Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1031

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: 35366
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31


Found at i:5382 original size:15 final size:16

Alignment explanation


    Indices: 5348--5382  Score: 54
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       5338 ATGTAACTTG

                           *
       5348 AATAAAAATTAATTTG
          1 AATAAAAATTAATTTA

                            
       5364 AATAAAAATT-ATTTA
          1 AATAAAAATTAATTTA

                
       5379 AATA
          1 AATA

       5383 TGAAATGACT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  15    8  0.44
  16   10  0.56

ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37


Consensus pattern (16 bp):   
AATAAAAATTAATTTA

Found at i:6288 original size:36 final size:36

Alignment explanation


    Indices: 6241--6315  Score: 123
    Period size: 36  Copynumber: 2.1  Consensus size: 36

       6231 GCTAGAACAA

                                 *              
       6241 TTACAACTCTTGATTTAATTCGTTCACAATCATGCT
          1 TTACAACTCTTGATTTAATTCATTCACAATCATGCT

                  *     *                       
       6277 TTACAATTCTTGGTTTAATTCATTCACAATCATGCT
          1 TTACAACTCTTGATTTAATTCATTCACAATCATGCT

               
       6313 TTA
          1 TTA

       6316 ACAAATGTTC


Statistics
Matches: 36,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  36   36  1.00

ACGTcount: A:0.28, C:0.20, G:0.08, T:0.44


Consensus pattern (36 bp):   
TTACAACTCTTGATTTAATTCATTCACAATCATGCT

Found at i:8014 original size:29 final size:29

Alignment explanation


    Indices: 7970--8035  Score: 78
    Period size: 29  Copynumber: 2.2  Consensus size: 29

       7960 TATATTATTG

                     *       *  * *       
       7970 TTTGATTCCTTTTAATAGTATATAGACTAA
          1 TTTGA-TCCATTTAATAATAGAAAGACTAA

                                     *   
       8000 TTTGATCCATTTAATAATAGAAAGATTAA
          1 TTTGATCCATTTAATAATAGAAAGACTAA

                   
       8029 TTTGATC
          1 TTTGATC

       8036 TAACCTCTAT


Statistics
Matches: 31,  Mismatches: 5, Indels: 1
        0.84            0.14        0.03

Matches are distributed among these distances:
  29   26  0.84
  30    5  0.16

ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44


Consensus pattern (29 bp):   
TTTGATCCATTTAATAATAGAAAGACTAA

Found at i:10242 original size:34 final size:34

Alignment explanation


    Indices: 10184--10270  Score: 133
    Period size: 34  Copynumber: 2.6  Consensus size: 34

      10174 AATAGGGTCC

                      *                       
      10184 TTAAAAGAAACAA-AT-TATATACATAAATAAAT
          1 TTAAAAGAAAAAATATATATATACATAAATAAAT

                                           *  
      10216 TTAAAAGAAAAAATATATATATACATAAATAGAT
          1 TTAAAAGAAAAAATATATATATACATAAATAAAT

                          *      
      10250 TTAAAAGAAAAAATTTATATA
          1 TTAAAAGAAAAAATATATATA

      10271 AAATAATATG


Statistics
Matches: 50,  Mismatches: 3, Indels: 2
        0.91            0.05        0.04

Matches are distributed among these distances:
  32   12  0.24
  33    2  0.04
  34   36  0.72

ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30


Consensus pattern (34 bp):   
TTAAAAGAAAAAATATATATATACATAAATAAAT

Found at i:29106 original size:20 final size:20

Alignment explanation


    Indices: 29081--29129  Score: 71
    Period size: 20  Copynumber: 2.5  Consensus size: 20

      29071 GTGGCTGCAG

                         *   *  
      29081 CACACGGGCATGTTCCAGGC
          1 CACACGGGCATGTCCCAAGC

                     *          
      29101 CACACGGGCTTGTCCCAAGC
          1 CACACGGGCATGTCCCAAGC

                     
      29121 CACACGGGC
          1 CACACGGGC

      29130 GTGTGCCCCT


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  20   26  1.00

ACGTcount: A:0.20, C:0.39, G:0.29, T:0.12


Consensus pattern (20 bp):   
CACACGGGCATGTCCCAAGC
Done.