Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018481.1 Corchorus olitorius cultivar O-4 contig18514, 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: 19593
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:5883 original size:8 final size:8

Alignment explanation


    Indices: 5870--5901  Score: 64
    Period size: 8  Copynumber: 4.0  Consensus size: 8

       5860 AATCTATACT

                    
       5870 TCTTCAAA
          1 TCTTCAAA

                    
       5878 TCTTCAAA
          1 TCTTCAAA

                    
       5886 TCTTCAAA
          1 TCTTCAAA

                    
       5894 TCTTCAAA
          1 TCTTCAAA

       5902 CTCTAATTTG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   24  1.00

ACGTcount: A:0.38, C:0.25, G:0.00, T:0.38


Consensus pattern (8 bp):   
TCTTCAAA

Found at i:9452 original size:21 final size:18

Alignment explanation


    Indices: 9404--9457  Score: 108
    Period size: 18  Copynumber: 3.0  Consensus size: 18

       9394 TAGTTTGAAG

                              
       9404 TGAAGAATCATCATTTGC
          1 TGAAGAATCATCATTTGC

                              
       9422 TGAAGAATCATCATTTGC
          1 TGAAGAATCATCATTTGC

                              
       9440 TGAAGAATCATCATTTGC
          1 TGAAGAATCATCATTTGC

       9458 AGGCAAGATC


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   36  1.00

ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Consensus pattern (18 bp):   
TGAAGAATCATCATTTGC

Found at i:13551 original size:2 final size:2

Alignment explanation


    Indices: 13544--13575  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      13534 TTTGCCTTAC

                                                           
      13544 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

      13576 AATCGGTCTG


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:16777 original size:2 final size:2

Alignment explanation


    Indices: 16772--16825  Score: 72
    Period size: 2  Copynumber: 26.5  Consensus size: 2

      16762 AGATGCGCAG

                                                               *        * 
      16772 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT GT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                      *      
      16814 GAT AT AT TT AT A
          1 -AT AT AT AT AT A

      16826 CTCAAACAAA


Statistics
Matches: 45,  Mismatches: 6, Indels: 2
        0.85            0.11        0.04

Matches are distributed among these distances:
   2   44  0.98
   3    1  0.02

ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50


Consensus pattern (2 bp):   
AT

Done.