Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga13g02230.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: 2984
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29


Found at i:1065 original size:137 final size:137

Alignment explanation


    Indices: 783--1058  Score: 525
    Period size: 137  Copynumber: 2.0  Consensus size: 137

        773 GAGTAGTCTC

                     *                                                       
        783 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
          1 CCCAAATGGACTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC

                                        *                                    
        848 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTATAATCTGAAAAGGGCTCTGGCCCAGTACC
         66 TGTTATCTGAATAAGGGGCTAAGGCCCAATTTATTATAATCTGAAAAGGGCTCTGGCCCAGTACC

                   
        913 ACTGTTA
        131 ACTGTTA

                                                                             
        920 CCCAAATGGACTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
          1 CCCAAATGGACTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC

                                               *                             
        985 TGTTATCTGAATAAGGGGCTAAGGCCCAATTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
         66 TGTTATCTGAATAAGGGGCTAAGGCCCAATTTATTATAATCTGAAAAGGGCTCTGGCCCAGTACC

                   
       1050 ACTGTTA
        131 ACTGTTA

              
       1057 CC
          1 CC

       1059 TGAATGGGCT


Statistics
Matches: 136,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 137  136  1.00

ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31


Consensus pattern (137 bp):   
CCCAAATGGACTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAATTTATTATAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA

Found at i:2813 original size:17 final size:17

Alignment explanation


    Indices: 2763--2813  Score: 66
    Period size: 19  Copynumber: 2.9  Consensus size: 17

       2753 TGGAAACATG

                 *           
       2763 ATCTTCGAAGATATGCA
          1 ATCTTAGAAGATATGCA

                             * 
       2780 ATCTTAGATATGATATGTA
          1 ATCTTAGA-A-GATATGCA

                           
       2799 ATCTTAGAAGATATG
          1 ATCTTAGAAGATATG

       2814 ATTTTGTAAT


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  17   13  0.43
  18    2  0.07
  19   15  0.50

ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35


Consensus pattern (17 bp):   
ATCTTAGAAGATATGCA

Found at i:2813 original size:22 final size:21

Alignment explanation


    Indices: 2785--2842  Score: 80
    Period size: 22  Copynumber: 2.7  Consensus size: 21

       2775 ATGCAATCTT

                     *           
       2785 AGATATGATATGTAATCTTAG
          1 AGATATGATTTGTAATCTTAG

                                   
       2806 AAGATATGATTTTGTAATCTTAG
          1 -AGATATGA-TTTGTAATCTTAG

                *         
       2829 AGATTTGATTTGTA
          1 AGATATGATTTGTA

       2843 GATACCCTTT


Statistics
Matches: 33,  Mismatches: 2, Indels: 3
        0.87            0.05        0.08

Matches are distributed among these distances:
  21    6  0.18
  22   15  0.45
  23   12  0.36

ACGTcount: A:0.34, C:0.03, G:0.19, T:0.43


Consensus pattern (21 bp):   
AGATATGATTTGTAATCTTAG

Done.