Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020801.1 Corchorus olitorius cultivar O-4 contig20834, 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: 20290
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33


Found at i:563 original size:15 final size:14

Alignment explanation


    Indices: 539--582  Score: 52
    Period size: 15  Copynumber: 3.0  Consensus size: 14

        529 ATAAAAATTA

                          
        539 AATATATTTATTTT
          1 AATATATTTATTTT

                           
        553 AATATATTTTATTTT
          1 AATATA-TTTATTTT

             *   *         
        568 ATTGAAATTTATTTT
          1 AAT-ATATTTATTTT

        583 TAAAAATAAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  14    6  0.23
  15   18  0.69
  16    2  0.08

ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64


Consensus pattern (14 bp):   
AATATATTTATTTT

Found at i:4071 original size:6 final size:6

Alignment explanation


    Indices: 4060--4099  Score: 55
    Period size: 6  Copynumber: 6.7  Consensus size: 6

       4050 CTGTCACCAT

                           *                               
       4060 CTCTTC CTCTTC CCCTTC C-CATTC CTCTTC CTCTTC CTCT
          1 CTCTTC CTCTTC CTCTTC CTC-TTC CTCTTC CTCTTC CTCT

       4100 ATCACCACCG


Statistics
Matches: 31,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
   5    1  0.03
   6   29  0.94
   7    1  0.03

ACGTcount: A:0.03, C:0.53, G:0.00, T:0.45


Consensus pattern (6 bp):   
CTCTTC

Found at i:5870 original size:3 final size:3

Alignment explanation


    Indices: 5862--5893  Score: 57
    Period size: 3  Copynumber: 11.0  Consensus size: 3

       5852 TTACTATCTC

                                                       
       5862 CTT CTT CTT CTT -TT CTT CTT CTT CTT CTT CTT
          1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT

       5894 TTTTTTTCGC


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   2    2  0.07
   3   26  0.93

ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69


Consensus pattern (3 bp):   
CTT

Found at i:12765 original size:35 final size:36

Alignment explanation


    Indices: 12719--12795  Score: 113
    Period size: 35  Copynumber: 2.2  Consensus size: 36

      12709 CGAGCAAACC

                               *                 
      12719 AAAGTCACTAAATTTGCATGAA-CA-ATTCTTTCATT
          1 AAAGTCACTAAATTTGCATAAAGCATA-TCTTTCATT

                                                
      12754 AAAGTCACTAAATTTGCATAAAGCATATCTTTCATT
          1 AAAGTCACTAAATTTGCATAAAGCATATCTTTCATT

            *     
      12790 GAAGTC
          1 AAAGTC

      12796 TATGCTTGAG


Statistics
Matches: 38,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  35   21  0.55
  36   16  0.42
  37    1  0.03

ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35


Consensus pattern (36 bp):   
AAAGTCACTAAATTTGCATAAAGCATATCTTTCATT

Done.