Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012180.1 Corchorus olitorius cultivar O-4 contig12213, 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: 1765
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31


Found at i:867 original size:21 final size:21

Alignment explanation


    Indices: 843--934  Score: 159
    Period size: 21  Copynumber: 4.4  Consensus size: 21

        833 CTTAGGCAAT

                         *       
        843 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
        864 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
        885 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
        906 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
        927 TCCAATGA
          1 TCCAATGA

        935 TCTCCTAGCA


Statistics
Matches: 69,  Mismatches: 1, Indels: 2
        0.96            0.01        0.03

Matches are distributed among these distances:
  20    3  0.04
  21   66  0.96

ACGTcount: A:0.26, C:0.27, G:0.18, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:1582 original size:17 final size:17

Alignment explanation


    Indices: 1551--1594  Score: 70
    Period size: 17  Copynumber: 2.5  Consensus size: 17

       1541 GTCCTTAATG

                              
       1551 AATAAAATAAAATAAAAT
          1 AATAAAAT-AAATAAAAT

                             
       1569 AATAAAATAAATAAAAT
          1 AATAAAATAAATAAAAT

                *    
       1586 AATATAATA
          1 AATAAAATA

       1595 TAATTTTTAT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  17   17  0.68
  18    8  0.32

ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25


Consensus pattern (17 bp):   
AATAAAATAAATAAAAT

Found at i:1598 original size:5 final size:5

Alignment explanation


    Indices: 1551--1597  Score: 55
    Period size: 5  Copynumber: 10.0  Consensus size: 5

       1541 GTCCTTAATG

                                                            *     *    
       1551 AATAA AATAA AATAA AAT-- AATAA AAT-A AATAA AATAA TATAA TATAA
          1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA

       1598 TTTTTATATG


Statistics
Matches: 38,  Mismatches: 1, Indels: 6
        0.84            0.02        0.13

Matches are distributed among these distances:
   3    3  0.08
   4    4  0.11
   5   31  0.82

ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26


Consensus pattern (5 bp):   
AATAA
Done.