Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g00474.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: 1875
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29


Found at i:1472 original size:18 final size:18

Alignment explanation


    Indices: 1446--1503  Score: 71
    Period size: 18  Copynumber: 3.2  Consensus size: 18

       1436 GCCGCCATTG

                *             
       1446 CCGCCACGACAACCTCCA
          1 CCGCAACGACAACCTCCA

                            * 
       1464 CCGCAACGACAACCTCGA
          1 CCGCAACGACAACCTCCA

                 *     *  *   
       1482 CCGCAGCGACAGCCGCCA
          1 CCGCAACGACAACCTCCA

                
       1500 CCGC
          1 CCGC

       1504 TGCCTCGACA


Statistics
Matches: 34,  Mismatches: 6, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  18   34  1.00

ACGTcount: A:0.26, C:0.52, G:0.19, T:0.03


Consensus pattern (18 bp):   
CCGCAACGACAACCTCCA

Found at i:1519 original size:57 final size:57

Alignment explanation


    Indices: 1428--1563  Score: 173
    Period size: 57  Copynumber: 2.4  Consensus size: 57

       1418 GCTTCTACTA

                           **                                   *    
       1428 CAGCGACAGCCGCCATTGCCGCCACGACAACCTCCACCGCAACGACAACCTCGACCG
          1 CAGCGACAGCCGCCACCGCCGCCACGACAACCTCCACCGCAACGACAACCTCAACCG

                               *   *     *       *   *               
       1485 CAGCGACAGCCGCCACCGCTGCCTCGACAGCCTCCACTGCAGCGACAACCTCAACCG
          1 CAGCGACAGCCGCCACCGCCGCCACGACAACCTCCACCGCAACGACAACCTCAACCG

                *      * *        
       1542 CAGCAACAGCCTCAACCGCCGC
          1 CAGCGACAGCCGCCACCGCCGC

       1564 GACAGCTGCC


Statistics
Matches: 67,  Mismatches: 12, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  57   67  1.00

ACGTcount: A:0.25, C:0.48, G:0.20, T:0.07


Consensus pattern (57 bp):   
CAGCGACAGCCGCCACCGCCGCCACGACAACCTCCACCGCAACGACAACCTCAACCG

Found at i:1530 original size:18 final size:18

Alignment explanation


    Indices: 1452--1578  Score: 103
    Period size: 18  Copynumber: 6.9  Consensus size: 18

       1442 ATTGCCGCCA

                 *           *
       1452 CGACAACCTCCACCGCAA
          1 CGACAGCCTCCACCGCAG

                 *    *       
       1470 CGACAACCTCGACCGCAG
          1 CGACAGCCTCCACCGCAG

                    *       * 
       1488 CGACAGCCGCCACCGCTG
          1 CGACAGCCTCCACCGCAG

                            *    
       1506 CCTCGACAGCCTCCACTGCAG
          1 ---CGACAGCCTCCACCGCAG

                 *    *       
       1527 CGACAACCTCAACCGCAG
          1 CGACAGCCTCCACCGCAG

             *        *     * 
       1545 CAACAGCCTCAACCGCCG
          1 CGACAGCCTCCACCGCAG

                             
       1563 CGACAG-CTGCCACCGC
          1 CGACAGCCT-CCACCGC

       1579 CGCCGCGATA


Statistics
Matches: 88,  Mismatches: 17, Indels: 8
        0.78            0.15        0.07

Matches are distributed among these distances:
  17    2  0.02
  18   71  0.81
  21   15  0.17

ACGTcount: A:0.25, C:0.48, G:0.20, T:0.07


Consensus pattern (18 bp):   
CGACAGCCTCCACCGCAG

Found at i:1605 original size:75 final size:74

Alignment explanation


    Indices: 1452--1627  Score: 210
    Period size: 75  Copynumber: 2.4  Consensus size: 74

       1442 ATTGCCGCCA

                             * *   *    *                       *   *        
       1452 CGACAACCTCCACCGCAACGACAACCTCGACCGCAGCGACAGCCGCCACCGCTGCCTCGACAGCC
          1 CGACAACCTCCACCGCAGCAACAGCCTCAACCGCAGCGACAGCCGCCACCGCCGCCGCGACAGCC

                      
       1517 TCCACTGCAG
         66 TCCAC-GCAG

                      *                       *        *                *    
       1527 CGACAACCTCAACCGCAGCAACAGCCTCAACCGCCGCGACAGCTGCCACCGCCGCCGCGATAGCC
          1 CGACAACCTCCACCGCAGCAACAGCCTCAACCGCAGCGACAGCCGCCACCGCCGCCGCGACAGCC

                       
       1592 TCCAC-CAATG
         66 TCCACGC-A-G

                         *  *         
       1602 CGACAACCTCCACAGCTGCAACAGCC
          1 CGACAACCTCCACCGCAGCAACAGCC

       1628 GCCGCCACAG


Statistics
Matches: 86,  Mismatches: 13, Indels: 4
        0.83            0.13        0.04

Matches are distributed among these distances:
  73    1  0.01
  74    1  0.01
  75   84  0.98

ACGTcount: A:0.26, C:0.47, G:0.19, T:0.08


Consensus pattern (74 bp):   
CGACAACCTCCACCGCAGCAACAGCCTCAACCGCAGCGACAGCCGCCACCGCCGCCGCGACAGCC
TCCACGCAG
Done.