Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3136

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: 36174
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:1915 original size:48 final size:46

Alignment explanation


    Indices: 1845--1937  Score: 134
    Period size: 48  Copynumber: 2.0  Consensus size: 46

       1835 TCCTTTTAAA

                     *   *                                  
       1845 TCTCTGAAAGGCATTAAAACACAATACTT-AAGAAAACCAAATGAAAT
          1 TCTCTGAAAAGCAGTAAAACACAATACTTCAA-AAAACCAAA-GAAAT

                                                          
       1892 TCTCTGAAAAAGCAGTAAAACACAATACTTCAAAAAACCAAAGAAA
          1 TCTCTG-AAAAGCAGTAAAACACAATACTTCAAAAAACCAAAGAAA

       1938 ACACCAATAT


Statistics
Matches: 42,  Mismatches: 2, Indels: 4
        0.88            0.04        0.08

Matches are distributed among these distances:
  47   10  0.24
  48   30  0.71
  49    2  0.05

ACGTcount: A:0.54, C:0.18, G:0.10, T:0.18


Consensus pattern (46 bp):   
TCTCTGAAAAGCAGTAAAACACAATACTTCAAAAAACCAAAGAAAT

Found at i:12318 original size:16 final size:16

Alignment explanation


    Indices: 12297--12328  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

      12287 TCCTTTTACC

                            
      12297 GTCTCTCTCTGTCTCT
          1 GTCTCTCTCTGTCTCT

                  *         
      12313 GTCTCTGTCTGTCTCT
          1 GTCTCTCTCTGTCTCT

      12329 TTTTTTTTTC


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.00, C:0.34, G:0.16, T:0.50


Consensus pattern (16 bp):   
GTCTCTCTCTGTCTCT

Found at i:17836 original size:3 final size:3

Alignment explanation


    Indices: 17790--17824  Score: 52
    Period size: 3  Copynumber: 11.7  Consensus size: 3

      17780 TTGCATTCCT

                              *   *                       
      17790 TTA TTA TTA TTA TTG TTG TTA TTA TTA TTA TTA TT
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT

      17825 TTGTCATTAT


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   3   30  1.00

ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69


Consensus pattern (3 bp):   
TTA

Found at i:20055 original size:17 final size:17

Alignment explanation


    Indices: 20025--20067  Score: 50
    Period size: 17  Copynumber: 2.5  Consensus size: 17

      20015 TTGACTTTTT

                    *        
      20025 TTTTCTTTCACTTTTAA
          1 TTTTCTTTTACTTTTAA

                     *     **
      20042 TTTTCTTTTTCTTTTTC
          1 TTTTCTTTTACTTTTAA

                     
      20059 TTTTCTTTT
          1 TTTTCTTTT

      20068 CCAATTAAAG


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  17   22  1.00

ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77


Consensus pattern (17 bp):   
TTTTCTTTTACTTTTAA

Found at i:24894 original size:30 final size:31

Alignment explanation


    Indices: 24835--24894  Score: 88
    Period size: 31  Copynumber: 2.0  Consensus size: 31

      24825 GCCTAATGTC

                                           
      24835 TTAAATAAAAATTTACGAATAGTTTAGTGAT
          1 TTAAATAAAAATTTACGAATAGTTTAGTGAT

                  *                        
      24866 TTAAATGAAAATTT-CGAATA-TTTCAGTGA
          1 TTAAATAAAAATTTACGAATAGTTT-AGTGA

      24895 CTATTTTATA


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  29    3  0.11
  30   11  0.41
  31   13  0.48

ACGTcount: A:0.43, C:0.05, G:0.13, T:0.38


Consensus pattern (31 bp):   
TTAAATAAAAATTTACGAATAGTTTAGTGAT

Found at i:25473 original size:13 final size:14

Alignment explanation


    Indices: 25446--25474  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

      25436 TATATTATAT

                          
      25446 TAAAATTTAAATTA
          1 TAAAATTTAAATTA

                          
      25460 TAAAATTT-AATTA
          1 TAAAATTTAAATTA

              
      25473 TA
          1 TA

      25475 CTTATTTAAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    7  0.47
  14    8  0.53

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (14 bp):   
TAAAATTTAAATTA

Found at i:29654 original size:31 final size:29

Alignment explanation


    Indices: 29584--29663  Score: 90
    Period size: 29  Copynumber: 2.7  Consensus size: 29

      29574 GAATTTGATC

                                     *    
      29584 AAATTAAAATTTCATGTATAAAATTGTACA
          1 AAATTAAAA-TTCATGTATAAAATTATACA

                               *       * 
      29614 AAATTAAAATTCATGTATATAATTATATA
          1 AAATTAAAATTCATGTATAAAATTATACA

                  *               
      29643 TTAAATCAAAATT-ATGTATAA
          1 --AAATTAAAATTCATGTATAA

      29664 TTTTAAGATT


Statistics
Matches: 43,  Mismatches: 5, Indels: 4
        0.83            0.10        0.08

Matches are distributed among these distances:
  29   17  0.40
  30   16  0.37
  31   10  0.23

ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39


Consensus pattern (29 bp):   
AAATTAAAATTCATGTATAAAATTATACA
Done.