Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_21509

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: 3269
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26


Found at i:870 original size:231 final size:231

Alignment explanation


    Indices: 488--961  Score: 630
    Period size: 231  Copynumber: 2.1  Consensus size: 231

        478 GATCTCCAAT

                    *                                            * *     *   
        488 TTAGTGTAGAACAATGTGAGCAGCAATGTAAGGAGTTTAAGTTGATGGAGGAAGTGGTAAATGAT
          1 TTAGTGTAAAACAATGTGAGCAGCAATGTAAGGAGTTTAAGTTGATGGAGGAAATAGTAAAAGAT

                   *          *                      *        *  *    *     *
        553 AAGTTGGGGGAAATTAGGTTAAAAGAGAATGATTTGGAGAATTGCTTGAGTGATTATGTGTTGAG
         66 AAGTTGGAGGAAATTAGGGTAAAAGAGAATGATTTGGAGAAGTGCTTGAGCGAGTATGAGTTGAA

                      *   *                             *            ***     
        618 AGAACAACAATTTGGGTTGAAAGAGAAGAGTTTTGAGAAGCGGTGTATGGAGTTTGAGTTGGAAG
        131 AGAACAACAAATTGAGTTGAAAGAGAAGAGTTTTGAGAAGCGGTATATGGAGTTTGAAAGGGAAG

                      **                        
        683 AAAAGGCTTTGGAAGAACGTCGCAGAGATCTTGAAG
        196 AAAAGGCTTTCAAAGAACGTCGCAGAGATCTTGAAG

                                 *                                           
        719 TTAGTGTAAAACAATGTGAGCGGCAATGTGAA-GAGTTTAAGTTGATGGA-GAAATCAGTAAAAG
          1 TTAGTGTAAAACAATGTGAGCAGCAATGT-AAGGAGTTTAAGTTGATGGAGGAAAT-AGTAAAAG

                          *  *    *                                          
        782 ATAAGTTGGAGGAAGTTGGGGTGAAAGAGAAAT-ATTTGGAGAAGTGCTTGAGCGAGTATGAGTT
         64 ATAAGTTGGAGGAAATTAGGGTAAAAGAG-AATGATTTGGAGAAGTGCTTGAGCGAGTATGAGTT

                   *                              *      *                   
        846 GAAAGAAGAACAAATTGAGTTGAAAGAGAAGAGTTTTGTGAAGCGTTATATGGAGTTTGAAAGGG
        128 GAAAGAACAACAAATTGAGTTGAAAGAGAAGAGTTTTGAGAAGCGGTATATGGAGTTTGAAAGGG

                *                  * *             
        911 AAGAGAAGGCTTTCAAAGAACGTTGTAGAGATCTTGAAG
        193 AAGAAAAGGCTTTCAAAGAACGTCGCAGAGATCTTGAAG

               *        
        950 TTAATGTAAAAC
          1 TTAGTGTAAAAC

        962 TGTATGAGCA


Statistics
Matches: 210,  Mismatches: 30, Indels: 6
        0.85            0.12        0.02

Matches are distributed among these distances:
 230    4  0.02
 231  201  0.96
 232    5  0.02

ACGTcount: A:0.36, C:0.05, G:0.32, T:0.26


Consensus pattern (231 bp):   
TTAGTGTAAAACAATGTGAGCAGCAATGTAAGGAGTTTAAGTTGATGGAGGAAATAGTAAAAGAT
AAGTTGGAGGAAATTAGGGTAAAAGAGAATGATTTGGAGAAGTGCTTGAGCGAGTATGAGTTGAA
AGAACAACAAATTGAGTTGAAAGAGAAGAGTTTTGAGAAGCGGTATATGGAGTTTGAAAGGGAAG
AAAAGGCTTTCAAAGAACGTCGCAGAGATCTTGAAG

Found at i:1041 original size:231 final size:231

Alignment explanation


    Indices: 574--1041  Score: 507
    Period size: 231  Copynumber: 2.0  Consensus size: 231

        564 AATTAGGTTA

                                *        *  *    *     *          *   *      
        574 AAAGAGAATGATTTGGAGAATTGCTTGAGTGATTATGTGTTGAGAGAACAACAATTTGGGTTGAA
          1 AAAGAGAATGATTTGGAGAAGTGCTTGAGCGAGTATGAGTTGAAAGAACAACAAATTGAGTTGAA

                                   *            ***               **         
        639 AGAGAAGAGTTTTGAGAAGCGGTGTATGGAGTTTGAGTTGGAAGAAAAGGCTTTGGAAGAACGTC
         66 AGAGAAGAGTTTTGAGAAGCGGTATATGGAGTTTGAAAGGGAAGAAAAGGCTTTCAAAGAACGTC

                              *           *     * *   *         *       **   
        704 GCAGAGATCTTGAAGTTAGTGTAAAACAATGTGAGCGGCAATGTGAAGAGTTTAAGTTGATGGAG
        131 GCAGAGATCTTGAAGTTAATGTAAAACAATATGAGCAGAAATATGAAGAGTTGAAGTTGACAGAG

                                   *   *  ***   
        769 AAATCAGTAAAAGATAAGTTGGAGGAAGTTGGGGTG
        196 AAATCAGTAAAAGATAAGTTGGAAGAAATTAAAGTG

                                                             *               
        805 AAAGAGAAAT-ATTTGGAGAAGTGCTTGAGCGAGTATGAGTTGAAAGAAGAACAAATTGAGTTGA
          1 AAAGAG-AATGATTTGGAGAAGTGCTTGAGCGAGTATGAGTTGAAAGAACAACAAATTGAGTTGA

                           *      *                       *                  
        869 AAGAGAAGAGTTTTGTGAAGCGTTATATGGAGTTTGAAAGGGAAGAGAAGGCTTTCAAAGAACGT
         65 AAGAGAAGAGTTTTGAGAAGCGGTATATGGAGTTTGAAAGGGAAGAAAAGGCTTTCAAAGAACGT

            * *                         **                                   
        934 TGTAGAGATCTTGAAGTTAATGTAAAACTGTATGAGCAGAAATAT-AAGAGGCTTGAAG-TGACA
        130 CGCAGAGATCTTGAAGTTAATGTAAAACAATATGAGCAGAAATATGAAGA-G-TTGAAGTTGACA

                   **           *                     
        997 GAGAAATGGGTGCAAAA-A-CAGTTGGAAGAAATTAAAAG-G
        193 GAGAAATCAGT--AAAAGATAAGTTGGAAGAAATT-AAAGTG

                  
       1036 AAAGAG
          1 AAAGAG

       1042 GAGGAATTTG


Statistics
Matches: 194,  Mismatches: 37, Indels: 12
        0.80            0.15        0.05

Matches are distributed among these distances:
 230    4  0.02
 231  176  0.91
 232   10  0.05
 233    4  0.02

ACGTcount: A:0.38, C:0.06, G:0.31, T:0.25


Consensus pattern (231 bp):   
AAAGAGAATGATTTGGAGAAGTGCTTGAGCGAGTATGAGTTGAAAGAACAACAAATTGAGTTGAA
AGAGAAGAGTTTTGAGAAGCGGTATATGGAGTTTGAAAGGGAAGAAAAGGCTTTCAAAGAACGTC
GCAGAGATCTTGAAGTTAATGTAAAACAATATGAGCAGAAATATGAAGAGTTGAAGTTGACAGAG
AAATCAGTAAAAGATAAGTTGGAAGAAATTAAAGTG
Done.