Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_08497

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, 934

Length: 1557
ACGTcount: A:0.30, C:0.21, G:0.29, T:0.20


Found at i:285 original size:11 final size:11

Alignment explanation


    Indices: 260--318  Score: 54
    Period size: 11  Copynumber: 5.7  Consensus size: 11

        250 AAAGAAGCCG

                       
        260 AGAAGCCGA-A
          1 AGAAGCCGAGA

                  *    
        270 AGAAGCTGAGA
          1 AGAAGCCGAGA

                       
        281 AGAAGCCG-GA
          1 AGAAGCCGAGA

                *  *   
        291 A-AAACCCA-A
          1 AGAAGCCGAGA

                  *    
        300 AGAAGCTGAGA
          1 AGAAGCCGAGA

                    
        311 AGAAGCCG
          1 AGAAGCCG

        319 GAAAAACCCA


Statistics
Matches: 37,  Mismatches: 8, Indels: 7
        0.71            0.15        0.13

Matches are distributed among these distances:
   9    6  0.16
  10   15  0.41
  11   16  0.43

ACGTcount: A:0.47, C:0.19, G:0.31, T:0.03


Consensus pattern (11 bp):   
AGAAGCCGAGA

Found at i:304 original size:30 final size:30

Alignment explanation


    Indices: 251--333  Score: 132
    Period size: 30  Copynumber: 2.8  Consensus size: 30

        241 GACAAACCTA

                       *  *  *            
        251 AAGAAGCC-GAGAAGCCGAAAGAAGCTGAG
          1 AAGAAGCCGGAAAAACCCAAAGAAGCTGAG

                                          
        280 AAGAAGCCGGAAAAACCCAAAGAAGCTGAG
          1 AAGAAGCCGGAAAAACCCAAAGAAGCTGAG

                                    
        310 AAGAAGCCGGAAAAACCCAAAGAA
          1 AAGAAGCCGGAAAAACCCAAAGAA

        334 CCGGAAAAAC


Statistics
Matches: 50,  Mismatches: 3, Indels: 1
        0.93            0.06        0.02

Matches are distributed among these distances:
  29    8  0.16
  30   42  0.84

ACGTcount: A:0.51, C:0.19, G:0.28, T:0.02


Consensus pattern (30 bp):   
AAGAAGCCGGAAAAACCCAAAGAAGCTGAG

Found at i:339 original size:18 final size:18

Alignment explanation


    Indices: 310--381  Score: 117
    Period size: 18  Copynumber: 3.9  Consensus size: 18

        300 AGAAGCTGAG

                               
        310 AAGAAGCCGGAAAAACCCA
          1 AAGAA-CCGGAAAAACCCA

                              
        329 AAGAACCGGAAAAACCCA
          1 AAGAACCGGAAAAACCCA

               *              
        347 AAGCACCGGAAAAACCCA
          1 AAGAACCGGAAAAACCCA

               *             
        365 AAGCACCGGAAAAACCC
          1 AAGAACCGGAAAAACCC

        382 GCGGAACCTG


Statistics
Matches: 52,  Mismatches: 1, Indels: 1
        0.96            0.02        0.02

Matches are distributed among these distances:
  18   47  0.90
  19    5  0.10

ACGTcount: A:0.51, C:0.31, G:0.18, T:0.00


Consensus pattern (18 bp):   
AAGAACCGGAAAAACCCA
Done.