Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_31136

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, 271

Length: 453
ACGTcount: A:0.39, C:0.15, G:0.30, T:0.16


Found at i:166 original size:21 final size:21

Alignment explanation


    Indices: 142--183  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        132 CACTGGTGAT

                     *           
        142 AAAGATGACGATAAGCACAAG
          1 AAAGATGACCATAAGCACAAG

                                 
        163 AAAGATGACCATAAGCACAAG
          1 AAAGATGACCATAAGCACAAG

        184 GAACGCAAAG


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.52, C:0.17, G:0.21, T:0.10


Consensus pattern (21 bp):   
AAAGATGACCATAAGCACAAG

Found at i:183 original size:105 final size:105

Alignment explanation


    Indices: 1--213  Score: 383
    Period size: 105  Copynumber: 2.0  Consensus size: 105

                                                                 *           
          1 ATGATGGATAAAATCAAGGACATGATCACGGGTGATAAAGATGACGATAAGCATAAGAAAGATGA
          1 ATGATGGATAAAATCAAGGACATGATCACGGGTGATAAAGATGACGATAAGCACAAGAAAGATGA

                                     *               
         66 CCATAAGCACAAGG-ACAGCAAAGACCACAAGGATGAAGGG
         66 CCATAAGCACAAGGAAC-GCAAAGAACACAAGGATGAAGGG

                                         *                                   
        106 ATGATGGATAAAATCAAGGACATGATCACTGGTGATAAAGATGACGATAAGCACAAGAAAGATGA
          1 ATGATGGATAAAATCAAGGACATGATCACGGGTGATAAAGATGACGATAAGCACAAGAAAGATGA

                                                    
        171 CCATAAGCACAAGGAACGCAAAGAACACAAGGATGAAGGG
         66 CCATAAGCACAAGGAACGCAAAGAACACAAGGATGAAGGG

               
        211 ATG
          1 ATG

        214 CTAGATAAGA


Statistics
Matches: 104,  Mismatches: 3, Indels: 2
        0.95            0.03        0.02

Matches are distributed among these distances:
 105  102  0.98
 106    2  0.02

ACGTcount: A:0.46, C:0.14, G:0.26, T:0.14


Consensus pattern (105 bp):   
ATGATGGATAAAATCAAGGACATGATCACGGGTGATAAAGATGACGATAAGCACAAGAAAGATGA
CCATAAGCACAAGGAACGCAAAGAACACAAGGATGAAGGG

Found at i:420 original size:15 final size:16

Alignment explanation


    Indices: 383--420  Score: 53
    Period size: 15  Copynumber: 2.5  Consensus size: 16

        373 AGTGATGACG

                            
        383 AGAAG-AAGAAAAAGA
          1 AGAAGAAAGAAAAAGA

                     *      
        398 AGAAGAAAGGAAAA-A
          1 AGAAGAAAGAAAAAGA

                    
        413 AGAAGAAA
          1 AGAAGAAA

        421 CACGATGGCA


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  15   14  0.67
  16    7  0.33

ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00


Consensus pattern (16 bp):   
AGAAGAAAGAAAAAGA
Done.