Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g03527.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: 3502
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.24


Found at i:680 original size:18 final size:18

Alignment explanation


    Indices: 653--699  Score: 58
    Period size: 18  Copynumber: 2.6  Consensus size: 18

        643 AGATAGGGAC

                              
        653 AGAGAAAAGGAAAAGGAA
          1 AGAGAAAAGGAAAAGGAA

                 *    **      
        671 AGAGACAAGGCCAAGGAA
          1 AGAGAAAAGGAAAAGGAA

              *        
        689 AGGGAAAAGGA
          1 AGAGAAAAGGA

        700 GAGAGACAAA


Statistics
Matches: 23,  Mismatches: 6, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  18   23  1.00

ACGTcount: A:0.57, C:0.06, G:0.36, T:0.00


Consensus pattern (18 bp):   
AGAGAAAAGGAAAAGGAA

Found at i:759 original size:18 final size:18

Alignment explanation


    Indices: 720--764  Score: 56
    Period size: 18  Copynumber: 2.5  Consensus size: 18

        710 CTTAAGGATC

                         *    
        720 GAGAGAAGGAGAGGGAAG
          1 GAGAGAAGGAGAGAGAAG

                      *        
        738 GAGAGAAGGATAGAGATA-
          1 GAGAGAAGGAGAGAGA-AG

                     
        756 GAGAGAAGG
          1 GAGAGAAGG

        765 GAAAAGATAG


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  18   23  0.96
  19    1  0.04

ACGTcount: A:0.47, C:0.00, G:0.49, T:0.04


Consensus pattern (18 bp):   
GAGAGAAGGAGAGAGAAG

Found at i:772 original size:18 final size:18

Alignment explanation


    Indices: 738--775  Score: 51
    Period size: 18  Copynumber: 2.1  Consensus size: 18

        728 GAGAGGGAAG

                        *     
        738 GAGAGAAGGATAGAGATA
          1 GAGAGAAGGATAAAGATA

                               
        756 GAGAGAAGGGA-AAAGATA
          1 GAGAGAA-GGATAAAGATA

              
        774 GA
          1 GA

        776 AGTAAACAGA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  18   15  0.83
  19    3  0.17

ACGTcount: A:0.53, C:0.00, G:0.39, T:0.08


Consensus pattern (18 bp):   
GAGAGAAGGATAAAGATA

Found at i:1690 original size:76 final size:76

Alignment explanation


    Indices: 1602--1755  Score: 229
    Period size: 76  Copynumber: 2.0  Consensus size: 76

       1592 TTTTTTTGGG

                           *      *           *                              
       1602 TGTGTAATTTACCTATTAGCAGGTTTAATA-TATTCCTTTAATATGGATTATGTTAATTAAGGTT
          1 TGTGTAATTTACCTACTAGCAGATTTAATAGT-TACCTTTAATATGGATTATGTTAATTAAGGTT

               *        
       1666 CAATGAAGAGCC
         65 CAACGAAGAGCC

                                       *                              *      
       1678 TGTGTAATTTACCTACTAGCAGATTTAGTAGTTACCTTTAATATGGATTATGTTAATTTAGGTTC
          1 TGTGTAATTTACCTACTAGCAGATTTAATAGTTACCTTTAATATGGATTATGTTAATTAAGGTTC

                    *  
       1743 AACGAAGATCC
         66 AACGAAGAGCC

              
       1754 TG
          1 TG

       1756 GTTCTGAGAA


Statistics
Matches: 70,  Mismatches: 7, Indels: 2
        0.89            0.09        0.03

Matches are distributed among these distances:
  76   69  0.99
  77    1  0.01

ACGTcount: A:0.31, C:0.12, G:0.18, T:0.40


Consensus pattern (76 bp):   
TGTGTAATTTACCTACTAGCAGATTTAATAGTTACCTTTAATATGGATTATGTTAATTAAGGTTC
AACGAAGAGCC
Done.