Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold657

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: 6513
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:2621 original size:13 final size:13

Alignment explanation


    Indices: 2603--2628  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       2593 AATATTTTTG

                         
       2603 TGTATCGATACAT
          1 TGTATCGATACAT

                         
       2616 TGTATCGATACAT
          1 TGTATCGATACAT

       2629 GCTTGCTGTA


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:3372 original size:21 final size:21

Alignment explanation


    Indices: 3331--3374  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       3321 CTCTCCTTTA

                       *  *      
       3331 TCTCCCCCGTTTATTAATAAT
          1 TCTCCCCCGTTAATCAATAAT

                                  
       3352 TCTCCCCC-TTAATCAAGTAAT
          1 TCTCCCCCGTTAATCAA-TAAT

              
       3373 TC
          1 TC

       3375 ATATCAAAAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  20    6  0.30
  21   14  0.70

ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39


Consensus pattern (21 bp):   
TCTCCCCCGTTAATCAATAAT

Found at i:3538 original size:21 final size:20

Alignment explanation


    Indices: 3514--3555  Score: 50
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       3504 AAGAGATTAA

                                  
       3514 AAAT-CAAAGTACAATGCAAAT
          1 AAATACAAAGT-CAA-GCAAAT

                    *           
       3535 AAATACAAGGTCAAGCAAAT
          1 AAATACAAAGTCAAGCAAAT

             
       3555 A
          1 A

       3556 CAAAACACTA


Statistics
Matches: 19,  Mismatches: 1, Indels: 3
        0.83            0.04        0.13

Matches are distributed among these distances:
  20    7  0.37
  21    7  0.37
  22    5  0.26

ACGTcount: A:0.57, C:0.14, G:0.12, T:0.17


Consensus pattern (20 bp):   
AAATACAAAGTCAAGCAAAT

Found at i:5182 original size:13 final size:13

Alignment explanation


    Indices: 5164--5189  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       5154 AATAATCACC

                         
       5164 CTGTATCGATACA
          1 CTGTATCGATACA

                         
       5177 CTGTATCGATACA
          1 CTGTATCGATACA

       5190 AAGAAAATGT


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:0.23, G:0.15, T:0.31


Consensus pattern (13 bp):   
CTGTATCGATACA
Done.