Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2751

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: 31990
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.32


Found at i:18078 original size:26 final size:26

Alignment explanation


    Indices: 18048--18099  Score: 79
    Period size: 26  Copynumber: 2.0  Consensus size: 26

      18038 AATAGTAGTT

                                       
      18048 AAATGTTA-AATATATATGTTGTTATG
          1 AAATGTTAGAATATATAT-TTGTTATG

                        *             
      18074 AAATGTTAGAATTTATATTTGTTATG
          1 AAATGTTAGAATATATATTTGTTATG

      18100 GCCGAATATG


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  26   16  0.67
  27    8  0.33

ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48


Consensus pattern (26 bp):   
AAATGTTAGAATATATATTTGTTATG

Found at i:22601 original size:30 final size:30

Alignment explanation


    Indices: 22557--22645  Score: 101
    Period size: 30  Copynumber: 3.0  Consensus size: 30

      22547 CAAAGATAAC

                  *                       
      22557 AAGAAAGCC-GAATAAAGAAATCCAAGATA
          1 AAGAAACCCAGAATAAAGAAATCCAAGATA

            *                              
      22586 GAGAAACCCAGAATAAAGAAATCC-AGAATA
          1 AAGAAACCCAGAATAAAGAAATCCAAG-ATA

                * *    *         *        
      22616 AAGAGATCCAGGATAAAGAAACCCAAGATA
          1 AAGAAACCCAGAATAAAGAAATCCAAGATA

      22646 CGATACTATG


Statistics
Matches: 50,  Mismatches: 7, Indels: 5
        0.81            0.11        0.08

Matches are distributed among these distances:
  29    9  0.18
  30   39  0.78
  31    2  0.04

ACGTcount: A:0.56, C:0.16, G:0.18, T:0.10


Consensus pattern (30 bp):   
AAGAAACCCAGAATAAAGAAATCCAAGATA

Found at i:22605 original size:15 final size:15

Alignment explanation


    Indices: 22557--22636  Score: 92
    Period size: 15  Copynumber: 5.4  Consensus size: 15

      22547 CAAAGATAAC

                  *        
      22557 AAGAAAGCC-GAATA
          1 AAGAAATCCAGAATA

                            
      22571 AAGAAATCCA-AGATA
          1 AAGAAATCCAGA-ATA

            *     *        
      22586 GAGAAACCCAGAATA
          1 AAGAAATCCAGAATA

                           
      22601 AAGAAATCCAGAATA
          1 AAGAAATCCAGAATA

                *      *   
      22616 AAGAGATCCAGGATA
          1 AAGAAATCCAGAATA

                  
      22631 AAGAAA
          1 AAGAAA

      22637 CCCAAGATAC


Statistics
Matches: 55,  Mismatches: 8, Indels: 5
        0.81            0.12        0.07

Matches are distributed among these distances:
  14    9  0.16
  15   45  0.82
  16    1  0.02

ACGTcount: A:0.57, C:0.14, G:0.19, T:0.10


Consensus pattern (15 bp):   
AAGAAATCCAGAATA

Found at i:22645 original size:15 final size:15

Alignment explanation


    Indices: 22568--22645  Score: 79
    Period size: 15  Copynumber: 5.2  Consensus size: 15

      22558 AGAAAGCCGA

                           
      22568 ATAAAGAAATCCAAG
          1 ATAAAGAAATCCAAG

               *        *  
      22583 ATAGAGAAA-CCCAG
          1 ATAAAGAAATCCAAG

                            
      22597 AATAAAGAAATCC-AG
          1 -ATAAAGAAATCCAAG

                    *     * 
      22612 AATAAAGAGATCCAGG
          1 -ATAAAGAAATCCAAG

                     *     
      22628 ATAAAGAAACCCAAG
          1 ATAAAGAAATCCAAG

               
      22643 ATA
          1 ATA

      22646 CGATACTATG


Statistics
Matches: 52,  Mismatches: 8, Indels: 6
        0.79            0.12        0.09

Matches are distributed among these distances:
  14    4  0.08
  15   45  0.87
  16    3  0.06

ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12


Consensus pattern (15 bp):   
ATAAAGAAATCCAAG

Found at i:28058 original size:15 final size:15

Alignment explanation


    Indices: 28036--28112  Score: 79
    Period size: 15  Copynumber: 5.2  Consensus size: 15

      28026 AAGAAACCGA

                           
      28036 ATAAAGAAATCCAAG
          1 ATAAAGAAATCCAAG

               *           
      28051 ATAGAGAAA-CC-AG
          1 ATAAAGAAATCCAAG

                            
      28064 AATAAAGAAATCC-AG
          1 -ATAAAGAAATCCAAG

                    *     * 
      28079 AATAAAGAGATCCAGG
          1 -ATAAAGAAATCCAAG

                     *     
      28095 ATAAAGAAACCCAAG
          1 ATAAAGAAATCCAAG

               
      28110 ATA
          1 ATA

      28113 CGATACTATG


Statistics
Matches: 52,  Mismatches: 7, Indels: 6
        0.80            0.11        0.09

Matches are distributed among these distances:
  13    2  0.04
  14   10  0.19
  15   39  0.75
  16    1  0.02

ACGTcount: A:0.57, C:0.14, G:0.17, T:0.12


Consensus pattern (15 bp):   
ATAAAGAAATCCAAG

Found at i:28069 original size:29 final size:29

Alignment explanation


    Indices: 28026--28112  Score: 106
    Period size: 29  Copynumber: 3.0  Consensus size: 29

      28016 CAAAGATAAC

                                         
      28026 AAGAAACC-GAATAAAGAAATCCAAGATA
          1 AAGAAACCAGAATAAAGAAATCCAAGATA

            *                             
      28054 GAGAAACCAGAATAAAGAAATCC-AGAATA
          1 AAGAAACCAGAATAAAGAAATCCAAG-ATA

                  *    *         *        
      28083 AAGAGATCCAGGATAAAGAAACCCAAGATA
          1 AAGA-AACCAGAATAAAGAAATCCAAGATA

      28113 CGATACTATG


Statistics
Matches: 50,  Mismatches: 5, Indels: 6
        0.82            0.08        0.10

Matches are distributed among these distances:
  28    9  0.18
  29   20  0.40
  30   19  0.38
  31    2  0.04

ACGTcount: A:0.57, C:0.15, G:0.17, T:0.10


Consensus pattern (29 bp):   
AAGAAACCAGAATAAAGAAATCCAAGATA
Done.