Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold605

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: 7767
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31


Found at i:285 original size:13 final size:13

Alignment explanation


    Indices: 267--314  Score: 53
    Period size: 13  Copynumber: 3.7  Consensus size: 13

        257 AAAATTTTAT

                         
        267 TTTCTTTTAAGAA
          1 TTTCTTTTAAGAA

                    * *  
        280 TTTCTTTTGATAA
          1 TTTCTTTTAAGAA

                *         
        293 TTTTATTTTAAGAA
          1 -TTTCTTTTAAGAA

                     
        307 -TTCTTTTA
          1 TTTCTTTTA

        315 TACATTTCGT


Statistics
Matches: 28,  Mismatches: 6, Indels: 3
        0.76            0.16        0.08

Matches are distributed among these distances:
  12    7  0.25
  13   11  0.39
  14   10  0.36

ACGTcount: A:0.27, C:0.06, G:0.06, T:0.60


Consensus pattern (13 bp):   
TTTCTTTTAAGAA

Found at i:308 original size:14 final size:14

Alignment explanation


    Indices: 265--308  Score: 54
    Period size: 14  Copynumber: 3.2  Consensus size: 14

        255 GAAAAATTTT

                          
        265 ATTTTCTTTTAAGA
          1 ATTTTCTTTTAAGA

                      * * 
        279 A-TTTCTTTTGATA
          1 ATTTTCTTTTAAGA

                 *        
        292 ATTTTATTTTAAGA
          1 ATTTTCTTTTAAGA

               
        306 ATT
          1 ATT

        309 CTTTTATACA


Statistics
Matches: 24,  Mismatches: 5, Indels: 2
        0.77            0.16        0.06

Matches are distributed among these distances:
  13   11  0.46
  14   13  0.54

ACGTcount: A:0.30, C:0.05, G:0.07, T:0.59


Consensus pattern (14 bp):   
ATTTTCTTTTAAGA

Found at i:321 original size:26 final size:27

Alignment explanation


    Indices: 265--321  Score: 82
    Period size: 27  Copynumber: 2.1  Consensus size: 27

        255 GAAAAATTTT

                 *                     
        265 ATTTTCTTTTAAGAATTTCTTTTGATA
          1 ATTTTATTTTAAGAATTTCTTTTGATA

                                       
        292 ATTTTATTTTAAGAA-TTCTTTT-ATA
          1 ATTTTATTTTAAGAATTTCTTTTGATA

                 
        317 CATTT
          1 -ATTT

        322 CGTTTTCATC


Statistics
Matches: 28,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  25    3  0.11
  26   11  0.39
  27   14  0.50

ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60


Consensus pattern (27 bp):   
ATTTTATTTTAAGAATTTCTTTTGATA

Found at i:327 original size:26 final size:26

Alignment explanation


    Indices: 267--327  Score: 72
    Period size: 26  Copynumber: 2.3  Consensus size: 26

        257 AAAATTTTAT

                                      
        267 TTTCTTTTAAGAATTTCTTTTGATAA
          1 TTTCTTTTAAGAATTTCTTTTGATAA

                *                       
        293 TTTTATTTTAAGAA-TTCTTTT-ATACA
          1 -TTTCTTTTAAGAATTTCTTTTGATA-A

                     
        319 TTTCGTTTT
          1 TTTC-TTTT

        328 CATCAATTTT


Statistics
Matches: 30,  Mismatches: 2, Indels: 5
        0.81            0.05        0.14

Matches are distributed among these distances:
  25    6  0.20
  26   12  0.40
  27   12  0.40

ACGTcount: A:0.25, C:0.08, G:0.07, T:0.61


Consensus pattern (26 bp):   
TTTCTTTTAAGAATTTCTTTTGATAA

Found at i:3783 original size:19 final size:19

Alignment explanation


    Indices: 3739--3794  Score: 85
    Period size: 19  Copynumber: 2.9  Consensus size: 19

       3729 CTGCCAGTTT

                              **
       3739 CATGTATCGATACAATTGTC
          1 CATGTATCGATACAA-TGAA

                               
       3759 CATGTATCGATACAATGAA
          1 CATGTATCGATACAATGAA

                             
       3778 CATGTATCGATACAATG
          1 CATGTATCGATACAATG

       3795 TATCGATACA


Statistics
Matches: 34,  Mismatches: 2, Indels: 1
        0.92            0.05        0.03

Matches are distributed among these distances:
  19   19  0.56
  20   15  0.44

ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30


Consensus pattern (19 bp):   
CATGTATCGATACAATGAA

Found at i:3797 original size:13 final size:13

Alignment explanation


    Indices: 3779--3805  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       3769 TACAATGAAC

                         
       3779 ATGTATCGATACA
          1 ATGTATCGATACA

                         
       3792 ATGTATCGATACA
          1 ATGTATCGATACA

             
       3805 A
          1 A

       3806 AGCAGCATGT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30


Consensus pattern (13 bp):   
ATGTATCGATACA

Found at i:3820 original size:33 final size:32

Alignment explanation


    Indices: 3760--3824  Score: 103
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       3750 ACAATTGTCC

                          *                 
       3760 ATGTATCGATACAATGAACATGTATCGATACA
          1 ATGTATCGATACAAAGAACATGTATCGATACA

                              *              
       3792 ATGTATCGATACAAAGCAGCATGTATCGATACA
          1 ATGTATCGATACAAAG-AACATGTATCGATACA

       3825 TCTGGGTGTG


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  32   15  0.50
  33   15  0.50

ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26


Consensus pattern (32 bp):   
ATGTATCGATACAAAGAACATGTATCGATACA
Done.