Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018292.1 Corchorus olitorius cultivar O-4 contig18325, 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: 31749
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33


Found at i:13915 original size:32 final size:32

Alignment explanation


    Indices: 13879--13942  Score: 128
    Period size: 32  Copynumber: 2.0  Consensus size: 32

      13869 ATTAAAAGAC

                                            
      13879 ATTCATCCCCTTTCCTATATAAAATAAATTAT
          1 ATTCATCCCCTTTCCTATATAAAATAAATTAT

                                            
      13911 ATTCATCCCCTTTCCTATATAAAATAAATTAT
          1 ATTCATCCCCTTTCCTATATAAAATAAATTAT

      13943 CAAATAATTA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   32  1.00

ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41


Consensus pattern (32 bp):   
ATTCATCCCCTTTCCTATATAAAATAAATTAT

Found at i:13975 original size:11 final size:11

Alignment explanation


    Indices: 13932--13969  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

      13922 TTCCTATATA

                *      
      13932 AAATAAATTAT
          1 AAATTAATTAT

                        
      13943 CAAA-TAATTAT
          1 -AAATTAATTAT

                       
      13954 AAATTAATTAT
          1 AAATTAATTAT

                 
      13965 AAATT
          1 AAATT

      13970 TGTTATGAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  10    3  0.12
  11   18  0.75
  12    3  0.12

ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39


Consensus pattern (11 bp):   
AAATTAATTAT

Found at i:14522 original size:74 final size:74

Alignment explanation


    Indices: 14430--14583  Score: 290
    Period size: 74  Copynumber: 2.1  Consensus size: 74

      14420 TGCAGTCTGC

                        **                                                   
      14430 TAAACTCCACTGGTAGTGAATTGTATAATTTTCCTACTTATTTGTAAAATTAATCGAACAATAGA
          1 TAAACTCCACTGACAGTGAATTGTATAATTTTCCTACTTATTTGTAAAATTAATCGAACAATAGA

                     
      14495 TATATTTAA
         66 TATATTTAA

                                                                             
      14504 TAAACTCCACTGACAGTGAATTGTATAATTTTCCTACTTATTTGTAAAATTAATCGAACAATAGA
          1 TAAACTCCACTGACAGTGAATTGTATAATTTTCCTACTTATTTGTAAAATTAATCGAACAATAGA

                     
      14569 TATATTTAA
         66 TATATTTAA

                  
      14578 TAAACT
          1 TAAACT

      14584 TTAATAAATT


Statistics
Matches: 78,  Mismatches: 2, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
  74   78  1.00

ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38


Consensus pattern (74 bp):   
TAAACTCCACTGACAGTGAATTGTATAATTTTCCTACTTATTTGTAAAATTAATCGAACAATAGA
TATATTTAA

Found at i:30526 original size:2 final size:2

Alignment explanation


    Indices: 30519--30545  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      30509 TTCAGCTTAC

                                                    
      30519 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

      30546 CTAATAAAGT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:30793 original size:102 final size:102

Alignment explanation


    Indices: 30617--30817  Score: 393
    Period size: 102  Copynumber: 2.0  Consensus size: 102

      30607 ACATAATAGG

                                                                 *           
      30617 AGGAGAAAGTGAAATGACAAAAAACCCAATCCAACCCTCTTATCTCATGACTTGAAGAACAAATG
          1 AGGAGAAAGTGAAATGACAAAAAACCCAATCCAACCCTCTTATCTCATGACTTCAAGAACAAATG

                                                 
      30682 AGTAAGGGTATTTAGGTCATTTCATGCTCGGTTTAAT
         66 AGTAAGGGTATTTAGGTCATTTCATGCTCGGTTTAAT

                                                                             
      30719 AGGAGAAAGTGAAATGACAAAAAACCCAATCCAACCCTCTTATCTCATGACTTCAAGAACAAATG
          1 AGGAGAAAGTGAAATGACAAAAAACCCAATCCAACCCTCTTATCTCATGACTTCAAGAACAAATG

                                              
      30784 AGTAAGGGTATTTAGGTCATTTCATGCTCGGTTT
         66 AGTAAGGGTATTTAGGTCATTTCATGCTCGGTTT

      30818 TTTCGTTATT


Statistics
Matches: 98,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 102   98  1.00

ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26


Consensus pattern (102 bp):   
AGGAGAAAGTGAAATGACAAAAAACCCAATCCAACCCTCTTATCTCATGACTTCAAGAACAAATG
AGTAAGGGTATTTAGGTCATTTCATGCTCGGTTTAAT
Done.