Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold8125.1

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: 5520
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28


Found at i:2899 original size:183 final size:183

Alignment explanation


    Indices: 2591--2957  Score: 698
    Period size: 183  Copynumber: 2.0  Consensus size: 183

       2581 TACCACATGA

                                                                      *      
       2591 CCCAAGAAGCTAACCTCTCTTAACCAGAACTCACACTTACTGAACTTAGCATATAACTGCTTATC
          1 CCCAAGAAGCTAACCTCTCTTAACCAGAACTCACACTTACTGAACTTAGCATATAACTACTTATC

                                *                                            
       2656 CCGCAAAATTTGCAACACTAGCCTCAGATGCTCAGCATGTTCGGTCTCATCTCTTGAATAGACCA
         66 CCGCAAAATTTGCAACACTAACCTCAGATGCTCAGCATGTTCGGTCTCATCTCTTGAATAGACCA

                                                                 
       2721 AGATGTCATCAATGAACACAACTATGAACCGGTCCAAATACTGTCTGAAGATC
        131 AGATGTCATCAATGAACACAACTATGAACCGGTCCAAATACTGTCTGAAGATC

                                                                             
       2774 CCCAAGAAGCTAACCTCTCTTAACCAGAACTCACACTTACTGAACTTAGCATATAACTACTTATC
          1 CCCAAGAAGCTAACCTCTCTTAACCAGAACTCACACTTACTGAACTTAGCATATAACTACTTATC

                                 *     *                                     
       2839 CCGCAAAATTTGCAACACTAATCTCAGGTGCTCAGCATGTTCGGTCTCATCTCTTGAATAGACCA
         66 CCGCAAAATTTGCAACACTAACCTCAGATGCTCAGCATGTTCGGTCTCATCTCTTGAATAGACCA

                                                                 
       2904 AGATGTCATCAATGAACACAACTATGAACCGGTCCAAATACTGTCTGAAGATC
        131 AGATGTCATCAATGAACACAACTATGAACCGGTCCAAATACTGTCTGAAGATC

             
       2957 C
          1 C

       2958 GATTCATCAA


Statistics
Matches: 180,  Mismatches: 4, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 183  180  1.00

ACGTcount: A:0.33, C:0.28, G:0.14, T:0.25


Consensus pattern (183 bp):   
CCCAAGAAGCTAACCTCTCTTAACCAGAACTCACACTTACTGAACTTAGCATATAACTACTTATC
CCGCAAAATTTGCAACACTAACCTCAGATGCTCAGCATGTTCGGTCTCATCTCTTGAATAGACCA
AGATGTCATCAATGAACACAACTATGAACCGGTCCAAATACTGTCTGAAGATC

Found at i:3191 original size:47 final size:47

Alignment explanation


    Indices: 3129--3221  Score: 159
    Period size: 47  Copynumber: 2.0  Consensus size: 47

       3119 ACTAAGGCTC

                *                                          
       3129 CCTTTAGTTGATCAAACAAATCATCAATACGCGGTAACGGATATTTA
          1 CCTTCAGTTGATCAAACAAATCATCAATACGCGGTAACGGATATTTA

                      *              *                    
       3176 CCTTCAGTTGGTCAAACAAATCATCGATACGCGGTAACGGATATTT
          1 CCTTCAGTTGATCAAACAAATCATCAATACGCGGTAACGGATATTT

       3222 GTTCTTTATC


Statistics
Matches: 43,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  47   43  1.00

ACGTcount: A:0.33, C:0.20, G:0.17, T:0.29


Consensus pattern (47 bp):   
CCTTCAGTTGATCAAACAAATCATCAATACGCGGTAACGGATATTTA
Done.