Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold671

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: 11046
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32


Found at i:4008 original size:15 final size:15

Alignment explanation


    Indices: 3988--4022  Score: 70
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       3978 AAAAAGATAG

                           
       3988 AGAAATCCAGAATAA
          1 AGAAATCCAGAATAA

                           
       4003 AGAAATCCAGAATAA
          1 AGAAATCCAGAATAA

                 
       4018 AGAAA
          1 AGAAA

       4023 CCCAAGATAC


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

Matches are distributed among these distances:
  15   20  1.00

ACGTcount: A:0.63, C:0.11, G:0.14, T:0.11


Consensus pattern (15 bp):   
AGAAATCCAGAATAA

Found at i:7078 original size:93 final size:93

Alignment explanation


    Indices: 6966--7136  Score: 306
    Period size: 93  Copynumber: 1.8  Consensus size: 93

       6956 GCCCATAAGT

                                        * *                                  
       6966 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
          1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA

                                        
       7031 CGAGCTCGGATGCCTAGTTACATCTCTC
         66 CGAGCTCGGATGCCTAGTTACATCTCTC

                                   *                                         
       7059 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
          1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA

                *        
       7124 CGAGTTCGGATGC
         66 CGAGCTCGGATGC

       7137 TCAACCATCC


Statistics
Matches: 74,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  93   74  1.00

ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21


Consensus pattern (93 bp):   
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC

Found at i:7133 original size:46 final size:46

Alignment explanation


    Indices: 6958--7133  Score: 214
    Period size: 46  Copynumber: 3.8  Consensus size: 46

       6948 TGTAACCCGC

                                                * *       
       6958 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT

                                                    *        
       7004 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T

            *   ***                         *              
       7050 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
          1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT

                                           *     
       7097 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA

       7134 TGCTCAACCA


Statistics
Matches: 111,  Mismatches: 12, Indels: 14
        0.81            0.09        0.10

Matches are distributed among these distances:
  43    1  0.01
  44    3  0.03
  46   70  0.63
  47   32  0.29
  49    4  0.04
  50    1  0.01

ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21


Consensus pattern (46 bp):   
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT

Found at i:10816 original size:10 final size:10

Alignment explanation


    Indices: 10781--10825  Score: 54
    Period size: 10  Copynumber: 4.3  Consensus size: 10

      10771 ATTTTCAGCA

                      
      10781 ATTTTTATTG
          1 ATTTTTATTG

               *     *  
      10791 ATTCTTAGCGTG
          1 ATTTTTA--TTG

                      
      10803 ATTTTTATTG
          1 ATTTTTATTG

                      
      10813 ATTTTTATTG
          1 ATTTTTATTG

               
      10823 ATT
          1 ATT

      10826 CAGGCCAAAA


Statistics
Matches: 29,  Mismatches: 4, Indels: 4
        0.78            0.11        0.11

Matches are distributed among these distances:
  10   21  0.72
  12    8  0.28

ACGTcount: A:0.20, C:0.04, G:0.13, T:0.62


Consensus pattern (10 bp):   
ATTTTTATTG
Done.