Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009949.1 Corchorus olitorius cultivar O-4 contig09981, 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: 14909
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35


Found at i:8468 original size:19 final size:19

Alignment explanation


    Indices: 8444--8482  Score: 78
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       8434 GGCCTGACAT

                               
       8444 TCGGGCTTGGTCATTTGAC
          1 TCGGGCTTGGTCATTTGAC

                               
       8463 TCGGGCTTGGTCATTTGAC
          1 TCGGGCTTGGTCATTTGAC

             
       8482 T
          1 T

       8483 AAAGCCCGCC


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.10, C:0.21, G:0.31, T:0.38


Consensus pattern (19 bp):   
TCGGGCTTGGTCATTTGAC

Found at i:11643 original size:11 final size:11

Alignment explanation


    Indices: 11600--11637  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

      11590 TTCCTATATA

                *      
      11600 AAATAAATTAT
          1 AAATTAATTAT

                        
      11611 CAAA-TAATTAT
          1 -AAATTAATTAT

                       
      11622 AAATTAATTAT
          1 AAATTAATTAT

                 
      11633 AAATT
          1 AAATT

      11638 TGTTATGATC


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  10    3  0.12
  11   18  0.75
  12    3  0.12

ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39


Consensus pattern (11 bp):   
AAATTAATTAT

Found at i:14508 original size:112 final size:112

Alignment explanation


    Indices: 14345--14567  Score: 437
    Period size: 112  Copynumber: 2.0  Consensus size: 112

      14335 AAAAGATGAG

                                  *                                          
      14345 TTGAGAAAATAATTAAAAGAAACCTCCAACATAGAATTAATATCCCTCTTGACAACAATACCATG
          1 TTGAGAAAATAATTAAAAGAAAACTCCAACATAGAATTAATATCCCTCTTGACAACAATACCATG

                                                           
      14410 GATCATTGATATCTAAAGATTATGAAAACAATGGATAGCTTGCTTGC
         66 GATCATTGATATCTAAAGATTATGAAAACAATGGATAGCTTGCTTGC

                                                                             
      14457 TTGAGAAAATAATTAAAAGAAAACTCCAACATAGAATTAATATCCCTCTTGACAACAATACCATG
          1 TTGAGAAAATAATTAAAAGAAAACTCCAACATAGAATTAATATCCCTCTTGACAACAATACCATG

                                                          
      14522 GATCATTGATATCTAAAGATTATGAAAACAATGGATAGCTTGCTTG
         66 GATCATTGATATCTAAAGATTATGAAAACAATGGATAGCTTGCTTG

      14568 GAATTTAATC


Statistics
Matches: 110,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 112  110  1.00

ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28


Consensus pattern (112 bp):   
TTGAGAAAATAATTAAAAGAAAACTCCAACATAGAATTAATATCCCTCTTGACAACAATACCATG
GATCATTGATATCTAAAGATTATGAAAACAATGGATAGCTTGCTTGC
Done.