Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1730

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: 8004
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37


Found at i:1449 original size:2 final size:2

Alignment explanation


    Indices: 1442--1471  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       1432 TTATTCTTTA

                                                        
       1442 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT

       1472 TCCTGAGCAT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
CT

Found at i:5228 original size:2 final size:2

Alignment explanation


    Indices: 5221--5246  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       5211 ATTTCTGTAG

                                                  
       5221 TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC

       5247 AGAGTACAAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
TC

Found at i:7772 original size:118 final size:117

Alignment explanation


    Indices: 7626--7841  Score: 326
    Period size: 118  Copynumber: 1.8  Consensus size: 117

       7616 AGAATGAAAA

                 *      *   *                  *                             
       7626 TGCTTCGTTTAATAATGAGAAACTAAAATGCATTTGTCATTATAATATAAAGATTGTAGAAGAAC
          1 TGCTTAGTTTAACAATAAGAAACTAAAATGCATTTCTCATTATAATATAAAGATTGTAGAAGAAC

              *             *    *                               
       7691 TCTTATCTAC-AGTATGTTAATTTTTTTATTTTTTTCAAAAATACTTATTTCT
         66 TCCTATCTACAAGTATATTAACTTTTTT-TTTTTTTCAAAAATACTTATTTCT

                                   *                                         
       7743 TGCTTAGTTTAACAATAAAGAAATTAAAATGCATTTCTCATTATAATATAAAGATTGTAGAAGAA
          1 TGCTTAGTTTAACAAT-AAGAAACTAAAATGCATTTCTCATTATAATATAAAGATTGTAGAAGAA

                                 *            
       7808 CTCCTATCTACAAGTATATTAGCTTTTTTTTTTT
         65 CTCCTATCTACAAGTATATTAACTTTTTTTTTTT

       7842 AAAAAATATT


Statistics
Matches: 88,  Mismatches: 9, Indels: 3
        0.88            0.09        0.03

Matches are distributed among these distances:
 117   14  0.16
 118   60  0.68
 119   14  0.16

ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43


Consensus pattern (117 bp):   
TGCTTAGTTTAACAATAAGAAACTAAAATGCATTTCTCATTATAATATAAAGATTGTAGAAGAAC
TCCTATCTACAAGTATATTAACTTTTTTTTTTTTTCAAAAATACTTATTTCT
Done.