Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold580

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: 7600
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31


Found at i:1964 original size:40 final size:40

Alignment explanation


    Indices: 1890--2111  Score: 340
    Period size: 40  Copynumber: 5.6  Consensus size: 40

       1880 AACCCAAGTA

                     *               *     *         
       1890 CCTTCGGGATTTAG-CCGGATAT-AGCAACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAATCAA-TAGCACAAATG

                    *               *             * 
       1929 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAAAG
          1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG

                                        *           
       1969 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG

                                                    
       2009 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG

                                        *     *     
       2049 CCTTCGGGACTTAGCCCGGATATAATCACTAGCATAAATG
          1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG

                                   
       2089 CCTTCGGGACTTAGCCCGGATAT
          1 CCTTCGGGACTTAGCCCGGATAT

       2112 CATTCGAATA


Statistics
Matches: 168,  Mismatches: 13, Indels: 3
        0.91            0.07        0.02

Matches are distributed among these distances:
  39   12  0.07
  40  153  0.91
  41    3  0.02

ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23


Consensus pattern (40 bp):   
CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG

Done.