Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1321

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: 5850
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31


Found at i:2837 original size:19 final size:19

Alignment explanation


    Indices: 2813--2852  Score: 71
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       2803 TGTGAGGAAT

                        *      
       2813 AGGTGTGAAGCACTAATGA
          1 AGGTGTGAAGCAATAATGA

                               
       2832 AGGTGTGAAGCAATAATGA
          1 AGGTGTGAAGCAATAATGA

              
       2851 AG
          1 AG

       2853 AAAAAAGAAA


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

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.40, C:0.07, G:0.33, T:0.20


Consensus pattern (19 bp):   
AGGTGTGAAGCAATAATGA

Found at i:4663 original size:2 final size:2

Alignment explanation


    Indices: 4656--4684  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       4646 ATATACATAA

                                                       
       4656 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
          1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A

       4685 TATAATATAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00


Consensus pattern (2 bp):   
AC

Found at i:5415 original size:15 final size:15

Alignment explanation


    Indices: 5370--5415  Score: 56
    Period size: 15  Copynumber: 3.0  Consensus size: 15

       5360 TTTTTTATGG

                    *     *
       5370 TTTAAATTGAATTAA
          1 TTTAAATTTAATTAT

                      *     
       5385 TTTAAATTATTATTAT
          1 TTTAAATT-TAATTAT

                           
       5401 TTTAAATTTAATTAT
          1 TTTAAATTTAATTAT

       5416 AAAAATATAT


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

Matches are distributed among these distances:
  15   14  0.54
  16   12  0.46

ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57


Consensus pattern (15 bp):   
TTTAAATTTAATTAT

Found at i:5461 original size:18 final size:19

Alignment explanation


    Indices: 5426--5464  Score: 53
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       5416 AAAAATATAT

                         *     
       5426 AAATATTAATATTTTTTTA
          1 AAATATTAATATTATTTTA

                *              
       5445 AAATTTTAATA-TATTTTA
          1 AAATATTAATATTATTTTA

              
       5463 AA
          1 AA

       5465 TAATTATATA


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  18    8  0.44
  19   10  0.56

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (19 bp):   
AAATATTAATATTATTTTA
Done.