Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2588

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: 15156
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:679 original size:2 final size:2

Alignment explanation


    Indices: 672--704  Score: 59
    Period size: 2  Copynumber: 17.0  Consensus size: 2

        662 GAAAGAAATT

                                                              
        672 AG AG AG AG AG AG AG AG AG AG -G AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

        705 GCTGATGATA


Statistics
Matches: 30,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   29  0.97

ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00


Consensus pattern (2 bp):   
AG

Found at i:2952 original size:40 final size:40

Alignment explanation


    Indices: 2908--2984  Score: 102
    Period size: 40  Copynumber: 1.9  Consensus size: 40

       2898 TTAGTAATTT

                 *                                   
       2908 TTTTATTATATTT-AATTTAAAAATTATATATTTATATAAA
          1 TTTTAATATATTTAAATTTAAAAATTA-ATATTTATATAAA

                               *  *      *       
       2948 TTTTAATATATTTAAATTTTAATATTAATTTTTATAT
          1 TTTTAATATATTTAAATTTAAAAATTAATATTTATAT

       2985 TATATTCACA


Statistics
Matches: 32,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  40   21  0.66
  41   11  0.34

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58


Consensus pattern (40 bp):   
TTTTAATATATTTAAATTTAAAAATTAATATTTATATAAA

Found at i:3331 original size:5 final size:5

Alignment explanation


    Indices: 3321--3345  Score: 50
    Period size: 5  Copynumber: 5.0  Consensus size: 5

       3311 ATTTCATACT

                                         
       3321 ATAAA ATAAA ATAAA ATAAA ATAAA
          1 ATAAA ATAAA ATAAA ATAAA ATAAA

       3346 TTATTTTTAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   20  1.00

ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20


Consensus pattern (5 bp):   
ATAAA

Found at i:4066 original size:2 final size:2

Alignment explanation


    Indices: 4053--4100  Score: 87
    Period size: 2  Copynumber: 24.0  Consensus size: 2

       4043 TCCAAATAAC

                   *                                                      
       4053 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                    
       4095 AT AT AT
          1 AT AT AT

       4101 GCAAAAAAAA


Statistics
Matches: 44,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   2   44  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:4227 original size:3 final size:3

Alignment explanation


    Indices: 4219--4265  Score: 94
    Period size: 3  Copynumber: 15.7  Consensus size: 3

       4209 GAAGTCTATT

                                                                          
       4219 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
          1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA

       4266 GATGCTGTCT


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   44  1.00

ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00


Consensus pattern (3 bp):   
GAA

Found at i:8925 original size:99 final size:99

Alignment explanation


    Indices: 8715--8894  Score: 254
    Period size: 99  Copynumber: 1.8  Consensus size: 99

       8705 CTAGAATTCA

                     *                              *                  *     
       8715 CAAATGGCAAAACAGAAACCCATAAGCAATGCAGAATTATTAAAGACTGAAACAAAGTTGGACGA
          1 CAAATGGCACAACAGAAACCCATAAGCAATGCAGAATTATCAAAGACTGAAACAAAGTTAGACGA

                                           *  
       8780 CTAAATGGAGGTCCACCAGGTTCTGACGCTCCAG
         66 CTAAATGGAGGTCCACCAGGTTCTGACGCTCAAG

                *                *                              **         * 
       8814 CAAAAGGCACAACAGAAACCCCTAAGCAGA-GCAGAATTATCAAAGACTGAATTAAAGTTAGATG
          1 CAAATGGCACAACAGAAACCCATAAGCA-ATGCAGAATTATCAAAGACTGAAACAAAGTTAGACG

             *               
       8878 ATTAAATGGAGGTCCAC
         65 ACTAAATGGAGGTCCAC

       8895 TACAGTCTGT


Statistics
Matches: 71,  Mismatches: 9, Indels: 2
        0.87            0.11        0.02

Matches are distributed among these distances:
  99   70  0.99
 100    1  0.01

ACGTcount: A:0.42, C:0.20, G:0.21, T:0.17


Consensus pattern (99 bp):   
CAAATGGCACAACAGAAACCCATAAGCAATGCAGAATTATCAAAGACTGAAACAAAGTTAGACGA
CTAAATGGAGGTCCACCAGGTTCTGACGCTCAAG

Found at i:12596 original size:23 final size:24

Alignment explanation


    Indices: 12570--12615  Score: 58
    Period size: 23  Copynumber: 2.0  Consensus size: 24

      12560 AAATTTAATA

                                    
      12570 TAAATATTAATATAAA-AATATTT
          1 TAAATATTAATATAAACAATATTT

                 *   * *           
      12593 TAAATTTTATTTTAAACAATATT
          1 TAAATATTAATATAAACAATATT

      12616 GACTTATCTT


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  23   13  0.68
  24    6  0.32

ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48


Consensus pattern (24 bp):   
TAAATATTAATATAAACAATATTT
Done.