Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_15982

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, 378

Length: 630
ACGTcount: A:0.22, C:0.09, G:0.45, T:0.24


Found at i:419 original size:15 final size:15

Alignment explanation


    Indices: 386--419  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

        376 GGAGGAGGAG

                       *  *
        386 GAGGTGGTGGCGGTG
          1 GAGGTGGTGGCAGTA

                           
        401 GAGGTGGTGGCAGTA
          1 GAGGTGGTGGCAGTA

                
        416 GAGG
          1 GAGG

        420 AGGGTCCGGA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.15, C:0.06, G:0.62, T:0.18


Consensus pattern (15 bp):   
GAGGTGGTGGCAGTA

Found at i:422 original size:18 final size:15

Alignment explanation


    Indices: 382--411  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

        372 TGGAGGAGGA

                           
        382 GGAGGAGGTGGTGGC
          1 GGAGGAGGTGGTGGC

              *            
        397 GGTGGAGGTGGTGGC
          1 GGAGGAGGTGGTGGC

        412 AGTAGAGGAG


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.10, C:0.07, G:0.67, T:0.17


Consensus pattern (15 bp):   
GGAGGAGGTGGTGGC

Found at i:447 original size:111 final size:111

Alignment explanation


    Indices: 308--521  Score: 383
    Period size: 111  Copynumber: 1.9  Consensus size: 111

        298 TCAGATGGAA

                                                                            *
        308 GAGGGTCCGGATACGGAAGTGGATCTGGATATGGAAGTGGAGGTGGTAGTGCTAGTAGTGGTGGT
          1 GAGGGTCCGGATACGGAAGTGGATCTGGATATGGAAGTGGAGGTGGTAGTGCTAGTAGTGGTGGA

                             *              *             
        373 GGAGGAGGAGGAGGAGGTGGTGGCGGTGGAGGTGGTGGCAGTAGAG
         66 GGAGGAGGAGGAGGAGGAGGTGGCGGTGGAGGAGGTGGCAGTAGAG

                                                                 *  *        
        419 GAGGGTCCGGATACGGAAGTGGATCTGGATATGGAAGTGGAGGTGGTAGTGCTGGTGGTGGTGGA
          1 GAGGGTCCGGATACGGAAGTGGATCTGGATATGGAAGTGGAGGTGGTAGTGCTAGTAGTGGTGGA

                                                  
        484 GGAGGAGGAGGAGGAGGAGGTGGCGGTGGAGGAGGTGG
         66 GGAGGAGGAGGAGGAGGAGGTGGCGGTGGAGGAGGTGG

        522 TGGTGGAGGA


Statistics
Matches: 98,  Mismatches: 5, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 111   98  1.00

ACGTcount: A:0.21, C:0.06, G:0.55, T:0.19


Consensus pattern (111 bp):   
GAGGGTCCGGATACGGAAGTGGATCTGGATATGGAAGTGGAGGTGGTAGTGCTAGTAGTGGTGGA
GGAGGAGGAGGAGGAGGAGGTGGCGGTGGAGGAGGTGGCAGTAGAG

Found at i:487 original size:3 final size:3

Alignment explanation


    Indices: 481--539  Score: 55
    Period size: 3  Copynumber: 19.7  Consensus size: 3

        471 TGGTGGTGGT

                                          *   *   *           *   *   *    
        481 GGA GGA GGA GGA GGA GGA GGA GGT GGC GGT GGA GGA GGT GGT GGT GGA
          1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA

                    *     
        529 GGA GGA AGA GG
          1 GGA GGA GGA GG

        540 TGGTGGAAGT


Statistics
Matches: 48,  Mismatches: 8, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
   3   48  1.00

ACGTcount: A:0.24, C:0.02, G:0.66, T:0.08


Consensus pattern (3 bp):   
GGA

Found at i:499 original size:15 final size:15

Alignment explanation


    Indices: 478--542  Score: 76
    Period size: 15  Copynumber: 4.3  Consensus size: 15

        468 TGCTGGTGGT

                           
        478 GGTGGAGGAGGAGGA
          1 GGTGGAGGAGGAGGA

              *        *  *
        493 GGAGGAGGAGGTGGC
          1 GGTGGAGGAGGAGGA

                       *  *
        508 GGTGGAGGAGGTGGT
          1 GGTGGAGGAGGAGGA

                        *  
        523 GGTGGAGGAGGAAGA
          1 GGTGGAGGAGGAGGA

                 
        538 GGTGG
          1 GGTGG

        543 TGGAAGTAGA


Statistics
Matches: 42,  Mismatches: 8, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  15   42  1.00

ACGTcount: A:0.22, C:0.02, G:0.66, T:0.11


Consensus pattern (15 bp):   
GGTGGAGGAGGAGGA

Found at i:543 original size:18 final size:18

Alignment explanation


    Indices: 490--546  Score: 78
    Period size: 18  Copynumber: 3.2  Consensus size: 18

        480 TGGAGGAGGA

                             *
        490 GGAGGAGGAGGAGGTGGC
          1 GGAGGAGGAGGAGGTGGT

              *        *      
        508 GGTGGAGGAGGTGGTGGT
          1 GGAGGAGGAGGAGGTGGT

                     *        
        526 GGAGGAGGAAGAGGTGGT
          1 GGAGGAGGAGGAGGTGGT

               
        544 GGA
          1 GGA

        547 AGTAGAGGCA


Statistics
Matches: 33,  Mismatches: 6, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  18   33  1.00

ACGTcount: A:0.21, C:0.02, G:0.65, T:0.12


Consensus pattern (18 bp):   
GGAGGAGGAGGAGGTGGT

Found at i:593 original size:30 final size:30

Alignment explanation


    Indices: 552--608  Score: 78
    Period size: 30  Copynumber: 1.9  Consensus size: 30

        542 GTGGAAGTAG

                           *              
        552 AGGCAATGGCTCAAGTTATGGAAGTGGATC
          1 AGGCAATGGCTCAAGGTATGGAAGTGGATC

                *        *       *     
        582 AGGCTATGGCTCAGGGTATGGTAGTGG
          1 AGGCAATGGCTCAAGGTATGGAAGTGG

        609 GGAAGGTGGT


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  30   23  1.00

ACGTcount: A:0.25, C:0.12, G:0.39, T:0.25


Consensus pattern (30 bp):   
AGGCAATGGCTCAAGGTATGGAAGTGGATC
Done.