Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021089.1 Corchorus olitorius cultivar O-4 contig21122, 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: 7176
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36


Found at i:523 original size:13 final size:13

Alignment explanation


    Indices: 505--530  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

        495 GGTGGTGGAG

                         
        505 AAGGAAAAAGGAA
          1 AAGGAAAAAGGAA

                         
        518 AAGGAAAAAGGAA
          1 AAGGAAAAAGGAA

        531 GAAGAGGAGA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00


Consensus pattern (13 bp):   
AAGGAAAAAGGAA

Found at i:2993 original size:31 final size:33

Alignment explanation


    Indices: 2925--2995  Score: 94
    Period size: 31  Copynumber: 2.2  Consensus size: 33

       2915 TGCAAGTCTT

                                  *   *      
       2925 GAAGACAATTTTGCAAGCCATTTATGGCAAATA
          1 GAAGACAATTTTGCAAGCCATTAATGACAAATA

                                     *       
       2958 -AAGACAATTTTGCAA-CCATTAATTACAAA-A
          1 GAAGACAATTTTGCAAGCCATTAATGACAAATA

                    
       2988 GAAGACAA
          1 GAAGACAA

       2996 AATTATAAAA


Statistics
Matches: 34,  Mismatches: 3, Indels: 4
        0.83            0.07        0.10

Matches are distributed among these distances:
  30    1  0.03
  31   18  0.53
  32   15  0.44

ACGTcount: A:0.46, C:0.15, G:0.14, T:0.24


Consensus pattern (33 bp):   
GAAGACAATTTTGCAAGCCATTAATGACAAATA

Found at i:3299 original size:25 final size:25

Alignment explanation


    Indices: 3271--3322  Score: 61
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       3261 TAGTTAAGAA

                                 *    
       3271 TTTAGTATTTCTTAAAT-TTTTTTAT
          1 TTTA-TATTTCTTAAATATTTATTAT

                     *  *            
       3296 TTTATATTTTTTTAATATTTATTAT
          1 TTTATATTTCTTAAATATTTATTAT

              
       3321 TT
          1 TT

       3323 CAATTAACCT


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  24   10  0.43
  25   13  0.57

ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71


Consensus pattern (25 bp):   
TTTATATTTCTTAAATATTTATTAT

Found at i:4065 original size:22 final size:22

Alignment explanation


    Indices: 4017--4065  Score: 71
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       4007 TAGAAATGGT

                            *   * 
       4017 TTCATTTGCTGTTGGATTTGGA
          1 TTCATTTGCTGTTGGACTTGAA

            *                     
       4039 CTCATTTGCTGTTGGACTTGAA
          1 TTCATTTGCTGTTGGACTTGAA

                 
       4061 TTCAT
          1 TTCAT

       4066 ATAACTGAAC


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.16, C:0.14, G:0.22, T:0.47


Consensus pattern (22 bp):   
TTCATTTGCTGTTGGACTTGAA

Found at i:4963 original size:11 final size:11

Alignment explanation


    Indices: 4949--4986  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       4939 ATTCATAACA

                       
       4949 AATTTATAATT
          1 AATTTATAATT

                       
       4960 AATTTATAATT
          1 AATTTATAATT

                        
       4971 -ATTTGATAATT
          1 AATTT-ATAATT

            *    
       4982 TATTT
          1 AATTT

       4987 TATATATGAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  10    4  0.16
  11   17  0.68
  12    4  0.16

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


Consensus pattern (11 bp):   
AATTTATAATT

Found at i:5432 original size:31 final size:31

Alignment explanation


    Indices: 5339--5438  Score: 107
    Period size: 31  Copynumber: 3.3  Consensus size: 31

       5329 AGTACCTAAA

                    *  *          *     *  
       5339 TAGTCCCTGTACTATTGAAAAAGGATCATTT
          1 TAGTCCCTCTATTATTGAAAAACGATCAATT

                     *           *          
       5370 TAGTCCCTCCATTA-TG-AAATCTG-TCAATT
          1 TAGTCCCTCTATTATTGAAAAAC-GATCAATT

                                     *     
       5399 TAGTCCCTCTATTATTGAAAAACGACCAATT
          1 TAGTCCCTCTATTATTGAAAAACGATCAATT

                     
       5430 TAGTCCCTC
          1 TAGTCCCTC

       5439 CGTGAAACGA


Statistics
Matches: 56,  Mismatches: 9, Indels: 8
        0.77            0.12        0.11

Matches are distributed among these distances:
  29   21  0.38
  30    6  0.11
  31   29  0.52

ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35


Consensus pattern (31 bp):   
TAGTCCCTCTATTATTGAAAAACGATCAATT

Found at i:6828 original size:31 final size:31

Alignment explanation


    Indices: 6793--6889  Score: 92
    Period size: 31  Copynumber: 3.2  Consensus size: 31

       6783 TTTCATGGAG

                                           
       6793 GGACTAAATTGATCGTTTTTCAATAGTAGAA
          1 GGACTAAATTGATCGTTTTTCAATAGTAGAA

                   *         *        * *  *
       6824 GGACTAATTTGA-CAG-ATTTC-ATAATGGAG
          1 GGACTAAATTGATC-GTTTTTCAATAGTAGAA

                    *     *             *  
       6853 GGACTAAAGTGATCCTTTTTCAATAGTACAA
          1 GGACTAAATTGATCGTTTTTCAATAGTAGAA

                  
       6884 GGACTA
          1 GGACTA

       6890 TTTAGGTACT


Statistics
Matches: 49,  Mismatches: 13, Indels: 8
        0.70            0.19        0.11

Matches are distributed among these distances:
  29   16  0.33
  30   10  0.20
  31   23  0.47

ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32


Consensus pattern (31 bp):   
GGACTAAATTGATCGTTTTTCAATAGTAGAA
Done.