Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016528.1 Corchorus olitorius cultivar O-4 contig16561, 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: 2804
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36


Found at i:546 original size:6 final size:6

Alignment explanation


    Indices: 535--582  Score: 51
    Period size: 6  Copynumber: 7.8  Consensus size: 6

        525 TTTTTTGGGT

                                    *      *         *      *      
        535 TATTAA TATTAA TATATAA TAATAA TAATAA TATTAT TATTAT TATTA
          1 TATTAA TATTAA TAT-TAA TATTAA TATTAA TATTAA TATTAA TATTA

        583 TGATGACTGA


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

Matches are distributed among these distances:
   6   33  0.87
   7    5  0.13

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


Consensus pattern (6 bp):   
TATTAA

Found at i:1560 original size:38 final size:38

Alignment explanation


    Indices: 1516--1603  Score: 160
    Period size: 38  Copynumber: 2.3  Consensus size: 38

       1506 TGTGTTCGAG

                                                   
       1516 TTCGGGTTTGGGCTTGGGTTGTCCCAGGTTC-AGATAAA
          1 TTCGGGTTTGGGCTTGGGTTGTCCCAGGTTCAAG-TAAA

                                                  
       1554 TTCGGGTTTGGGCTTGGGTTGTCCCAGGTTCAAGTAAA
          1 TTCGGGTTTGGGCTTGGGTTGTCCCAGGTTCAAGTAAA

                        
       1592 TTCGGGTTTGGG
          1 TTCGGGTTTGGG

       1604 TAATTTCAGG


Statistics
Matches: 49,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
  38   47  0.96
  39    2  0.04

ACGTcount: A:0.14, C:0.15, G:0.36, T:0.35


Consensus pattern (38 bp):   
TTCGGGTTTGGGCTTGGGTTGTCCCAGGTTCAAGTAAA

Found at i:1812 original size:15 final size:15

Alignment explanation


    Indices: 1781--1828  Score: 53
    Period size: 15  Copynumber: 3.3  Consensus size: 15

       1771 TTTCTAACCA

                    *      
       1781 AATCTAATCTAA-CT
          1 AATCTAATTTAATCT

                         * 
       1795 AATCTAATTTAATTT
          1 AATCTAATTTAATCT

               *          *
       1810 AATTTAATTTAATCA
          1 AATCTAATTTAATCT

                
       1825 AATC
          1 AATC

       1829 AAATCAAATC


Statistics
Matches: 27,  Mismatches: 6, Indels: 1
        0.79            0.18        0.03

Matches are distributed among these distances:
  14   11  0.41
  15   16  0.59

ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44


Consensus pattern (15 bp):   
AATCTAATTTAATCT
Done.