Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold404

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: 9280
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31


Found at i:2270 original size:40 final size:41

Alignment explanation


    Indices: 2211--2362  Score: 211
    Period size: 40  Copynumber: 3.8  Consensus size: 41

       2201 CATTTGAATG

                          *             *   *        
       2211 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
          1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT

            *                                        
       2251 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
          1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT

                                                   * 
       2291 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
          1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT

               *     *               *      
       2331 ATACCCGGGTTAAGACCCGAAGGCAATTGTGC
          1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC

       2363 TTGTGGTTAT


Statistics
Matches: 102,  Mismatches: 8, Indels: 4
        0.89            0.07        0.04

Matches are distributed among these distances:
  40   99  0.97
  41    3  0.03

ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26


Consensus pattern (41 bp):   
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT

Found at i:2374 original size:80 final size:80

Alignment explanation


    Indices: 2211--2382  Score: 213
    Period size: 80  Copynumber: 2.2  Consensus size: 80

       2201 CATTTGAATG

                          *                 *     * *  *                     
       2211 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
          1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCA

            *          *   
       2276 TTTGTGCGAGTTGAT
         66 ATTGTGCGAGTGGAT

                                        *                     *              
       2291 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATACCCGGGTTAAGACCCGAAGGC
          1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAG-TGACTATACCCGGGCTAAGACCCGAAGGC

                    **    * 
       2355 AATTGTGCTTGTGGTT
         65 AATTGTGCGAGTGGAT

                         
       2371 ATATCC-GGCTAA
          1 ATATCCGGGCTAA

       2383 ATTCCGAAGA


Statistics
Matches: 79,  Mismatches: 12, Indels: 3
        0.84            0.13        0.03

Matches are distributed among these distances:
  79    6  0.08
  80   71  0.90
  81    2  0.03

ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27


Consensus pattern (80 bp):   
ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCA
ATTGTGCGAGTGGAT
Done.