Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2472

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: 13991
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36


Found at i:4414 original size:191 final size:191

Alignment explanation


    Indices: 4090--4472  Score: 748
    Period size: 191  Copynumber: 2.0  Consensus size: 191

       4080 AGTTCCAAAG

                                     *                                       
       4090 AGGAAATAGTGACTTTAAAAGCAGCTAAAGCAAAAAGAAGACTATGATTGCACTAATACAGCAAT
          1 AGGAAATAGTGACTTTAAAAGCAGCCAAAGCAAAAAGAAGACTATGATTGCACTAATACAGCAAT

                                                                             
       4155 ATGTATCAACCAAAGTGATTAAGCAGAAGATCACCAATTCATAGCAACTCATAGAGAAGAAAAAT
         66 ATGTATCAACCAAAGTGATTAAGCAGAAGATCACCAATTCATAGCAACTCATAGAGAAGAAAAAT

                                                                         
       4220 GGCCTACGTACAAACACATAACTCTATCTACTATAAACATTTGCATCTATGCTCGTTATAT
        131 GGCCTACGTACAAACACATAACTCTATCTACTATAAACATTTGCATCTATGCTCGTTATAT

                                                                             
       4281 AGGAAATAGTGACTTTAAAAGCAGCCAAAGCAAAAAGAAGACTATGATTGCACTAATACAGCAAT
          1 AGGAAATAGTGACTTTAAAAGCAGCCAAAGCAAAAAGAAGACTATGATTGCACTAATACAGCAAT

                                            *                                
       4346 ATGTATCAACCAAAGTGATTAAGCAGAAGATCGCCAATTCATAGCAACTCATAGAGAAGAAAAAT
         66 ATGTATCAACCAAAGTGATTAAGCAGAAGATCACCAATTCATAGCAACTCATAGAGAAGAAAAAT

                                                                         
       4411 GGCCTACGTACAAACACATAACTCTATCTACTATAAACATTTGCATCTATGCTCGTTATAT
        131 GGCCTACGTACAAACACATAACTCTATCTACTATAAACATTTGCATCTATGCTCGTTATAT

             
       4472 A
          1 A

       4473 TCTTGATACC


Statistics
Matches: 190,  Mismatches: 2, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 191  190  1.00

ACGTcount: A:0.43, C:0.19, G:0.15, T:0.24


Consensus pattern (191 bp):   
AGGAAATAGTGACTTTAAAAGCAGCCAAAGCAAAAAGAAGACTATGATTGCACTAATACAGCAAT
ATGTATCAACCAAAGTGATTAAGCAGAAGATCACCAATTCATAGCAACTCATAGAGAAGAAAAAT
GGCCTACGTACAAACACATAACTCTATCTACTATAAACATTTGCATCTATGCTCGTTATAT

Found at i:13352 original size:24 final size:25

Alignment explanation


    Indices: 13297--13352  Score: 60
    Period size: 25  Copynumber: 2.3  Consensus size: 25

      13287 AGTAAGCTCA

                                     
      13297 ATAAAAAAATCCCCAAGAAAGGACT
          1 ATAAAAAAATCCCCAAGAAAGGACT

             **        **            
      13322 AGCAAAAAATCTTCAAGAAA-GACT
          1 ATAAAAAAATCCCCAAGAAAGGACT

            *      
      13346 TTAAAAA
          1 ATAAAAA

      13353 TTTGCAATAA


Statistics
Matches: 24,  Mismatches: 7, Indels: 1
        0.75            0.22        0.03

Matches are distributed among these distances:
  24    8  0.33
  25   16  0.67

ACGTcount: A:0.57, C:0.16, G:0.11, T:0.16


Consensus pattern (25 bp):   
ATAAAAAAATCCCCAAGAAAGGACT
Done.