Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold270

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: 28770
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33


Found at i:833 original size:30 final size:31

Alignment explanation


    Indices: 799--862  Score: 112
    Period size: 30  Copynumber: 2.1  Consensus size: 31

        789 TCCATATTTA

                                           
        799 TGGAAAGTCAAAGATATGGGTATC-AAATAT
          1 TGGAAAGTCAAAGATATGGGTATCGAAATAT

                                      *    
        829 TGGAAAGTCAAAGATATGGGTATCGAGATAT
          1 TGGAAAGTCAAAGATATGGGTATCGAAATAT

               
        860 TGG
          1 TGG

        863 CATAAGAAAT


Statistics
Matches: 32,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  30   24  0.75
  31    8  0.25

ACGTcount: A:0.39, C:0.06, G:0.28, T:0.27


Consensus pattern (31 bp):   
TGGAAAGTCAAAGATATGGGTATCGAAATAT

Found at i:839 original size:15 final size:16

Alignment explanation


    Indices: 797--847  Score: 61
    Period size: 15  Copynumber: 3.3  Consensus size: 16

        787 CATCCATATT

                            
        797 TATGGAAAGTCAAAGA
          1 TATGGAAAGTCAAAGA

                 **       * 
        813 TATGGGTA-TCAAATA
          1 TATGGAAAGTCAAAGA

                            
        828 T-TGGAAAGTCAAAGA
          1 TATGGAAAGTCAAAGA

                 
        843 TATGG
          1 TATGG

        848 GTATCGAGAT


Statistics
Matches: 27,  Mismatches: 6, Indels: 4
        0.73            0.16        0.11

Matches are distributed among these distances:
  14    4  0.15
  15   14  0.52
  16    9  0.33

ACGTcount: A:0.43, C:0.06, G:0.25, T:0.25


Consensus pattern (16 bp):   
TATGGAAAGTCAAAGA

Found at i:4281 original size:18 final size:18

Alignment explanation


    Indices: 4250--4289  Score: 57
    Period size: 18  Copynumber: 2.3  Consensus size: 18

       4240 ATAAAGTTCT

                              
       4250 TAAATATATAAAGGTATA
          1 TAAATATATAAAGGTATA

                               
       4268 TAAATCATAT-AAGGTATA
          1 TAAAT-ATATAAAGGTATA

                 
       4286 -AAAT
          1 TAAAT

       4290 GTAGTAATAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  17    4  0.19
  18   13  0.62
  19    4  0.19

ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33


Consensus pattern (18 bp):   
TAAATATATAAAGGTATA

Found at i:7838 original size:25 final size:25

Alignment explanation


    Indices: 7801--7851  Score: 84
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       7791 ATATTTATGG

                    *                
       7801 AAAGTCAATGATATGGGAATCAAAT
          1 AAAGTCAAAGATATGGGAATCAAAT

                             *       
       7826 AAAGTCAAAGATATGGGTATCAAAT
          1 AAAGTCAAAGATATGGGAATCAAAT

             
       7851 A
          1 A

       7852 TAGGAAAGTC


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  25   24  1.00

ACGTcount: A:0.49, C:0.08, G:0.20, T:0.24


Consensus pattern (25 bp):   
AAAGTCAAAGATATGGGAATCAAAT

Found at i:7862 original size:30 final size:27

Alignment explanation


    Indices: 7797--7876  Score: 101
    Period size: 30  Copynumber: 2.9  Consensus size: 27

       7787 ATTCATATTT

                        *        *     
       7797 ATGGAAAGTCAATGATATGGGAATCAA
          1 ATGGAAAGTCAAAGATATGGGTATCAA

                                        
       7824 AT--AAAGTCAAAGATATGGGTATCAAA
          1 ATGGAAAGTCAAAGATATGGGTATC-AA

                                       
       7850 TATAGGAAAGTCAAAGATATGGGTATC
          1 -AT-GGAAAGTCAAAGATATGGGTATC

       7877 GAGATATTGG


Statistics
Matches: 46,  Mismatches: 2, Indels: 7
        0.84            0.04        0.13

Matches are distributed among these distances:
  25   19  0.41
  26    2  0.04
  27    4  0.09
  30   21  0.46

ACGTcount: A:0.45, C:0.07, G:0.24, T:0.24


Consensus pattern (27 bp):   
ATGGAAAGTCAAAGATATGGGTATCAA

Found at i:8038 original size:2 final size:2

Alignment explanation


    Indices: 8031--8069  Score: 69
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       8021 AAGGCATTTT

                            *                                         
       8031 TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T

       8070 TTATAAATTC


Statistics
Matches: 35,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54


Consensus pattern (2 bp):   
TC

Found at i:19196 original size:29 final size:30

Alignment explanation


    Indices: 19140--19197  Score: 73
    Period size: 29  Copynumber: 2.0  Consensus size: 30

      19130 CGTTTGGCTG

                          **     * *      
      19140 GAAAAAGTTTAAAATTAATTTTAGAAAAAT
          1 GAAAAAGTTTAAAAGAAATTTAAAAAAAAT

                                         
      19170 GAAAAAG-TTAAAAGAAATTTAAAAAAAA
          1 GAAAAAGTTTAAAAGAAATTTAAAAAAAA

      19198 AGTGATTTTT


Statistics
Matches: 24,  Mismatches: 4, Indels: 1
        0.83            0.14        0.03

Matches are distributed among these distances:
  29   17  0.71
  30    7  0.29

ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26


Consensus pattern (30 bp):   
GAAAAAGTTTAAAAGAAATTTAAAAAAAAT
Done.