Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold4540

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, 311

Length: 519
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30


Found at i:62 original size:13 final size:14

Alignment explanation


    Indices: 44--79  Score: 56
    Period size: 15  Copynumber: 2.6  Consensus size: 14

         34 GTAGTTTCGA

                          
         44 AAAAAAAATC-AAG
          1 AAAAAAAATCAAAG

                           
         57 AAAAAAAATCGAAAG
          1 AAAAAAAATC-AAAG

                    
         72 AAAAAAAA
          1 AAAAAAAA

         80 ATTTGAAAAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  13   10  0.48
  15   11  0.52

ACGTcount: A:0.81, C:0.06, G:0.08, T:0.06


Consensus pattern (14 bp):   
AAAAAAAATCAAAG

Found at i:87 original size:17 final size:15

Alignment explanation


    Indices: 43--92  Score: 50
    Period size: 16  Copynumber: 3.3  Consensus size: 15

         33 TGTAGTTTCG

                           
         43 AAAAAAAAATC--AA
          1 AAAAAAAAATCGAAA

            *              
         56 GAAAAAAAATCGAAA
          1 AAAAAAAAATCGAAA

                        *    
         71 GAAAAAAAAATTTGAAA
          1 -AAAAAAAAA-TCGAAA

                 
         88 AAAAA
          1 AAAAA

         93 TTGCATACGG


Statistics
Matches: 30,  Mismatches: 3, Indels: 5
        0.79            0.08        0.13

Matches are distributed among these distances:
  13   10  0.33
  15    2  0.07
  16   13  0.43
  17    5  0.17

ACGTcount: A:0.78, C:0.04, G:0.08, T:0.10


Consensus pattern (15 bp):   
AAAAAAAAATCGAAA

Found at i:92 original size:16 final size:16

Alignment explanation


    Indices: 42--81  Score: 59
    Period size: 13  Copynumber: 2.7  Consensus size: 16

         32 TTGTAGTTTC

                            
         42 GAAAAAAAAATC--AA
          1 GAAAAAAAAATCGAAA

                            
         56 G-AAAAAAAATCGAAA
          1 GAAAAAAAAATCGAAA

                       
         71 GAAAAAAAAAT
          1 GAAAAAAAAAT

         82 TTGAAAAAAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  13   10  0.43
  14    1  0.04
  15    3  0.13
  16    9  0.39

ACGTcount: A:0.78, C:0.05, G:0.10, T:0.07


Consensus pattern (16 bp):   
GAAAAAAAAATCGAAA
Done.