Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_22872

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, 434

Length: 724
ACGTcount: A:0.22, C:0.06, G:0.48, T:0.24


Found at i:181 original size:27 final size:27

Alignment explanation


    Indices: 136--191  Score: 76
    Period size: 27  Copynumber: 2.1  Consensus size: 27

        126 AGGTGGCTTT

                                *  *   
        136 GGAGCTGGAGGCGGGGGTGGTTTTGGA
          1 GGAGCTGGAGGCGGGGGTGGATTCGGA

                       *  *            
        163 GGAGCTGGAGGTGGTGGTGGATTCGGA
          1 GGAGCTGGAGGCGGGGGTGGATTCGGA

              
        190 GG
          1 GG

        192 TGGGCATGGT


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  27   25  1.00

ACGTcount: A:0.12, C:0.07, G:0.59, T:0.21


Consensus pattern (27 bp):   
GGAGCTGGAGGCGGGGGTGGATTCGGA

Found at i:274 original size:30 final size:30

Alignment explanation


    Indices: 240--338  Score: 80
    Period size: 30  Copynumber: 3.3  Consensus size: 30

        230 GTGGTGGATA

                                          
        240 TGGTGGTGGGATTGGCAAAGGAGGAGGTGT
          1 TGGTGGTGGGATTGGCAAAGGAGGAGGTGT

                         *        *        ***
        270 TGGTGGT-GGATACGG---AGGTGGCATAGGAAA
          1 TGGTGGTGGGAT-TGGCAAAGGAGG---AGGTGT

            *                             
        300 GGGTGGTGGGATTGGCAAAGGAGGAGGTGT
          1 TGGTGGTGGGATTGGCAAAGGAGGAGGTGT

                     
        330 TGGTGGTGG
          1 TGGTGGTGG

        339 AATCGGAAAG


Statistics
Matches: 49,  Mismatches: 12, Indels: 16
        0.64            0.16        0.21

Matches are distributed among these distances:
  27    5  0.10
  29    4  0.08
  30   31  0.63
  31    4  0.08
  33    5  0.10

ACGTcount: A:0.20, C:0.04, G:0.54, T:0.22


Consensus pattern (30 bp):   
TGGTGGTGGGATTGGCAAAGGAGGAGGTGT

Found at i:365 original size:78 final size:78

Alignment explanation


    Indices: 271--478  Score: 382
    Period size: 78  Copynumber: 2.7  Consensus size: 78

        261 AGGAGGTGTT

                 *                       *                                   
        271 GGTGGTGGATACGGAGGTGGCATAGGAAAGGGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGTGG
          1 GGTGGAGGATACGGAGGTGGCATAGGAAAAGGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGTGG

                         
        336 TGGAATCGGAAAG
         66 TGGAATCGGAAAG

                                                                             
        349 GGTGGAGGATACGGAGGTGGCATAGGAAAAGGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGTGG
          1 GGTGGAGGATACGGAGGTGGCATAGGAAAAGGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGTGG

                         
        414 TGGAATCGGAAAG
         66 TGGAATCGGAAAG

                                 *                               
        427 GGTGGAGGATACGGAGGTGGCGTAGGAAAAGGTGGT-GGATTGGCAAAGGAGG
          1 GGTGGAGGATACGGAGGTGGCATAGGAAAAGGTGGTGGGATTGGCAAAGGAGG

        479 CGGATATGGA


Statistics
Matches: 127,  Mismatches: 3, Indels: 1
        0.97            0.02        0.01

Matches are distributed among these distances:
  77   16  0.13
  78  111  0.87

ACGTcount: A:0.26, C:0.05, G:0.51, T:0.18


Consensus pattern (78 bp):   
GGTGGAGGATACGGAGGTGGCATAGGAAAAGGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGTGG
TGGAATCGGAAAG

Found at i:380 original size:60 final size:57

Alignment explanation


    Indices: 228--368  Score: 167
    Period size: 60  Copynumber: 2.4  Consensus size: 57

        218 GCTTTGGTAA

                  *     *                                            
        228 AGGTGGTGGATATGGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGTGGTGGATACGG
          1 AGGTGGAGGATACGGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGTGGTGGATACGG

                         * *                                             
        285 AGGTGGCATAGGAAAGGGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGTGGTGGA-ATCGG
          1 AGGTGG---AGGATACGGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGTGGTGGATA-CGG

                              *     
        345 AAAGGGTGGAGGATACGGAGGTGG
          1 --A-GGTGGAGGATACGGTGGTGG

        369 CATAGGAAAA


Statistics
Matches: 71,  Mismatches: 6, Indels: 11
        0.81            0.07        0.12

Matches are distributed among these distances:
  57    6  0.08
  59    1  0.01
  60   58  0.82
  62    1  0.01
  63    5  0.07

ACGTcount: A:0.23, C:0.04, G:0.52, T:0.21


Consensus pattern (57 bp):   
AGGTGGAGGATACGGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGTGGTGGATACGG

Found at i:683 original size:23 final size:23

Alignment explanation


    Indices: 653--701  Score: 98
    Period size: 23  Copynumber: 2.1  Consensus size: 23

        643 GAGGTGGAAA

                                   
        653 GGGCGGTGGTTTTGGAGGTGGTG
          1 GGGCGGTGGTTTTGGAGGTGGTG

                                   
        676 GGGCGGTGGTTTTGGAGGTGGTG
          1 GGGCGGTGGTTTTGGAGGTGGTG

               
        699 GGG
          1 GGG

        702 GTGGTGGAAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   26  1.00

ACGTcount: A:0.04, C:0.04, G:0.63, T:0.29


Consensus pattern (23 bp):   
GGGCGGTGGTTTTGGAGGTGGTG

Found at i:707 original size:24 final size:24

Alignment explanation


    Indices: 605--708  Score: 102
    Period size: 24  Copynumber: 4.4  Consensus size: 24

        595 GATATGGCAA

                                   *
        605 GGGTGGTGGTTTTGGAGGTGGAGT
          1 GGGTGGTGGTTTTGGAGGTGGAGG

            *        ***          **
        629 AGGTGGTGGAGCTGGAGGTGGAAA
          1 GGGTGGTGGTTTTGGAGGTGGAGG

               *                  * 
        653 GGGCGGTGGTTTTGGAGGTGG-TG
          1 GGGTGGTGGTTTTGGAGGTGGAGG

               *                 *  
        676 GGGCGGTGGTTTTGGAGGTGGTGG
          1 GGGTGGTGGTTTTGGAGGTGGAGG

                     
        700 GGGTGGTGG
          1 GGGTGGTGG

        709 AAATGGACAC


Statistics
Matches: 64,  Mismatches: 15, Indels: 2
        0.79            0.19        0.02

Matches are distributed among these distances:
  23   21  0.33
  24   43  0.67

ACGTcount: A:0.10, C:0.03, G:0.61, T:0.27


Consensus pattern (24 bp):   
GGGTGGTGGTTTTGGAGGTGGAGG
Done.