Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_D_gene_10030422

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, 562

Length: 938
ACGTcount: A:0.43, C:0.11, G:0.27, T:0.19


Found at i:322 original size:21 final size:22

Alignment explanation


    Indices: 298--351  Score: 69
    Period size: 21  Copynumber: 2.5  Consensus size: 22

        288 AAAAGCAAAA

                                   
        298 GAATAAAATAAA-TAAACAT-AT
          1 GAATAAAATAAATTAAA-ATAAT

                                  
        319 GAAT-AAATAAATTAAAATAAT
          1 GAATAAAATAAATTAAAATAAT

                        
        340 GAAATAAAATAA
          1 G-AATAAAATAA

        352 TAATAATAAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 6
        0.83            0.00        0.17

Matches are distributed among these distances:
  20    9  0.31
  21   11  0.38
  22    3  0.10
  23    6  0.21

ACGTcount: A:0.69, C:0.02, G:0.06, T:0.24


Consensus pattern (22 bp):   
GAATAAAATAAATTAAAATAAT

Found at i:359 original size:14 final size:13

Alignment explanation


    Indices: 272--370  Score: 76
    Period size: 14  Copynumber: 7.2  Consensus size: 13

        262 TAAATATCAT

                         
        272 AAATAAAATAA-A
          1 AAATAAAATAATA

                     *    
        284 AAATAAAAGCAA-A
          1 AAATAAAA-TAATA

                           
        297 AGAATAAAATAAATA
          1 A-AATAAAAT-AATA

                   *        
        312 AACATATGAATAAATA
          1 AA-ATA-AAAT-AATA

              *         *
        328 AATTAAAATAATG
          1 AAATAAAATAATA

                         
        341 AAATAAAATAATA
          1 AAATAAAATAATA

                    *     
        354 ATAATAAACTAATA
          1 A-AATAAAATAATA

               
        368 AAA
          1 AAA

        371 ATAATAAGAA


Statistics
Matches: 71,  Mismatches: 9, Indels: 13
        0.76            0.10        0.14

Matches are distributed among these distances:
  12    8  0.11
  13   21  0.30
  14   25  0.35
  15    7  0.10
  16   10  0.14

ACGTcount: A:0.72, C:0.03, G:0.04, T:0.21


Consensus pattern (13 bp):   
AAATAAAATAATA

Done.