Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga13g00336.F3

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: 2460
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26


Found at i:1419 original size:21 final size:21

Alignment explanation


    Indices: 1415--1470  Score: 67
    Period size: 21  Copynumber: 2.7  Consensus size: 21

       1405 ATCCAATCTC

                                 
       1415 CACCACCACCACCAATGCACT
          1 CACCACCACCACCAATGCACT

                      *  ** *  * 
       1436 CACCACCACCGCCCGTCCATT
          1 CACCACCACCACCAATGCACT

                          
       1457 CACCACCACCACCA
          1 CACCACCACCACCA

       1471 TCGGTTCCTT


Statistics
Matches: 28,  Mismatches: 7, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  21   28  1.00

ACGTcount: A:0.29, C:0.57, G:0.05, T:0.09


Consensus pattern (21 bp):   
CACCACCACCACCAATGCACT

Found at i:1643 original size:62 final size:63

Alignment explanation


    Indices: 1460--1848  Score: 638
    Period size: 63  Copynumber: 6.2  Consensus size: 63

       1450 GTCCATTCAC

                       * *                 *                 *        *    
       1460 CACCACCACCATCGGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCCCCACCGGTACCCT
          1 CACCACCACCACCAGTTCCTTCACCCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCCT

                             *             *           *                   
       1523 CACCACCACCACCAGTTTCTTCACCCCCACCGCCAGTAAAATCTCCACCTCCACCGGTGCCCT
          1 CACCACCACCACCAGTTCCTTCACCCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCCT

                                                                           
       1586 CACCACCACCACCAGTTCCTTCA-CCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCCT
          1 CACCACCACCACCAGTTCCTTCACCCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCCT

                                                               *           
       1648 CACCACCACCACCAGTTCCTTCA-CCCCACCCCCAGTAAAATCCCCACCTCTACCGGTGCCCT
          1 CACCACCACCACCAGTTCCTTCACCCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCCT

                                                                           
       1710 CACCACCACCACCAGTTCCTTCACCCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCCT
          1 CACCACCACCACCAGTTCCTTCACCCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCCT

                           *          *    *             *                 
       1773 CACCACCACCACCAGATCCTTCACCCTCACCACCAGTAAAATCCCTACCTCCACCGGTGCCCT
          1 CACCACCACCACCAGTTCCTTCACCCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCCT

                   *     
       1836 CACCACCCCCACC
          1 CACCACCACCACC

       1849 TGTGCCATCT


Statistics
Matches: 308,  Mismatches: 17, Indels: 2
        0.94            0.05        0.01

Matches are distributed among these distances:
  62  121  0.39
  63  187  0.61

ACGTcount: A:0.23, C:0.54, G:0.08, T:0.15


Consensus pattern (63 bp):   
CACCACCACCACCAGTTCCTTCACCCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCCT

Found at i:1950 original size:62 final size:63

Alignment explanation


    Indices: 1814--2122  Score: 277
    Period size: 62  Copynumber: 5.0  Consensus size: 63

       1804 ACCAGTAAAA

                *   *     *        *           *         *                * 
       1814 TCCCTACCTCCACCGGTGCCCTCACCACCCCCACCTGTGCCA-TCTCCACCCCCACCCGTCCGC
          1 TCCCCACCCCCACCTGTGCCCTCTCCACCCCCACCCGT-CCACTCACCACCCCCACCCGTCCAC

                                           *                        *      
       1877 TCCCCACCCCCACCTGTGCCCTCTCCACCCCTACCCGTCCACTC-CCACCCCCACCTGTCCAC
          1 TCCCCACCCCCACCTGTGCCCTCTCCACCCCCACCCGTCCACTCACCACCCCCACCCGTCCAC

              *                                **   *   *           *  * * 
       1939 TCTCCACCCCCACCTGTGCCCTCTCCACCCCCACCTATCCTCTCTCCA-CCCCACCGGTGCGC
          1 TCCCCACCCCCACCTGTGCCCTCTCCACCCCCACCCGTCCACTCACCACCCCCACCCGTCCAC

