Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_32703

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, 356

Length: 594
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.18


Found at i:321 original size:15 final size:15

Alignment explanation


    Indices: 301--350  Score: 64
    Period size: 15  Copynumber: 3.3  Consensus size: 15

        291 AGGGCCAGAG

                           
        301 AAGAAGGAGGAGCCA
          1 AAGAAGGAGGAGCCA

                    *  *  *
        316 AAGAAGGAAGAACCC
          1 AAGAAGGAGGAGCCA

                 *         
        331 AAGAAAGAGGAGCCA
          1 AAGAAGGAGGAGCCA

                 
        346 AAGAA
          1 AAGAA

        351 AGAAGAACCC


Statistics
Matches: 28,  Mismatches: 7, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  15   28  1.00

ACGTcount: A:0.54, C:0.14, G:0.32, T:0.00


Consensus pattern (15 bp):   
AAGAAGGAGGAGCCA

Found at i:335 original size:30 final size:30

Alignment explanation


    Indices: 301--434  Score: 146
    Period size: 30  Copynumber: 4.4  Consensus size: 30

        291 AGGGCCAGAG

                                *         
        301 AAGAAGGAGGAGCCAAAGAAGGAAGAACCC
          1 AAGAAGGAGGAGCCAAAGAAAGAAGAACCC

                 *                        
        331 AAGAAAGAGGAGCCAAAGAAAGAAGAACCC
          1 AAGAAGGAGGAGCCAAAGAAAGAAGAACCC

                                          *  *
        361 AAGAAGGAAGAAGAG-CAGAAGAAAGAAGAGCCT
          1 AAGAAGG-AG--GAGCCA-AAGAAAGAAGAACCC

                    *  *                   
        394 AAGAAGGAAGAACCAAA-AAAGGAAGAACCC
          1 AAGAAGGAGGAGCCAAAGAAA-GAAGAACCC

                 *     
        424 AAGAAAGAGGA
          1 AAGAAGGAGGA

        435 AGAGAAGAAG


Statistics
Matches: 87,  Mismatches: 11, Indels: 12
        0.79            0.10        0.11

Matches are distributed among these distances:
  29    3  0.03
  30   54  0.62
  31    4  0.05
  32    3  0.03
  33   23  0.26

ACGTcount: A:0.56, C:0.13, G:0.30, T:0.01


Consensus pattern (30 bp):   
AAGAAGGAGGAGCCAAAGAAAGAAGAACCC

Found at i:364 original size:15 final size:15

Alignment explanation


    Indices: 316--431  Score: 90
    Period size: 15  Copynumber: 7.5  Consensus size: 15

        306 GGAGGAGCCA

                 *         
        316 AAGAAGGAAGAACCC
          1 AAGAAAGAAGAACCC

                    *  *  *
        331 AAGAAAGAGGAGCCA
          1 AAGAAAGAAGAACCC

                           
        346 AAGAAAGAAGAACCC
          1 AAGAAAGAAGAACCC

                          * **
        361 AAGAAGGAAGAAGAGCAG
          1 AAG-A--AAGAAGAACCC

                       *  *
        379 AAGAAAGAAGAGCCT
          1 AAGAAAGAAGAACCC

                 *         
        394 AAGAAGGAAGAA-CC
          1 AAGAAAGAAGAACCC

              *             
        408 AAAAAAGGAAGAACCC
          1 AAGAAA-GAAGAACCC

                    
        424 AAGAAAGA
          1 AAGAAAGA

        432 GGAAGAGAAG


Statistics
Matches: 78,  Mismatches: 18, Indels: 10
        0.74            0.17        0.09

Matches are distributed among these distances:
  14    5  0.06
  15   53  0.68
  16    8  0.10
  17    1  0.01
  18   11  0.14

ACGTcount: A:0.58, C:0.14, G:0.28, T:0.01


Consensus pattern (15 bp):   
AAGAAAGAAGAACCC

Found at i:398 original size:63 final size:63

Alignment explanation


    Indices: 316--453  Score: 179
    Period size: 63  Copynumber: 2.2  Consensus size: 63

        306 GGAGGAGCCA

                       *           *  *                        *         *  
        316 AAGAAGGAAGAACCCAAGAAAGAGGAGCCAAAGAAA-GAAGAACCCAAGAAGGAAGAAGAGCAG
          1 AAGAAGGAAGAGCCCAAGAAAGAAGAACCAAA-AAAGGAAGAACCCAAGAAAGAAGAAGAGAAG

                 *        *     *                                *         
        379 AAGAAAGAAGAGCCTAAGAAGGAAGAACCAAAAAAGGAAGAACCCAAGAAAGAGGAAGAGAAG
          1 AAGAAGGAAGAGCCCAAGAAAGAAGAACCAAAAAAGGAAGAACCCAAGAAAGAAGAAGAGAAG

                        
        442 AAGAAGGAAGAG
          1 AAGAAGGAAGAG

        454 GAGAAAAAGC


Statistics
Matches: 64,  Mismatches: 10, Indels: 2
        0.84            0.13        0.03

Matches are distributed among these distances:
  62    3  0.05
  63   61  0.95

ACGTcount: A:0.57, C:0.12, G:0.30, T:0.01


Consensus pattern (63 bp):   
AAGAAGGAAGAGCCCAAGAAAGAAGAACCAAAAAAGGAAGAACCCAAGAAAGAAGAAGAGAAG
Done.