Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3805

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: 28164
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30


Found at i:6867 original size:14 final size:16

Alignment explanation


    Indices: 6838--6869  Score: 50
    Period size: 14  Copynumber: 2.1  Consensus size: 16

       6828 AATTCGCCAC

                            
       6838 AAGTATAAGCAAAGAA
          1 AAGTATAAGCAAAGAA

                            
       6854 AAGTA-AAG-AAAGAA
          1 AAGTATAAGCAAAGAA

              
       6868 AA
          1 AA

       6870 TCGAAAGAAC


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  14    8  0.50
  15    3  0.19
  16    5  0.31

ACGTcount: A:0.69, C:0.03, G:0.19, T:0.09


Consensus pattern (16 bp):   
AAGTATAAGCAAAGAA

Found at i:15345 original size:4 final size:4

Alignment explanation


    Indices: 15336--15365  Score: 60
    Period size: 4  Copynumber: 7.5  Consensus size: 4

      15326 ACTAATATAG

                                                 
      15336 AATA AATA AATA AATA AATA AATA AATA AA
          1 AATA AATA AATA AATA AATA AATA AATA AA

      15366 AATAAAACTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   26  1.00

ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23


Consensus pattern (4 bp):   
AATA

Found at i:16755 original size:23 final size:22

Alignment explanation


    Indices: 16703--16755  Score: 56
    Period size: 23  Copynumber: 2.4  Consensus size: 22

      16693 TCCCACGTCT

                    *             
      16703 TTTCTTTTGTTTCTTTTTCTAA
          1 TTTCTTTTCTTTCTTTTTCTAA

                                     
      16725 -TTCATTTTCTCTTCTTTCTTC-AA
          1 TTTC-TTTTCT-TTCTTT-TTCTAA

                    
      16748 TTTCTTTT
          1 TTTCTTTT

      16756 TCACTTCAAT


Statistics
Matches: 26,  Mismatches: 1, Indels: 7
        0.76            0.03        0.21

Matches are distributed among these distances:
  21    3  0.12
  22    5  0.19
  23   12  0.46
  24    6  0.23

ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70


Consensus pattern (22 bp):   
TTTCTTTTCTTTCTTTTTCTAA

Found at i:16762 original size:24 final size:23

Alignment explanation


    Indices: 16713--16762  Score: 57
    Period size: 24  Copynumber: 2.1  Consensus size: 23

      16703 TTTCTTTTGT

                                 * 
      16713 TTCTTTTTCTAATTCATTTTCTC
          1 TTCTTTTTCTAATTCATTTTCAC

                             *       
      16736 TTCTTTCTTC-AATTTCTTTTTCAC
          1 TTCTTT-TTCTAA-TTCATTTTCAC

               
      16760 TTC
          1 TTC

      16763 AATCTCTTTT


Statistics
Matches: 23,  Mismatches: 2, Indels: 3
        0.82            0.07        0.11

Matches are distributed among these distances:
  23    8  0.35
  24   15  0.65

ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64


Consensus pattern (23 bp):   
TTCTTTTTCTAATTCATTTTCAC
Done.