Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2222

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: 15050
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32


Found at i:544 original size:3 final size:3

Alignment explanation


    Indices: 536--616  Score: 72
    Period size: 3  Copynumber: 27.0  Consensus size: 3

        526 TTTTTAGTTA

                         *   *                  *   *       *   *          
        536 ATC ATC ATC ACC ACC ATC ATC ATC ATC GTC GTC ATC GTC GTC ATC ATC
          1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC

                    * *                 *   *          
        584 ATC ATC TTG ATC ATC ATC ATC GTC GTC ATC ATC
          1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC

        617 TTCTTTTCCC


Statistics
Matches: 66,  Mismatches: 12, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
   3   66  1.00

ACGTcount: A:0.25, C:0.35, G:0.09, T:0.32


Consensus pattern (3 bp):   
ATC

Found at i:1745 original size:23 final size:22

Alignment explanation


    Indices: 1700--1743  Score: 88
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       1690 CGTGAATCCT

                                  
       1700 TTTCAACCATTTGATAAACCCC
          1 TTTCAACCATTTGATAAACCCC

                                  
       1722 TTTCAACCATTTGATAAACCCC
          1 TTTCAACCATTTGATAAACCCC

       1744 CTAAACCTAG


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.32, C:0.32, G:0.05, T:0.32


Consensus pattern (22 bp):   
TTTCAACCATTTGATAAACCCC

Found at i:5338 original size:32 final size:31

Alignment explanation


    Indices: 5268--5339  Score: 76
    Period size: 32  Copynumber: 2.3  Consensus size: 31

       5258 TATATATGAT

                 *                         
       5268 AATATTAATGTATTAAAATTGTTATAATAAA
          1 AATATAAATGTATTAAAATTGTTATAATAAA

                      *                        
       5299 AATTATAAATTTATTAAAATATGAATTAT-AT-AA
          1 AA-TATAAATGTATTAAAAT-TG--TTATAATAAA

                    
       5332 AATATAAA
          1 AATATAAA

       5340 AATATAGATA


Statistics
Matches: 35,  Mismatches: 2, Indels: 7
        0.80            0.05        0.16

Matches are distributed among these distances:
  31    2  0.06
  32   21  0.60
  33    6  0.17
  34    2  0.06
  35    4  0.11

ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40


Consensus pattern (31 bp):   
AATATAAATGTATTAAAATTGTTATAATAAA

Found at i:5356 original size:19 final size:18

Alignment explanation


    Indices: 5331--5379  Score: 62
    Period size: 19  Copynumber: 2.7  Consensus size: 18

       5321 GAATTATATA

                              
       5331 AAATATAAAAATATAGAT
          1 AAATATAAAAATATAGAT

                      *     *  
       5349 ATAATATAAATATATATAT
          1 A-AATATAAAAATATAGAT

               *        
       5368 AAAGATAAAAAT
          1 AAATATAAAAAT

       5380 TATTAATAAA


Statistics
Matches: 26,  Mismatches: 4, Indels: 2
        0.81            0.12        0.06

Matches are distributed among these distances:
  18   10  0.38
  19   16  0.62

ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31


Consensus pattern (18 bp):   
AAATATAAAAATATAGAT

Found at i:5631 original size:24 final size:22

Alignment explanation


    Indices: 5582--5642  Score: 86
    Period size: 23  Copynumber: 2.6  Consensus size: 22

       5572 ATAATTATAT

                                   
       5582 TTATATAAATATTAAATTATTGA
          1 TTAT-TAAATATTAAATTATTGA

                                  * 
       5605 TTATTAAAATATTCAAATTATTTA
          1 TTATT-AAATATT-AAATTATTGA

                          
       5629 TTATTAAATATTAA
          1 TTATTAAATATTAA

       5643 TAGTTTAAAA


Statistics
Matches: 35,  Mismatches: 1, Indels: 5
        0.85            0.02        0.12

Matches are distributed among these distances:
  22    3  0.09
  23   18  0.51
  24   14  0.40

ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49


Consensus pattern (22 bp):   
TTATTAAATATTAAATTATTGA

Found at i:5655 original size:14 final size:15

Alignment explanation


    Indices: 5632--5667  Score: 56
    Period size: 14  Copynumber: 2.5  Consensus size: 15

       5622 TTATTTATTA

                           
       5632 TTAAATATTAATAGT
          1 TTAAATATTAATAGT

                         * 
       5647 TTAAA-ATTAATATT
          1 TTAAATATTAATAGT

                   
       5661 TTAAATA
          1 TTAAATA

       5668 GTAAATCAAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  14   13  0.68
  15    6  0.32

ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47


Consensus pattern (15 bp):   
TTAAATATTAATAGT

Found at i:8376 original size:25 final size:26

Alignment explanation


    Indices: 8343--8400  Score: 77
    Period size: 25  Copynumber: 2.3  Consensus size: 26

       8333 ATTATAAATT

                                       
       8343 TAATAAATATT-ATTAAAATTTATT-A
          1 TAATAAATATTAATTAAAA-TTATTAA

                            *         
       8368 TAATAAATATTAATTATAATTATTAA
          1 TAATAAATATTAATTAAAATTATTAA

                    
       8394 TAA-AAAT
          1 TAATAAAT

       8401 TAAAATATCA


Statistics
Matches: 30,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  25   20  0.67
  26   10  0.33

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


Consensus pattern (26 bp):   
TAATAAATATTAATTAAAATTATTAA
Done.