Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g00082.N3

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: 3079
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31


Found at i:1542 original size:27 final size:26

Alignment explanation


    Indices: 1481--1546  Score: 69
    Period size: 27  Copynumber: 2.5  Consensus size: 26

       1471 TCCCCCTTCA

                          *         * 
       1481 CCACCTCCACCTCCGCCGCCACCTGT
          1 CCACCTCCACCTCCACCGCCACCTCT

            **       *                  
       1507 GTACTCTCCTCCTCCACCGCCACCATCT
          1 CCAC-CTCCACCTCCACCGCCACC-TCT

                        
       1535 CCACCTCCACCT
          1 CCACCTCCACCT

       1547 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:1560 original size:42 final size:42

Alignment explanation


    Indices: 1499--1631  Score: 131
    Period size: 42  Copynumber: 3.1  Consensus size: 42

       1489 ACCTCCGCCG

                    *                 *        *      
       1499 CCACCTGTGTACTCTCCTCCTCCACCGCCACCATCTCCACCT
          1 CCACCTGTTTACTCTCCTCCTCCACCACCACCATCACCACCT

                           *    *               *       *
       1541 CCACCTGTTTATTCACCTCCACCTCCACCACCACCACCACCACCA
          1 CCACCTGTTTA--C-TCTCCTCCTCCACCACCACCATCACCACCT

                 *           *  *        *     *      
       1586 CCACCAGTTTACTCTCCACCACCACCACCTCCATCCCCACCT
          1 CCACCTGTTTACTCTCCTCCTCCACCACCACCATCACCACCT

                
       1628 CCAC
          1 CCAC

       1632 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:1568 original size:45 final size:42

Alignment explanation


    Indices: 1512--1631  Score: 123
    Period size: 45  Copynumber: 2.8  Consensus size: 42

       1502 CCTGTGTACT

                *        *        *           *          
       1512 CTCCTCCTCCACCGCCACCATCTCCACCTCCACCTGTTTATTCAC
          1 CTCCACCTCCACCACCACCATCACCACCTCCACCAGTTTA--C-C

                                *       *            *
       1557 CTCCACCTCCACCACCACCACCACCACCACCACCAGTTTACT
          1 CTCCACCTCCACCACCACCATCACCACCTCCACCAGTTTACC

                   *        *     *          
       1599 CTCCACCACCACCACCTCCATCCCCACCTCCAC
          1 CTCCACCTCCACCACCACCATCACCACCTCCAC

       1632 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:1611 original size:3 final size:3

Alignment explanation


    Indices: 1554--1591  Score: 58
    Period size: 3  Copynumber: 12.7  Consensus size: 3

       1544 CCTGTTTATT

                 *       *                                    
       1554 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

       1592 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:2037 original size:42 final size:42

Alignment explanation


    Indices: 1990--2097  Score: 207
    Period size: 42  Copynumber: 2.6  Consensus size: 42

       1980 ACCGCCGCCA

                                                      
       1990 CCATCACCATCACCCCCACCCCCAATTCATTACAAACCACCT
          1 CCATCACCATCACCCCCACCCCCAATTCATTACAAACCACCT

                                                      
       2032 CCATCACCATCACCCCCACCCCCAATTCATTACAAACCACCT
          1 CCATCACCATCACCCCCACCCCCAATTCATTACAAACCACCT

                    *               
       2074 CCATCACCTTCACCCCCACCCCCA
          1 CCATCACCATCACCCCCACCCCCA

       2098 CCAATCCATT


Statistics
Matches: 65,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  42   65  1.00

ACGTcount: A:0.29, C:0.56, G:0.00, T:0.16


Consensus pattern (42 bp):   
CCATCACCATCACCCCCACCCCCAATTCATTACAAACCACCT

Found at i:2071 original size:21 final size:21

Alignment explanation


    Indices: 2005--2072  Score: 59
    Period size: 21  Copynumber: 3.2  Consensus size: 21

       1995 ACCATCACCC

                                 
       2005 CCACCCCCAATTCATTACAAA
          1 CCACCCCCAATTCATTACAAA

                 *        **     **
       2026 CCACCTCC-A-TCACCATCACCC
          1 CCACCCCCAATTCATTA-CA-AA

                                 
       2047 CCACCCCCAATTCATTACAAA
          1 CCACCCCCAATTCATTACAAA

                 
       2068 CCACC
          1 CCACC

       2073 TCCATCACCT


Statistics
Matches: 33,  Mismatches: 10, Indels: 8
        0.65            0.20        0.16

Matches are distributed among these distances:
  19    4  0.12
  20    3  0.09
  21   19  0.58
  22    3  0.09
  23    4  0.12

ACGTcount: A:0.32, C:0.51, G:0.00, T:0.16


Consensus pattern (21 bp):   
CCACCCCCAATTCATTACAAA
Done.