Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_14261

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, 297

Length: 495
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.23


Found at i:157 original size:33 final size:30

Alignment explanation


    Indices: 118--179  Score: 79
    Period size: 30  Copynumber: 2.0  Consensus size: 30

        108 TCCTGGCGGA

                    *                        
        118 TATCCACCTGCTGGAGCTTACCCACCTCAAGGC
          1 TATCCACCAGCT-G-GC-TACCCACCTCAAGGC

                                *        
        151 TATCCACCAGCTGGCTACCCTCCTCAAGG
          1 TATCCACCAGCTGGCTACCCACCTCAAGG

        180 AGGATACCCC


Statistics
Matches: 27,  Mismatches: 2, Indels: 3
        0.84            0.06        0.09

Matches are distributed among these distances:
  30   13  0.48
  31    2  0.07
  32    1  0.04
  33   11  0.41

ACGTcount: A:0.21, C:0.40, G:0.18, T:0.21


Consensus pattern (30 bp):   
TATCCACCAGCTGGCTACCCACCTCAAGGC

Found at i:323 original size:9 final size:9

Alignment explanation


    Indices: 311--353  Score: 68
    Period size: 9  Copynumber: 4.8  Consensus size: 9

        301 CACCACGTGT

                *    
        311 CTCACGGTG
          1 CTCATGGTG

                     
        320 CTCATGGTG
          1 CTCATGGTG

                     
        329 CTCATGGTG
          1 CTCATGGTG

              *      
        338 CTTATGGTG
          1 CTCATGGTG

                   
        347 CTCATGG
          1 CTCATGG

        354 GTTTGGTCAT


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   9   31  1.00

ACGTcount: A:0.12, C:0.23, G:0.33, T:0.33


Consensus pattern (9 bp):   
CTCATGGTG

Found at i:430 original size:21 final size:24

Alignment explanation


    Indices: 372--431  Score: 72
    Period size: 24  Copynumber: 2.6  Consensus size: 24

        362 ATGGTCATCA

                        *           
        372 TGGGAAGTTCAAACATCATGGTGG
          1 TGGGAAGTTCAAGCATCATGGTGG

                     *              
        396 TGGGAAGTTTAAGCATCAT-G-GG
          1 TGGGAAGTTCAAGCATCATGGTGG

                  *        
        418 -GGGAAATTCAAGCA
          1 TGGGAAGTTCAAGCA

        432 CGGGAAGCAT


Statistics
Matches: 32,  Mismatches: 4, Indels: 3
        0.82            0.10        0.08

Matches are distributed among these distances:
  21   12  0.38
  22    2  0.06
  23    1  0.03
  24   17  0.53

ACGTcount: A:0.32, C:0.12, G:0.33, T:0.23


Consensus pattern (24 bp):   
TGGGAAGTTCAAGCATCATGGTGG

Found at i:447 original size:24 final size:24

Alignment explanation


    Indices: 418--467  Score: 91
    Period size: 24  Copynumber: 2.1  Consensus size: 24

        408 GCATCATGGG

                             *      
        418 GGGAAATTCAAGCACGGGAAGCAT
          1 GGGAAATTCAAGCACGGAAAGCAT

                                    
        442 GGGAAATTCAAGCACGGAAAGCAT
          1 GGGAAATTCAAGCACGGAAAGCAT

              
        466 GG
          1 GG

        468 AGGCGGCAAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.38, C:0.16, G:0.34, T:0.12


Consensus pattern (24 bp):   
GGGAAATTCAAGCACGGAAAGCAT
Done.