Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g00441.F6

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: 3285
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27


Found at i:700 original size:24 final size:24

Alignment explanation


    Indices: 547--705  Score: 207
    Period size: 24  Copynumber: 6.8  Consensus size: 24

        537 GAGGCATGCT

                    *               
        547 CAGCAACAACAGCAGCAGCAACAA
          1 CAGCAACAGCAGCAGCAGCAACAA

              *                 *  *
        571 CAACAACAGCAGCA--A-CAGCAG
          1 CAGCAACAGCAGCAGCAGCAACAA

                 *                  
        592 CAGCAGCAGCAGCAGCAGCAACAA
          1 CAGCAACAGCAGCAGCAGCAACAA

                                    
        616 CAGCAACAGCAGCAGCAGCAACAA
          1 CAGCAACAGCAGCAGCAGCAACAA

                                    
        640 CAGCAACAGCAGCAGCAGCAACAA
          1 CAGCAACAGCAGCAGCAGCAACAA

              *     *     *         
        664 CAACAACAACAGCAACAGCAACAA
          1 CAGCAACAGCAGCAGCAGCAACAA

                 * *          
        688 CAGCAGCCGCAGCAGCAG
          1 CAGCAACAGCAGCAGCAG

        706 TCTCCCCAGC


Statistics
Matches: 115,  Mismatches: 17, Indels: 6
        0.83            0.12        0.04

Matches are distributed among these distances:
  21   16  0.14
  22    1  0.01
  23    1  0.01
  24   97  0.84

ACGTcount: A:0.46, C:0.34, G:0.20, T:0.00


Consensus pattern (24 bp):   
CAGCAACAGCAGCAGCAGCAACAA

Found at i:718 original size:3 final size:3

Alignment explanation


    Indices: 556--705  Score: 120
    Period size: 3  Copynumber: 50.0  Consensus size: 3

        546 TCAGCAACAA

                          *   *   *   *           *                        
        556 CAG CAG CAG CAA CAA CAA CAA CAG CAG CAA CAG CAG CAG CAG CAG CAG
          1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG

                      *   *       *                   *   *       *        
        604 CAG CAG CAA CAA CAG CAA CAG CAG CAG CAG CAA CAA CAG CAA CAG CAG
          1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG

                      *   *   *   *   *       *       *   *          *     
        652 CAG CAG CAA CAA CAA CAA CAA CAG CAA CAG CAA CAA CAG CAG CCG CAG
          1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG

                   
        700 CAG CAG
          1 CAG CAG

        706 TCTCCCCAGC


Statistics
Matches: 127,  Mismatches: 20, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
   3  127  1.00

ACGTcount: A:0.45, C:0.34, G:0.21, T:0.00


Consensus pattern (3 bp):   
CAG

Found at i:1114 original size:13 final size:14

Alignment explanation


    Indices: 1081--1127  Score: 71
    Period size: 14  Copynumber: 3.4  Consensus size: 14

       1071 GGTAGGTTTG

                          
       1081 TTTGATCTCTTTCA
          1 TTTGATCTCTTTCA

                          
       1095 TTTGATCTC-TT-A
          1 TTTGATCTCTTTCA

                           
       1107 TATTGATCTCTTTCA
          1 T-TTGATCTCTTTCA

                  
       1122 TTTGAT
          1 TTTGAT

       1128 GCTTCTCTTT


Statistics
Matches: 30,  Mismatches: 0, Indels: 6
        0.83            0.00        0.17

Matches are distributed among these distances:
  12    2  0.07
  13   10  0.33
  14   16  0.53
  15    2  0.07

ACGTcount: A:0.17, C:0.17, G:0.09, T:0.57


Consensus pattern (14 bp):   
TTTGATCTCTTTCA

Found at i:1618 original size:6 final size:6

Alignment explanation


    Indices: 1607--1657  Score: 56
    Period size: 6  Copynumber: 9.2  Consensus size: 6

       1597 TGGCTCAGTT

                                      *        *                   
       1607 GCAACA GCAACA G---CA GCAACT GCAACA ACAACA GCAACA GCAACA
          1 GCAACA GCAACA GCAACA GCAACA GCAACA GCAACA GCAACA GCAACA

                    
       1652 G-AACA G
          1 GCAACA G

       1658 TAGCTCACAG


Statistics
Matches: 38,  Mismatches: 4, Indels: 7
        0.78            0.08        0.14

Matches are distributed among these distances:
   3    3  0.08
   5    5  0.13
   6   30  0.79

ACGTcount: A:0.49, C:0.31, G:0.18, T:0.02


Consensus pattern (6 bp):   
GCAACA

Done.