Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024243.1 Corchorus olitorius cultivar O-4 contig24276, 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: 13301
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28


Found at i:5262 original size:30 final size:30

Alignment explanation


    Indices: 5228--5288  Score: 122
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       5218 TCGAAAAATT

                                          
       5228 GTTCAACTTGGCATCTGAGCCCTTCGCAAA
          1 GTTCAACTTGGCATCTGAGCCCTTCGCAAA

                                          
       5258 GTTCAACTTGGCATCTGAGCCCTTCGCAAA
          1 GTTCAACTTGGCATCTGAGCCCTTCGCAAA

             
       5288 G
          1 G

       5289 ATCGTGGTGA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   31  1.00

ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26


Consensus pattern (30 bp):   
GTTCAACTTGGCATCTGAGCCCTTCGCAAA

Found at i:7705 original size:11 final size:10

Alignment explanation


    Indices: 7689--7740  Score: 54
    Period size: 11  Copynumber: 5.1  Consensus size: 10

       7679 AAGTTCGTGT

                       
       7689 TTGAAGATTTA
          1 TTGAAGA-TTA

                    * 
       7700 TTGAAGATAA
          1 TTGAAGATTA

                       
       7710 TTTGAAGA-T-
          1 -TTGAAGATTA

                      
       7719 TTGAAGATTA
          1 TTGAAGATTA

                       
       7729 TTGAAGAATTA
          1 TTGAAG-ATTA

             
       7740 T
          1 T

       7741 CTCAAGAGCA


Statistics
Matches: 35,  Mismatches: 2, Indels: 8
        0.78            0.04        0.18

Matches are distributed among these distances:
   8    7  0.20
   9    1  0.03
  10    8  0.23
  11   19  0.54

ACGTcount: A:0.40, C:0.00, G:0.19, T:0.40


Consensus pattern (10 bp):   
TTGAAGATTA

Found at i:7724 original size:19 final size:18

Alignment explanation


    Indices: 7700--7735  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       7690 TGAAGATTTA

                               
       7700 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
       7719 TTGAAGATTATTGAAGA
          1 TTGAAGATAATTGAAGA

       7736 ATTATCTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT
Done.