Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_18506

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: 2793
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24


Found at i:1160 original size:90 final size:90

Alignment explanation


    Indices: 691--1148  Score: 772
    Period size: 90  Copynumber: 5.1  Consensus size: 90

        681 AATGTTTGAA

                                                              *        *     
        691 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCTGATTGGACTTCCTT
          1 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCCGATTGGACATCCTT

                                     
        756 TTTAGAACGAAACAAGGAATGGAAT
         66 TTTAGAACGAAACAAGGAATGGAAT

                          *                                      *           
        781 CGTCGCCGTCTTCTTCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCCGACTGGACATCCTT
          1 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCCGATTGGACATCCTT

                                     
        846 TTTAGAACGAAACAAGGAATGGAAT
         66 TTTAGAACGAAACAAGGAATGGAAT

                 *        *            *                                     
        871 CGTCGTCGTCTTCTTCAAGACGAAGATAGACTTCCGGTTATTGGCCATTCCGATTGGACATCCTT
          1 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCCGATTGGACATCCTT

                                     
        936 TTTAGAACGAAACAAGGAATGGAAT
         66 TTTAGAACGAAACAAGGAATGGAAT

                                                   * *                       
        961 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTGTCGGCCATTCCGATTGGACATCCTT
          1 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCCGATTGGACATCCTT

                           *         
       1026 TTTAGAACGAAACAAAGAATGGAAT
         66 TTTAGAACGAAACAAGGAATGGAAT

                 *                     *                                  *  
       1051 CGTCGTCGTCTTCTCCAAGACGAAGATAGACTTCCGGTTATTGGCCATTCCGATTGGACATCATT
          1 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCCGATTGGACATCCTT

                     *              *
       1116 TTTAGAACGGAACAAGGAATGGAAC
         66 TTTAGAACGAAACAAGGAATGGAAT

              *     
       1141 CGCCGCCG
          1 CGTCGCCG

       1149 GATGCTCCAA


Statistics
Matches: 345,  Mismatches: 23, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  90  345  1.00

ACGTcount: A:0.26, C:0.23, G:0.23, T:0.27


Consensus pattern (90 bp):   
CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTATTGGCCATTCCGATTGGACATCCTT
TTTAGAACGAAACAAGGAATGGAAT

Found at i:2273 original size:51 final size:51

Alignment explanation


    Indices: 2213--2613  Score: 516
    Period size: 51  Copynumber: 7.9  Consensus size: 51

       2203 AAAACTGAAG

                *     *        *    *                   *      
       2213 ACAAAGGGTTGATCCCTACGTCCCTAGATGTTCCCGCTAGTAAATCCGAAA
          1 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA

                                                          *    
       2264 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCTGAAA
          1 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA

                                                               
       2315 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA
          1 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA

               *    *             *                            
       2366 ACAGTGGGCTCATCCCTACCTCTCCAGATGTTCCCGCTAGTAAACCCGAAA
          1 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA

               *       *               *         *              
       2417 ACAGTGAGG-TGATCCCTACCTCCCCAAATGTTCCCGTTAGTAAACCCGAAA
          1 ACAATG-GGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA

                                            *   *              
       2468 ACAATGGGTTCATCCCTACCTCCCCAGATGTTTCCGTTAGTAAACCCGAAA
          1 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA

               *      *       *   *      *  *             *    
       2519 ACAGTGGGTTGATCCCTATCTCTCCAGATCTTTCCGCTAGTAAACCTGAAA
          1 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA

                    * **  *   *       *  *  *           
       2570 ACAATGGGGTGGTCTCTATCTCCCCAAATCTTTCCGCTAGTAAA
          1 ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAA

       2614 GCCGCACACA


Statistics
Matches: 317,  Mismatches: 31, Indels: 4
        0.90            0.09        0.01

Matches are distributed among these distances:
  50    2  0.01
  51  313  0.99
  52    2  0.01

ACGTcount: A:0.27, C:0.31, G:0.17, T:0.24


Consensus pattern (51 bp):   
ACAATGGGTTCATCCCTACCTCCCCAGATGTTCCCGCTAGTAAACCCGAAA

Found at i:2686 original size:21 final size:21

Alignment explanation


    Indices: 2662--2730  Score: 120
    Period size: 21  Copynumber: 3.3  Consensus size: 21

       2652 ACACAAGAAA

                                 
       2662 AAGAAGCACCATGGGAAAGGG
          1 AAGAAGCACCATGGGAAAGGG

                          *      
       2683 AAGAAGCACCATGGAAAAGGG
          1 AAGAAGCACCATGGGAAAGGG

                        *        
       2704 AAGAAGCACCATAGGAAAGGG
          1 AAGAAGCACCATGGGAAAGGG

                  
       2725 AAGAAG
          1 AAGAAG

       2731 AAAGGGAAGA


Statistics
Matches: 45,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  21   45  1.00

ACGTcount: A:0.48, C:0.13, G:0.35, T:0.04


Consensus pattern (21 bp):   
AAGAAGCACCATGGGAAAGGG
Done.