Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3137

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: 21954
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:1713 original size:31 final size:31

Alignment explanation


    Indices: 1678--1770  Score: 108
    Period size: 31  Copynumber: 3.2  Consensus size: 31

       1668 TTATTTTTAA

                    *                      
       1678 ATTTTTAACAAAATAAAAATATATAAAAAAT
          1 ATTTTTAAAAAAATAAAAATATATAAAAAAT

                                            
       1709 ATTTTTAAAAAAATAAAAATCAT-T--AAAAT
          1 ATTTTTAAAAAAATAAAAAT-ATATAAAAAAT

              *     *                      
       1738 -TATTT-AGAAAATAAAAAT-TATAAAAAAT
          1 ATTTTTAAAAAAATAAAAATATATAAAAAAT

                 
       1766 ATTTT
          1 ATTTT

       1771 AATCTTTTTA


Statistics
Matches: 53,  Mismatches: 4, Indels: 12
        0.77            0.06        0.17

Matches are distributed among these distances:
  25    1  0.02
  26    1  0.02
  27   12  0.23
  28    9  0.17
  29    8  0.15
  31   20  0.38
  32    2  0.04

ACGTcount: A:0.61, C:0.02, G:0.01, T:0.35


Consensus pattern (31 bp):   
ATTTTTAAAAAAATAAAAATATATAAAAAAT

Found at i:1753 original size:27 final size:27

Alignment explanation


    Indices: 1687--1769  Score: 85
    Period size: 27  Copynumber: 2.9  Consensus size: 27

       1677 AATTTTTAAC

                        *                 *
       1687 AAAATAAAAATATATAAAAAATATTTTTAAA
          1 AAAATAAAAAT-CATAAAAAATA--TTT-AG

                          *    *       
       1718 AAAATAAAAATCATTAAAATTATTTAG
          1 AAAATAAAAATCATAAAAAATATTTAG

                       *             
       1745 AAAATAAAAATTATAAAAAATATTT
          1 AAAATAAAAATCATAAAAAATATTT

       1770 TAATCTTTTT


Statistics
Matches: 45,  Mismatches: 7, Indels: 4
        0.80            0.12        0.07

Matches are distributed among these distances:
  27   23  0.51
  28    3  0.07
  30    8  0.18
  31   11  0.24

ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33


Consensus pattern (27 bp):   
AAAATAAAAATCATAAAAAATATTTAG

Found at i:3752 original size:22 final size:23

Alignment explanation


    Indices: 3724--3788  Score: 73
    Period size: 22  Copynumber: 3.0  Consensus size: 23

       3714 CACTAATAAT

                                 * 
       3724 CAGAGAGCACTAAA-GTGCTATA
          1 CAGAGAGCACTAAATGTGCTAAA

                   *               
       3746 CAGAGAGAAC-AAATGTGCTAAA
          1 CAGAGAGCACTAAATGTGCTAAA

             *           *        
       3768 CGGAGAGCACT-ACTGTGCTAA
          1 CAGAGAGCACTAAATGTGCTAA

       3789 TAATCGAATA


Statistics
Matches: 36,  Mismatches: 5, Indels: 4
        0.80            0.11        0.09

Matches are distributed among these distances:
  21    3  0.08
  22   33  0.92

ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17


Consensus pattern (23 bp):   
CAGAGAGCACTAAATGTGCTAAA
Done.