Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1668

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: 41203
ACGTcount: A:0.02, C:0.01, G:0.01, T:0.02

Warning! 39064 characters in sequence are not A, C, G, or T


Found at i:345 original size:125 final size:125

Alignment explanation


    Indices: 123--369  Score: 467
    Period size: 125  Copynumber: 2.0  Consensus size: 125

        113 CTTTTAACCT

                                                                             
        123 TAAATGAACCATAAACACCTTCATTGAACAAATATAACTCTTTGAATCAAGACGAACGAAACTTC
          1 TAAATGAACCATAAACACCTTCATTGAACAAATATAACTCTTTGAATCAAGACGAACGAAACTTC

                                                                        
        188 ATCATTAAGACGATCGGGCAACGAAAACGACTCGAATTCATCAACGAGGACGGGGTCGTA
         66 ATCATTAAGACGATCGGGCAACGAAAACGACTCGAATTCATCAACGAGGACGGGGTCGTA

                                                                             
        248 TAAATGAACCATAAACACCTTCATTGAACAAATATAACTCTTTGAATCAAGACGAACGAAACTTC
          1 TAAATGAACCATAAACACCTTCATTGAACAAATATAACTCTTTGAATCAAGACGAACGAAACTTC

               *                       *      *                      
        313 ATCGTTAAGACGATCGGGCAACGAAAATGACTCGGATTCATCAACGAGGACGGGGTC
         66 ATCATTAAGACGATCGGGCAACGAAAACGACTCGAATTCATCAACGAGGACGGGGTC

        370 ATATCATTTG


Statistics
Matches: 119,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 125  119  1.00

ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21


Consensus pattern (125 bp):   
TAAATGAACCATAAACACCTTCATTGAACAAATATAACTCTTTGAATCAAGACGAACGAAACTTC
ATCATTAAGACGATCGGGCAACGAAAACGACTCGAATTCATCAACGAGGACGGGGTCGTA

Found at i:463 original size:14 final size:13

Alignment explanation


    Indices: 440--466  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

        430 TAAGTAGATT

                         
        440 TTTGAAAAAAAAA
          1 TTTGAAAAAAAAA

                         
        453 TTTGAAAAAAAAA
          1 TTTGAAAAAAAAA

             
        466 T
          1 T

        467 CAAAAAAAAA


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:0.67, C:0.00, G:0.07, T:0.26


Consensus pattern (13 bp):   
TTTGAAAAAAAAA

Found at i:472 original size:12 final size:11

Alignment explanation


    Indices: 457--488  Score: 55
    Period size: 11  Copynumber: 2.8  Consensus size: 11

        447 AAAAAATTTG

                       
        457 AAAAAAAAATC
          1 AAAAAAAAATC

                       
        468 AAAAAAAAATC
          1 AAAAAAAAATC

                      
        479 AAAAGAAAAA
          1 AAAA-AAAAA

        489 AAATTGAAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  11   15  0.75
  12    5  0.25

ACGTcount: A:0.84, C:0.06, G:0.03, T:0.06


Consensus pattern (11 bp):   
AAAAAAAAATC

Found at i:508 original size:16 final size:16

Alignment explanation


    Indices: 468--510  Score: 68
    Period size: 16  Copynumber: 2.7  Consensus size: 16

        458 AAAAAAAATC

                    * *     
        468 AAAAAAAAATCAAAAG
          1 AAAAAAAATTGAAAAG

                            
        484 AAAAAAAATTGAAAAG
          1 AAAAAAAATTGAAAAG

                       
        500 AAAAAAAATTG
          1 AAAAAAAATTG

        511 TATACGGTCT


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   25  1.00

ACGTcount: A:0.77, C:0.02, G:0.09, T:0.12


Consensus pattern (16 bp):   
AAAAAAAATTGAAAAG
Done.