Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1081

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: 2900
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35


Found at i:166 original size:53 final size:55

Alignment explanation


    Indices: 64--167  Score: 142
    Period size: 55  Copynumber: 1.9  Consensus size: 55

         54 CCACCTTTAA

                                            *                      
         64 AAAACTGCCAACCGTTCTCCCTTTTTTATTGATTCCTTTTTTTTCTTTTTTTTTT
          1 AAAACTGCCAACCGTTCTCCCTTTTTTATTGACTCCTTTTTTTTCTTTTTTTTTT

                       *        *          *        *           
        119 AAAACTGCCAATCGTTCT-CTTTTTTTATT-CCTCCTTTTCTTT-TTTTTTT
          1 AAAACTGCCAACCGTTCTCCCTTTTTTATTGACTCCTTTTTTTTCTTTTTTT

        168 CTAACAATGA


Statistics
Matches: 44,  Mismatches: 5, Indels: 3
        0.85            0.10        0.06

Matches are distributed among these distances:
  52    7  0.16
  53   10  0.23
  54   10  0.23
  55   17  0.39

ACGTcount: A:0.14, C:0.22, G:0.05, T:0.59


Consensus pattern (55 bp):   
AAAACTGCCAACCGTTCTCCCTTTTTTATTGACTCCTTTTTTTTCTTTTTTTTTT

Found at i:325 original size:21 final size:21

Alignment explanation


    Indices: 299--348  Score: 91
    Period size: 21  Copynumber: 2.4  Consensus size: 21

        289 AATCATATCT

                      *          
        299 TCTAAGATTGTATATATCATA
          1 TCTAAGATTGCATATATCATA

                                 
        320 TCTAAGATTGCATATATCATA
          1 TCTAAGATTGCATATATCATA

                    
        341 TCTAAGAT
          1 TCTAAGAT

        349 CTAAGATTGT


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  21   28  1.00

ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40


Consensus pattern (21 bp):   
TCTAAGATTGCATATATCATA
Done.