Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1165

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: 2537
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28


Found at i:921 original size:34 final size:30

Alignment explanation


    Indices: 878--1007  Score: 113
    Period size: 29  Copynumber: 4.2  Consensus size: 30

        868 GAAGAAAAAG

                                    *    *    
        878 AAAAATCAAAATCAAAGTCAAAATGAAAATGCAA
          1 AAAAATCAAAAT-AAA--CAAAATCAAAAAG-AA

                                          
        912 AAAAATCAAAATAAA-AAAA-CAAAAAGAA
          1 AAAAATCAAAATAAACAAAATCAAAAAGAA

                           *    *         
        940 AAAAATCAAAATAAAAAAAAACAAAAAG-A
          1 AAAAATCAAAATAAACAAAATCAAAAAGAA

                                    *    *    
        969 AAAAATCAAAATCAAGATCAAAATGAAAATGAGA
          1 AAAAATCAAAAT-AA-A-CAAAATCAAAAAGA-A

                 
       1003 AAAAA
          1 AAAAA

       1008 GAATGAAGAA


Statistics
Matches: 83,  Mismatches: 6, Indels: 14
        0.81            0.06        0.14

Matches are distributed among these distances:
  28   17  0.20
  29   22  0.27
  30   13  0.16
  31    1  0.01
  32    9  0.11
  33    3  0.04
  34   18  0.22

ACGTcount: A:0.74, C:0.08, G:0.07, T:0.11


Consensus pattern (30 bp):   
AAAAATCAAAATAAACAAAATCAAAAAGAA

Found at i:942 original size:29 final size:27

Alignment explanation


    Indices: 910--980  Score: 99
    Period size: 28  Copynumber: 2.5  Consensus size: 27

        900 ATGAAAATGC

                                        
        910 AAAAAAATCAAAATAAAAAAACAA-AAA
          1 AAAAAAATCAAAATAAAAAAA-AACAAA

                                         
        937 GAAAAAAATCAAAATAAAAAAAAACAAAA
          1 -AAAAAAATCAAAATAAAAAAAAAC-AAA

                           
        966 AGAAAAAATCAAAAT
          1 A-AAAAAATCAAAAT

        981 CAAGATCAAA


Statistics
Matches: 40,  Mismatches: 0, Indels: 5
        0.89            0.00        0.11

Matches are distributed among these distances:
  27    2  0.05
  28   22  0.55
  29   16  0.40

ACGTcount: A:0.82, C:0.07, G:0.03, T:0.08


Consensus pattern (27 bp):   
AAAAAAATCAAAATAAAAAAAAACAAA

Found at i:1025 original size:20 final size:19

Alignment explanation


    Indices: 990--1030  Score: 55
    Period size: 20  Copynumber: 2.1  Consensus size: 19

        980 TCAAGATCAA

                       *       
        990 AATGAAAATGAGAAAAAAG
          1 AATGAAAATGAAAAAAAAG

                             *  
       1009 AATGAAGAATGAAAAAAGAG
          1 AATGAA-AATGAAAAAAAAG

              
       1029 AA
          1 AA

       1031 ATCTAGATGA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  19    6  0.32
  20   13  0.68

ACGTcount: A:0.68, C:0.00, G:0.22, T:0.10


Consensus pattern (19 bp):   
AATGAAAATGAAAAAAAAG
Done.