Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_33159

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, 645

Length: 1076
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.19


Found at i:299 original size:24 final size:24

Alignment explanation


    Indices: 267--325  Score: 82
    Period size: 24  Copynumber: 2.5  Consensus size: 24

        257 AGGGCACACA

                         *       *  
        267 TAAACCTCCACGATACTCAGGTGG
          1 TAAACCTCCACGACACTCAGGAGG

                      *       *     
        291 TAAACCTCCAAGACACTCGGGAGG
          1 TAAACCTCCACGACACTCAGGAGG

                       
        315 TAAACCTCCAC
          1 TAAACCTCCAC

        326 ATGTTGAGGG


Statistics
Matches: 30,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  24   30  1.00

ACGTcount: A:0.32, C:0.32, G:0.19, T:0.17


Consensus pattern (24 bp):   
TAAACCTCCACGACACTCAGGAGG

Found at i:500 original size:24 final size:24

Alignment explanation


    Indices: 468--527  Score: 93
    Period size: 24  Copynumber: 2.5  Consensus size: 24

        458 AGGGCACACA

                                 *  
        468 TAAACCTCCACAACACTCAGGTGG
          1 TAAACCTCCACAACACTCAGGGGG

                       *   *        
        492 TAAACCTCCACGACATTCAGGGGG
          1 TAAACCTCCACAACACTCAGGGGG

                        
        516 TAAACCTCCACA
          1 TAAACCTCCACA

        528 TGTTGAAGGA


Statistics
Matches: 32,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  24   32  1.00

ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17


Consensus pattern (24 bp):   
TAAACCTCCACAACACTCAGGGGG

Found at i:583 original size:171 final size:171

Alignment explanation


    Indices: 366--957  Score: 812
    Period size: 171  Copynumber: 3.4  Consensus size: 171

        356 CCATGAAGCC

                                 *        * *                     *          
        366 ATTCCCTGGTGACAAACCATCTAAGGGTAATGAAAAGGGAGCACCTCATGAACCTAAACCTCCTC
          1 ATTCCCTGGTGACAAACCATCCAAGGGTAAGGGAAAGGGAGCACCTCATGAACCAAAACCTCCTC

                    *                                                        
        431 ATAGACACTTATTGAGTGTGGAAGTTGAGGGCACACATAAACCTCCACAACACTCAGGTGGTAAA
         66 ATAGACACATATTGAGTGTGGAAGTTGAGGGCACACATAAACCTCCACAACACTCAGGTGGTAAA

                                                     
        496 CCTCCACGACATTCAGGGGGTAAACCTCCACATGTTGAAGG
        131 CCTCCACGACATTCAGGGGGTAAACCTCCACATGTTGAAGG

               *                                   *              *          
        537 ATTTCCTGGTGACAAACCATCCAAGGGTAAGGGAAAGGGGGCACCTCATGAACCCAAACCTCCTC
          1 ATTCCCTGGTGACAAACCATCCAAGGGTAAGGGAAAGGGAGCACCTCATGAACCAAAACCTCCTC

             *                               *                  *            
        602 ACAGACACATATTGAGTGTGGAAGTTGAGGGCATACATAAACCTCCACAACAATCAGGTGGTAAA
         66 ATAGACACATATTGAGTGTGGAAGTTGAGGGCACACATAAACCTCCACAACACTCAGGTGGTAAA

                                                     
        667 CCTCCACGACATTCAGGGGGTAAACCTCCACATGTTGAAGG
        131 CCTCCACGACATTCAGGGGGTAAACCTCCACATGTTGAAGG

                                                                             
        708 ATTCCCTGGTGACAAACCATCCAAGGGTAAGGGAAAGGGAGCACCTCATGAACCAAAACCTCCTC
          1 ATTCCCTGGTGACAAACCATCCAAGGGTAAGGGAAAGGGAGCACCTCATGAACCAAAACCTCCTC

                    *      *   *          *         *                 *      
        773 ATAGACACCTATTGAATGTCGAAGTTGAGGACACACATAAGCCTCCACAACACTCAGGGGGTAAA
         66 ATAGACACATATTGAGTGTGGAAGTTGAGGGCACACATAAACCTCCACAACACTCAGGTGGTAAA

                            *      * **     *  *        **  **
        838 CCTCCACATGTTGAAGGATTCCCCGACGGTAAGCCACC-CA--TAAAACC
        131 CCTCCAC-----G-A-CATT--CAGGGGGTAAACCTCCACATGTTGAAGG

                  *                                  *            *          
        885 ATTCCCCGGTGACAAACCATCCAAGGGTAAGGGAAAGGGAGTACCTCATGAACCTAAACCTCCTC
          1 ATTCCCTGGTGACAAACCATCCAAGGGTAAGGGAAAGGGAGCACCTCATGAACCAAAACCTCCTC

                    
        950 ATAGACAC
         66 ATAGACAC

        958 CTCTTAAGTG


Statistics
Matches: 377,  Mismatches: 35, Indels: 12
        0.89            0.08        0.03

Matches are distributed among these distances:
 171  286  0.76
 176    1  0.00
 177   74  0.20
 178    3  0.01
 179    2  0.01
 180   11  0.03

ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18


Consensus pattern (171 bp):   
ATTCCCTGGTGACAAACCATCCAAGGGTAAGGGAAAGGGAGCACCTCATGAACCAAAACCTCCTC
ATAGACACATATTGAGTGTGGAAGTTGAGGGCACACATAAACCTCCACAACACTCAGGTGGTAAA
CCTCCACGACATTCAGGGGGTAAACCTCCACATGTTGAAGG

Found at i:671 original size:24 final size:24

Alignment explanation


    Indices: 639--698  Score: 93
    Period size: 24  Copynumber: 2.5  Consensus size: 24

        629 AGGGCATACA

                                 *  
        639 TAAACCTCCACAACAATCAGGTGG
          1 TAAACCTCCACAACAATCAGGGGG

                       *   *        
        663 TAAACCTCCACGACATTCAGGGGG
          1 TAAACCTCCACAACAATCAGGGGG

                        
        687 TAAACCTCCACA
          1 TAAACCTCCACA

        699 TGTTGAAGGA


Statistics
Matches: 32,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  24   32  1.00

ACGTcount: A:0.35, C:0.32, G:0.17, T:0.17


Consensus pattern (24 bp):   
TAAACCTCCACAACAATCAGGGGG

Done.