Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g02140.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, 982

Length: 1638
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29


Found at i:1039 original size:15 final size:16

Alignment explanation


    Indices: 1003--1040  Score: 53
    Period size: 15  Copynumber: 2.5  Consensus size: 16

        993 GAGCAGTTGC

                            
       1003 AGAAGCAGAAGCTGCA
          1 AGAAGCAGAAGCTGCA

              *             
       1019 A-TAGCAGAAGCTG-A
          1 AGAAGCAGAAGCTGCA

                    
       1033 AGAAGCAG
          1 AGAAGCAG

       1041 CAAGAGAGGC


Statistics
Matches: 19,  Mismatches: 2, Indels: 3
        0.79            0.08        0.12

Matches are distributed among these distances:
  14    2  0.11
  15   16  0.84
  16    1  0.05

ACGTcount: A:0.45, C:0.16, G:0.32, T:0.08


Consensus pattern (16 bp):   
AGAAGCAGAAGCTGCA

Found at i:1086 original size:21 final size:21

Alignment explanation


    Indices: 1062--1101  Score: 53
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       1052 GAGGTTGCTG

                         *       
       1062 AAGCTGATGCAGAGGCAGCGC
          1 AAGCTGATGCAGAAGCAGCGC

                 **            
       1083 AAGCTTTTGCAGAAGCAGC
          1 AAGCTGATGCAGAAGCAGC

       1102 AATGAAAACT


Statistics
Matches: 16,  Mismatches: 3, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   16  1.00

ACGTcount: A:0.30, C:0.23, G:0.33, T:0.15


Consensus pattern (21 bp):   
AAGCTGATGCAGAAGCAGCGC

Found at i:1257 original size:30 final size:29

Alignment explanation


    Indices: 1186--1272  Score: 138
    Period size: 29  Copynumber: 3.0  Consensus size: 29

       1176 TGTTGACGAT

                                         
       1186 TTTTGCAGCAGGCACCCAGTCATCATCCC
          1 TTTTGCAGCAGGCACCCAGTCATCATCCC

                                    *    
       1215 TTTTGCAGCAGGCACCCAGTCATCGTCCC
          1 TTTTGCAGCAGGCACCCAGTCATCATCCC

                  *              *       
       1244 TATTTGTAGCAGGCACCCAGTGATCATCC
          1 T-TTTGCAGCAGGCACCCAGTCATCATCC

       1273 TTATTATTTG


Statistics
Matches: 53,  Mismatches: 4, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  29   29  0.55
  30   24  0.45

ACGTcount: A:0.21, C:0.34, G:0.20, T:0.25


Consensus pattern (29 bp):   
TTTTGCAGCAGGCACCCAGTCATCATCCC
Done.