Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_17376

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: 2572
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25


Found at i:1391 original size:36 final size:35

Alignment explanation


    Indices: 1314--1392  Score: 97
    Period size: 36  Copynumber: 2.2  Consensus size: 35

       1304 GAACACTCAG

                            *                   
       1314 AAAGTACCCAAGGAACCAACCTGAGTGAAAACAATC
          1 AAAGT-CCCAAGGAACAAACCTGAGTGAAAACAATC

            *                           *        
       1350 TAAGTCCACAAGGAACAAACCTGAGTGAGAACACA-C
          1 AAAGTCC-CAAGGAACAAACCTGAGTGAAAACA-ATC

                   
       1386 AAAGTCC
          1 AAAGTCC

       1393 TTCAGAGATT


Statistics
Matches: 37,  Mismatches: 4, Indels: 4
        0.82            0.09        0.09

Matches are distributed among these distances:
  35    2  0.05
  36   34  0.92
  37    1  0.03

ACGTcount: A:0.46, C:0.25, G:0.18, T:0.11


Consensus pattern (35 bp):   
AAAGTCCCAAGGAACAAACCTGAGTGAAAACAATC

Found at i:1458 original size:36 final size:36

Alignment explanation


    Indices: 1418--1521  Score: 95
    Period size: 36  Copynumber: 2.9  Consensus size: 36

       1408 GGAGGGAGAA

                                             *  
       1418 ACACAAAGTCCTCAAGATGTAAACCGGAATGAAGAT
          1 ACACAAAGTCCTCAAGATGTAAACCGGAATGAAAAT

                 *           *     *   *         
       1454 ACACACAGTCCTCAA-AAGATAAGCCGCAATGAAAAT
          1 ACACAAAGTCCTCAAGATG-TAAACCGGAATGAAAAT

            *           *  *          *      
       1490 GCACAGAA-TCCACAGGATGTAAACCAGAATGA
          1 ACACA-AAGTCCTCAAGATGTAAACCGGAATGA

       1522 CAGCAAGCAA


Statistics
Matches: 52,  Mismatches: 13, Indels: 6
        0.73            0.18        0.08

Matches are distributed among these distances:
  35    2  0.04
  36   47  0.90
  37    3  0.06

ACGTcount: A:0.45, C:0.22, G:0.18, T:0.14


Consensus pattern (36 bp):   
ACACAAAGTCCTCAAGATGTAAACCGGAATGAAAAT
Done.