Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold539

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: 9747
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33


Found at i:5139 original size:14 final size:14

Alignment explanation


    Indices: 5120--5154  Score: 61
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       5110 AAATAACATG

                          
       5120 AAAATATAATATAA
          1 AAAATATAATATAA

                          
       5134 AAAATATAATATAA
          1 AAAATATAATATAA

                   
       5148 AATAATA
          1 AA-AATA

       5155 CGAACAAGCT


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  14   16  0.80
  15    4  0.20

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


Consensus pattern (14 bp):   
AAAATATAATATAA

Found at i:5330 original size:26 final size:24

Alignment explanation


    Indices: 5296--5352  Score: 69
    Period size: 26  Copynumber: 2.2  Consensus size: 24

       5286 AATACGATAA

                      *                
       5296 AAAACATAAATATAAAATTAAAAAATT
          1 AAAA-ATAAAAATAAAA-TAAAAAA-T

                          *         
       5323 AAAAATAAAAATAACATAAAAAAT
          1 AAAAATAAAAATAAAATAAAAAAT

                  
       5347 AAAAAT
          1 AAAAAT

       5353 TACATGTAGG


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  24    7  0.25
  25    7  0.25
  26   10  0.36
  27    4  0.14

ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21


Consensus pattern (24 bp):   
AAAAATAAAAATAAAATAAAAAAT

Found at i:5346 original size:18 final size:18

Alignment explanation


    Indices: 5323--5357  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       5313 TTAAAAAATT

                              
       5323 AAAAATAAAAATAACATA
          1 AAAAATAAAAATAACATA

                        *    
       5341 AAAAATAAAAATTACAT
          1 AAAAATAAAAATAACAT

       5358 GTAGGTAAAA


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

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20


Consensus pattern (18 bp):   
AAAAATAAAAATAACATA

Found at i:5404 original size:14 final size:14

Alignment explanation


    Indices: 5363--5406  Score: 54
    Period size: 13  Copynumber: 3.1  Consensus size: 14

       5353 TACATGTAGG

                            
       5363 TAAAAATAATAATATT
          1 TAAAAATAAT--TATT

             *            
       5379 TTAAAA-AATTATT
          1 TAAAAATAATTATT

                          
       5392 TAAAAATAATTATT
          1 TAAAAATAATTATT

             
       5406 T
          1 T

       5407 TGATAAGTAG


Statistics
Matches: 25,  Mismatches: 2, Indels: 4
        0.81            0.06        0.13

Matches are distributed among these distances:
  13    9  0.36
  14    8  0.32
  15    3  0.12
  16    5  0.20

ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43


Consensus pattern (14 bp):   
TAAAAATAATTATT

Found at i:9577 original size:26 final size:28

Alignment explanation


    Indices: 9548--9612  Score: 66
    Period size: 25  Copynumber: 2.4  Consensus size: 28

       9538 ATATATTTGT

                                        
       9548 ATTTTTTTTATAAT-TTTT-AAATTTTA
          1 ATTTTTTTTATAATATTTTAAAATTTTA

                 * *                    
       9574 A-TTTATATA-AATATTTTAAAATTTTA
          1 ATTTTTTTTATAATATTTTAAAATTTTA

                         
       9600 ATTTATTTATTAT
          1 ATTT-TTT-TTAT

       9613 CTACATTAAA


Statistics
Matches: 29,  Mismatches: 4, Indels: 8
        0.71            0.10        0.20

Matches are distributed among these distances:
  24    3  0.10
  25   10  0.34
  26   10  0.34
  27    2  0.07
  28    2  0.07
  29    2  0.07

ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63


Consensus pattern (28 bp):   
ATTTTTTTTATAATATTTTAAAATTTTA

Found at i:9692 original size:17 final size:18

Alignment explanation


    Indices: 9666--9699  Score: 61
    Period size: 17  Copynumber: 1.9  Consensus size: 18

       9656 ATATTATTCG

                              
       9666 TAAAATATTTAAATTCAC
          1 TAAAATATTTAAATTCAC

                             
       9684 TAAAA-ATTTAAATTCA
          1 TAAAATATTTAAATTCA

       9700 ATACATAACT


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

Matches are distributed among these distances:
  17   11  0.69
  18    5  0.31

ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38


Consensus pattern (18 bp):   
TAAAATATTTAAATTCAC
Done.