Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1567

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: 10681
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35


Found at i:3819 original size:45 final size:45

Alignment explanation


    Indices: 3724--3819  Score: 106
    Period size: 46  Copynumber: 2.1  Consensus size: 45

       3714 TAAATATTTT

                                                **  *    
       3724 TATAATATTTTAATAATAATAGTATTATTTTAGTATTTAATATTA
          1 TATAATATTTTAATAATAATAGTATTATTTTAGTATAAAAAATTA

                        *  *      *                        
       3769 TATAATATTTTAGTATTAAATATTATTATTTTATGT-TAAAAAATTA
          1 TATAATATTTTAATAAT-AATAGTATTATTTTA-GTATAAAAAATTA

                  
       3815 -ATAAT
          1 TATAAT

       3820 TTCATGATAA


Statistics
Matches: 43,  Mismatches: 6, Indels: 4
        0.81            0.11        0.08

Matches are distributed among these distances:
  45   20  0.47
  46   21  0.49
  47    2  0.05

ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52


Consensus pattern (45 bp):   
TATAATATTTTAATAATAATAGTATTATTTTAGTATAAAAAATTA

Found at i:3901 original size:16 final size:17

Alignment explanation


    Indices: 3871--3903  Score: 59
    Period size: 16  Copynumber: 2.0  Consensus size: 17

       3861 CTTTGAAAAT

                             
       3871 TATTAAAATATATTATA
          1 TATTAAAATATATTATA

                             
       3888 TATTAAAA-ATATTATA
          1 TATTAAAATATATTATA

       3904 ATAATAATAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16    8  0.50
  17    8  0.50

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


Consensus pattern (17 bp):   
TATTAAAATATATTATA

Found at i:9272 original size:23 final size:23

Alignment explanation


    Indices: 9242--9304  Score: 78
    Period size: 23  Copynumber: 2.8  Consensus size: 23

       9232 TATACAAAAA

                                   
       9242 ATAATTAAAATATATATAAATAT
          1 ATAATTAAAATATATATAAATAT

                       *            
       9265 ATAATTAAAATTTACT-TAAATAT
          1 ATAATTAAAATATA-TATAAATAT

                    *          
       9288 ATAA-TAATATA-ATATAA
          1 ATAATTAAAATATATATAA

       9305 TTAAAAATAA


Statistics
Matches: 35,  Mismatches: 3, Indels: 6
        0.80            0.07        0.14

Matches are distributed among these distances:
  20    1  0.03
  21    4  0.11
  22    5  0.14
  23   24  0.69
  24    1  0.03

ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40


Consensus pattern (23 bp):   
ATAATTAAAATATATATAAATAT

Found at i:9314 original size:15 final size:15

Alignment explanation


    Indices: 9296--9333  Score: 60
    Period size: 15  Copynumber: 2.6  Consensus size: 15

       9286 ATATAATAAT

                           
       9296 ATAATATAATTAAAA
          1 ATAATATAATTAAAA

                  *        
       9311 ATAATAAAATTAAAA
          1 ATAATATAATTAAAA

                     
       9326 A-AATATAA
          1 ATAATATAA

       9334 GATAAATATA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  14    6  0.29
  15   15  0.71

ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29


Consensus pattern (15 bp):   
ATAATATAATTAAAA
Done.