Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_18191

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: 2189
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32


Found at i:297 original size:144 final size:144

Alignment explanation


    Indices: 100--363  Score: 474
    Period size: 144  Copynumber: 1.8  Consensus size: 144

         90 AAACAATTGG

                                                                  *         *
        100 TTTTTGGTCCAATCCCATCATCTATCAGCAACTTAACCAATCTTGCCTCGTTGTTCCTTCAAAGC
          1 TTTTTGGTCCAATCCCATCATCTATCAGCAACTTAACCAATCTTGCCTCGTTGTCCCTTCAAAGA

                     *                                 *                     
        165 AACCAACTTGATGGATCCATTCCAGAAGATATTGGGAGACTAATGAATTTGGTTGCACTGAATCT
         66 AACCAACTTAATGGATCCATTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGCACTGAATCT

                          
        230 ATCCTCCAATTATC
        131 ATCCTCCAATTATC

                               *   *                                         
        244 TTTTTGGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGCCTCGTTGTCCCTTCAAAGA
          1 TTTTTGGTCCAATCCCATCATCTATCAGCAACTTAACCAATCTTGCCTCGTTGTCCCTTCAAAGA

                                                                   
        309 AACCAACTTAATGGATCCATTCCAGAAGATATTGGGAGACTAACGAATTTGGTTG
         66 AACCAACTTAATGGATCCATTCCAGAAGATATTGGGAGACTAACGAATTTGGTTG

        364 AATTAGATCT


Statistics
Matches: 114,  Mismatches: 6, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 144  114  1.00

ACGTcount: A:0.28, C:0.25, G:0.16, T:0.32


Consensus pattern (144 bp):   
TTTTTGGTCCAATCCCATCATCTATCAGCAACTTAACCAATCTTGCCTCGTTGTCCCTTCAAAGA
AACCAACTTAATGGATCCATTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGCACTGAATCT
ATCCTCCAATTATC

Found at i:403 original size:144 final size:144

Alignment explanation


    Indices: 105--396  Score: 444
    Period size: 144  Copynumber: 2.0  Consensus size: 144

         95 ATTGGTTTTT

                                                             *         *     
        105 GGTCCAATCCCATCATCTATCAGCAACTTAACCAATCTTGCCTCGTTGTTCCTTCAAAGCAACCA
          1 GGTCCAATCCCATCATCTATCAGCAACTTAACCAATCTTGCCTCGTTGTCCCTTCAAAGAAACCA

                *                                 *           *            * 
        170 ACTTGATGGATCCATTCCAGAAGATATTGGGAGACTAATGAATTTGGTTGCACTGAATCTATCCT
         66 ACTTAATGGATCCATTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGAACTGAATCTATCAT

                   *    **
        235 CCAATTATCTTTTT
        131 CCAATTAGCTTTCA

                          *   *                                              
        249 GGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGCCTCGTTGTCCCTTCAAAGAAACCA
          1 GGTCCAATCCCATCATCTATCAGCAACTTAACCAATCTTGCCTCGTTGTCCCTTCAAAGAAACCA

                                                                  *          
        314 ACTTAATGGATCCATTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGAA-TTAGATCTATCA
         66 ACTTAATGGATCCATTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGAACTGA-ATCTATCA

                            
        378 TCCAA-TAGGCTTTCA
        130 TCCAATTA-GCTTTCA

                
        393 GGTC
          1 GGTC

        397 ACATCCCTTC


Statistics
Matches: 134,  Mismatches: 12, Indels: 4
        0.89            0.08        0.03

Matches are distributed among these distances:
 143    4  0.03
 144  130  0.97

ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31


Consensus pattern (144 bp):   
GGTCCAATCCCATCATCTATCAGCAACTTAACCAATCTTGCCTCGTTGTCCCTTCAAAGAAACCA
ACTTAATGGATCCATTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGAACTGAATCTATCAT
CCAATTAGCTTTCA

Done.