Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023598.1 Corchorus olitorius cultivar O-4 contig23631, 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: 20200
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30


Found at i:5199 original size:21 final size:21

Alignment explanation


    Indices: 5175--5224  Score: 75
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       5165 TTGCCGCTGG

                                  
       5175 GCGCCCAGGCGA-AATGCCTCA
          1 GCGCCCAGGCGACAA-GCCTCA

                            *    
       5196 GCGCCCAGGCGACAAGGCTCA
          1 GCGCCCAGGCGACAAGCCTCA

                    
       5217 GCGCCCAG
          1 GCGCCCAG

       5225 CTCGATCCCT


Statistics
Matches: 27,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  21   25  0.93
  22    2  0.07

ACGTcount: A:0.22, C:0.40, G:0.32, T:0.06


Consensus pattern (21 bp):   
GCGCCCAGGCGACAAGCCTCA

Found at i:10712 original size:13 final size:14

Alignment explanation


    Indices: 10685--10713  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

      10675 TGGTCGAAAC

                          
      10685 TTTTTTTTTATTAT
          1 TTTTTTTTTATTAT

                          
      10699 TTTTTTTTTA-TAT
          1 TTTTTTTTTATTAT

              
      10712 TT
          1 TT

      10714 GTCGATTAAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    5  0.33
  14   10  0.67

ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86


Consensus pattern (14 bp):   
TTTTTTTTTATTAT

Found at i:10865 original size:25 final size:24

Alignment explanation


    Indices: 10828--10874  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

      10818 CTAGAAAATT

                                      
      10828 TGAAAAACTTTGATGGATGAGATGGA
          1 TGAAAAACTTTGAT-GAT-AGATGGA

                                  
      10854 TGAAAAAC-TTGATGATAGATG
          1 TGAAAAACTTTGATGATAGATG

      10875 AATAGAAGGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    3  0.14
  25    5  0.24
  26    8  0.38

ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28


Consensus pattern (24 bp):   
TGAAAAACTTTGATGATAGATGGA

Found at i:11719 original size:21 final size:21

Alignment explanation


    Indices: 11695--11790  Score: 174
    Period size: 21  Copynumber: 4.6  Consensus size: 21

      11685 CTTAGGCAAT

                         *       
      11695 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
      11716 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
      11737 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                           *     
      11758 TCCAATGAGCTTGGACCCTTC
          1 TCCAATGAGCTTGGAACCTTC

                        
      11779 TCCAATGAGCTT
          1 TCCAATGAGCTT

      11791 CTAGCATCTT


Statistics
Matches: 73,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  21   73  1.00

ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Done.