              *           *      *              *  * *                *     
       2001 TCACCA-CCCCACCCGT-CCTTTCTCCACCCCCACCAGTGCGCTCACCACCCCCACCCATCCAC
          1 TCCCCACCCCCACCTGTGCC-CTCTCCACCCCCACCCGTCCACTCACCACCCCCACCCGTCCAC

                          *  * **  *     *         *          *         
       2063 TCCCCACCCCCACCAGTACATTCACCACCACCACCCGTCTACTCACCACCTCCACCCGTC
          1 TCCCCACCCCCACCTGTGCCCTCTCCACCCCCACCCGTCCACTCACCACCCCCACCCGTC

       2123 AAGTCTCCAC


Statistics
Matches: 201,  Mismatches: 39, Indels: 12
        0.80            0.15        0.05

Matches are distributed among these distances:
  60    2  0.01
  61   31  0.15
  62   89  0.44
  63   78  0.39
  64    1  0.00

ACGTcount: A:0.15, C:0.61, G:0.08, T:0.16


Consensus pattern (63 bp):   
TCCCCACCCCCACCTGTGCCCTCTCCACCCCCACCCGTCCACTCACCACCCCCACCCGTCCAC

Found at i:2069 original size:21 final size:21

Alignment explanation


    Indices: 1838--2139  Score: 238
    Period size: 21  Copynumber: 14.5  Consensus size: 21

       1828 GGTGCCCTCA

                       *          
       1838 CCACCCCCACCTGTGCCA-TCT
          1 CCACCCCCACCCGT-CCACTCT

                            *   *
       1859 CCACCCCCACCCGTCCGCTCC
          1 CCACCCCCACCCGTCCACTCT

                       *          
       1880 CCACCCCCACCTGTGCC-CTCT
          1 CCACCCCCACCCGT-CCACTCT

                   *             
       1901 CCACCCCTACCCGTCCACTC-
          1 CCACCCCCACCCGTCCACTCT

                       *         
       1921 CCACCCCCACCTGTCCACTCT
          1 CCACCCCCACCCGTCCACTCT

                       *          
       1942 CCACCCCCACCTGTGCC-CTCT
          1 CCACCCCCACCCGT-CCACTCT

                       **   *    
       1963 CCACCCCCACCTATCCTCTCT
          1 CCACCCCCACCCGTCCACTCT

                       *  * *   *
       1984 CCA-CCCCACCGGTGCGCTCA
          1 CCACCCCCACCCGTCCACTCT

                            **   
       2004 CCA-CCCCACCCGTCCTTTCT
          1 CCACCCCCACCCGTCCACTCT

                       *  * *   *
       2024 CCACCCCCACCAGTGCGCTCA
          1 CCACCCCCACCCGTCCACTCT

                        *       *
       2045 CCACCCCCACCCATCCACTCC
          1 CCACCCCCACCCGTCCACTCT

                       *  *  *  *
       2066 CCACCCCCACCAGTACATTCA
          1 CCACCCCCACCCGTCCACTCT

                 *         *    *
       2087 CCACCACCACCCGTCTACTCA
          1 CCACCCCCACCCGTCCACTCT

                 *         * *   
       2108 CCACCTCCACCCGTCAAGTCT
          1 CCACCCCCACCCGTCCACTCT

                 *     
       2129 CCACCACCACC
          1 CCACCCCCACC

       2140 AGTAAAATCT


Statistics
Matches: 229,  Mismatches: 45, Indels: 14
        0.80            0.16        0.05

Matches are distributed among these distances:
  20   54  0.24
  21  171  0.75
  22    4  0.02

ACGTcount: A:0.16, C:0.61, G:0.07, T:0.16


Consensus pattern (21 bp):   
CCACCCCCACCCGTCCACTCT

Done.