Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1497

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: 22098
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31


Found at i:2009 original size:51 final size:49

Alignment explanation


    Indices: 1933--2033  Score: 166
    Period size: 51  Copynumber: 2.0  Consensus size: 49

       1923 TTAGAAGTGC

                                                               
       1933 ATGCATGATTTATTGGTCACCAGATACGGATAGAGTCCGTAGGACTTGCTA
          1 ATGCATGATTTATTGGTCACCAGATACGGAT--AGTCCGTAGGACTTGCTA

                           *                   *             
       1984 ATGCATGATTTATTGTTCACCAGATACGGATAGTCTGTAGGACTTGCTA
          1 ATGCATGATTTATTGGTCACCAGATACGGATAGTCCGTAGGACTTGCTA

             
       2033 A
          1 A

       2034 CTGATATTTG


Statistics
Matches: 48,  Mismatches: 2, Indels: 2
        0.92            0.04        0.04

Matches are distributed among these distances:
  49   18  0.38
  51   30  0.62

ACGTcount: A:0.28, C:0.17, G:0.24, T:0.32


Consensus pattern (49 bp):   
ATGCATGATTTATTGGTCACCAGATACGGATAGTCCGTAGGACTTGCTA

Found at i:10063 original size:11 final size:12

Alignment explanation


    Indices: 10049--10082  Score: 52
    Period size: 12  Copynumber: 2.8  Consensus size: 12

      10039 TTTAACTTTT

                        
      10049 AAAAAATTATTA
          1 AAAAAATTATTA

                         
      10061 AAATAAATT-TTA
          1 AAA-AAATTATTA

                      
      10073 AAAAAATTAT
          1 AAAAAATTAT

      10083 GTTTAAAAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 4
        0.83            0.00        0.17

Matches are distributed among these distances:
  11    5  0.25
  12   10  0.50
  13    5  0.25

ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35


Consensus pattern (12 bp):   
AAAAAATTATTA

Found at i:13056 original size:5 final size:5

Alignment explanation


    Indices: 13043--13072  Score: 51
    Period size: 5  Copynumber: 6.0  Consensus size: 5

      13033 TAGTGTACAG

                *                              
      13043 ACAAC ACAAT ACAAT ACAAT ACAAT ACAAT
          1 ACAAT ACAAT ACAAT ACAAT ACAAT ACAAT

      13073 TGCCCCCAGC


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   5   24  1.00

ACGTcount: A:0.60, C:0.23, G:0.00, T:0.17


Consensus pattern (5 bp):   
ACAAT

Found at i:20599 original size:32 final size:34

Alignment explanation


    Indices: 20539--20604  Score: 118
    Period size: 32  Copynumber: 2.0  Consensus size: 34

      20529 CCAAATGATA

                                              
      20539 AGTGTTAAAAGTTAACATACTTTAGTCTCATTCT
          1 AGTGTTAAAAGTTAACATACTTTAGTCTCATTCT

                                              
      20573 AGTGTTAAAAG-TAACAT-CTTTAGTCTCATTCT
          1 AGTGTTAAAAGTTAACATACTTTAGTCTCATTCT

      20605 TAATGCATCT


Statistics
Matches: 32,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  32   15  0.47
  33    6  0.19
  34   11  0.34

ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41


Consensus pattern (34 bp):   
AGTGTTAAAAGTTAACATACTTTAGTCTCATTCT
Done.