Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_15699

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: 1752
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24


Found at i:1229 original size:162 final size:162

Alignment explanation


    Indices: 962--1282  Score: 545
    Period size: 162  Copynumber: 2.0  Consensus size: 162

        952 GTAGGAAGAT

                                                          *             *    
        962 CTGCAAAGCTAGATGGTACTGTCAATGGTGGTTCATTGTTGCCCCGGAAAAGGAAAACTGCGAAG
          1 CTGCAAAGCTAGATGGTACTGTCAATGGTGGTTCATTGTTGCCCCGAAAAAGGAAAACTGAGAAG

                                                             *               
       1027 AAAAGTTCTAAAATTGATCCACATCAGGTCTGTTTTCCTGAAGAAAACACTGCAGATGAGATTAA
         66 AAAAGTTCTAAAATTGATCCACATCAGGTCTGTTTTCCTGAAGAAAACAATGCAGATGAGATTAA

                  *                         
       1092 GCAAACGACATATAGGACTGAAACTCCACCGC
        131 GCAAACAACATATAGGACTGAAACTCCACCGC

                        *                     *                    *         
       1124 CTGCAAAGCTAGCTGGTACTGTCAATGGTGGTTCGTTGTTGCCCCAGAAAAAGG-GAACTGAGAA
          1 CTGCAAAGCTAGATGGTACTGTCAATGGTGGTTCATTGTTGCCCC-GAAAAAGGAAAACTGAGAA

                                        *                                    
       1188 GAAAAGTTCTAAAATTGATCCACATCAGTTCTGTTTTCCTGAAGAAAACAATGCAGATGAGATTA
         65 GAAAAGTTCTAAAATTGATCCACATCAGGTCTGTTTTCCTGAAGAAAACAATGCAGATGAGATTA

                              *           
       1253 AGCAAACAACATATAGGAGTGAAACTCCAC
        130 AGCAAACAACATATAGGACTGAAACTCCAC

       1283 TTCCTTCAGA


Statistics
Matches: 149,  Mismatches: 9, Indels: 2
        0.93            0.06        0.01

Matches are distributed among these distances:
 162  142  0.95
 163    7  0.05

ACGTcount: A:0.35, C:0.19, G:0.22, T:0.23


Consensus pattern (162 bp):   
CTGCAAAGCTAGATGGTACTGTCAATGGTGGTTCATTGTTGCCCCGAAAAAGGAAAACTGAGAAG
AAAAGTTCTAAAATTGATCCACATCAGGTCTGTTTTCCTGAAGAAAACAATGCAGATGAGATTAA
GCAAACAACATATAGGACTGAAACTCCACCGC
Done.