Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1062

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: 16941
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.32


Found at i:4959 original size:16 final size:17

Alignment explanation


    Indices: 4935--4967  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       4925 ATTATCACCC

                             
       4935 TATGA-TTTTCTTGTAT
          1 TATGATTTTTCTTGTAT

                *            
       4951 TATGCTTTTTCTTGTAT
          1 TATGATTTTTCTTGTAT

       4968 AGCCCTTATT


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  16    4  0.27
  17   11  0.73

ACGTcount: A:0.15, C:0.09, G:0.12, T:0.64


Consensus pattern (17 bp):   
TATGATTTTTCTTGTAT

Found at i:10138 original size:16 final size:16

Alignment explanation


    Indices: 10100--10138  Score: 53
    Period size: 16  Copynumber: 2.4  Consensus size: 16

      10090 GCCCATTCCG

                  *         
      10100 AAGTATATATATACAT
          1 AAGTATGTATATACAT

                             
      10116 ATA-TATGTATATACAT
          1 A-AGTATGTATATACAT

                   
      10132 AAGTATG
          1 AAGTATG

      10139 CCCATTCGTG


Statistics
Matches: 20,  Mismatches: 1, Indels: 4
        0.80            0.04        0.16

Matches are distributed among these distances:
  15    1  0.05
  16   18  0.90
  17    1  0.05

ACGTcount: A:0.46, C:0.05, G:0.10, T:0.38


Consensus pattern (16 bp):   
AAGTATGTATATACAT

Found at i:10646 original size:13 final size:13

Alignment explanation


    Indices: 10628--10653  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      10618 GCGAGTTGAT

                         
      10628 TATGTAGCACTAA
          1 TATGTAGCACTAA

                         
      10641 TATGTAGCACTAA
          1 TATGTAGCACTAA

      10654 GTGTGCGAGT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31


Consensus pattern (13 bp):   
TATGTAGCACTAA

Found at i:10679 original size:27 final size:27

Alignment explanation


    Indices: 10641--10785  Score: 193
    Period size: 27  Copynumber: 5.7  Consensus size: 27

      10631 GTAGCACTAA

                                       
      10641 TATGTAGCACTAAGTGTGCGAGTTGAT
          1 TATGTAGCACTAAGTGTGCGAGTTGAT

                                       
      10668 TATGTAGCACTAAGTGTGCGA---G-T
          1 TATGTAGCACTAAGTGTGCGAGTTGAT

                                       
      10691 TATG-AGCACTAAGTGTGCGA-TTGAT
          1 TATGTAGCACTAAGTGTGCGAGTTGAT

                                       
      10716 TA--T-GCACTAAGTGTGCGAGTTGAT
          1 TATGTAGCACTAAGTGTGCGAGTTGAT

               *                       
      10740 TATATAG-ACTAAGTGTGCGAGTTGAT
          1 TATGTAGCACTAAGTGTGCGAGTTGAT

               *       *        
      10766 TATATAGCACTGAGTGTGCG
          1 TATGTAGCACTAAGTGTGCG

      10786 GACTTAATAT


Statistics
Matches: 108,  Mismatches: 1, Indels: 18
        0.85            0.01        0.14

Matches are distributed among these distances:
  22   16  0.15
  23   20  0.19
  24    9  0.08
  25    3  0.03
  26   27  0.25
  27   33  0.31

ACGTcount: A:0.27, C:0.12, G:0.29, T:0.32


Consensus pattern (27 bp):   
TATGTAGCACTAAGTGTGCGAGTTGAT

Found at i:10734 original size:45 final size:49

Alignment explanation


    Indices: 10641--10785  Score: 174
    Period size: 49  Copynumber: 2.9  Consensus size: 49

      10631 GTAGCACTAA

                                                              
      10641 TATGTAGCACTAAGTGTGCGAGTTGATTATGTAGCACTAAGTGTGCGAGT
          1 TATGTAGCACTAAGTGTGCGAGTTGATTA-GTAGCACTAAGTGTGCGAGT

                                                                 
      10691 TATG-AGCACTAAGTGTGCGA-TTGATTA-T-GCACTAAGTGTGCGAGTTGAT
          1 TATGTAGCACTAAGTGTGCGAGTTGATTAGTAGCACTAAGTGTGCGA---G-T

               *                          *       *        
      10740 TATATAG-ACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
          1 TATGTAGCACTAAGTGTGCGAGTTGATTA-GTAGCACTAAGTGTGCG

      10786 GACTTAATAT


Statistics
Matches: 84,  Mismatches: 2, Indels: 15
        0.83            0.02        0.15

Matches are distributed among these distances:
  45   15  0.18
  46    1  0.01
  48    8  0.10
  49   33  0.39
  50   13  0.15
  52    1  0.01
  53   13  0.15

ACGTcount: A:0.27, C:0.12, G:0.29, T:0.32


Consensus pattern (49 bp):   
TATGTAGCACTAAGTGTGCGAGTTGATTAGTAGCACTAAGTGTGCGAGT

Found at i:10756 original size:26 final size:27

Alignment explanation


    Indices: 10645--10785  Score: 185
    Period size: 26  Copynumber: 5.6  Consensus size: 27

      10635 CACTAATATG

                                      *
      10645 TAGCACTAAGTGTGCGAGTTGATTATG
          1 TAGCACTAAGTGTGCGAGTTGATTATA

                                       
      10672 TAGCACTAAGTGTGCGA---G-TTAT-
          1 TAGCACTAAGTGTGCGAGTTGATTATA

            *                          
      10694 GAGCACTAAGTGTGCGA-TTGA-T-TA
          1 TAGCACTAAGTGTGCGAGTTGATTATA

                                       
      10718 T-GCACTAAGTGTGCGAGTTGATTATA
          1 TAGCACTAAGTGTGCGAGTTGATTATA

                                       
      10744 TAG-ACTAAGTGTGCGAGTTGATTATA
          1 TAGCACTAAGTGTGCGAGTTGATTATA

                   *        
      10770 TAGCACTGAGTGTGCG
          1 TAGCACTAAGTGTGCG

      10786 GACTTAATAT


Statistics
Matches: 102,  Mismatches: 3, Indels: 18
        0.83            0.02        0.15

Matches are distributed among these distances:
  22   16  0.16
  23   20  0.20
  24    7  0.07
  25    1  0.01
  26   29  0.28
  27   29  0.28

ACGTcount: A:0.27, C:0.12, G:0.29, T:0.32


Consensus pattern (27 bp):   
TAGCACTAAGTGTGCGAGTTGATTATA
Done.