Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1239

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: 2296
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37


Found at i:1258 original size:35 final size:35

Alignment explanation


    Indices: 1196--1281  Score: 106
    Period size: 35  Copynumber: 2.5  Consensus size: 35

       1186 TTTTATTTGT

                                   *           
       1196 TTTA-ATTATATAATTAATGATATTTAAA-TATAA
          1 TTTATATTATATAATTAATGATAATTAAATTATAA

                             *                  
       1229 TTTATATTATATGAATTTATGATAATTAAATTATAA
          1 TTTATATTATAT-AATTAATGATAATTAAATTATAA

              *         *     
       1265 -TGATATTATATTATTAA
          1 TTTATATTATATAATTAA

       1282 ATAAATCAAA


Statistics
Matches: 45,  Mismatches: 5, Indels: 5
        0.82            0.09        0.09

Matches are distributed among these distances:
  33    4  0.09
  34   11  0.24
  35   25  0.56
  36    5  0.11

ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50


Consensus pattern (35 bp):   
TTTATATTATATAATTAATGATAATTAAATTATAA

Found at i:1267 original size:25 final size:23

Alignment explanation


    Indices: 1223--1283  Score: 61
    Period size: 24  Copynumber: 2.5  Consensus size: 23

       1213 TGATATTTAA

                      *              
       1223 ATATAATTTATATTATATGA-ATTT
          1 ATATAA-TTAAATTATATGATA-TT

                                     
       1247 ATGATAATTAAATTATAATGATATT
          1 AT-ATAATTAAATTAT-ATGATATT

                *       
       1272 ATATTATTAAAT
          1 ATATAATTAAAT

       1284 AAATCAAAAT


Statistics
Matches: 32,  Mismatches: 2, Indels: 6
        0.80            0.05        0.15

Matches are distributed among these distances:
  24   19  0.59
  25   12  0.38
  26    1  0.03

ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49


Consensus pattern (23 bp):   
ATATAATTAAATTATATGATATT
Done.