Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold6744.1

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: 10079
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30


Found at i:796 original size:24 final size:24

Alignment explanation


    Indices: 752--797  Score: 58
    Period size: 24  Copynumber: 1.9  Consensus size: 24

        742 GAAAGAGAGC

                            *       
        752 AAAAAGAGATCGAGATTGAAAAAG
          1 AAAAAGAGATCGAGATAGAAAAAG

                           *       
        776 AAAAAGAG-TGCGAGCTAGAAAA
          1 AAAAAGAGAT-CGAGATAGAAAA

        798 GCATATCGAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 2
        0.83            0.09        0.09

Matches are distributed among these distances:
  23    1  0.05
  24   18  0.95

ACGTcount: A:0.57, C:0.07, G:0.26, T:0.11


Consensus pattern (24 bp):   
AAAAAGAGATCGAGATAGAAAAAG

Found at i:1231 original size:19 final size:20

Alignment explanation


    Indices: 1191--1231  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 20

       1181 CCCATTTTTG

                 *               
       1191 ATTTGTTGGAATAAGCATTTA
          1 ATTTGCTGGAATAA-CATTTA

                                
       1212 ATTTGCTGGAATAA-ATTTA
          1 ATTTGCTGGAATAACATTTA

             
       1231 A
          1 A

       1232 ATAATATTTA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  19    6  0.32
  21   13  0.68

ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41


Consensus pattern (20 bp):   
ATTTGCTGGAATAACATTTA

Found at i:1554 original size:19 final size:19

Alignment explanation


    Indices: 1530--1569  Score: 53
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       1520 AGCTCCCATG

                               
       1530 TAGCTCCACACCAGCTCAT
          1 TAGCTCCACACCAGCTCAT

                  ***          
       1549 TAGCTCGGGACCAGCTCAT
          1 TAGCTCCACACCAGCTCAT

              
       1568 TA
          1 TA

       1570 TCAGCTCACG


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23


Consensus pattern (19 bp):   
TAGCTCCACACCAGCTCAT

Found at i:1826 original size:14 final size:14

Alignment explanation


    Indices: 1809--1848  Score: 53
    Period size: 14  Copynumber: 2.9  Consensus size: 14

       1799 CGAATGGAAT

                     *    
       1809 GGTAGGAACGAAAG
          1 GGTAGGAACAAAAG

                          
       1823 GGTAGGAACAAAAG
          1 GGTAGGAACAAAAG

             *  *       
       1837 GATATGAACAAA
          1 GGTAGGAACAAA

       1849 TTGGTCAGTT


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  14   23  1.00

ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10


Consensus pattern (14 bp):   
GGTAGGAACAAAAG

Found at i:7314 original size:15 final size:15

Alignment explanation


    Indices: 7294--7341  Score: 53
    Period size: 15  Copynumber: 3.3  Consensus size: 15

       7284 TCAAAGATGG

                           
       7294 GTTTATGGATATGAA
          1 GTTTATGGATATGAA

                   * *    *
       7309 GTTTATGTAGATG-G
          1 GTTTATGGATATGAA

                        *  
       7323 GTTTATGGATATAAA
          1 GTTTATGGATATGAA

                
       7338 GTTT
          1 GTTT

       7342 TTGTAGGTTT


Statistics
Matches: 25,  Mismatches: 7, Indels: 2
        0.74            0.21        0.06

Matches are distributed among these distances:
  14   10  0.40
  15   15  0.60

ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44


Consensus pattern (15 bp):   
GTTTATGGATATGAA

Found at i:7328 original size:14 final size:14

Alignment explanation


    Indices: 7288--7331  Score: 52
    Period size: 14  Copynumber: 3.1  Consensus size: 14

       7278 AAGGATTCAA

                          
       7288 AGATGGGTTTATGG
          1 AGATGGGTTTATGG

             *    *       *
       7302 ATATGAAGTTTATGT
          1 AGATG-GGTTTATGG

                          
       7317 AGATGGGTTTATGG
          1 AGATGGGTTTATGG

             
       7331 A
          1 A

       7332 TATAAAGTTT


Statistics
Matches: 23,  Mismatches: 6, Indels: 2
        0.74            0.19        0.06

Matches are distributed among these distances:
  14   12  0.52
  15   11  0.48

ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39


Consensus pattern (14 bp):   
AGATGGGTTTATGG

Found at i:7357 original size:29 final size:29

Alignment explanation


    Indices: 7288--7347  Score: 102
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       7278 AAGGATTCAA

                              *          
       7288 AGATGGGTTTATGGATATGAAGTTTATGT
          1 AGATGGGTTTATGGATATAAAGTTTATGT

                                     *   
       7317 AGATGGGTTTATGGATATAAAGTTTTTGT
          1 AGATGGGTTTATGGATATAAAGTTTATGT

              
       7346 AG
          1 AG

       7348 GTTTGGTTAT


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  29   29  1.00

ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42


Consensus pattern (29 bp):   
AGATGGGTTTATGGATATAAAGTTTATGT
Done.