Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold975

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: 10369
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30


Found at i:2164 original size:28 final size:28

Alignment explanation


    Indices: 2101--2251  Score: 241
    Period size: 28  Copynumber: 5.4  Consensus size: 28

       2091 ATATTAAGTC

                    *                   
       2101 CGCACACTCAGTGCTATATAATC-AACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                                        
       2128 CGCACACTTAGTGCTATATAATCAAACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                                        
       2156 CGCACACTTAGTGCTATATAATCAAACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                                        
       2184 CGCACACTTAGTGCTATATAATCAAACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                           *  *    *    *
       2212 CGCACACTTAGTGCTGTACAATTTAAACC
          1 CGCACACTTAGTGCTATATAA-TCAAACT

                       
       2241 CGCACACTTAG
          1 CGCACACTTAG

       2252 CGCCAATCTC


Statistics
Matches: 117,  Mismatches: 5, Indels: 2
        0.94            0.04        0.02

Matches are distributed among these distances:
  27   22  0.19
  28   79  0.68
  29   16  0.14

ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27


Consensus pattern (28 bp):   
CGCACACTTAGTGCTATATAATCAAACT

Found at i:10110 original size:28 final size:28

Alignment explanation


    Indices: 10077--10199  Score: 185
    Period size: 28  Copynumber: 4.4  Consensus size: 28

      10067 ATATTAAGTC

                    *                   
      10077 CGCACACTCAGTGCTATATAATCAAACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                                        
      10105 CGCACACTTAGTGCTATATAATC-AACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                                        
      10132 CGCACACTTAGTGCTATATAATCAAACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                           *  *    *    *
      10160 CGCACACTTAGTGCTGTACAATTTAAACC
          1 CGCACACTTAGTGCTATATAA-TCAAACT

                       
      10189 CGCACACTTAG
          1 CGCACACTTAG

      10200 CGCCAATCTC


Statistics
Matches: 88,  Mismatches: 5, Indels: 3
        0.92            0.05        0.03

Matches are distributed among these distances:
  27   27  0.31
  28   45  0.51
  29   16  0.18

ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27


Consensus pattern (28 bp):   
CGCACACTTAGTGCTATATAATCAAACT
Done.