Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_03540

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: 2367
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.22


Found at i:1283 original size:18 final size:18

Alignment explanation


    Indices: 1260--1308  Score: 53
    Period size: 18  Copynumber: 2.7  Consensus size: 18

       1250 GGAGGACTCA

                              
       1260 TAGCCGGAGCCCAAGTCT
          1 TAGCCGGAGCCCAAGTCT

                  *    *    * 
       1278 TAGCCGAAGCCGAAGTGT
          1 TAGCCGGAGCCCAAGTCT

            *   *        
       1296 GAGCAGGAGCCCA
          1 TAGCCGGAGCCCA

       1309 GTTGCAAGTA


Statistics
Matches: 24,  Mismatches: 7, Indels: 0
        0.77            0.23        0.00

Matches are distributed among these distances:
  18   24  1.00

ACGTcount: A:0.27, C:0.29, G:0.33, T:0.12


Consensus pattern (18 bp):   
TAGCCGGAGCCCAAGTCT

Found at i:1600 original size:33 final size:35

Alignment explanation


    Indices: 1560--1643  Score: 100
    Period size: 33  Copynumber: 2.4  Consensus size: 35

       1550 GACTTTCAAA

                    *                          
       1560 GAGAAGCACAAGTAGAAGTCCTGCAAGATC-TC-G
          1 GAGAAGCATAAGTAGAAGTCCTGCAAGATCTTCAG

                     *  **         *            
       1593 GAGAAGCATTAGCGGAAGTCCTGTAAGATCTTCTAG
          1 GAGAAGCATAAGTAGAAGTCCTGCAAGATCTTC-AG

                           
       1629 GAGAAGCATAAGTAG
          1 GAGAAGCATAAGTAG

       1644 GAGCTCTGCT


Statistics
Matches: 40,  Mismatches: 8, Indels: 3
        0.78            0.16        0.06

Matches are distributed among these distances:
  33   25  0.62
  34    2  0.05
  36   13  0.32

ACGTcount: A:0.36, C:0.17, G:0.29, T:0.19


Consensus pattern (35 bp):   
GAGAAGCATAAGTAGAAGTCCTGCAAGATCTTCAG

Found at i:2164 original size:36 final size:36

Alignment explanation


    Indices: 2086--2164  Score: 106
    Period size: 36  Copynumber: 2.2  Consensus size: 36

       2076 TGGTCATGGC

                               *          *     
       2086 CGCAGCCGTAGTCCAAGTCGAAGTCGAACCTCTATT
          1 CGCAGCCGTAGTCCAAGTCAAAGTCGAACCCCTATT

             *                                *  
       2122 CACAGCCGTAG-CTCAAGTCAAAGTCGAACCCCTGTT
          1 CGCAGCCGTAGTC-CAAGTCAAAGTCGAACCCCTATT

                   
       2158 CGCAGCC
          1 CGCAGCC

       2165 ATATTGCAGT


Statistics
Matches: 37,  Mismatches: 5, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  35    1  0.03
  36   36  0.97

ACGTcount: A:0.25, C:0.34, G:0.22, T:0.19


Consensus pattern (36 bp):   
CGCAGCCGTAGTCCAAGTCAAAGTCGAACCCCTATT
Done.