Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_10822

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, 325

Length: 543
ACGTcount: A:0.23, C:0.17, G:0.41, T:0.19


Found at i:424 original size:27 final size:24

Alignment explanation


    Indices: 393--446  Score: 72
    Period size: 24  Copynumber: 2.1  Consensus size: 24

        383 TATTCGGGAA

                                       
        393 TGGTGGAGGATATGACGGCGGAGGCGG
          1 TGGTGGAGGATAT---GGCGGAGGCGG

                  *                 
        420 TGGTGGCGGATATGGCGGAGGCGG
          1 TGGTGGAGGATATGGCGGAGGCGG

               
        444 TGG
          1 TGG

        447 AGGATATGGA


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  24   14  0.54
  27   12  0.46

ACGTcount: A:0.15, C:0.11, G:0.57, T:0.17


Consensus pattern (24 bp):   
TGGTGGAGGATATGGCGGAGGCGG

Found at i:460 original size:24 final size:24

Alignment explanation


    Indices: 394--461  Score: 70
    Period size: 24  Copynumber: 2.8  Consensus size: 24

        384 ATTCGGGAAT

                                      
        394 GGTGGAGGATATGACGGCGGAGGCGG
          1 GGTGGAGGATATGA-GGCGGAGGC-G

                  *                  
        420 TGGTGGCGGATAT--GGCGGAGGC-
          1 -GGTGGAGGATATGAGGCGGAGGCG

                                
        442 GGTGGAGGATATGGAGGCGG
          1 GGTGGAGGATAT-GAGGCGG

        462 TGGCCGATAT


Statistics
Matches: 36,  Mismatches: 2, Indels: 9
        0.77            0.04        0.19

Matches are distributed among these distances:
  21   11  0.31
  24   14  0.39
  27   11  0.31

ACGTcount: A:0.18, C:0.10, G:0.57, T:0.15


Consensus pattern (24 bp):   
GGTGGAGGATATGAGGCGGAGGCG

Found at i:464 original size:39 final size:39

Alignment explanation


    Indices: 421--539  Score: 184
    Period size: 39  Copynumber: 3.0  Consensus size: 39

        411 CGGAGGCGGT

                                                   
        421 GGTGGCGGATATGGCGGAGGCGGTGGAGGATATGGAGGC
          1 GGTGGCGGATATGGCGGAGGCGGTGGAGGATATGGAGGC

                  *                                
        460 GGTGGCCGATATGGCGGAGGCGGTGGAGGATATGGAGGC
          1 GGTGGCGGATATGGCGGAGGCGGTGGAGGATATGGAGGC

                                *        *           
        499 GGTGGCGGATATGGCGGCGGTGGCGGTGGTGGATATGGAGG
          1 GGTGGCGGATAT---GGCGGAGGCGGTGGAGGATATGGAGG

        540 TTGA


Statistics
Matches: 73,  Mismatches: 4, Indels: 3
        0.91            0.05        0.04

Matches are distributed among these distances:
  39   49  0.67
  42   24  0.33

ACGTcount: A:0.16, C:0.11, G:0.56, T:0.17


Consensus pattern (39 bp):   
GGTGGCGGATATGGCGGAGGCGGTGGAGGATATGGAGGC

Found at i:505 original size:24 final size:23

Alignment explanation


    Indices: 472--539  Score: 65
    Period size: 24  Copynumber: 3.1  Consensus size: 23

        462 TGGCCGATAT

                 *                  
        472 GGCGGAGGCGGTGGAGGATATGGA
          1 GGCGGTGGCGGTGG-GGATATGGA

                                  *
        496 GGCGGTGGC-----GGATATGGC
          1 GGCGGTGGCGGTGGGGATATGGA

                                    
        514 GGCGGTGGCGGTGGTGGATATGGA
          1 GGCGGTGGCGGTGG-GGATATGGA

              
        538 GG
          1 GG

        540 TTGA


Statistics
Matches: 35,  Mismatches: 3, Indels: 12
        0.70            0.06        0.24

Matches are distributed among these distances:
  18   17  0.49
  24   18  0.51

ACGTcount: A:0.15, C:0.10, G:0.59, T:0.16


Consensus pattern (23 bp):   
GGCGGTGGCGGTGGGGATATGGA

Found at i:522 original size:18 final size:18

Alignment explanation


    Indices: 415--524  Score: 112
    Period size: 18  Copynumber: 5.8  Consensus size: 18

        405 TGACGGCGGA

                 *            
        415 GGCGGTGGTGGCGGATAT
          1 GGCGGCGGTGGCGGATAT

                          *      
        433 GGCGGAGGCGGTGGAGGATAT
          1 GGC---GGCGGTGGCGGATAT

              *         *     
        454 GGAGGCGGTGGCCGATAT
          1 GGCGGCGGTGGCGGATAT

                          *      
        472 GGCGGAGGCGGTGGAGGATAT
          1 GGC---GGCGGTGGCGGATAT

              *               
        493 GGAGGCGGTGGCGGATAT
          1 GGCGGCGGTGGCGGATAT

                          
        511 GGCGGCGGTGGCGG
          1 GGCGGCGGTGGCGG

        525 TGGTGGATAT


Statistics
Matches: 75,  Mismatches: 11, Indels: 12
        0.77            0.11        0.12

Matches are distributed among these distances:
  18   45  0.60
  21   30  0.40

ACGTcount: A:0.15, C:0.13, G:0.57, T:0.15


Consensus pattern (18 bp):   
GGCGGCGGTGGCGGATAT
Done.