Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018706.1 Corchorus olitorius cultivar O-4 contig18739, 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: 5456
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31


Found at i:383 original size:21 final size:20

Alignment explanation


    Indices: 332--398  Score: 71
    Period size: 20  Copynumber: 3.2  Consensus size: 20

        322 TCTATATATG

                  *            *
        332 TCAGCACTTTTGGAGCCACG
          1 TCAGCATTTTTGGAGCCACA

                            *   
        352 TCAGCATTTTTGGAGCTACA
          1 TCAGCATTTTTGGAGCCACA

                            *      
        372 TCAGCAATTTTTTTGGTGCCACA
          1 TCAGC-A--TTTTTGGAGCCACA

                
        395 TCAG
          1 TCAG

        399 TATATTGGGC


Statistics
Matches: 39,  Mismatches: 5, Indels: 3
        0.83            0.11        0.06

Matches are distributed among these distances:
  20   22  0.56
  21    1  0.03
  23   16  0.41

ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33


Consensus pattern (20 bp):   
TCAGCATTTTTGGAGCCACA

Found at i:3862 original size:30 final size:30

Alignment explanation


    Indices: 3823--3892  Score: 124
    Period size: 30  Copynumber: 2.4  Consensus size: 30

       3813 TTTTTTTTGG

                                         *
       3823 TCTTT-CTCTCGATCCTTCCTCGCTTCCTT
          1 TCTTTACTCTCGATCCTTCCTCGCTTCCTC

                                          
       3852 TCTTTACTCTCGATCCTTCCTCGCTTCCTC
          1 TCTTTACTCTCGATCCTTCCTCGCTTCCTC

                       
       3882 TCTTTACTCTC
          1 TCTTTACTCTC

       3893 TCATCTATAA


Statistics
Matches: 39,  Mismatches: 1, Indels: 1
        0.95            0.02        0.02

Matches are distributed among these distances:
  29    5  0.13
  30   34  0.87

ACGTcount: A:0.06, C:0.41, G:0.06, T:0.47


Consensus pattern (30 bp):   
TCTTTACTCTCGATCCTTCCTCGCTTCCTC
Done.