Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2168

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: 9986
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29


Found at i:857 original size:1 final size:1

Alignment explanation


    Indices: 851--875  Score: 50
    Period size: 1  Copynumber: 25.0  Consensus size: 1

        841 TGCAGTGGAA

                                     
        851 TTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTT

        876 GGGGCAGGGA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   24  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:6767 original size:17 final size:15

Alignment explanation


    Indices: 6747--6786  Score: 55
    Period size: 17  Copynumber: 2.6  Consensus size: 15

       6737 TTAAAATGAG

                             
       6747 ATATATTATTATTATTT
          1 ATATATTATTA-TA-TT

                           
       6764 ATATATTATTATATT
          1 ATATATTATTATATT

                     
       6779 ATA-ATTAT
          1 ATATATTAT

       6787 ATAAAATGAG


Statistics
Matches: 23,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  14    5  0.22
  15    5  0.22
  16    2  0.09
  17   11  0.48

ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60


Consensus pattern (15 bp):   
ATATATTATTATATT

Found at i:7036 original size:18 final size:18

Alignment explanation


    Indices: 6998--7054  Score: 55
    Period size: 18  Copynumber: 3.2  Consensus size: 18

       6988 TTTCAAATAA

                   *           
       6998 TAATAAACT-AAATCAAAT
          1 TAATAAATTAAAATC-AAT

                        *      
       7016 TAACTAAATT-AGATCAAT
          1 TAA-TAAATTAAAATCAAT

                *             
       7034 TAATCAATTAAAATCAAT
          1 TAATAAATTAAAATCAAT

               
       7052 TAA
          1 TAA

       7055 AATTGACTTA


Statistics
Matches: 33,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  17    5  0.15
  18   19  0.58
  19    9  0.27

ACGTcount: A:0.56, C:0.11, G:0.02, T:0.32


Consensus pattern (18 bp):   
TAATAAATTAAAATCAAT
Done.