Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_01341

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, 1000

Length: 2474
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27


Found at i:1462 original size:71 final size:72

Alignment explanation


    Indices: 1345--1563  Score: 350
    Period size: 72  Copynumber: 3.1  Consensus size: 72

       1335 TGGCTTTCAT

                                                                             
       1345 TCTTCGGGTTCTACATTGGGTAATGGGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA
          1 TCTTCGGGTTCTACATTGGGTAATGGGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA

                   
       1410 TAGCAGC
         66 TAGCAGC

                         * *   *            *              *   *          *  
       1417 TCTTCGGGTTCTATAGTGGTTAAT-GGCTCTTTGGAAGCAGTAGCAGGTCTCACCCTAGTCTCAA
          1 TCTTCGGGTTCTACATTGGGTAATGGGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA

                   
       1481 TAGCAGC
         66 TAGCAGC

                     *                                                       
       1488 TCTTCGGGTGCTACATTGGGTAATGGGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA
          1 TCTTCGGGTTCTACATTGGGTAATGGGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA

              *    
       1553 TAACAGC
         66 TAGCAGC

                
       1560 TCTT
          1 TCTT

       1564 ACCCTACCCT


Statistics
Matches: 130,  Mismatches: 16, Indels: 2
        0.88            0.11        0.01

Matches are distributed among these distances:
  71   63  0.48
  72   67  0.52

ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30


Consensus pattern (72 bp):   
TCTTCGGGTTCTACATTGGGTAATGGGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA
TAGCAGC

Found at i:1575 original size:24 final size:24

Alignment explanation


    Indices: 1532--1577  Score: 74
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       1522 GAAGCAGTAG

                          **        
       1532 CAGCTCTTACCCTAGTCTGAATAA
          1 CAGCTCTTACCCTACCCTGAATAA

                                  
       1556 CAGCTCTTACCCTACCCTGAAT
          1 CAGCTCTTACCCTACCCTGAAT

       1578 CCTGGTTACA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  24   20  1.00

ACGTcount: A:0.26, C:0.35, G:0.11, T:0.28


Consensus pattern (24 bp):   
CAGCTCTTACCCTACCCTGAATAA

Found at i:2316 original size:6 final size:6

Alignment explanation


    Indices: 2301--2364  Score: 74
    Period size: 6  Copynumber: 10.7  Consensus size: 6

       2291 GACTGCCCCA

                 *                                  *      *      *
       2301 GCTCCT GCTCCC GCTCCC GCTCCC GCTCCC GCTCCT GCTCCA GCTCCT
          1 GCTCCC GCTCCC GCTCCC GCTCCC GCTCCC GCTCCC GCTCCC GCTCCC

                 *      *     
       2349 GCTCCT GCTCCA GCTC
          1 GCTCCC GCTCCC GCTC

       2365 TGGCTGTATA


Statistics
Matches: 53,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   6   53  1.00

ACGTcount: A:0.03, C:0.56, G:0.17, T:0.23


Consensus pattern (6 bp):   
GCTCCC

Found at i:2328 original size:18 final size:18

Alignment explanation


    Indices: 2301--2364  Score: 92
    Period size: 18  Copynumber: 3.6  Consensus size: 18

       2291 GACTGCCCCA

                 *           *
       2301 GCTCCTGCTCCCGCTCCC
          1 GCTCCAGCTCCCGCTCCT

                 *            
       2319 GCTCCCGCTCCCGCTCCT
          1 GCTCCAGCTCCCGCTCCT

                       *      
       2337 GCTCCAGCTCCTGCTCCT
          1 GCTCCAGCTCCCGCTCCT

                      
       2355 GCTCCAGCTC
          1 GCTCCAGCTC

       2365 TGGCTGTATA


Statistics
Matches: 42,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  18   42  1.00

ACGTcount: A:0.03, C:0.56, G:0.17, T:0.23


Consensus pattern (18 bp):   
GCTCCAGCTCCCGCTCCT
Done.