Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1584

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: 15136
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30


Found at i:471 original size:20 final size:20

Alignment explanation


    Indices: 446--520  Score: 78
    Period size: 20  Copynumber: 3.6  Consensus size: 20

        436 TACAAGCTAA

                                
        446 TGTATCGATACAATTTTTTG
          1 TGTATCGATACAATTTTTTG

                             *** **
        466 TGTATCGATACAATACAAGCTAA
          1 TGTATCGATACAAT---TTTTTG

                                
        489 TGTATCGATACAATTTTTTG
          1 TGTATCGATACAATTTTTTG

                        
        509 TGTATCGATACA
          1 TGTATCGATACA

        521 TTGTATCGAT


Statistics
Matches: 42,  Mismatches: 10, Indels: 6
        0.72            0.17        0.10

Matches are distributed among these distances:
  20   27  0.64
  23   15  0.36

ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40


Consensus pattern (20 bp):   
TGTATCGATACAATTTTTTG

Found at i:497 original size:43 final size:43

Alignment explanation


    Indices: 436--520  Score: 170
    Period size: 43  Copynumber: 2.0  Consensus size: 43

        426 TTCTAGCCGT

                                                       
        436 TACAAGCTAATGTATCGATACAATTTTTTGTGTATCGATACAA
          1 TACAAGCTAATGTATCGATACAATTTTTTGTGTATCGATACAA

                                                      
        479 TACAAGCTAATGTATCGATACAATTTTTTGTGTATCGATACA
          1 TACAAGCTAATGTATCGATACAATTTTTTGTGTATCGATACA

        521 TTGTATCGAT


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  43   42  1.00

ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38


Consensus pattern (43 bp):   
TACAAGCTAATGTATCGATACAATTTTTTGTGTATCGATACAA

Found at i:527 original size:13 final size:13

Alignment explanation


    Indices: 509--534  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

        499 CAATTTTTTG

                         
        509 TGTATCGATACAT
          1 TGTATCGATACAT

                         
        522 TGTATCGATACAT
          1 TGTATCGATACAT

        535 ACTTGCTGTA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38


Consensus pattern (13 bp):   
TGTATCGATACAT

Found at i:11744 original size:20 final size:20

Alignment explanation


    Indices: 11716--11790  Score: 87
    Period size: 20  Copynumber: 3.8  Consensus size: 20

      11706 TTTTACCCAG

                                
      11716 ATGTATCGATACATTTTTCA
          1 ATGTATCGATACATTTTTCA

              *           * * * 
      11736 ATATATCGATACATGTATGA
          1 ATGTATCGATACATTTTTCA

                   *   *   *    
      11756 ATGTATCAATATATTCTTCA
          1 ATGTATCGATACATTTTTCA

                           
      11776 ATGTATCGATACATT
          1 ATGTATCGATACATT

      11791 ATGTCTTTTT


Statistics
Matches: 42,  Mismatches: 13, Indels: 0
        0.76            0.24        0.00

Matches are distributed among these distances:
  20   42  1.00

ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41


Consensus pattern (20 bp):   
ATGTATCGATACATTTTTCA

Found at i:11760 original size:40 final size:39

Alignment explanation


    Indices: 11716--11793  Score: 111
    Period size: 40  Copynumber: 2.0  Consensus size: 39

      11706 TTTTACCCAG

                   *       *                        
      11716 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
          1 ATGTATCAATACATTCTTCAATATATCGATACAT-TATGA

                       *          *               
      11756 ATGTATCAATATATTCTTCAATGTATCGATACATTATG
          1 ATGTATCAATACATTCTTCAATATATCGATACATTATG

      11794 TCTTTTTACC


Statistics
Matches: 34,  Mismatches: 4, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  39    4  0.12
  40   30  0.88

ACGTcount: A:0.35, C:0.13, G:0.12, T:0.41


Consensus pattern (39 bp):   
ATGTATCAATACATTCTTCAATATATCGATACATTATGA
Done.