Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g00428.N1

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: 7014
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30


Found at i:533 original size:26 final size:26

Alignment explanation


    Indices: 504--556  Score: 72
    Period size: 26  Copynumber: 2.0  Consensus size: 26

        494 TTTACAGTTT

                                       
        504 TACCCCTAGGAGATAAATT-ACCGAAA
          1 TACCCCTAGG-GATAAATTGACCGAAA

                       *          *   
        530 TACCCCTAGGGTTAAATTGACCTAAA
          1 TACCCCTAGGGATAAATTGACCGAAA

             
        556 T
          1 T

        557 GCATGTTTGA


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

Matches are distributed among these distances:
  25    7  0.29
  26   17  0.71

ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25


Consensus pattern (26 bp):   
TACCCCTAGGGATAAATTGACCGAAA

Found at i:4785 original size:26 final size:26

Alignment explanation


    Indices: 4749--4858  Score: 177
    Period size: 26  Copynumber: 4.2  Consensus size: 26

       4739 TGATACAAAT

                                       
       4749 TGATAATAGGTTAGGTAAATG-TTCAA
          1 TGATAATAGGTTAGGTAAATGTTTC-A

                                   *  
       4775 TGATAATAGGTTAGGTAAATGTTCCA
          1 TGATAATAGGTTAGGTAAATGTTTCA

                   *                  
       4801 TGATAATGGGTTAGGTAAATGTTTCA
          1 TGATAATAGGTTAGGTAAATGTTTCA

                   *                  
       4827 TGATAATGGGTTAGGTAAATGTTTCA
          1 TGATAATAGGTTAGGTAAATGTTTCA

                  
       4853 TGATAA
          1 TGATAA

       4859 GAATTTCATG


Statistics
Matches: 80,  Mismatches: 3, Indels: 2
        0.94            0.04        0.02

Matches are distributed among these distances:
  26   78  0.98
  27    2  0.03

ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36


Consensus pattern (26 bp):   
TGATAATAGGTTAGGTAAATGTTTCA

Found at i:5479 original size:25 final size:25

Alignment explanation


    Indices: 5431--5479  Score: 64
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       5421 ACAGTTTTAC

                                     
       5431 CCCTAGGAGATAAATTACCGAAATA
          1 CCCTAGGAGATAAATTACCGAAATA

                     *          *    
       5456 CCCTAGG-GTTAAATTGACCTAAAT
          1 CCCTAGGAGATAAATT-ACCGAAAT

       5480 GCATGTTTGA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  24    7  0.33
  25   14  0.67

ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24


Consensus pattern (25 bp):   
CCCTAGGAGATAAATTACCGAAATA
Done.