Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021893.1 Corchorus olitorius cultivar O-4 contig21926, 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: 10493
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:850 original size:18 final size:19

Alignment explanation


    Indices: 816--853  Score: 60
    Period size: 18  Copynumber: 2.1  Consensus size: 19

        806 GTCCATCGTT

                      *        
        816 ATCTCCATGGTCTCCATGC
          1 ATCTCCATGGCCTCCATGC

                               
        835 ATCTCCAT-GCCTCCATGC
          1 ATCTCCATGGCCTCCATGC

             
        853 A
          1 A

        854 ACCCATGCAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18   10  0.56
  19    8  0.44

ACGTcount: A:0.18, C:0.39, G:0.13, T:0.29


Consensus pattern (19 bp):   
ATCTCCATGGCCTCCATGC

Found at i:6827 original size:67 final size:67

Alignment explanation


    Indices: 6719--6849  Score: 262
    Period size: 67  Copynumber: 2.0  Consensus size: 67

       6709 ATTTGCAAGG

                                                                             
       6719 AACCAGAAAACTTCCAAACCTTATACAGAACATTTCGAAGAATTTCAATCATCACCAGTTACTTC
          1 AACCAGAAAACTTCCAAACCTTATACAGAACATTTCGAAGAATTTCAATCATCACCAGTTACTTC

              
       6784 CA
         66 CA

                                                                            
       6786 AACCAGAAAACTTCCAAACCTTATACAGAACATTTCGAAGAATTTCAATCATCACCAGTTACTT
          1 AACCAGAAAACTTCCAAACCTTATACAGAACATTTCGAAGAATTTCAATCATCACCAGTTACTT

       6850 TGTGAGTAAT


Statistics
Matches: 64,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  67   64  1.00

ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26


Consensus pattern (67 bp):   
AACCAGAAAACTTCCAAACCTTATACAGAACATTTCGAAGAATTTCAATCATCACCAGTTACTTC
CA

Found at i:7194 original size:2 final size:2

Alignment explanation


    Indices: 7187--7220  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       7177 ACTTTTGCTG

                                                              
       7187 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       7221 CTTTATACTC


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:9261 original size:14 final size:15

Alignment explanation


    Indices: 9242--9270  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

       9232 AACTAGGAAA

                           
       9242 CATAAAT-AACAAGG
          1 CATAAATAAACAAGG

                           
       9256 CATAAATAAACAAGG
          1 CATAAATAAACAAGG

       9271 ATTAAACTTA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14    7  0.50
  15    7  0.50

ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14


Consensus pattern (15 bp):   
CATAAATAAACAAGG
Done.