Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_25931

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, 826

Length: 1377
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.21


Found at i:318 original size:3 final size:3

Alignment explanation


    Indices: 310--347  Score: 51
    Period size: 3  Copynumber: 12.7  Consensus size: 3

        300 CAAAGGTGGA

                              *                                
        310 AAC AAC AAC AAC AAG AAC AAC AACC AA- AAC AAC AAC AA
          1 AAC AAC AAC AAC AAC AAC AAC AA-C AAC AAC AAC AAC AA

        348 GGGTGGTCAG


Statistics
Matches: 31,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
   2    2  0.06
   3   26  0.84
   4    3  0.10

ACGTcount: A:0.68, C:0.29, G:0.03, T:0.00


Consensus pattern (3 bp):   
AAC

Found at i:581 original size:3 final size:3

Alignment explanation


    Indices: 573--650  Score: 59
    Period size: 3  Copynumber: 25.0  Consensus size: 3

        563 AAGATTTCAG

                         *                                           **    
        573 TGA TGA TGA TTA TGA TGA TGA TGA CTTGGA TGA TGA TTG- TGA TCT TGA
          1 TGA TGA TGA TGA TGA TGA TGA TGA --T-GA TGA TGA -TGA TGA TGA TGA

                             **           *        
        621 TGA TGA TGA TGA TTT TGA TGA TGG TGA TGA
          1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA

        651 GTTGGATGAT


Statistics
Matches: 58,  Mismatches: 12, Indels: 10
        0.73            0.15        0.12

Matches are distributed among these distances:
   2    2  0.03
   3   50  0.86
   4    3  0.05
   5    1  0.02
   6    2  0.03

ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40


Consensus pattern (3 bp):   
TGA

Found at i:596 original size:18 final size:17

Alignment explanation


    Indices: 573--660  Score: 83
    Period size: 18  Copynumber: 5.1  Consensus size: 17

        563 AAGATTTCAG

                             
        573 TGATGATGA-TT-ATGA
          1 TGATGATGATTTGATGA

                        *     
        588 TGATGATGACTTGGATGA
          1 TGATGATGA-TTTGATGA

                               
        606 TGATTG-TGATCTTGATGA
          1 TGA-TGATGAT-TTGATGA

                              
        624 TGATGATGATTTTGATGA
          1 TGATGATGA-TTTGATGA

              *         *     
        642 TGGTGATGAGTTGGATGA
          1 TGATGATGA-TTTGATGA

             
        660 T
          1 T

        661 CATCGTCATC


Statistics
Matches: 61,  Mismatches: 5, Indels: 11
        0.79            0.06        0.14

Matches are distributed among these distances:
  15    9  0.15
  17    4  0.07
  18   45  0.74
  19    3  0.05

ACGTcount: A:0.26, C:0.02, G:0.32, T:0.40


Consensus pattern (17 bp):   
TGATGATGATTTGATGA

Found at i:995 original size:15 final size:15

Alignment explanation


    Indices: 960--996  Score: 53
    Period size: 12  Copynumber: 2.7  Consensus size: 15

        950 CATATCAAGG

                           
        960 TGGCGGTGGTAAAAA
          1 TGGCGGTGGTAAAAA

                           
        975 ---CGGTGGTAAAAA
          1 TGGCGGTGGTAAAAA

                      
        987 TGGCGGTGGT
          1 TGGCGGTGGT

        997 TTACCTCAGG


Statistics
Matches: 19,  Mismatches: 0, Indels: 6
        0.76            0.00        0.24

Matches are distributed among these distances:
  12   12  0.63
  15    7  0.37

ACGTcount: A:0.27, C:0.08, G:0.43, T:0.22


Consensus pattern (15 bp):   
TGGCGGTGGTAAAAA
Done.