Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001696.1 Corchorus olitorius cultivar O-4 contig01696, 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: 9451
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Found at i:664 original size:12 final size:13

Alignment explanation


    Indices: 638--670  Score: 50
    Period size: 12  Copynumber: 2.6  Consensus size: 13

        628 TAAACTAATT

                         
        638 ACAAACTAAACAA
          1 ACAAACTAAACAA

                      *  
        651 ACAAA-TAAATAA
          1 ACAAACTAAACAA

                    
        663 ACAAACTA
          1 ACAAACTA

        671 TTAAACCCAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  12   11  0.61
  13    7  0.39

ACGTcount: A:0.70, C:0.18, G:0.00, T:0.12


Consensus pattern (13 bp):   
ACAAACTAAACAA

Found at i:4121 original size:29 final size:29

Alignment explanation


    Indices: 4079--4135  Score: 96
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       4069 ATAAGAGGTA

                                         
       4079 TTTTTATGACATAATTATTCGTAAAGTTT
          1 TTTTTATGACATAATTATTCGTAAAGTTT

                 *   *                  
       4108 TTTTTTTGAGATAATTATTCGTAAAGTT
          1 TTTTTATGACATAATTATTCGTAAAGTT

       4136 ATATCTATAT


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  29   26  1.00

ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53


Consensus pattern (29 bp):   
TTTTTATGACATAATTATTCGTAAAGTTT

Found at i:5886 original size:18 final size:18

Alignment explanation


    Indices: 5863--5904  Score: 84
    Period size: 18  Copynumber: 2.3  Consensus size: 18

       5853 TTTTGCTTTT

                              
       5863 AATATCCATGTTTGTTTG
          1 AATATCCATGTTTGTTTG

                              
       5881 AATATCCATGTTTGTTTG
          1 AATATCCATGTTTGTTTG

                  
       5899 AATATC
          1 AATATC

       5905 ATCCATAAGA


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

Matches are distributed among these distances:
  18   24  1.00

ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48


Consensus pattern (18 bp):   
AATATCCATGTTTGTTTG

Found at i:6814 original size:21 final size:21

Alignment explanation


    Indices: 6790--6856  Score: 57
    Period size: 21  Copynumber: 3.2  Consensus size: 21

       6780 AATTCTCTAT

                                 
       6790 AAATTAAGAAATACTCAACTC
          1 AAATTAAGAAATACTCAACTC

                *         *   **  *
       6811 AAATCATAGAAA-ATTC-TTTGT
          1 AAATTA-AGAAATACTCAACT-C

                                 
       6832 AAATTAAGAAATACTCAACTC
          1 AAATTAAGAAATACTCAACTC

                
       6853 AAAT
          1 AAAT

       6857 CCTGATCCTT


Statistics
Matches: 32,  Mismatches: 10, Indels: 8
        0.64            0.20        0.16

Matches are distributed among these distances:
  20    6  0.19
  21   20  0.62
  22    6  0.19

ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28


Consensus pattern (21 bp):   
AAATTAAGAAATACTCAACTC

Found at i:6836 original size:42 final size:42

Alignment explanation


    Indices: 6777--6857  Score: 144
    Period size: 42  Copynumber: 1.9  Consensus size: 42

       6767 GCTAAGTCTT

                                                      
       6777 GAAAATTCTCTATAAATTAAGAAATACTCAACTCAAATCATA
          1 GAAAATTCTCTATAAATTAAGAAATACTCAACTCAAATCATA

                     * *                           
       6819 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
          1 GAAAATTCTCTATAAATTAAGAAATACTCAACTCAAATC

       6858 CTGATCCTTA


Statistics
Matches: 37,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  42   37  1.00

ACGTcount: A:0.48, C:0.16, G:0.06, T:0.30


Consensus pattern (42 bp):   
GAAAATTCTCTATAAATTAAGAAATACTCAACTCAAATCATA

Found at i:6994 original size:57 final size:57

Alignment explanation


    Indices: 6923--7038  Score: 214
    Period size: 57  Copynumber: 2.0  Consensus size: 57

       6913 TTTATTTTGT

                                                      *              
       6923 AGAATAATTAAGTAGAGATAGGGGGGATAGGATTTATTATAATATTTATTGTGTGAA
          1 AGAATAATTAAGTAGAGATAGGGGGGATAGGATTTATTATAACATTTATTGTGTGAA

                            *                                        
       6980 AGAATAATTAAGTAGATATAGGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
          1 AGAATAATTAAGTAGAGATAGGGGGGATAGGATTTATTATAACATTTATTGTGTGAA

              
       7037 AG
          1 AG

       7039 GAAACGGATA


Statistics
Matches: 57,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  57   57  1.00

ACGTcount: A:0.39, C:0.01, G:0.26, T:0.34


Consensus pattern (57 bp):   
AGAATAATTAAGTAGAGATAGGGGGGATAGGATTTATTATAACATTTATTGTGTGAA

Found at i:8499 original size:31 final size:32

Alignment explanation


    Indices: 8432--8502  Score: 117
    Period size: 32  Copynumber: 2.2  Consensus size: 32

       8422 CTTCATGGAT

                    *               *       
       8432 AAAATGTCTTAAATTTGGAAATTTTAGGAGGC
          1 AAAATGTCCTAAATTTGGAAATTTAAGGAGGC

                                            
       8464 AAAATGTCCTAAATTTGGAAATTTAAGG-GGC
          1 AAAATGTCCTAAATTTGGAAATTTAAGGAGGC

                    
       8495 AAAATGTC
          1 AAAATGTC

       8503 ATTGGTGCAA


Statistics
Matches: 37,  Mismatches: 2, Indels: 1
        0.93            0.05        0.03

Matches are distributed among these distances:
  31   11  0.30
  32   26  0.70

ACGTcount: A:0.39, C:0.08, G:0.21, T:0.31


Consensus pattern (32 bp):   
AAAATGTCCTAAATTTGGAAATTTAAGGAGGC
Done.