Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1074

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: 2949
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25


Found at i:80 original size:31 final size:31

Alignment explanation


    Indices: 45--178  Score: 216
    Period size: 31  Copynumber: 4.3  Consensus size: 31

         35 ACCCCTAATG

                                           
         45 TGGGATATCCCAAACCGGGATAAGCGCAGAA
          1 TGGGATATCCCAAACCGGGATAAGCGCAGAA

                        *                  
         76 TGGGATATCCCAGACCGGGATAAGCGCAGAA
          1 TGGGATATCCCAAACCGGGATAAGCGCAGAA

                        *                  
        107 TGGGATATCCCAGACCGGGATAAGCGCAGAA
          1 TGGGATATCCCAAACCGGGATAAGCGCAGAA

                          * *               
        138 TGGGATATCCTC-ATCAGGGATAAGCGCAGAA
          1 TGGGATATCC-CAAACCGGGATAAGCGCAGAA

                      
        169 TGGGATATCC
          1 TGGGATATCC

        179 GGCCCGGGCT


Statistics
Matches: 98,  Mismatches: 4, Indels: 2
        0.94            0.04        0.02

Matches are distributed among these distances:
  31   97  0.99
  32    1  0.01

ACGTcount: A:0.32, C:0.22, G:0.31, T:0.16


Consensus pattern (31 bp):   
TGGGATATCCCAAACCGGGATAAGCGCAGAA

Found at i:82 original size:16 final size:16

Alignment explanation


    Indices: 61--175  Score: 92
    Period size: 16  Copynumber: 7.4  Consensus size: 16

         51 ATCCCAAACC

                            
         61 GGGATAAGCGCAGAAT
          1 GGGATAAGCGCAGAAT

                   * *    **
         77 GGGAT-ATCCCAGACC
          1 GGGATAAGCGCAGAAT

                            
         92 GGGATAAGCGCAGAAT
          1 GGGATAAGCGCAGAAT

                   * *    **
        108 GGGAT-ATCCCAGACC
          1 GGGATAAGCGCAGAAT

                            
        123 GGGATAAGCGCAGAAT
          1 GGGATAAGCGCAGAAT

                  ** *  **  
        139 GGGATATCCTCATCA-
          1 GGGATAAGCGCAGAAT

                            
        154 GGGATAAGCGCAGAAT
          1 GGGATAAGCGCAGAAT

                  
        170 GGGATA
          1 GGGATA

        176 TCCGGCCCGG


Statistics
Matches: 70,  Mismatches: 26, Indels: 6
        0.69            0.25        0.06

Matches are distributed among these distances:
  15   32  0.46
  16   38  0.54

ACGTcount: A:0.33, C:0.19, G:0.33, T:0.15


Consensus pattern (16 bp):   
GGGATAAGCGCAGAAT

Found at i:216 original size:21 final size:21

Alignment explanation


    Indices: 192--259  Score: 109
    Period size: 21  Copynumber: 3.2  Consensus size: 21

        182 CCGGGCTCAT

                  * *            
        192 AAAACAACAGAACCGGTCACC
          1 AAAACAGCCGAACCGGTCACC

                                 
        213 AAAACAGCCGAACCGGTCACC
          1 AAAACAGCCGAACCGGTCACC

                                 
        234 AAAACAGCCGAACCGGTCACC
          1 AAAACAGCCGAACCGGTCACC

                 
        255 TAAAA
          1 -AAAA

        260 TTCTGAACCG


Statistics
Matches: 44,  Mismatches: 2, Indels: 1
        0.94            0.04        0.02

Matches are distributed among these distances:
  21   40  0.91
  22    4  0.09

ACGTcount: A:0.44, C:0.34, G:0.16, T:0.06


Consensus pattern (21 bp):   
AAAACAGCCGAACCGGTCACC
Done.