Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g01309.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: 3198
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.33


Found at i:1578 original size:27 final size:27

Alignment explanation


    Indices: 1540--1648  Score: 112
    Period size: 27  Copynumber: 4.0  Consensus size: 27

       1530 AAGCGTTCTC

                  *                    
       1540 GTGGCTATGCCACAAATATCTGATCTG
          1 GTGGCTCTGCCACAAATATCTGATCTG

                          *       *   *
       1567 GTGGCTCTGCCACATATATCTGTTCTA
          1 GTGGCTCTGCCACAAATATCTGATCTG

                         * *            
       1594 GTGGCTCTGCCACGATTATCTGTATCTG
          1 GTGGCTCTGCCACAAATATCTG-ATCTG

               *     *     *      *    
       1622 GTGACTCTGTCAC-ATTATCTGTTCTG
          1 GTGGCTCTGCCACAAATATCTGATCTG

             
       1648 G
          1 G

       1649 CAGCCATGCT


Statistics
Matches: 69,  Mismatches: 12, Indels: 3
        0.82            0.14        0.04

Matches are distributed among these distances:
  26    5  0.07
  27   50  0.72
  28   14  0.20

ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36


Consensus pattern (27 bp):   
GTGGCTCTGCCACAAATATCTGATCTG

Found at i:1641 original size:54 final size:54

Alignment explanation


    Indices: 1534--1646  Score: 156
    Period size: 54  Copynumber: 2.1  Consensus size: 54

       1524 TGGAGGAAGC

                 *                              *                 
       1534 GTTCTCGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
          1 GTTCTAGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT

                        *      * *                     *           
       1588 GTTCTAGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
          1 GTTCTAGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT

                 
       1642 GTTCT
          1 GTTCT

       1647 GGCAGCCATG


Statistics
Matches: 52,  Mismatches: 6, Indels: 2
        0.87            0.10        0.03

Matches are distributed among these distances:
  54   34  0.65
  55   18  0.35

ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37


Consensus pattern (54 bp):   
GTTCTAGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT

Found at i:1734 original size:19 final size:22

Alignment explanation


    Indices: 1710--1749  Score: 59
    Period size: 19  Copynumber: 2.0  Consensus size: 22

       1700 CTCCCCACAC

                                  
       1710 GGTGTA-A-GGTTGG-TATGGG
          1 GGTGTATACGGTTGGATATGGG

                                 
       1729 GGTGTATACGGTTGGATATGG
          1 GGTGTATACGGTTGGATATGG

       1750 TTGGGTTTCT


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  19    6  0.33
  20    1  0.06
  21    6  0.33
  22    5  0.28

ACGTcount: A:0.17, C:0.03, G:0.47, T:0.33


Consensus pattern (22 bp):   
GGTGTATACGGTTGGATATGGG

Done.