Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1769

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: 12279
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30


Found at i:2145 original size:56 final size:55

Alignment explanation


    Indices: 2000--2148  Score: 194
    Period size: 56  Copynumber: 2.7  Consensus size: 55

       1990 ATATTAAGTC

                    *         *        *                           
       2000 CGCACACTCAGTGCTATATAATC-AACTCGCACACTTAGTGCTATATATCAAACT
          1 CGCACACTTAGTGCTATACAATCAAACCCGCACACTTAGTGCTATATATCAAACT

              *               *        *                            
       2054 CGTACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATATAATCAAACT
          1 CGCACACTTAGTGCTATACAATCAAACCCGCACACTTAGTGCTATAT-ATCAAACT

                           *       *                
       2110 CGCACACTTAGTGCTGTACAATTTAAACCCG-ACACTTAG
          1 CGCACACTTAGTGCTATACAA-TCAAACCCGCACACTTAG

       2149 CGCCAATCTC


Statistics
Matches: 85,  Mismatches: 7, Indels: 4
        0.89            0.07        0.04

Matches are distributed among these distances:
  54   21  0.25
  55   23  0.27
  56   34  0.40
  57    7  0.08

ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28


Consensus pattern (55 bp):   
CGCACACTTAGTGCTATACAATCAAACCCGCACACTTAGTGCTATATATCAAACT

Found at i:2148 original size:28 final size:28

Alignment explanation


    Indices: 2000--2124  Score: 218
    Period size: 28  Copynumber: 4.5  Consensus size: 28

       1990 ATATTAAGTC

                    *                   
       2000 CGCACACTCAGTGCTATATAATC-AACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                                        
       2027 CGCACACTTAGTGCTATAT-ATCAAACT
          1 CGCACACTTAGTGCTATATAATCAAACT

              *                         
       2054 CGTACACTTAGTGCTATATAATCAAACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                                        
       2082 CGCACACTTAGTGCTATATAATCAAACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                           
       2110 CGCACACTTAGTGCT
          1 CGCACACTTAGTGCT

       2125 GTACAATTTA


Statistics
Matches: 93,  Mismatches: 3, Indels: 3
        0.94            0.03        0.03

Matches are distributed among these distances:
  26    3  0.03
  27   40  0.43
  28   50  0.54

ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29


Consensus pattern (28 bp):   
CGCACACTTAGTGCTATATAATCAAACT

Found at i:10044 original size:28 final size:28

Alignment explanation


    Indices: 9981--10131  Score: 223
    Period size: 28  Copynumber: 5.4  Consensus size: 28

       9971 ATATTAAGTC

                    *                   
       9981 CGCACACTCAGTGCTATATAATC-AACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                                        
      10008 CGCACACTTAGTGCTATATAATCAAACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                            *           
      10036 CGCACACTTAGTGCTACATAATCAAACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                            *           
      10064 CGCACACTTAGTGCTACATAATCAAACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                           *  *    *    *
      10092 CGCACACTTAGTGCTGTACAATTTAAACC
          1 CGCACACTTAGTGCTATATAA-TCAAACT

                       
      10121 CGCACACTTAG
          1 CGCACACTTAG

      10132 CGCCAATCTC


Statistics
Matches: 115,  Mismatches: 7, Indels: 2
        0.93            0.06        0.02

Matches are distributed among these distances:
  27   22  0.19
  28   77  0.67
  29   16  0.14

ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26


Consensus pattern (28 bp):   
CGCACACTTAGTGCTATATAATCAAACT

Found at i:12235 original size:17 final size:17

Alignment explanation


    Indices: 12213--12245  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

      12203 AGCTGTCATA

                             
      12213 TGAATTAAATTAATTTT
          1 TGAATTAAATTAATTTT

                    *       
      12230 TGAATTAATTTAATTT
          1 TGAATTAAATTAATTT

      12246 GATAGTTAAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55


Consensus pattern (17 bp):   
TGAATTAAATTAATTTT
Done.