Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1614

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: 27536
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:4037 original size:6 final size:6

Alignment explanation


    Indices: 4026--4051  Score: 52
    Period size: 6  Copynumber: 4.3  Consensus size: 6

       4016 CTATATCTAC

                                          
       4026 CCCTGA CCCTGA CCCTGA CCCTGA CC
          1 CCCTGA CCCTGA CCCTGA CCCTGA CC

       4052 GACCCCTCTC


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   20  1.00

ACGTcount: A:0.15, C:0.54, G:0.15, T:0.15


Consensus pattern (6 bp):   
CCCTGA

Found at i:7387 original size:23 final size:23

Alignment explanation


    Indices: 7357--7405  Score: 82
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       7347 TTAAATTTGA

                                    
       7357 TTTATTAA-AATTAAAATTTTAAT
          1 TTTATTAATAA-TAAAATTTTAAT

                                   
       7380 TTTATTAATAATAAAATTTTAAT
          1 TTTATTAATAATAAAATTTTAAT

               
       7403 TTT
          1 TTT

       7406 TTATCATCTC


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

Matches are distributed among these distances:
  23   23  0.92
  24    2  0.08

ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55


Consensus pattern (23 bp):   
TTTATTAATAATAAAATTTTAAT

Found at i:9783 original size:3 final size:3

Alignment explanation


    Indices: 9775--9802  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

       9765 TATTAATCTC

                                                 
       9775 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A

       9803 AAAATAAAAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64


Consensus pattern (3 bp):   
ATT

Found at i:18547 original size:2 final size:2

Alignment explanation


    Indices: 18542--18589  Score: 96
    Period size: 2  Copynumber: 24.0  Consensus size: 2

      18532 GCATGCATGG

                                                                          
      18542 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                    
      18584 AT AT AT
          1 AT AT AT

      18590 GGGATAAGCC


Statistics
Matches: 46,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   46  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:18548 original size:24 final size:25

Alignment explanation


    Indices: 18503--18552  Score: 93
    Period size: 24  Copynumber: 2.0  Consensus size: 25

      18493 AAGATTAATA

                                     
      18503 AAATGCATGCATGGGATATATATAT
          1 AAATGCATGCATGGGATATATATAT

                                     
      18528 AAATGCATGCAT-GGATATATATAT
          1 AAATGCATGCATGGGATATATATAT

             
      18552 A
          1 A

      18553 TATATATATA


Statistics
Matches: 25,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24   13  0.52
  25   12  0.48

ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32


Consensus pattern (25 bp):   
AAATGCATGCATGGGATATATATAT

Found at i:20105 original size:17 final size:18

Alignment explanation


    Indices: 20072--20105  Score: 52
    Period size: 17  Copynumber: 1.9  Consensus size: 18

      20062 ATTTAAGATA

                        *     
      20072 AATTTATAAAAATTAAAC
          1 AATTTATAAAAAATAAAC

                             
      20090 AATTTA-AAAAAATAAA
          1 AATTTATAAAAAATAAA

      20106 AAATACTCAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    9  0.60
  18    6  0.40

ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29


Consensus pattern (18 bp):   
AATTTATAAAAAATAAAC
Done.