Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold8299.1

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: 5308
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28


Found at i:2732 original size:65 final size:65

Alignment explanation


    Indices: 2650--2777  Score: 211
    Period size: 65  Copynumber: 2.0  Consensus size: 65

       2640 GTGAGAAACT

                                           *         *    *                  
       2650 TGGTCGAGCAAAACCTCTATCCGTCAATTCTTGCAACTGAGCTTTCCACTCTTTTAACTCGGTCG
          1 TGGTCGAGCAAAACCTCTATCCGTCAATTCTAGCAACTGAGATTTCAACTCTTTTAACTCGGTCG

                        *                                *                 
       2715 TGGTCGAGCAAAGCCTCTATCCGTCAATTCTAGCAACTGAGATTTTAACTCTTTTAACTCGGT
          1 TGGTCGAGCAAAACCTCTATCCGTCAATTCTAGCAACTGAGATTTCAACTCTTTTAACTCGGT

       2778 TGGTGCCATA


Statistics
Matches: 58,  Mismatches: 5, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  65   58  1.00

ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33


Consensus pattern (65 bp):   
TGGTCGAGCAAAACCTCTATCCGTCAATTCTAGCAACTGAGATTTCAACTCTTTTAACTCGGTCG

Found at i:5284 original size:288 final size:288

Alignment explanation


    Indices: 4739--5301  Score: 968
    Period size: 288  Copynumber: 2.0  Consensus size: 288

       4729 CCACACTATC

                                              *                              
       4739 AAGTAATCACATAAAATGGCATGTATAGCTAGACCCAACGCATTACGGTAGTCCTAGAATCGACT
          1 AAGTAATCACATAAAATGGCATGTATAGCTAGACACAACGCATTACGGTAGTCCTAGAATCGACT

                                                                             
       4804 AAACCGTAGCTCTGATACCAATCAAATGTAACACCCCGAACCCGAGACCGACACCGGAGTCGAAC
         66 AAACCGTAGCTCTGATACCAATCAAATGTAACACCCCGAACCCGAGACCGACACCGGAGTCGAAC

                                     *          *                           *
       4869 ACGAGGTGTTAACAGACTTTAAACCCCTTATAAAAATATTTCCCAGACACTGCCAATCTGCGTAC
        131 ACGAGGTGTTAACAGACTTTAAACCACTTATAAAAAAATTTCCCAGACACTGCCAATCTGCGTAA

                                            *                **  * *         
       4934 TAGTCGCTTTAAAAATCATATCTTGAGTTTCACAACTCGAAAATCAGTTTTGTGATTTTTCCCCG
        196 TAGTCGCTTTAAAAATCATATCTTGAGTTTCAAAACTCGAAAATCAGTTCCGTAAATTTTCCCCG

                                        
       4999 AAACTAGACTCATATGCTCATCTACATA
        261 AAACTAGACTCATATGCTCATCTACATA

                                                                             
       5027 AAGTAATCACATAAAATGGCATGTATAGCTAGACACAACGCATTACGGTAGTCCTAGAATCGACT
          1 AAGTAATCACATAAAATGGCATGTATAGCTAGACACAACGCATTACGGTAGTCCTAGAATCGACT

                *                                             *   *          
       5092 AAACTGTAGCTCTGATACCAATCAAATGTAACACCCCGAACCCGAGACCGTCACTGGAGTCGAAC
         66 AAACCGTAGCTCTGATACCAATCAAATGTAACACCCCGAACCCGAGACCGACACCGGAGTCGAAC

                                                                             
       5157 ACGAGGTGTTAACAGACTTTAAACCACTTATAAAAAAATTTCCCAGACACTGCCAATCTGCGTAA
        131 ACGAGGTGTTAACAGACTTTAAACCACTTATAAAAAAATTTCCCAGACACTGCCAATCTGCGTAA

                                                     *                       
       5222 TAGTCGCTTTAAAAATCATATCTTGAG-TTCAGAAACTCG-GAATCCAGTTCCGTAAATTTTCCC
        196 TAGTCGCTTTAAAAATCATATCTTGAGTTTCA-AAACTCGAAAAT-CAGTTCCGTAAATTTTCCC

            *                
       5285 TGAAACTAGACTCATAT
        259 CGAAACTAGACTCATAT

       5302 AGCCATC


Statistics
Matches: 259,  Mismatches: 14, Indels: 4
        0.94            0.05        0.01

Matches are distributed among these distances:
 287    7  0.03
 288  252  0.97

ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25


Consensus pattern (288 bp):   
AAGTAATCACATAAAATGGCATGTATAGCTAGACACAACGCATTACGGTAGTCCTAGAATCGACT
AAACCGTAGCTCTGATACCAATCAAATGTAACACCCCGAACCCGAGACCGACACCGGAGTCGAAC
ACGAGGTGTTAACAGACTTTAAACCACTTATAAAAAAATTTCCCAGACACTGCCAATCTGCGTAA
TAGTCGCTTTAAAAATCATATCTTGAGTTTCAAAACTCGAAAATCAGTTCCGTAAATTTTCCCCG
AAACTAGACTCATATGCTCATCTACATA
Done.