Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_11855

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: 1740
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21


Found at i:953 original size:141 final size:141

Alignment explanation


    Indices: 673--944  Score: 481
    Period size: 141  Copynumber: 1.9  Consensus size: 141

        663 GCCGCCAACT

                                                                       *     
        673 CCGCCTCCTGCAGCTGCATATCGTAAACCAAGGCGAAGTTATCAAGCTGTTGGCCGGAACGAGAA
          1 CCGCCTCCTGCAGCTGCATATCGTAAACCAAGGCGAAGTTATCAAGCTGTTGGCCGGAAAGAGAA

                           *                                                 
        738 TGTGAATAATACTCAGAAGTTTCATGTTAAGTACGATGGAAGTGAGTCTCCGGCTCCGCAGCCAG
         66 TGTGAATAATACTCAAAAGTTTCATGTTAAGTACGATGGAAGTGAGTCTCCGGCTCCGCAGCCAG

                       
        803 TGAAGCCACCG
        131 TGAAGCCACCG

                        *   *                                                
        814 CCGCCTCCTGCATCTGGATATCGTAAACCAAGGCGAAGTTATCAAGCTGTTGGCCGGAAAGAGAA
          1 CCGCCTCCTGCAGCTGCATATCGTAAACCAAGGCGAAGTTATCAAGCTGTTGGCCGGAAAGAGAA

                      *                 *                            *       
        879 TGTGAATAATGCTCAAAAGTTTCATGTTGAGTACGATGGAAGTGAGTCTCCGGCTCCTCAGCCAG
         66 TGTGAATAATACTCAAAAGTTTCATGTTAAGTACGATGGAAGTGAGTCTCCGGCTCCGCAGCCAG

             
        944 T
        131 T

        945 AACTCCACCT


Statistics
Matches: 124,  Mismatches: 7, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 141  124  1.00

ACGTcount: A:0.28, C:0.24, G:0.26, T:0.23


Consensus pattern (141 bp):   
CCGCCTCCTGCAGCTGCATATCGTAAACCAAGGCGAAGTTATCAAGCTGTTGGCCGGAAAGAGAA
TGTGAATAATACTCAAAAGTTTCATGTTAAGTACGATGGAAGTGAGTCTCCGGCTCCGCAGCCAG
TGAAGCCACCG

Found at i:1356 original size:3 final size:3

Alignment explanation


    Indices: 1348--1393  Score: 56
    Period size: 3  Copynumber: 15.3  Consensus size: 3

       1338 CACTCAATCC

                                              * *     *     *            
       1348 CCA CCA CCA CCA CCA CCA CCA CCA CCT GCA CCG CCA ACA CCA CCA C
          1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA C

       1394 TCAGACCGTC


Statistics
Matches: 35,  Mismatches: 8, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
   3   35  1.00

ACGTcount: A:0.30, C:0.63, G:0.04, T:0.02


Consensus pattern (3 bp):   
CCA

Done.