Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold634

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: 12008
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.30


Found at i:1874 original size:18 final size:19

Alignment explanation


    Indices: 1851--1888  Score: 60
    Period size: 18  Copynumber: 2.1  Consensus size: 19

       1841 GGAAGCAAGT

                      *        
       1851 AATGATTGAAGA-AATCAG
          1 AATGATTGAAAAGAATCAG

                               
       1869 AATGATTGAAAAGAATCAG
          1 AATGATTGAAAAGAATCAG

             
       1888 A
          1 A

       1889 CCAGGAGTCT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18   11  0.61
  19    7  0.39

ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21


Consensus pattern (19 bp):   
AATGATTGAAAAGAATCAG

Found at i:4878 original size:81 final size:81

Alignment explanation


    Indices: 4724--4912  Score: 200
    Period size: 81  Copynumber: 2.3  Consensus size: 81

       4714 CCCACGAGTA

                         **                          *                 * *   
       4724 GTTATACCCCTTTATATGTTTGTATATCCGTATAATGAATATTGTGAGACAAAGAGAGCTCGCGA
          1 GTTATACCCCTTTGCATGTTTGTATATCCGTATAATGAATACTGTGAGACAAAGAGAGCCCACGA

                      ***   
       4789 AGGATTCCTGTGGGTG
         66 AGGATTCCTGCAAGTG

                   *                                      *  *     *       * 
       4805 GTTATACTCCTTTGCATGTTTGTATATCCGTATAAT-ATATACTGTTAGGCAAAGGGAGCCCATG
          1 GTTATACCCCTTTGCATGTTTGTATATCCGTATAATGA-ATACTGTGAGACAAAGAGAGCCCACG

             *  *            
       4869 AGGGGTTCCTGCAAGTG
         65 AAGGATTCCTGCAAGTG

                      * *      *       
       4886 GTTATACCCCGTGGCATGTATGTATAT
          1 GTTATACCCCTTTGCATGTTTGTATAT

       4913 TCATAGTGTT


Statistics
Matches: 88,  Mismatches: 19, Indels: 2
        0.81            0.17        0.02

Matches are distributed among these distances:
  80    1  0.01
  81   87  0.99

ACGTcount: A:0.25, C:0.16, G:0.24, T:0.34


Consensus pattern (81 bp):   
GTTATACCCCTTTGCATGTTTGTATATCCGTATAATGAATACTGTGAGACAAAGAGAGCCCACGA
AGGATTCCTGCAAGTG
Done.