Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_387 ID=scaffold_387-JGI_221_v2.0

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: 7578
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29


Found at i:3889 original size:7 final size:7

Alignment explanation


    Indices: 3846--3879  Score: 50
    Period size: 7  Copynumber: 4.7  Consensus size: 7

       3836 AGTCAAACAA

                   
       3846 AAAAATG
          1 AAAAATG

                   
       3853 AAAAATG
          1 AAAAATG

               *    
       3860 AATGAATG
          1 AA-AAATG

                   
       3868 AAAAATG
          1 AAAAATG

                 
       3875 AAAAA
          1 AAAAA

       3880 AAATGAAAAA


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

Matches are distributed among these distances:
   7   18  0.75
   8    6  0.25

ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15


Consensus pattern (7 bp):   
AAAAATG

Found at i:3896 original size:17 final size:17

Alignment explanation


    Indices: 3844--3889  Score: 60
    Period size: 15  Copynumber: 2.8  Consensus size: 17

       3834 TGAGTCAAAC

                             
       3844 AAAAAAATGAAAAATG-
          1 AAAAAAATGAAAAATGA

               **            
       3860 -AATGAATGAAAAATGA
          1 AAAAAAATGAAAAATGA

                          
       3876 AAAAAAATGAAAAA
          1 AAAAAAATGAAAAA

       3890 GTAAAAATGG


Statistics
Matches: 24,  Mismatches: 4, Indels: 3
        0.77            0.13        0.10

Matches are distributed among these distances:
  15   13  0.54
  17   11  0.46

ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13


Consensus pattern (17 bp):   
AAAAAAATGAAAAATGA

Found at i:5330 original size:46 final size:46

Alignment explanation


    Indices: 5077--5313  Score: 375
    Period size: 46  Copynumber: 5.2  Consensus size: 46

       5067 AACAGATCAA

                             *                            
       5077 CGAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGAT
          1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGAT

             *                                        *   
       5123 CAAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
          1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGAT

                     *                         *  *       
       5169 CGAAGATAGTAGATCTTGTCTTCCTGTATTTGGCAACGAAGGAGAT
          1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGAT

                *         *          *                    
       5215 CGAAAATAGCAGATATTGTCTTCCTATATTTGGCAGCGGAGGAGAT
          1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGAT

                                           *         *    
       5261 CGAAGATAGCAGATCTTGTCTTCCTGTATTTCGCAGCGGAGCAGAT
          1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGAT

                   
       5307 CGAAGAT
          1 CGAAGAT

       5314 GGTGAATCTT


Statistics
Matches: 172,  Mismatches: 19, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  46  172  1.00

ACGTcount: A:0.27, C:0.17, G:0.27, T:0.28


Consensus pattern (46 bp):   
CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGAT

Found at i:5450 original size:132 final size:132

Alignment explanation


    Indices: 5298--5703  Score: 697
    Period size: 132  Copynumber: 3.1  Consensus size: 132

       5288 ATTTCGCAGC

                                                                             
       5298 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
          1 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA

                                                                             
       5363 GTCCTATCACCCTAAGCAGTAGAGGAGTAGGTTAAAGATTACAGATTCTGTCACCCTAAGCAGTA
         66 GTCCTATCACCCTAAGCAGTAGAGGAGTAGGTTAAAGATTACAGATTCTGTCACCCTAAGCAGTA

              
       5428 GT
        131 GT

                                                    *                        
       5430 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAATGGAGAAGCAGATTTAAGCCATTA
          1 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA

                    *             *                                          
       5495 GTCCTATCGCCCTAAGCAGTAGTGGAGTAGGTTAAAGATTACAGATTCTGTCACCCTAAGCAGTA
         66 GTCCTATCACCCTAAGCAGTAGAGGAGTAGGTTAAAGATTACAGATTCTGTCACCCTAAGCAGTA

              
       5560 GT
        131 GT

                         *                                   *               
       5562 GGAGCAGATCGAAAATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGAAGATTTAAGCCATTA
          1 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA

                      *           *         *     * **                       
       5627 GTCCTATCACTCTAAGCAGTAGCGGAGTAGGTCAAAGACTGTAGATTCTGT-ACCCTTAAGCAGT
         66 GTCCTATCACCCTAAGCAGTAGAGGAGTAGGTTAAAGATTACAGATTCTGTCACCC-TAAGCAGT

               
       5691 AGT
        130 AGT

                      
       5694 GGAGCAGATC
          1 GGAGCAGATC

       5704 AACAATAACG


Statistics
Matches: 260,  Mismatches: 13, Indels: 2
        0.95            0.05        0.01

Matches are distributed among these distances:
 131    4  0.02
 132  256  0.98

ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25


Consensus pattern (132 bp):   
GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
GTCCTATCACCCTAAGCAGTAGAGGAGTAGGTTAAAGATTACAGATTCTGTCACCCTAAGCAGTA
GT

Found at i:6147 original size:13 final size:13

Alignment explanation


    Indices: 6129--6154  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       6119 GAAACAAAGA

                         
       6129 AACCCTAGCCTCT
          1 AACCCTAGCCTCT

                         
       6142 AACCCTAGCCTCT
          1 AACCCTAGCCTCT

       6155 GCCACCACCT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.23, C:0.46, G:0.08, T:0.23


Consensus pattern (13 bp):   
AACCCTAGCCTCT
Done.