copynumber: 3.1  Consensus size: 42

       1561 ACCTCCGCCG

                    *                 *        *      
       1571 CCACCTGTGTACTCTCCTCCTCCACCGCCACCATCTCCACCT
          1 CCACCTGTTTACTCTCCTCCTCCACCACCACCATCACCACCT

                           *    *               *       *
       1613 CCACCTGTTTATTCACCTCCACCTCCACCACCACCACCACCACCA
          1 CCACCTGTTTA--C-TCTCCTCCTCCACCACCACCATCACCACCT

                 *           *  *        *     *      
       1658 CCACCAGTTTACTCTCCACCACCACCACCTCCATCCCCACCT
          1 CCACCTGTTTACTCTCCTCCTCCACCACCACCATCACCACCT

                
       1700 CCAC
          1 CCAC

       1704 ATCACCCCCG


Statistics
Matches: 74,  Mismatches: 14, Indels: 6
        0.79            0.15        0.06

Matches are distributed among these distances:
  42   38  0.51
  43    1  0.01
  44    1  0.01
  45   34  0.46

ACGTcount: A:0.20, C:0.56, G:0.04, T:0.20


Consensus pattern (42 bp):   
CCACCTGTTTACTCTCCTCCTCCACCACCACCATCACCACCT

Found at i:1640 original size:45 final size:42

Alignment explanation


    Indices: 1584--1703  Score: 123
    Period size: 45  Copynumber: 2.8  Consensus size: 42

       1574 CCTGTGTACT

                *        *        *           *          
       1584 CTCCTCCTCCACCGCCACCATCTCCACCTCCACCTGTTTATTCAC
          1 CTCCACCTCCACCACCACCATCACCACCTCCACCAGTTTA--C-C

                                *       *            *
       1629 CTCCACCTCCACCACCACCACCACCACCACCACCAGTTTACT
          1 CTCCACCTCCACCACCACCATCACCACCTCCACCAGTTTACC

                   *        *     *          
       1671 CTCCACCACCACCACCTCCATCCCCACCTCCAC
          1 CTCCACCTCCACCACCACCATCACCACCTCCAC

       1704 ATCACCCCCG


Statistics
Matches: 63,  Mismatches: 12, Indels: 3
        0.81            0.15        0.04

Matches are distributed among these distances:
  42   28  0.44
  43    1  0.02
  45   34  0.54

ACGTcount: A:0.21, C:0.58, G:0.03, T:0.18


Consensus pattern (42 bp):   
CTCCACCTCCACCACCACCATCACCACCTCCACCAGTTTACC

Found at i:1683 original size:3 final size:3

Alignment explanation


    Indices: 1626--1663  Score: 58
    Period size: 3  Copynumber: 12.7  Consensus size: 3

       1616 CCTGTTTATT

                 *       *                                    
       1626 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

       1664 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.