Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold8239.1

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: 5378
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.24


Found at i:1485 original size:92 final size:92

Alignment explanation


    Indices: 1328--1510  Score: 357
    Period size: 92  Copynumber: 2.0  Consensus size: 92

       1318 ATTATCTGAG

                                                                             
       1328 GGGAGAGCTACATCAGGCTAAAGAACAGGTCAGAAAAAGGGATCATGTCATTGGTGAAGCCATAG
          1 GGGAGAGCTACATCAGGCTAAAGAACAGGTCAGAAAAAGGGATCATGTCATTGGTGAAGCCATAG

                        *              
       1393 CTCAGATTCGAGTGGTTGCTGAGTATA
         66 CTCAGATTCGAGAGGTTGCTGAGTATA

                                                                             
       1420 GGGAGAGCTACATCAGGCTAAAGAACAGGTCAGAAAAAGGGATCATGTCATTGGTGAAGCCATAG
          1 GGGAGAGCTACATCAGGCTAAAGAACAGGTCAGAAAAAGGGATCATGTCATTGGTGAAGCCATAG

                                      
       1485 CTCAGATTCGAGAGGTTGCTGAGTAT
         66 CTCAGATTCGAGAGGTTGCTGAGTAT

       1511 GTGCAAGACT


Statistics
Matches: 90,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  92   90  1.00

ACGTcount: A:0.33, C:0.15, G:0.31, T:0.21


Consensus pattern (92 bp):   
GGGAGAGCTACATCAGGCTAAAGAACAGGTCAGAAAAAGGGATCATGTCATTGGTGAAGCCATAG
CTCAGATTCGAGAGGTTGCTGAGTATA

Found at i:1829 original size:15 final size:15

Alignment explanation


    Indices: 1809--1839  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1799 TTTACTTTCC

                           
       1809 AGAGAGGTAGAAAAG
          1 AGAGAGGTAGAAAAG

                           
       1824 AGAGAGGTAGAAAAG
          1 AGAGAGGTAGAAAAG

             
       1839 A
          1 A

       1840 AAATCTGGAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.55, C:0.00, G:0.39, T:0.06


Consensus pattern (15 bp):   
AGAGAGGTAGAAAAG

Found at i:5242 original size:103 final size:104

Alignment explanation


    Indices: 5056--5269  Score: 412
    Period size: 103  Copynumber: 2.1  Consensus size: 104

       5046 TGATAAAGGA

                                                                             
       5056 AAGACATCAAGTTAATGCTGTACACAATGAAGGATCGGAGCAAGGAAGCCTCGAAGGCATTTGCC
          1 AAGACATCAAGTTAATGCTGTACACAATGAAGGATCGGAGCAAGGAAGCCTCGAAGGCATTTGCC

                                                   
       5121 CTCACGAACCGGGGAGCTCTCTGAATAATTAGACTGCGG
         66 CTCACGAACCGGGGAGCTCTCTGAATAATTAGACTGCGG

                                                                             
       5160 AAGACA-CAAGTTAATGCTGTACACAATGAAGGATCGGAGCAAGGAAGCCTCGAAGGCATTTGCC
          1 AAGACATCAAGTTAATGCTGTACACAATGAAGGATCGGAGCAAGGAAGCCTCGAAGGCATTTGCC

                                          *        
       5224 CTCACGAACCGGGGAGCTCTCTGAATAATTGGACTGCGG
         66 CTCACGAACCGGGGAGCTCTCTGAATAATTAGACTGCGG

                   
       5263 AAGACAT
          1 AAGACAT

       5270 TCCTGTAGTC


Statistics
Matches: 108,  Mismatches: 1, Indels: 2
        0.97            0.01        0.02

Matches are distributed among these distances:
 103  102  0.94
 104    6  0.06

ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19


Consensus pattern (104 bp):   
AAGACATCAAGTTAATGCTGTACACAATGAAGGATCGGAGCAAGGAAGCCTCGAAGGCATTTGCC
CTCACGAACCGGGGAGCTCTCTGAATAATTAGACTGCGG
Done.