Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_25287

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: 2964
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23


Found at i:1559 original size:42 final size:42

Alignment explanation


    Indices: 1513--1671  Score: 153
    Period size: 42  Copynumber: 3.8  Consensus size: 42

       1503 TCATGCAAGG

                            *      **                 
       1513 TCAAGATCCAAATCAAAATCACCCCTTAGTTATCGGAGAAGA
          1 TCAAGATCCAAATCAAGATCACCAATTAGTTATCGGAGAAGA

                           *                     *     
       1555 TCAAGAT-CAAAGTCTAGATCACCAATTAGTTATCGGCGAAGA
          1 TCAAGATCCAAA-TCAAGATCACCAATTAGTTATCGGAGAAGA

                 *     *              * *    *  *     
       1597 TCAAGGTCCAAGTCAAGATCACCAATCATTTATAGGCGAA-A
          1 TCAAGATCCAAATCAAGATCACCAATTAGTTATCGGAGAAGA

                  *                     *      
       1638 GTCAAGGT-CAAAGTCAAGATCACCAATCAGTTAT
          1 -TCAAGATCCAAA-TCAAGATCACCAATTAGTTAT

       1672 AGGCGAAGGA


Statistics
Matches: 100,  Mismatches: 13, Indels: 8
        0.83            0.11        0.07

Matches are distributed among these distances:
  41    8  0.08
  42   89  0.89
  43    3  0.03

ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23


Consensus pattern (42 bp):   
TCAAGATCCAAATCAAGATCACCAATTAGTTATCGGAGAAGA

Found at i:1672 original size:42 final size:43

Alignment explanation


    Indices: 1551--1678  Score: 188
    Period size: 42  Copynumber: 3.0  Consensus size: 43

       1541 GTTATCGGAG

                     *        *           *      *     
       1551 AAGATCAAGATCAAAGTCTAGATCACCAATTAGTTATCGGCG-
          1 AAGATCAAGGTCAAAGTCAAGATCACCAATCAGTTATAGGCGA

                        *                   *          
       1593 AAGATCAAGGTCCAAGTCAAGATCACCAATCATTTATAGGCGA
          1 AAGATCAAGGTCAAAGTCAAGATCACCAATCAGTTATAGGCGA

                                                       
       1636 AAG-TCAAGGTCAAAGTCAAGATCACCAATCAGTTATAGGCGA
          1 AAGATCAAGGTCAAAGTCAAGATCACCAATCAGTTATAGGCGA

             
       1678 A
          1 A

       1679 GGAGGAGATC


Statistics
Matches: 77,  Mismatches: 8, Indels: 2
        0.89            0.09        0.02

Matches are distributed among these distances:
  42   74  0.96
  43    3  0.04

ACGTcount: A:0.40, C:0.20, G:0.20, T:0.21


Consensus pattern (43 bp):   
AAGATCAAGGTCAAAGTCAAGATCACCAATCAGTTATAGGCGA

Found at i:2480 original size:45 final size:45

Alignment explanation


    Indices: 2407--2503  Score: 140
    Period size: 45  Copynumber: 2.2  Consensus size: 45

       2397 TAAGAAATCT

                            * *   **                     
       2407 AAGCATCGGGATAGAAGGCGGTTGAGGTCAAGATCTGCTGATGGC
          1 AAGCATCGGGATAGAAAGAGGTCAAGGTCAAGATCTGCTGATGGC

                                                **       
       2452 AAGCATCGGGATAGAAAGAGGTCAAGGTCAAGATCTTTTGATGGC
          1 AAGCATCGGGATAGAAAGAGGTCAAGGTCAAGATCTGCTGATGGC

                   
       2497 AAGCATC
          1 AAGCATC

       2504 ACAGAGGAAG


Statistics
Matches: 46,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  45   46  1.00

ACGTcount: A:0.31, C:0.15, G:0.33, T:0.21


Consensus pattern (45 bp):   
AAGCATCGGGATAGAAAGAGGTCAAGGTCAAGATCTGCTGATGGC
Done.