Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_29805

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: 3918
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28


Found at i:2485 original size:222 final size:222

Alignment explanation


    Indices: 2099--2527  Score: 705
    Period size: 222  Copynumber: 1.9  Consensus size: 222

       2089 ATAGAAGTTG

                       *       *                       *         *           
       2099 AAGGCATTTCTTATATGGTTACACCTGATACAAATTGCAAACATAAAATTTTGGTGAAAGAAACA
          1 AAGGCATTTCTGATATGGTAACACCTGATACAAATTGCAAACAAAAAATTTTGATGAAAGAAACA

                           *               *           *  *                  
       2164 CCTGGAAAACTTTCATTAGATTTAGAGCAGCTGCAAGACCCTGCATGTTCCCAGGAATTGCAGCC
         66 CCTGGAAAACTTTCACTAGATTTAGAGCAGCAGCAAGACCCTGAATATTCCCAGGAATTGCAGCC

                            *                      *                         
       2229 TTCAGAAGCATTTGCTGATGTTGCTGTTGAAATGAATGATGGATCTGACACAATGAATCAAACTG
        131 TTCAGAAGCATTTGCTAATGTTGCTGTTGAAATGAATGACGGATCTGACACAATGAATCAAACTG

                                       
       2294 GTGACAGCTACAATAACAGTGATGTTA
        196 GTGACAGCTACAATAACAGTGATGTTA

                                      *  *       *  *                     *  
       2321 AAGGCATTTCTGATATGGTAACACCTTATGCAAATTGTAAGCAAAAAATTTTGATGAAAGAAGCA
          1 AAGGCATTTCTGATATGGTAACACCTGATACAAATTGCAAACAAAAAATTTTGATGAAAGAAACA

                             *                                      *        
       2386 CCTGGAAAACTTTCACTGGATTTAGAGCAGCAGCAAGACCCTGAATATTCCCAGGATTTGCAGCC
         66 CCTGGAAAACTTTCACTAGATTTAGAGCAGCAGCAAGACCCTGAATATTCCCAGGAATTGCAGCC

                                                                             
       2451 TTCAGAAGCATTTGCTAATGTTGCTGTTGAAATGAATGACGGATCTGACACAATGAATCAAACTG
        131 TTCAGAAGCATTTGCTAATGTTGCTGTTGAAATGAATGACGGATCTGACACAATGAATCAAACTG

                        
       2516 GTGACAGCTACA
        196 GTGACAGCTACA

       2528 GTCATAATGA


Statistics
Matches: 190,  Mismatches: 17, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
 222  190  1.00

ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27


Consensus pattern (222 bp):   
AAGGCATTTCTGATATGGTAACACCTGATACAAATTGCAAACAAAAAATTTTGATGAAAGAAACA
CCTGGAAAACTTTCACTAGATTTAGAGCAGCAGCAAGACCCTGAATATTCCCAGGAATTGCAGCC
TTCAGAAGCATTTGCTAATGTTGCTGTTGAAATGAATGACGGATCTGACACAATGAATCAAACTG
GTGACAGCTACAATAACAGTGATGTTA
Done.