Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1337

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: 6735
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39


Found at i:237 original size:13 final size:13

Alignment explanation


    Indices: 219--244  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

        209 CAATTTTTTG

                         
        219 TGTATCGATACAT
          1 TGTATCGATACAT

                         
        232 TGTATCGATACAT
          1 TGTATCGATACAT

        245 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:5744 original size:13 final size:13

Alignment explanation


    Indices: 5726--5755  Score: 60
    Period size: 13  Copynumber: 2.3  Consensus size: 13

       5716 ACAATTCTTC

                         
       5726 ATGTATCGATACA
          1 ATGTATCGATACA

                         
       5739 ATGTATCGATACA
          1 ATGTATCGATACA

                
       5752 ATGT
          1 ATGT

       5756 CCCATATATC


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33


Consensus pattern (13 bp):   
ATGTATCGATACA

Found at i:5766 original size:33 final size:33

Alignment explanation


    Indices: 5705--5769  Score: 87
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       5695 CGTTGGGCAT

                               *   *         
       5705 AATGTATCAATACAATTCTTCATGTATCGATAC
          1 AATGTATCAATACAATTCTCCATATATCGATAC

                    *                        
       5738 AATGTATCGATACAATGTC-CCATATATCGATA
          1 AATGTATCAATACAAT-TCTCCATATATCGATA

       5770 TATTTCACTT


Statistics
Matches: 28,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  33   26  0.93
  34    2  0.07

ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34


Consensus pattern (33 bp):   
AATGTATCAATACAATTCTCCATATATCGATAC

Found at i:5832 original size:19 final size:20

Alignment explanation


    Indices: 5800--5853  Score: 85
    Period size: 19  Copynumber: 2.8  Consensus size: 20

       5790 TTGCCAGTTT

                                
       5800 CATGTATCGATACAATTAAG
          1 CATGTATCGATACAATTAAG

            *                   
       5820 TATGTAT-GATACAA-TAAG
          1 CATGTATCGATACAATTAAG

                            
       5838 CATGTATCGATACAAT
          1 CATGTATCGATACAAT

       5854 GTATCGATAC


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  18   10  0.33
  19   14  0.47
  20    6  0.20

ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31


Consensus pattern (20 bp):   
CATGTATCGATACAATTAAG

Found at i:5857 original size:13 final size:13

Alignment explanation


    Indices: 5839--5865  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       5829 TACAATAAGC

                         
       5839 ATGTATCGATACA
          1 ATGTATCGATACA

                         
       5852 ATGTATCGATACA
          1 ATGTATCGATACA

             
       5865 A
          1 A

       5866 AGCATAATGT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30


Consensus pattern (13 bp):   
ATGTATCGATACA
Done.