Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_33061

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, 909

Length: 1515
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.24


Found at i:205 original size:33 final size:33

Alignment explanation


    Indices: 163--248  Score: 118
    Period size: 33  Copynumber: 2.6  Consensus size: 33

        153 CAAACCTTCC

                             **              
        163 ACGGAAACCGCTGATTCGGAACCGCCGGCGACA
          1 ACGGAAACCGCTGATTCCAAACCGCCGGCGACA

                         *                  *
        196 ACGGAAACCGCTGGTTCCAAACCGCCGGCGACG
          1 ACGGAAACCGCTGATTCCAAACCGCCGGCGACA

                       *  *     
        229 ACGGAAACCGCCGACTCCAA
          1 ACGGAAACCGCTGATTCCAA

        249 GCAACCGGCG


Statistics
Matches: 46,  Mismatches: 7, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  33   46  1.00

ACGTcount: A:0.28, C:0.36, G:0.28, T:0.08


Consensus pattern (33 bp):   
ACGGAAACCGCTGATTCCAAACCGCCGGCGACA

Found at i:257 original size:33 final size:33

Alignment explanation


    Indices: 187--262  Score: 89
    Period size: 33  Copynumber: 2.3  Consensus size: 33

        177 TTCGGAACCG

                    *           * **       **
        187 CCGGCGACAACGGAAACCGCTGGTTCCAAACCG
          1 CCGGCGACGACGGAAACCGCCGACTCCAAACAA

                                         *   
        220 CCGGCGACGACGGAAACCGCCGACTCCAAGCAA
          1 CCGGCGACGACGGAAACCGCCGACTCCAAACAA

                      
        253 CCGGCGACGA
          1 CCGGCGACGA

        263 AACCATCGGA


Statistics
Matches: 36,  Mismatches: 7, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  33   36  1.00

ACGTcount: A:0.28, C:0.38, G:0.29, T:0.05


Consensus pattern (33 bp):   
CCGGCGACGACGGAAACCGCCGACTCCAAACAA

Found at i:273 original size:39 final size:39

Alignment explanation


    Indices: 229--347  Score: 141
    Period size: 39  Copynumber: 2.9  Consensus size: 39

        219 GCCGGCGACG

                          *     *                   
        229 ACGGAAACCGCCGACTCCAAGCAACCGGCGACGAAACCAT
          1 ACGGAAACC-CCGAATCCAAACAACCGGCGACGAAACCAT

                       *         *                * 
        269 -CGGAAAACCCGGAATCCAAAAAACCGGCGACGAAACCTT
          1 ACGG-AAACCCCGAATCCAAACAACCGGCGACGAAACCAT

                                                    
        308 CGACGGAAACCCCGGAATCCAAACAACCGGCGACGAAACC
          1 --ACGGAAACCCC-GAATCCAAACAACCGGCGACGAAACC

        348 TTTGAAAGAA


Statistics
Matches: 67,  Mismatches: 7, Indels: 8
        0.82            0.09        0.10

Matches are distributed among these distances:
  39   28  0.42
  40    5  0.07
  41    6  0.09
  42   28  0.42

ACGTcount: A:0.38, C:0.35, G:0.22, T:0.05


Consensus pattern (39 bp):   
ACGGAAACCCCGAATCCAAACAACCGGCGACGAAACCAT

Found at i:327 original size:42 final size:42

Alignment explanation


    Indices: 227--398  Score: 181
    Period size: 42  Copynumber: 4.2  Consensus size: 42

        217 CCGCCGGCGA

                             *     *                 * 
        227 CGACGGAAACCGCC-GACTCCAAGCAACCGGCGACGAAACCAT
          1 CGACGGAAACC-CCGGAATCCAAACAACCGGCGACGAAACCTT

                     *             *                  
        269 ---CGGAAAACCCGGAATCCAAAAAACCGGCGACGAAACCTT
          1 CGACGGAAACCCCGGAATCCAAACAACCGGCGACGAAACCTT

                                                      
        308 CGACGGAAACCCCGGAATCCAAACAACCGGCGACGAAACCTT
          1 CGACGGAAACCCCGGAATCCAAACAACCGGCGACGAAACCTT

            *  **      *       *      ***           * 
        350 TGAAAGAAACCTCGGAATCTAAACAATTAGCGACGAAACCGT
          1 CGACGGAAACCCCGGAATCCAAACAACCGGCGACGAAACCTT

                   
        392 CGACGGA
          1 CGACGGA

        399 CACATCAGAA


Statistics
Matches: 107,  Mismatches: 19, Indels: 8
        0.80            0.14        0.06

Matches are distributed among these distances:
  38    2  0.02
  39   31  0.29
  42   74  0.69

ACGTcount: A:0.38, C:0.31, G:0.22, T:0.09


Consensus pattern (42 bp):   
CGACGGAAACCCCGGAATCCAAACAACCGGCGACGAAACCTT
Done.