Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011842.1 Corchorus olitorius cultivar O-4 contig11875, whole genome shotgun sequence

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: 14791
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Found at i:941 original size:31 final size:31

Alignment explanation


    Indices: 903--967  Score: 130
    Period size: 31  Copynumber: 2.1  Consensus size: 31

        893 TACAATGCCG

                                           
        903 CAAGATTGTGATCTAAATTGTCCTAAAACCT
          1 CAAGATTGTGATCTAAATTGTCCTAAAACCT

                                           
        934 CAAGATTGTGATCTAAATTGTCCTAAAACCT
          1 CAAGATTGTGATCTAAATTGTCCTAAAACCT

               
        965 CAA
          1 CAA

        968 CCTAAGTCCT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   34  1.00

ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31


Consensus pattern (31 bp):   
CAAGATTGTGATCTAAATTGTCCTAAAACCT

Found at i:1577 original size:2 final size:2

Alignment explanation


    Indices: 1566--1607  Score: 77
    Period size: 2  Copynumber: 21.5  Consensus size: 2

       1556 CAAAATTCTT

                                                                          
       1566 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

             
       1607 T
          1 T

       1608 CAGTCTATGA


Statistics
Matches: 39,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   38  0.97

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:12818 original size:22 final size:22

Alignment explanation


    Indices: 12793--12837  Score: 90
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      12783 ACACGCGCCG

                                  
      12793 TTAACGCGCTGTTAACTCAAAA
          1 TTAACGCGCTGTTAACTCAAAA

                                  
      12815 TTAACGCGCTGTTAACTCAAAA
          1 TTAACGCGCTGTTAACTCAAAA

             
      12837 T
          1 T

      12838 ATGGATGCCA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29


Consensus pattern (22 bp):   
TTAACGCGCTGTTAACTCAAAA

Found at i:14772 original size:18 final size:18

Alignment explanation


    Indices: 14749--14784  Score: 54
    Period size: 18  Copynumber: 2.0  Consensus size: 18

      14739 ATTTTTTTTC

                         *    
      14749 TTTTCTAATTTAGCCTCA
          1 TTTTCTAATTTAGACTCA

                   *          
      14767 TTTTCTAGTTTAGACTCA
          1 TTTTCTAATTTAGACTCA

      14785 AGGTAAT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.22, C:0.19, G:0.08, T:0.50


Consensus pattern (18 bp):   
TTTTCTAATTTAGACTCA
Done.