Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g00622.F6

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: 4937
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28


Found at i:22 original size:7 final size:7

Alignment explanation


    Indices: 2--38  Score: 65
    Period size: 7  Copynumber: 5.1  Consensus size: 7

          1 A

                   
          2 TTCATTT
          1 TTCATTT

                    
          9 ATTCATTT
          1 -TTCATTT

                   
         17 TTCATTT
          1 TTCATTT

                   
         24 TTCATTT
          1 TTCATTT

                   
         31 TTCATTT
          1 TTCATTT

             
         38 T
          1 T

         39 CTTCTTCTCG


Statistics
Matches: 29,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
   7   22  0.76
   8    7  0.24

ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70


Consensus pattern (7 bp):   
TTCATTT

Found at i:3689 original size:33 final size:33

Alignment explanation


    Indices: 3647--3735  Score: 142
    Period size: 33  Copynumber: 2.7  Consensus size: 33

       3637 GGATTCTGGA

                                             
       3647 GGCCGTGGTGGAATGAGGGATGGAGGCTTTGGT
          1 GGCCGTGGTGGAATGAGGGATGGAGGCTTTGGT

                                   *         
       3680 GGCCGTGGTGGAATGAGGGATGGGGGCTTTGGT
          1 GGCCGTGGTGGAATGAGGGATGGAGGCTTTGGT

              *        *     *     
       3713 GGACGTGGTGGCATGAGAGATGG
          1 GGCCGTGGTGGAATGAGGGATGG

       3736 TTTTGGCGGT


Statistics
Matches: 52,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  33   52  1.00

ACGTcount: A:0.16, C:0.09, G:0.53, T:0.22


Consensus pattern (33 bp):   
GGCCGTGGTGGAATGAGGGATGGAGGCTTTGGT

Found at i:4037 original size:6 final size:6

Alignment explanation


    Indices: 4026--4053  Score: 56
    Period size: 6  Copynumber: 4.7  Consensus size: 6

       4016 CGAACTTGGC

                                            
       4026 GCCGTA GCCGTA GCCGTA GCCGTA GCCG
          1 GCCGTA GCCGTA GCCGTA GCCGTA GCCG

       4054 CAGTGGGAGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   22  1.00

ACGTcount: A:0.14, C:0.36, G:0.36, T:0.14


Consensus pattern (6 bp):   
GCCGTA

Found at i:4068 original size:6 final size:6

Alignment explanation


    Indices: 4059--4108  Score: 55
    Period size: 6  Copynumber: 7.8  Consensus size: 6

       4049 AGCCGCAGTG

                 *      *                                            
       4059 GGAGTC GGAGTT GGAGTA GTAGGAGTA GGAGTA GGAGTA GGAGTA GGAGT
          1 GGAGTA GGAGTA GGAGTA G--G-AGTA GGAGTA GGAGTA GGAGTA GGAGT

       4109 CGAAGCAGAA


Statistics
Matches: 39,  Mismatches: 2, Indels: 6
        0.83            0.04        0.13

Matches are distributed among these distances:
   6   32  0.82
   7    1  0.03
   8    1  0.03
   9    5  0.13

ACGTcount: A:0.28, C:0.02, G:0.50, T:0.20


Consensus pattern (6 bp):   
GGAGTA

Found at i:4089 original size:21 final size:21

Alignment explanation


    Indices: 4059--4098  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       4049 AGCCGCAGTG

                 *     *         
       4059 GGAGTCGGAGTTGGAGTAGTA
          1 GGAGTAGGAGTAGGAGTAGTA

                               
       4080 GGAGTAGGAGTAGGAGTAG
          1 GGAGTAGGAGTAGGAGTAG

       4099 GAGTAGGAGT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.28, C:0.03, G:0.50, T:0.20


Consensus pattern (21 bp):   
GGAGTAGGAGTAGGAGTAGTA

Found at i:4091 original size:12 final size:12

Alignment explanation


    Indices: 4076--4108  Score: 66
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       4066 GAGTTGGAGT

                        
       4076 AGTAGGAGTAGG
          1 AGTAGGAGTAGG

                        
       4088 AGTAGGAGTAGG
          1 AGTAGGAGTAGG

                     
       4100 AGTAGGAGT
          1 AGTAGGAGT

       4109 CGAAGCAGAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   21  1.00

ACGTcount: A:0.33, C:0.00, G:0.48, T:0.18


Consensus pattern (12 bp):   
AGTAGGAGTAGG

Found at i:4339 original size:63 final size:63

Alignment explanation


    Indices: 4240--4395  Score: 226
    Period size: 63  Copynumber: 2.5  Consensus size: 63

       4230 GCTATGAGCG

                              *                  **            *            
       4240 GAAGGATGTTGCAAAGCGGGCATTTGATTCTCCTCCTGGTTCCAACGAACATAACTT-GCAACA
          1 GAAGGATGTTGCAAAGCGAGCATTTGATTCTCCTCCTCCTTCCAACGAACAGAACTTCG-AACA

                        *                                               *  
       4303 GAAGGATGTTGCGAAGCGAGCATTTGATTCTCCTCCTCCTTCCAACGAACAGAACTTCGAGCA
          1 GAAGGATGTTGCAAAGCGAGCATTTGATTCTCCTCCTCCTTCCAACGAACAGAACTTCGAACA

                                           
       4366 GAAGGATGTTGCAAAGC-AGGCATTTGATTC
          1 GAAGGATGTTGCAAAGCGA-GCATTTGATTC

       4396 ACCTGGTGCA


Statistics
Matches: 84,  Mismatches: 7, Indels: 4
        0.88            0.07        0.04

Matches are distributed among these distances:
  62    1  0.01
  63   82  0.98
  64    1  0.01

ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25


Consensus pattern (63 bp):   
GAAGGATGTTGCAAAGCGAGCATTTGATTCTCCTCCTCCTTCCAACGAACAGAACTTCGAACA
Done.