Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_22961

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: 3000
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25


Found at i:1368 original size:258 final size:261

Alignment explanation


    Indices: 905--1430  Score: 781
    Period size: 258  Copynumber: 2.0  Consensus size: 261

        895 GAAAAATTAA

                       *            *   * *          *         *             
        905 AGAATGGGAAGTACATTGTCAAAGTTTCGGGTGAAACTTATTCGTGCCCCTTTTGTCCTCAGAAG
          1 AGAATGGGAAGCACATTGTCAAAGCTTCAGATGAAACTTATACGTGCCCCTATTGTCCT-AGAAG

                                   *  *                                      
        970 AAAAAGCCAAATTACCGATACATGGATCTTGTCCAGCATGCTTCTGCTGTGGCAAATAGTAGTTC
         65 AAAAA--CAAATTACCGATACATAGACCTTGTCCAGCATGCTTCTGCTGTGGCAAATAGTAGTTC

                               *              *     *  *                     
       1035 TGCAAGAAGAACACCAATAGTGAAAGCCAATCACTTGGCTTTGTCGAAGTATTTGGAAAAGGATC
        128 TGCAAGAAGAACACCAATAATGAAAGCCAATCACCTGGCTCTGGCGAAGTATTTGGAAAAGGATC

                                           *      *                          
       1100 TTGCGCCTTTGGTTAGTTCATTGAAACCTG-TGACTCAGGAGGATCCTCTTAGTGGTTGTGACCA
        193 TTGCGCCTTTGGTTAGTTCATTGAAACCTGCAG-CTCAAGAGGATCCTCTTAGTGGTTGTGACCA

                 
       1164 TGATG
        257 TGATG

                                                                             
       1169 AGAATGGGAAGCACATTGTCAAAGCTTCAGATGAAACTTATACGTGCCCCTATTGTCCT-G-AGA
          1 AGAATGGGAAGCACATTGTCAAAGCTTCAGATGAAACTTATACGTGCCCCTATTGTCCTAGAAGA

             *     *         **                        *     *               
       1232 AGAA-AATTTACCGATATTTAGACCTTGTCCAGCATGCTTCTGGTGTGGGAAATAGTAGTTCTGC
         66 AAAACAAATTACCGATACATAGACCTTGTCCAGCATGCTTCTGCTGTGGCAAATAGTAGTTCTGC

                                                      *                *     
       1296 AAGAAGAACACCAATAATGAAAGCCAATCACCTGGCTCTGGCTAAGTATTTGGAAAAGGGTCTTG
        131 AAGAAGAACACCAATAATGAAAGCCAATCACCTGGCTCTGGCGAAGTATTTGGAAAAGGATCTTG

            *                                                                
       1361 TGCCTTTGGTTAGTTCATTGAAACCTGCAGCTCAAGAGGATCCTCTTAGTGGTTGTGACCATGAT
        196 CGCCTTTGGTTAGTTCATTGAAACCTGCAGCTCAAGAGGATCCTCTTAGTGGTTGTGACCATGAT

             
       1426 G
        261 G

                
       1427 AGAA
          1 AGAA

       1431 AATTGTTTGG


Statistics
Matches: 238,  Mismatches: 23, Indels: 8
        0.88            0.09        0.03

Matches are distributed among these distances:
 258  177  0.74
 259    1  0.00
 261    6  0.03
 262    1  0.00
 264   53  0.22

ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29


Consensus pattern (261 bp):   
AGAATGGGAAGCACATTGTCAAAGCTTCAGATGAAACTTATACGTGCCCCTATTGTCCTAGAAGA
AAAACAAATTACCGATACATAGACCTTGTCCAGCATGCTTCTGCTGTGGCAAATAGTAGTTCTGC
AAGAAGAACACCAATAATGAAAGCCAATCACCTGGCTCTGGCGAAGTATTTGGAAAAGGATCTTG
CGCCTTTGGTTAGTTCATTGAAACCTGCAGCTCAAGAGGATCCTCTTAGTGGTTGTGACCATGAT
G
Done.