Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2206

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: 30558
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31


Found at i:2352 original size:12 final size:12

Alignment explanation


    Indices: 2318--2352  Score: 52
    Period size: 12  Copynumber: 2.9  Consensus size: 12

       2308 TAAATTAAGT

                      * 
       2318 AAAAAATAAATA
          1 AAAAAATAAAAA

              *         
       2330 AATAAATAAAAA
          1 AAAAAATAAAAA

                       
       2342 AAAAAATAAAA
          1 AAAAAATAAAA

       2353 CTTTACAACT


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  12   20  1.00

ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14


Consensus pattern (12 bp):   
AAAAAATAAAAA

Found at i:7405 original size:12 final size:12

Alignment explanation


    Indices: 7383--7433  Score: 66
    Period size: 13  Copynumber: 4.0  Consensus size: 12

       7373 GTATTACGAG

                         
       7383 ATTGTAAAAAAAA
          1 ATTG-AAAAAAAA

                        
       7396 ATTGAAAAAAAA
          1 ATTGAAAAAAAA

                          
       7408 ATTCGAAAAAAATA
          1 ATT-GAAAAAAA-A

               *        
       7422 ATTCAAAAAAAA
          1 ATTGAAAAAAAA

       7434 GTTTGTATTC


Statistics
Matches: 35,  Mismatches: 1, Indels: 5
        0.85            0.02        0.12

Matches are distributed among these distances:
  12   12  0.34
  13   19  0.54
  14    4  0.11

ACGTcount: A:0.71, C:0.04, G:0.06, T:0.20


Consensus pattern (12 bp):   
ATTGAAAAAAAA

Found at i:9546 original size:15 final size:14

Alignment explanation


    Indices: 9510--9564  Score: 65
    Period size: 15  Copynumber: 3.8  Consensus size: 14

       9500 TCTATTGAGC

                          
       9510 GAGAAAAAGAAAAA
          1 GAGAAAAAGAAAAA

                    *     
       9524 GAGAAAAACAAAAA
          1 GAGAAAAAGAAAAA

                *          
       9538 GAGTGAAAAGAAAAA
          1 GAG-AAAAAGAAAAA

              *         
       9553 GAAAGAAAAGAA
          1 GAGA-AAAAGAA

       9565 TGAGGAGAGT


Statistics
Matches: 34,  Mismatches: 5, Indels: 3
        0.81            0.12        0.07

Matches are distributed among these distances:
  14   16  0.47
  15   18  0.53

ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02


Consensus pattern (14 bp):   
GAGAAAAAGAAAAA

Found at i:16981 original size:4 final size:4

Alignment explanation


    Indices: 16972--17010  Score: 57
    Period size: 4  Copynumber: 10.5  Consensus size: 4

      16962 TAAACTAAGT

                                                                
      16972 AATA AATA AATA AATA AATA AAT- AA-A AATA AA-A AATA AA
          1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AA

      17011 ACTTTACAAC


Statistics
Matches: 32,  Mismatches: 0, Indels: 6
        0.84            0.00        0.16

Matches are distributed among these distances:
   3    7  0.22
   4   25  0.78

ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21


Consensus pattern (4 bp):   
AATA

Done.