Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3466

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: 24520
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38


Found at i:838 original size:27 final size:27

Alignment explanation


    Indices: 800--854  Score: 101
    Period size: 27  Copynumber: 2.0  Consensus size: 27

        790 ATATCGACCC

                                       
        800 ATTGGAGGGTTTGGCTTTGAATAAACA
          1 ATTGGAGGGTTTGGCTTTGAATAAACA

                          *            
        827 ATTGGAGGGTTTGGTTTTGAATAAACA
          1 ATTGGAGGGTTTGGCTTTGAATAAACA

             
        854 A
          1 A

        855 CACTTGGAAG


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27   27  1.00

ACGTcount: A:0.31, C:0.05, G:0.29, T:0.35


Consensus pattern (27 bp):   
ATTGGAGGGTTTGGCTTTGAATAAACA

Found at i:3795 original size:20 final size:19

Alignment explanation


    Indices: 3770--3829  Score: 65
    Period size: 20  Copynumber: 3.3  Consensus size: 19

       3760 CAATATATTT

                                
       3770 AAATTTAATCATTAAACTTG
          1 AAATTTAATCATT-AACTTG

                   *           
       3790 AAATTTAGT-A-T-ACTTG
          1 AAATTTAATCATTAACTTG

                                
       3806 -AATTTAATCATTGAACTTG
          1 AAATTTAATCATT-AACTTG

                 
       3825 AAATT
          1 AAATT

       3830 AGTATCATTC


Statistics
Matches: 33,  Mismatches: 2, Indels: 10
        0.73            0.04        0.22

Matches are distributed among these distances:
  15    7  0.21
  16    6  0.18
  17    1  0.03
  18    1  0.03
  19    6  0.18
  20   12  0.36

ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42


Consensus pattern (19 bp):   
AAATTTAATCATTAACTTG

Found at i:3825 original size:19 final size:18

Alignment explanation


    Indices: 3771--3826  Score: 55
    Period size: 19  Copynumber: 3.1  Consensus size: 18

       3761 AATATATTTA

                               
       3771 AATTTAATCATTAAACTTG
          1 AATTTAATCATT-AACTTG

                   *           
       3790 AAATTTAGT-A-T-ACTTG
          1 -AATTTAATCATTAACTTG

                               
       3806 AATTTAATCATTGAACTTG
          1 AATTTAATCATT-AACTTG

              
       3825 AA
          1 AA

       3827 ATTAGTATCA


Statistics
Matches: 30,  Mismatches: 2, Indels: 9
        0.73            0.05        0.22

Matches are distributed among these distances:
  15    7  0.23
  16    6  0.20
  17    1  0.03
  18    1  0.03
  19    8  0.27
  20    7  0.23

ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41


Consensus pattern (18 bp):   
AATTTAATCATTAACTTG

Found at i:21698 original size:16 final size:15

Alignment explanation


    Indices: 21670--21700  Score: 53
    Period size: 16  Copynumber: 2.0  Consensus size: 15

      21660 ATCAATAAGA

                           
      21670 GCACATAATATATAT
          1 GCACATAATATATAT

                            
      21685 GCACATATATATATAT
          1 GCACATA-ATATATAT

      21701 TATATTATAG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    7  0.47
  16    8  0.53

ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35


Consensus pattern (15 bp):   
GCACATAATATATAT
Done.