Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold784

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: 9146
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36


Found at i:1990 original size:14 final size:14

Alignment explanation


    Indices: 1963--2003  Score: 50
    Period size: 14  Copynumber: 2.9  Consensus size: 14

       1953 ATATCCTTTC

                           
       1963 ATAAAAT-ATAAATA
          1 ATAAAATAAT-AATA

                           
       1977 ATAATAA-AATAATA
          1 ATAA-AATAATAATA

                         
       1991 ATAAAATAATAAT
          1 ATAAAATAATAAT

       2004 TAATTAATTA


Statistics
Matches: 24,  Mismatches: 0, Indels: 6
        0.80            0.00        0.20

Matches are distributed among these distances:
  13    2  0.08
  14   18  0.75
  15    4  0.17

ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29


Consensus pattern (14 bp):   
ATAAAATAATAATA

Found at i:2011 original size:11 final size:11

Alignment explanation


    Indices: 1963--2003  Score: 66
    Period size: 11  Copynumber: 3.7  Consensus size: 11

       1953 ATATCCTTTC

                        
       1963 ATAA-AATATAA
          1 ATAATAATA-AA

                       
       1974 ATAATAATAAA
          1 ATAATAATAAA

                       
       1985 ATAATAATAAA
          1 ATAATAATAAA

                    
       1996 ATAATAAT
          1 ATAATAAT

       2004 TAATTAATTA


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  11   25  0.86
  12    4  0.14

ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29


Consensus pattern (11 bp):   
ATAATAATAAA

Found at i:2011 original size:22 final size:23

Alignment explanation


    Indices: 1967--2019  Score: 65
    Period size: 22  Copynumber: 2.3  Consensus size: 23

       1957 CCTTTCATAA

                                    
       1967 AATATAAATAATAATAAAATAA-T
          1 AATA-AAATAATAATAAAATAATT

                          *  *     
       1990 AATAAAATAATAATTAATTAATT
          1 AATAAAATAATAATAAAATAATT

                    
       2013 AA-AAAAT
          1 AATAAAAT

       2020 TAATTTTGCA


Statistics
Matches: 27,  Mismatches: 2, Indels: 3
        0.84            0.06        0.09

Matches are distributed among these distances:
  22   20  0.74
  23    7  0.26

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (23 bp):   
AATAAAATAATAATAAAATAATT

Found at i:7695 original size:23 final size:24

Alignment explanation


    Indices: 7661--7719  Score: 70
    Period size: 23  Copynumber: 2.5  Consensus size: 24

       7651 TTATAGATAT

                           *        
       7661 TAAAAT-TTAATTTTTAAAT-TTA
          1 TAAAATATTAATTTTAAAATATTA

                                     
       7683 TAAAATATTAATTTTAAAATAATTA
          1 TAAAATATTAATTTTAAAAT-ATTA

              *          
       7708 TATAA-ATTAATT
          1 TAAAATATTAATT

       7720 AAATTTTTTT


Statistics
Matches: 32,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
  22    6  0.19
  23   12  0.38
  24    7  0.22
  25    7  0.22

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (24 bp):   
TAAAATATTAATTTTAAAATATTA

Found at i:8682 original size:2 final size:2

Alignment explanation


    Indices: 8675--8709  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       8665 AACCTCTTTA

                                                                
       8675 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
          1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T

       8710 ATAATGGTAT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51


Consensus pattern (2 bp):   
TG

Done.