Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold8402.1

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: 5177
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.27


Found at i:584 original size:158 final size:158

Alignment explanation


    Indices: 293--598  Score: 504
    Period size: 158  Copynumber: 1.9  Consensus size: 158

        283 TTGAAGATCA

                                      *                                      
        293 GGGGGCAAAATCAATCGATACACAACTGGACCAACTCGTTCGGAGATTTCGTACGGCCCAATGAA
          1 GGGGGCAAAATCAATCGATACACAACCGGACCAACTCGTTCGGAGATTTCGTACGGCCCAATGAA

                                          *                          *       
        358 TCTCGGACTCAACTTGCCCTTACGGCCAAATCTGAGTACCTTTTTCCAAGGCGAAACTTTAAGAA
         66 TCTCGGACTCAACTTGCCCTTACGGCCAAACCTGAGTACCTTTTTCCAAGGCGAAACCTTAAGAA

                                        
        423 ACACTTTATCTCCCACCTGTCAAGCTCC
        131 ACACTTTATCTCCCACCTGTCAAGCTCC

                            *    *                                           
        451 GGGGGCAAAATCAATCTATACGCAACCGGACCAACTCGTTCGGAGATTTCGTACGGCCCAATGAA
          1 GGGGGCAAAATCAATCGATACACAACCGGACCAACTCGTTCGGAGATTTCGTACGGCCCAATGAA

               *  *                    *          *            *           * 
        516 TCTTGGGCTCAACTTGCCCTTACGGCCGAACCTGAGTATCTTTTTCCAAGGTGAAACCTTAAGGA
         66 TCTCGGACTCAACTTGCCCTTACGGCCAAACCTGAGTACCTTTTTCCAAGGCGAAACCTTAAGAA

                   *          
        581 ACACTTTGTCTCCCACCT
        131 ACACTTTATCTCCCACCT

        599 AAAACTCGAT


Statistics
Matches: 136,  Mismatches: 12, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
 158  136  1.00

ACGTcount: A:0.27, C:0.29, G:0.20, T:0.25


Consensus pattern (158 bp):   
GGGGGCAAAATCAATCGATACACAACCGGACCAACTCGTTCGGAGATTTCGTACGGCCCAATGAA
TCTCGGACTCAACTTGCCCTTACGGCCAAACCTGAGTACCTTTTTCCAAGGCGAAACCTTAAGAA
ACACTTTATCTCCCACCTGTCAAGCTCC

Found at i:2501 original size:48 final size:48

Alignment explanation


    Indices: 2430--2522  Score: 168
    Period size: 48  Copynumber: 1.9  Consensus size: 48

       2420 GCTCAGCATG

                     *                                      
       2430 TTCGGTCTCGTCTCTTGAATAGACCAAAATGTCATCAATGAACACCAC
          1 TTCGGTCTCATCTCTTGAATAGACCAAAATGTCATCAATGAACACCAC

                                       *                 
       2478 TTCGGTCTCATCTCTTGAATAGACCAAGATGTCATCAATGAACAC
          1 TTCGGTCTCATCTCTTGAATAGACCAAAATGTCATCAATGAACAC

       2523 AACTACGAAC


Statistics
Matches: 43,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  48   43  1.00

ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28


Consensus pattern (48 bp):   
TTCGGTCTCATCTCTTGAATAGACCAAAATGTCATCAATGAACACCAC

Found at i:3400 original size:42 final size:42

Alignment explanation


    Indices: 3333--3414  Score: 128
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       3323 CATCAAACGG

                                *      *              
       3333 CAAAAGCATCAAGTCCACCGGAAAACAGGAACCTCGAATTTC
          1 CAAAAGCATCAAGTCCACCGAAAAACAAGAACCTCGAATTTC

                            *                 *     
       3375 CAAAAGCATCAAGTCCGCCGAAAAACAAGAACCTTGAATT
          1 CAAAAGCATCAAGTCCACCGAAAAACAAGAACCTCGAATT

       3415 ACTAGGGGAC


Statistics
Matches: 36,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  42   36  1.00

ACGTcount: A:0.43, C:0.27, G:0.16, T:0.15


Consensus pattern (42 bp):   
CAAAAGCATCAAGTCCACCGAAAAACAAGAACCTCGAATTTC
Done.