Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1250

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: 2268
ACGTcount: A:0.04, C:0.07, G:0.04, T:0.08

Warning! 1749 characters in sequence are not A, C, G, or T


Found at i:83 original size:52 final size:52

Alignment explanation


    Indices: 27--225  Score: 305
    Period size: 52  Copynumber: 3.8  Consensus size: 52

         17 GCCCAAACCG

                                                  *              
         27 ACTTCCGGTACGTC-CGCCCTTCATTTCCGGTCGATACGGCACGCCACGGTCC
          1 ACTTCCGGTACGTCGC-CCCTTCATTTCCGGTCGATACCGCACGCCACGGTCC

                                                                 
         79 ACTTCCGGTACGTCGCCCCTTCATTTCCGGTCGATACCGCAC-CCTACGGTCC
          1 ACTTCCGGTACGTCGCCCCTTCATTTCCGGTCGATACCGCACGCC-ACGGTCC

                          *               *             *       *
        131 ACTTCCGGTACGTCCCCCCTTCATTTCCGGCCGATACCGCACGCTA-GAGTCG
          1 ACTTCCGGTACGTCGCCCCTTCATTTCCGGTCGATACCGCACGCCACG-GTCC

                                                       
        183 ACTTCCGGTACGTCGCCCCTTCATTTCCGGTCGATACCGCACG
          1 ACTTCCGGTACGTCGCCCCTTCATTTCCGGTCGATACCGCACG

        226 TCTTGACGTC


Statistics
Matches: 136,  Mismatches: 7, Indels: 8
        0.90            0.05        0.05

Matches are distributed among these distances:
  51    3  0.02
  52  131  0.96
  53    2  0.01

ACGTcount: A:0.14, C:0.41, G:0.21, T:0.24


Consensus pattern (52 bp):   
ACTTCCGGTACGTCGCCCCTTCATTTCCGGTCGATACCGCACGCCACGGTCC

Found at i:321 original size:18 final size:18

Alignment explanation


    Indices: 229--346  Score: 98
    Period size: 18  Copynumber: 6.6  Consensus size: 18

        219 CCGCACGTCT

                            *  
        229 TGACGTCACGTACGC-CGA
          1 TGACGTCACGTAC-CTTGA

                          *   
        247 TGACGTCACGTACCGTGA
          1 TGACGTCACGTACCTTGA

                       **      
        265 TGACGTCACGCGCCCTT-A
          1 TGACGTCACG-TACCTTGA

                       **      
        283 TGACGTCACGCGCCCTT-A
          1 TGACGTCACG-TACCTTGA

                         *    
        301 TGACGTCACGTACTTTGA
          1 TGACGTCACGTACCTTGA

                      * **    
        319 TGACGTCACGCATTTTGA
          1 TGACGTCACGTACCTTGA

                      
        337 TGACGTCACG
          1 TGACGTCACG

        347 NNNNNNNNNN


Statistics
Matches: 88,  Mismatches: 9, Indels: 6
        0.85            0.09        0.06

Matches are distributed among these distances:
  17    4  0.05
  18   81  0.92
  19    3  0.03

ACGTcount: A:0.20, C:0.31, G:0.25, T:0.25


Consensus pattern (18 bp):   
TGACGTCACGTACCTTGA

Found at i:2102 original size:1 final size:1

Alignment explanation


    Indices: 2096--2158  Score: 117
    Period size: 1  Copynumber: 63.0  Consensus size: 1

       2086 NNNNNNNNNN

                                                                *          
       2096 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

       2159 CCTCGCACCA


Statistics
Matches: 60,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
   1   60  1.00

ACGTcount: A:0.02, C:0.00, G:0.00, T:0.98


Consensus pattern (1 bp):   
T

Done.