Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_00785

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: 8532
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.25


Found at i:4362 original size:381 final size:381

Alignment explanation


    Indices: 3746--4634  Score: 1616
    Period size: 381  Copynumber: 2.3  Consensus size: 381

       3736 AGAAAGCTTG

                                  *                                          
       3746 AGGACAGAATGAAGATGGCTGACGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
          1 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT

                                                                        *  * 
       3811 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGCACGA
         66 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGACAA

                                                               **            
       3876 ACAACTTGCAGAATCAGCAAAGGCAATCTTGAGTAAGGATGCTCTTTTGATTGACCAAGCTACCA
        131 ACAACTTGCAGAATCAGCAAAGGCAATCTTGAGTAAGGATGCTCTTTTGATCAACCAAGCTACCA

                                                                          *  
       3941 TGATTGAAGAAGCAGAAAAACATATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAATCT
        196 TGATTGAAGAAGCAGAAAAACATATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAGCT

                                                                             
       4006 TGCACTGAACTTAGCCAGAGGCTTCTGGAGGAGGAGCAGCATGCTGCTGCTATTGAACAAAAGCT
        261 TGCACTGAACTTAGCCAGAGGCTTCTGGAGGAGGAGCAGCATGCTGCTGCTATTGAACAAAAGCT

                                                               *    
       4071 TGAAGATATGGTGGAGAATGACATTTTGAAGACACAGGAGGAGCTGTCTAATCTTA
        326 TGAAGATATGGTGGAGAATGACATTTTGAAGACACAGGAGGAGCTGTCTAAACTTA

                                                                   *         
       4127 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACCGTTGCTTTT
          1 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT

                                                                             
       4192 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGACAA
         66 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGACAA

                               *    *                                        
       4257 ACAACTTGCAGAATCAGCAGAGGCGATCTTGAGTAAGGATGCTCTTTTGATCAACCAAGCTACCA
        131 ACAACTTGCAGAATCAGCAAAGGCAATCTTGAGTAAGGATGCTCTTTTGATCAACCAAGCTACCA

                              *  *                                           
       4322 TGATTGAAGAAGCAGAAACACGTATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAGCT
        196 TGATTGAAGAAGCAGAAAAACATATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAGCT

                        *                          **                        
       4387 TGCACTGAACTTCGCCAGAGGCTTCTGGAGGAGGAGCAGTGTGCTGCTGCTATTGAACAAAAGCT
        261 TGCACTGAACTTAGCCAGAGGCTTCTGGAGGAGGAGCAGCATGCTGCTGCTATTGAACAAAAGCT

                                  *                                *
       4452 TGAAGATATGGTGGAGAATGACTTTTTGAAGACACAGGAGGAGCTGTCTAAACTTG
        326 TGAAGATATGGTGGAGAATGACATTTTGAAGACACAGGAGGAGCTGTCTAAACTTA

                                           *                                 
       4508 AGGACAGAATGAAGATGGCTGAAGATGACCTAAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
          1 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT

                                                                          
       4573 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGA
         66 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGA

       4635 TGCTCTTCTA


Statistics
Matches: 489,  Mismatches: 19, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
 381  489  1.00

ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25


Consensus pattern (381 bp):   
AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGACAA
ACAACTTGCAGAATCAGCAAAGGCAATCTTGAGTAAGGATGCTCTTTTGATCAACCAAGCTACCA
TGATTGAAGAAGCAGAAAAACATATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAGCT
TGCACTGAACTTAGCCAGAGGCTTCTGGAGGAGGAGCAGCATGCTGCTGCTATTGAACAAAAGCT
TGAAGATATGGTGGAGAATGACATTTTGAAGACACAGGAGGAGCTGTCTAAACTTA
Done.