Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold758

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: 7221
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:71 original size:12 final size:12

Alignment explanation


    Indices: 56--106  Score: 63
    Period size: 12  Copynumber: 4.4  Consensus size: 12

         46 AATTATAATT

                        
         56 AATATTTAGGTA
          1 AATATTTAGGTA

                        
         68 AATA--TA-GTA
          1 AATATTTAGGTA

               *         
         77 TAAAATTTAGGTA
          1 -AATATTTAGGTA

                        
         90 AATATTTAGGTA
          1 AATATTTAGGTA

                 
        102 AATAT
          1 AATAT

        107 AGTACAAAAT


Statistics
Matches: 33,  Mismatches: 2, Indels: 8
        0.77            0.05        0.19

Matches are distributed among these distances:
   9    3  0.09
  10    5  0.15
  12   22  0.67
  13    3  0.09

ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39


Consensus pattern (12 bp):   
AATATTTAGGTA

Found at i:2361 original size:39 final size:37

Alignment explanation


    Indices: 2318--2394  Score: 86
    Period size: 39  Copynumber: 2.0  Consensus size: 37

       2308 TCTATTCAGA

                                                     
       2318 TTTATTCTGATTTA-AGTTTGAA-TATATTTTAGCTTTTAG
          1 TTTATTCTGATTTATA--TTGAATTA-ATTTTAG-TTTTAG

                  *  *                           
       2357 TTTATTGTGCTTTATATTGAATTAATTTTAGTTTTAG
          1 TTTATTCTGATTTATATTGAATTAATTTTAGTTTTAG

             
       2394 T
          1 T

       2395 GAATTAAATA


Statistics
Matches: 34,  Mismatches: 2, Indels: 6
        0.81            0.05        0.14

Matches are distributed among these distances:
  37    7  0.21
  38   12  0.35
  39   14  0.41
  40    1  0.03

ACGTcount: A:0.25, C:0.04, G:0.13, T:0.58


Consensus pattern (37 bp):   
TTTATTCTGATTTATATTGAATTAATTTTAGTTTTAG

Found at i:6734 original size:19 final size:20

Alignment explanation


    Indices: 6710--6747  Score: 60
    Period size: 19  Copynumber: 1.9  Consensus size: 20

       6700 AAATAAAAAT

                    *           
       6710 AAAAATTATAAAAT-TATTA
          1 AAAAATTAAAAAATCTATTA

                               
       6729 AAAAATTAAAAAATCTATT
          1 AAAAATTAAAAAATCTATT

       6748 GGAGTGATTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  19   13  0.76
  20    4  0.24

ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34


Consensus pattern (20 bp):   
AAAAATTAAAAAATCTATTA
Done.