Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold633

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: 15283
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32

Warning! 144 characters in sequence are not A, C, G, or T


Found at i:467 original size:22 final size:22

Alignment explanation


    Indices: 442--496  Score: 58
    Period size: 22  Copynumber: 2.5  Consensus size: 22

        432 ATTATATGTA

                  *      *        
        442 TTAATTCATAATATAATTTAAT
          1 TTAATTAATAATACAATTTAAT

                  *     *         
        464 TTAATTTAT-ATCCAATTTAAT
          1 TTAATTAATAATACAATTTAAT

                        
        485 TTGAATTAATAA
          1 TT-AATTAATAA

        497 ATTATTATTA


Statistics
Matches: 27,  Mismatches: 4, Indels: 3
        0.79            0.12        0.09

Matches are distributed among these distances:
  21   12  0.44
  22   14  0.52
  23    1  0.04

ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49


Consensus pattern (22 bp):   
TTAATTAATAATACAATTTAAT

Found at i:1938 original size:13 final size:13

Alignment explanation


    Indices: 1920--1949  Score: 60
    Period size: 13  Copynumber: 2.3  Consensus size: 13

       1910 TATTTCAGGT

                         
       1920 GTTTTGCATTTTG
          1 GTTTTGCATTTTG

                         
       1933 GTTTTGCATTTTG
          1 GTTTTGCATTTTG

                
       1946 GTTT
          1 GTTT

       1950 ATTTTTTGAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.07, C:0.07, G:0.23, T:0.63


Consensus pattern (13 bp):   
GTTTTGCATTTTG

Found at i:5943 original size:19 final size:19

Alignment explanation


    Indices: 5921--5958  Score: 51
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       5911 TCAATCATCC

                                
       5921 CTCATCCCATCA-TCTCTCA
          1 CTCAT-CCATCATTCTCTCA

                 *             
       5940 CTCATTCATCATTCTCTCA
          1 CTCATCCATCATTCTCTCA

       5959 AATCTTTTAG


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  18    5  0.29
  19   12  0.71

ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37


Consensus pattern (19 bp):   
CTCATCCATCATTCTCTCA

Found at i:12589 original size:3 final size:3

Alignment explanation


    Indices: 12581--12609  Score: 58
    Period size: 3  Copynumber: 9.7  Consensus size: 3

      12571 TTCATGCTTA

                                                  
      12581 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
          1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA

      12610 AGAAAAAAAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   26  1.00

ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00


Consensus pattern (3 bp):   
AAC

Found at i:13525 original size:14 final size:14

Alignment explanation


    Indices: 13506--13533  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

      13496 TAAATTTATA

                          
      13506 TTTAATATTTCATT
          1 TTTAATATTTCATT

                          
      13520 TTTAATATTTCATT
          1 TTTAATATTTCATT

      13534 AATAAATTAG


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64


Consensus pattern (14 bp):   
TTTAATATTTCATT
Done.