Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1946

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: 2298
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.41


Found at i:1754 original size:3 final size:3

Alignment explanation


    Indices: 1746--1792  Score: 71
    Period size: 3  Copynumber: 16.3  Consensus size: 3

       1736 ATATACTTAA

                              *                                            
       1746 TAT TAT TA- TAT TAC TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

             
       1792 T
          1 T

       1793 GGATTTGGTT


Statistics
Matches: 40,  Mismatches: 2, Indels: 4
        0.87            0.04        0.09

Matches are distributed among these distances:
   2    4  0.10
   3   36  0.90

ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66


Consensus pattern (3 bp):   
TAT

Found at i:1756 original size:17 final size:17

Alignment explanation


    Indices: 1743--1776  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       1733 CAAATATACT

                             
       1743 TAATATTATTATATTAC
          1 TAATATTATTATATTAC

              *              
       1760 TATTATTATTATTATTA
          1 TAATATTATTA-TATTA

       1777 TTATTTTATT


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

Matches are distributed among these distances:
  17   10  0.67
  18    5  0.33

ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59


Consensus pattern (17 bp):   
TAATATTATTATATTAC

Found at i:1769 original size:20 final size:20

Alignment explanation


    Indices: 1746--1792  Score: 69
    Period size: 20  Copynumber: 2.4  Consensus size: 20

       1736 ATATACTTAA

                                 
       1746 TATTATTA-TATTACTATTAT
          1 TATTATTATTATTA-TATTAT

                           *    
       1766 TATTATTATTATTATTTTAT
          1 TATTATTATTATTATATTAT

                   
       1786 TATTATT
          1 TATTATT

       1793 GGATTTGGTT


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  20   20  0.80
  21    5  0.20

ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66


Consensus pattern (20 bp):   
TATTATTATTATTATATTAT
Done.