Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_13355

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: 5235
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27


Found at i:1267 original size:42 final size:42

Alignment explanation


    Indices: 1208--1294  Score: 174
    Period size: 42  Copynumber: 2.1  Consensus size: 42

       1198 CCAAAAAGTG

                                                      
       1208 CATTGATGGAGTCTCATGGGAGGCAAGAAGAACATCCTGGTC
          1 CATTGATGGAGTCTCATGGGAGGCAAGAAGAACATCCTGGTC

                                                      
       1250 CATTGATGGAGTCTCATGGGAGGCAAGAAGAACATCCTGGTC
          1 CATTGATGGAGTCTCATGGGAGGCAAGAAGAACATCCTGGTC

               
       1292 CAT
          1 CAT

       1295 CAGAAACATC


Statistics
Matches: 45,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  42   45  1.00

ACGTcount: A:0.29, C:0.20, G:0.30, T:0.22


Consensus pattern (42 bp):   
CATTGATGGAGTCTCATGGGAGGCAAGAAGAACATCCTGGTC

Found at i:4930 original size:21 final size:21

Alignment explanation


    Indices: 4906--4953  Score: 78
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       4896 CATCTTAAAG

                                 
       4906 GCTGCAGAACAGTTTGTCATC
          1 GCTGCAGAACAGTTTGTCATC

                 *               
       4927 GCTGCGGAACAGTTTGTCATC
          1 GCTGCAGAACAGTTTGTCATC

            *     
       4948 ACTGCA
          1 GCTGCA

       4954 AAGAAGCTGG


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27


Consensus pattern (21 bp):   
GCTGCAGAACAGTTTGTCATC
Done.