Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1640

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: 166584
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


File 2 of 2

Found at i:163902 original size:32 final size:32

Alignment explanation


    Indices: 163861--163932  Score: 126
    Period size: 32  Copynumber: 2.2  Consensus size: 32

     163851 ACAAACAGTA

                               *       *    
     163861 AATGTATCGATACATAAGTTTTGTATCGATAC
          1 AATGTATCGATACATAAGTGTTGTATCAATAC

                                            
     163893 AATGTATCGATACATAAGTGTTGTATCAATAC
          1 AATGTATCGATACATAAGTGTTGTATCAATAC

                    
     163925 AATGTATC
          1 AATGTATC

     163933 ACTACAAAGC


Statistics
Matches: 38,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  32   38  1.00

ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36


Consensus pattern (32 bp):   
AATGTATCGATACATAAGTGTTGTATCAATAC

Found at i:163980 original size:20 final size:20

Alignment explanation


    Indices: 163955--164019  Score: 81
    Period size: 20  Copynumber: 3.6  Consensus size: 20

     163945 CTGCCAAGGA

                                
     163955 AATGTATCGATACATTACTC
          1 AATGTATCGATACATTACTC

                                
     163975 AATGTATCGAT--A-TA-T-
          1 AATGTATCGATACATTACTC

                                
     163990 --TGTATCGATACATTACTC
          1 AATGTATCGATACATTACTC

                        
     164008 AATGTATCGATA
          1 AATGTATCGATA

     164020 TATTGTATCG


Statistics
Matches: 38,  Mismatches: 0, Indels: 14
        0.73            0.00        0.27

Matches are distributed among these distances:
  13    9  0.24
  15    1  0.03
  16    3  0.08
  17    3  0.08
  18    1  0.03
  20   21  0.55

ACGTcount: A:0.35, C:0.15, G:0.12, T:0.37


Consensus pattern (20 bp):   
AATGTATCGATACATTACTC

Found at i:163995 original size:13 final size:13

Alignment explanation


    Indices: 163977--164037  Score: 50
    Period size: 13  Copynumber: 4.2  Consensus size: 13

     163967 CATTACTCAA

                         
     163977 TGTATCGATATAT
          1 TGTATCGATATAT

                             
     163990 TGTATCGATACATTACT
          1 TGTATCGAT--A-TA-T

                            
     164007 CAATGTATCGATATAT
          1 ---TGTATCGATATAT

                      *  
     164023 TGTATCGATACAT
          1 TGTATCGATATAT

              
     164036 TG
          1 TG

     164038 ATCTTTGTAT


Statistics
Matches: 40,  Mismatches: 1, Indels: 14
        0.73            0.02        0.25

Matches are distributed among these distances:
  13   23  0.57
  15    1  0.03
  16    3  0.08
  17    3  0.08
  18    1  0.03
  20    9  0.22

ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41


Consensus pattern (13 bp):   
TGTATCGATATAT

Found at i:164052 original size:33 final size:33

Alignment explanation


    Indices: 163957--164036  Score: 160
    Period size: 33  Copynumber: 2.4  Consensus size: 33

     163947 GCCAAGGAAA

                                             
     163957 TGTATCGATACATTACTCAATGTATCGATATAT
          1 TGTATCGATACATTACTCAATGTATCGATATAT

                                             
     163990 TGTATCGATACATTACTCAATGTATCGATATAT
          1 TGTATCGATACATTACTCAATGTATCGATATAT

                          
     164023 TGTATCGATACATT
          1 TGTATCGATACATT

     164037 GATCTTTGTA


Statistics
Matches: 47,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  33   47  1.00

ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40


Consensus pattern (33 bp):   
TGTATCGATACATTACTCAATGTATCGATATAT

Done.