Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017810.1 Corchorus olitorius cultivar O-4 contig17843, 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: 31400
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30


Found at i:250 original size:24 final size:24

Alignment explanation


    Indices: 223--270  Score: 96
    Period size: 24  Copynumber: 2.0  Consensus size: 24

        213 TAGGAACTGC

                                    
        223 AGATGATCTAGCTCACATTTATCG
          1 AGATGATCTAGCTCACATTTATCG

                                    
        247 AGATGATCTAGCTCACATTTATCG
          1 AGATGATCTAGCTCACATTTATCG

        271 TATACATGTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33


Consensus pattern (24 bp):   
AGATGATCTAGCTCACATTTATCG

Found at i:723 original size:69 final size:69

Alignment explanation


    Indices: 609--743  Score: 225
    Period size: 69  Copynumber: 2.0  Consensus size: 69

        599 GTATGCATAT

                  *                              *  *                        
        609 ATACTTTTGCTTCAAGAACTCTCAATTACTCAAAGCTGTATTAAGAAAAGCATAAACATTTCAAA
          1 ATACTTCTGCTTCAAGAACTCTCAATTACTCAAAGCTATACTAAGAAAAGCATAAACATTTCAAA

                
        674 AATA
         66 AATA

                             *                                           *   
        678 ATACTTCTGCTTCAAGAGCTCTCAATTACTCAAAGCTATACTAAGAAAAGCATAAACATTTTAAA
          1 ATACTTCTGCTTCAAGAACTCTCAATTACTCAAAGCTATACTAAGAAAAGCATAAACATTTCAAA

             
        743 A
         66 A

        744 GCAACAACCT


Statistics
Matches: 61,  Mismatches: 5, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  69   61  1.00

ACGTcount: A:0.43, C:0.19, G:0.09, T:0.30


Consensus pattern (69 bp):   
ATACTTCTGCTTCAAGAACTCTCAATTACTCAAAGCTATACTAAGAAAAGCATAAACATTTCAAA
AATA

Found at i:3117 original size:26 final size:26

Alignment explanation


    Indices: 3088--3139  Score: 104
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       3078 ACAAAATGAA

                                      
       3088 GATTTGTTTTATGTAGAAAAAAATGC
          1 GATTTGTTTTATGTAGAAAAAAATGC

                                      
       3114 GATTTGTTTTATGTAGAAAAAAATGC
          1 GATTTGTTTTATGTAGAAAAAAATGC

       3140 AGTGGTAGCA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   26  1.00

ACGTcount: A:0.38, C:0.04, G:0.19, T:0.38


Consensus pattern (26 bp):   
GATTTGTTTTATGTAGAAAAAAATGC

Found at i:20096 original size:2 final size:2

Alignment explanation


    Indices: 20089--20113  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      20079 CCCCAGAAAC

                                                 
      20089 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 A

      20114 CATACATACA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:20132 original size:10 final size:10

Alignment explanation


    Indices: 20087--20137  Score: 52
    Period size: 10  Copynumber: 5.3  Consensus size: 10

      20077 TACCCCAGAA

                   *  
      20087 ACATATATAT
          1 ACATATACAT

             *     *  
      20097 ATATATATAT
          1 ACATATACAT

             *        
      20107 ATATATACAT
          1 ACATATACAT

                      
      20117 AC--ATACAT
          1 ACATATACAT

                      
      20125 ACATATACAT
          1 ACATATACAT

               
      20135 ACA
          1 ACA

      20138 CGTATTATTA


Statistics
Matches: 36,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
   8    8  0.22
  10   28  0.78

ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35


Consensus pattern (10 bp):   
ACATATACAT

Found at i:27937 original size:32 final size:31

Alignment explanation


    Indices: 27890--27951  Score: 90
    Period size: 32  Copynumber: 2.0  Consensus size: 31

      27880 GCACTAGTTA

                *                           
      27890 TATGGTATGGTGTAAAAA-TCCATTTTGATTG
          1 TATGCTATGGTGTAAAAACT-CATTTTGATTG

                                           
      27921 TATGCTATGGTTGTAAAAACTCATTTTGATT
          1 TATGCTATGG-TGTAAAAACTCATTTTGATT

      27952 ATTAATATAT


Statistics
Matches: 28,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  31    9  0.32
  32   18  0.64
  33    1  0.04

ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44


Consensus pattern (31 bp):   
TATGCTATGGTGTAAAAACTCATTTTGATTG

Found at i:30927 original size:11 final size:11

Alignment explanation


    Indices: 30889--30927  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

      30879 TACCTATGGG

                   *   
      30889 AACCGGTAAAA
          1 AACCGGTCAAA

              *        
      30900 AAACGGTCAAA
          1 AACCGGTCAAA

                       
      30911 AACCGGTCAAA
          1 AACCGGTCAAA

             *    
      30922 ACCCGG
          1 AACCGG

      30928 ATAATCGAGA


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  11   24  1.00

ACGTcount: A:0.46, C:0.26, G:0.21, T:0.08


Consensus pattern (11 bp):   
AACCGGTCAAA
Done.