Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g02498.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: 3188
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.22


Found at i:523 original size:27 final size:27

Alignment explanation


    Indices: 485--539  Score: 110
    Period size: 27  Copynumber: 2.0  Consensus size: 27

        475 CCCTGATACG

                                       
        485 GCTGCTGGGGATCCAAAGTCCAAGGAC
          1 GCTGCTGGGGATCCAAAGTCCAAGGAC

                                       
        512 GCTGCTGGGGATCCAAAGTCCAAGGAC
          1 GCTGCTGGGGATCCAAAGTCCAAGGAC

             
        539 G
          1 G

        540 AGACATCTGA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   28  1.00

ACGTcount: A:0.25, C:0.25, G:0.35, T:0.15


Consensus pattern (27 bp):   
GCTGCTGGGGATCCAAAGTCCAAGGAC

Found at i:1351 original size:6 final size:6

Alignment explanation


    Indices: 1336--1411  Score: 80
    Period size: 6  Copynumber: 12.7  Consensus size: 6

       1326 AGGCACGTGA

                        *                         **            ** 
       1336 ACAGGC ACAGGA ACAGGC ACAGGC ACAGGC ACAACC ACAGGC ACAACC
          1 ACAGGC ACAGGC ACAGGC ACAGGC ACAGGC ACAGGC ACAGGC ACAGGC

                        *    **             
       1384 ACAGGC ACAGGA ACAACC ACAGGC ACAG
          1 ACAGGC ACAGGC ACAGGC ACAGGC ACAG

       1412 CAAGGGAAGG


Statistics
Matches: 54,  Mismatches: 16, Indels: 0
        0.77            0.23        0.00

Matches are distributed among these distances:
   6   54  1.00

ACGTcount: A:0.41, C:0.34, G:0.25, T:0.00


Consensus pattern (6 bp):   
ACAGGC

Found at i:1537 original size:45 final size:45

Alignment explanation


    Indices: 1488--1760  Score: 410
    Period size: 45  Copynumber: 6.2  Consensus size: 45

       1478 AAATTAGAGG

                                                         
       1488 AGCAAGAACGAAAAGAAAAGGACAAGAAGAGAAAAGAGGATGAGA
          1 AGCAAGAACGAAAAGAAAAGGACAAGAAGAGAAAAGAGGATGAGA

                                                         
       1533 AGCAAGAACGAAAAGAAAAGGACAAGAAGAGAAAAGAGGATGAGA
          1 AGCAAGAACGAAAAGAAAAGGACAAGAAGAGAAAAGAGGATGAGA

                                                     *   
       1578 AGCAAGAACGAAAAGAAAAGGAC---AAGAGAAAAGAGGATAAGA
          1 AGCAAGAACGAAAAGAAAAGGACAAGAAGAGAAAAGAGGATGAGA

             *                *   *       *   *          
       1620 ACCAAGAACGAAAAGAAATGGAGAAGAAGATAAACGAGGATGAGA
          1 AGCAAGAACGAAAAGAAAAGGACAAGAAGAGAAAAGAGGATGAGA

             *             *  *                          
       1665 ACCAAGAACGAAAAGCAATGGACAAGAAGAGAAAAGAGGATGAGA
          1 AGCAAGAACGAAAAGAAAAGGACAAGAAGAGAAAAGAGGATGAGA

                               *  *          *           
       1710 AGCAAGAACGAAAAGAAAAAGAGAAGAAGAGAATAGAGGATGAGA
          1 AGCAAGAACGAAAAGAAAAGGACAAGAAGAGAAAAGAGGATGAGA

                   
       1755 AG-AAGA
          1 AGCAAGA

       1761 GAGGAAAGCT


Statistics
Matches: 208,  Mismatches: 17, Indels: 7
        0.90            0.07        0.03

Matches are distributed among these distances:
  42   38  0.18
  44    4  0.02
  45  166  0.80

ACGTcount: A:0.59, C:0.07, G:0.30, T:0.04


Consensus pattern (45 bp):   
AGCAAGAACGAAAAGAAAAGGACAAGAAGAGAAAAGAGGATGAGA

Found at i:1659 original size:132 final size:135

Alignment explanation


    Indices: 1490--1755  Score: 421
    Period size: 132  Copynumber: 2.0  Consensus size: 135

       1480 ATTAGAGGAG

                                                        *                    
       1490 CAAGAACGAAAAGAAAAGGACAAGAAGAGAAAAGAGGATGAGAAGCAAGAACGAAAAGAAAAGGA
          1 CAAGAACGAAAAGAAAAGGACAAGAAGAGAAAAGAGGATGAGAACCAAGAACGAAAAGAAAAGGA

                                                                             
       1555 CAAGAAGAGAAAAGAGGATGAGAAGCAAGAACGAAAAG-AAAAG-G-ACAAGAGAAAAGAGGATA
         66 CAAGAAGAGAAAAGAGGATGAGAAGCAAGAACGAAAAGAAAAAGAGAACAAGAGAAAAGAGGATA

                 
       1617 AGAAC
        131 AGAAC

                            *   *       *   *                         *  *   
       1622 CAAGAACGAAAAGAAATGGAGAAGAAGATAAACGAGGATGAGAACCAAGAACGAAAAGCAATGGA
          1 CAAGAACGAAAAGAAAAGGACAAGAAGAGAAAAGAGGATGAGAACCAAGAACGAAAAGAAAAGGA

                                                            *       *       *
       1687 CAAGAAGAGAAAAGAGGATGAGAAGCAAGAACGAAAAGAAAAAGAGAAGAAGAGAATAGAGGATG
         66 CAAGAAGAGAAAAGAGGATGAGAAGCAAGAACGAAAAGAAAAAGAGAACAAGAGAAAAGAGGATA

                
       1752 AGAA
        131 AGAA

       1756 GAAGAGAGGA


Statistics
Matches: 121,  Mismatches: 10, Indels: 3
        0.90            0.07        0.02

Matches are distributed among these distances:
 132   96  0.79
 133    5  0.04
 134    1  0.01
 135   19  0.16

ACGTcount: A:0.59, C:0.08, G:0.30, T:0.04


Consensus pattern (135 bp):   
CAAGAACGAAAAGAAAAGGACAAGAAGAGAAAAGAGGATGAGAACCAAGAACGAAAAGAAAAGGA
CAAGAAGAGAAAAGAGGATGAGAAGCAAGAACGAAAAGAAAAAGAGAACAAGAGAAAAGAGGATA
AGAAC

Done.