Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017719.1 Corchorus olitorius cultivar O-4 contig17752, 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: 27207
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33


Found at i:2112 original size:2 final size:2

Alignment explanation


    Indices: 2105--2129  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       2095 AATGTCTTTT

                                                 
       2105 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

       2130 CATTTTGCCT


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

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:6178 original size:22 final size:23

Alignment explanation


    Indices: 6139--6181  Score: 79
    Period size: 22  Copynumber: 1.9  Consensus size: 23

       6129 AATCCTAATC

                                   
       6139 CTGGTAGGAATAGTAAAACCTTT
          1 CTGGTAGGAATAGTAAAACCTTT

                                 
       6162 CTGGTAGGAA-AGTAAAACCT
          1 CTGGTAGGAATAGTAAAACCT

       6182 ACTCCTTCTA


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  22   10  0.50
  23   10  0.50

ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26


Consensus pattern (23 bp):   
CTGGTAGGAATAGTAAAACCTTT

Found at i:14881 original size:24 final size:22

Alignment explanation


    Indices: 14838--14884  Score: 58
    Period size: 24  Copynumber: 2.0  Consensus size: 22

      14828 TGGTAGAAAT

                       *   *      
      14838 AGTAAAACCTTTCTTGTAGGAA
          1 AGTAAAACCTTCCTTCTAGGAA

                                    
      14860 AGTAAAACCTACTCCTTCTAGGAA
          1 AGTAAAACCT--TCCTTCTAGGAA

             
      14884 A
          1 A

      14885 AACCATAAAC


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  22   10  0.48
  24   11  0.52

ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28


Consensus pattern (22 bp):   
AGTAAAACCTTCCTTCTAGGAA

Found at i:22531 original size:21 final size:21

Alignment explanation


    Indices: 22505--22546  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      22495 GTTCATTATC

                                 
      22505 TATGAATGCCTAACAAAGATT
          1 TATGAATGCCTAACAAAGATT

                           *     
      22526 TATGAATGCCTAACATAGATT
          1 TATGAATGCCTAACAAAGATT

      22547 CCTTCATAAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31


Consensus pattern (21 bp):   
TATGAATGCCTAACAAAGATT
Done.