Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1171

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: 44392
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31


Found at i:8111 original size:28 final size:28

Alignment explanation


    Indices: 8079--8148  Score: 99
    Period size: 28  Copynumber: 2.5  Consensus size: 28

       8069 ATAGTAAGTC

                                          
       8079 CGCACACTTAGTGCT-TA-ATAGTCAAACT
          1 CGCACACTTAGTGCTATACA-A-TCAAACT

                                  *     
       8107 CGCACACTTAGTGCTATACAATTAAACT
          1 CGCACACTTAGTGCTATACAATCAAACT

                          
       8135 CGCACACTTAGTGC
          1 CGCACACTTAGTGC

       8149 CAATCTCATT


Statistics
Matches: 39,  Mismatches: 1, Indels: 4
        0.89            0.02        0.09

Matches are distributed among these distances:
  28   35  0.90
  29    3  0.08
  30    1  0.03

ACGTcount: A:0.31, C:0.27, G:0.14, T:0.27


Consensus pattern (28 bp):   
CGCACACTTAGTGCTATACAATCAAACT

Found at i:29343 original size:28 final size:28

Alignment explanation


    Indices: 29312--29369  Score: 89
    Period size: 28  Copynumber: 2.1  Consensus size: 28

      29302 TAAATTGTAG

                  * *      *            
      29312 TTTAAATTGGTTTACGCCATATACGATT
          1 TTTAAACTAGTTTACACCATATACGATT

                                        
      29340 TTTAAACTAGTTTACACCATATACGATT
          1 TTTAAACTAGTTTACACCATATACGATT

              
      29368 TT
          1 TT

      29370 AAGGATAACG


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  28   27  1.00

ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43


Consensus pattern (28 bp):   
TTTAAACTAGTTTACACCATATACGATT

Found at i:34501 original size:29 final size:28

Alignment explanation


    Indices: 34435--34503  Score: 86
    Period size: 29  Copynumber: 2.4  Consensus size: 28

      34425 TATATTAAGT

                                        
      34435 CCGCACACTTAGTGCTACATAATCAAAC
          1 CCGCACACTTAGTGCTACATAATCAAAC

            *                      * *    
      34463 TCGCACACTTAGTGCTGTACA-ATTTAAAC
          1 CCGCACACTTAGTGC--TACATAATCAAAC

                        
      34492 CCGCACACTTAG
          1 CCGCACACTTAG

      34504 CGCCAATCTC


Statistics
Matches: 35,  Mismatches: 4, Indels: 3
        0.83            0.10        0.07

Matches are distributed among these distances:
  28   14  0.40
  29   17  0.49
  30    4  0.11

ACGTcount: A:0.32, C:0.30, G:0.13, T:0.25


Consensus pattern (28 bp):   
CCGCACACTTAGTGCTACATAATCAAAC

Found at i:42626 original size:28 final size:28

Alignment explanation


    Indices: 42563--42685  Score: 176
    Period size: 28  Copynumber: 4.4  Consensus size: 28

      42553 ATATTAAGTC

                    *                   
      42563 CGCACACTCAGTGCTATATAATC-AACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                                        
      42590 CGCACACTTAGTGCTATATAATCAAACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                            *           
      42618 CGCACACTTAGTGCTACATAATCAAACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                           *  *    *    *
      42646 CGCACACTTAGTGCTGTACAATTTAAACC
          1 CGCACACTTAGTGCTATATAA-TCAAACT

                       
      42675 CGCACACTTAG
          1 CGCACACTTAG

      42686 CGCCAATCTC


Statistics
Matches: 87,  Mismatches: 7, Indels: 2
        0.91            0.07        0.02

Matches are distributed among these distances:
  27   22  0.25
  28   49  0.56
  29   16  0.18

ACGTcount: A:0.33, C:0.28, G:0.12, T:0.26


Consensus pattern (28 bp):   
CGCACACTTAGTGCTATATAATCAAACT
Done.