Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017126.1 Corchorus olitorius cultivar O-4 contig17159, 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: 5152
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31


Found at i:1740 original size:2 final size:2

Alignment explanation


    Indices: 1733--1772  Score: 71
    Period size: 2  Copynumber: 20.0  Consensus size: 2

       1723 TGCTAAGTGC

                        *                                              
       1733 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       1773 GTCTGCAAAC


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:2599 original size:21 final size:20

Alignment explanation


    Indices: 2557--2600  Score: 52
    Period size: 21  Copynumber: 2.1  Consensus size: 20

       2547 TGAAATTAAA

                       *   *    
       2557 TGACAAACAATGATCCTAAT
          1 TGACAAACAATAATCATAAT

                              *  
       2577 TGACAAAGCAATAATCATGAT
          1 TGACAAA-CAATAATCATAAT

               
       2598 TGA
          1 TGA

       2601 AATTGAATCA


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  20    7  0.35
  21   13  0.65

ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25


Consensus pattern (20 bp):   
TGACAAACAATAATCATAAT

Found at i:2797 original size:39 final size:40

Alignment explanation


    Indices: 2754--2830  Score: 113
    Period size: 41  Copynumber: 1.9  Consensus size: 40

       2744 AAATGACATG

                                  *                  
       2754 ATACCCAGAGGTTT-T-ATTTATTGCCCGGAGGACTTATTA
          1 ATACCCAGAGGTTTCTAATTT-GTGCCCGGAGGACTTATTA

                                                  
       2793 ATACCCAGAGGTTTCTGAATTTGTGCCCGGAGGACTTA
          1 ATACCCAGAGGTTTCT-AATTTGTGCCCGGAGGACTTA

       2831 CCTATGCAAA


Statistics
Matches: 34,  Mismatches: 1, Indels: 4
        0.87            0.03        0.10

Matches are distributed among these distances:
  39   14  0.41
  40    1  0.03
  41   15  0.44
  42    4  0.12

ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32


Consensus pattern (40 bp):   
ATACCCAGAGGTTTCTAATTTGTGCCCGGAGGACTTATTA

Found at i:3143 original size:69 final size:69

Alignment explanation


    Indices: 3074--3568  Score: 758
    Period size: 69  Copynumber: 7.2  Consensus size: 69

       3064 ACTTGACTTA

                       *   *            *    * *     *                       
       3074 TGGAAAAGCCTCTGTTG-TATGGATGGACCCAATGTTTAAAATGACTCGTATGGAAACGAGTTTG
          1 TGGAAAAGCCTATGTGGCT-TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTG

            *   *
       3138 ACTTA
         65 GCTTG

                    *    *                  *    *          *                
       3143 TGGAAAAGTCTATATGGCTTGGATGGAACCAATGCTTGAACTGACTCGCATGGAAACGAGTTTGG
          1 TGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGG

                
       3208 CTTG
         66 CTTG

                         *                  *    *           *       *       
       3212 TGGAAAAGCCTATATGGCTTGGATGGAACCAAAGCTTGAACTGACTCGTCTGGAAACAAGTTTGG
          1 TGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGG

                
       3277 CTTG
         66 CTTG

                                                          *          * *     
       3281 TGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTAGTATGGAAACCATTTTGG
          1 TGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGG

                
       3346 CTTG
         66 CTTG

              *            *                     *                           
       3350 TGAAAAAGCCTATGTTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGG
          1 TGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGG

                
       3415 CTTG
         66 CTTG

                                                                             
       3419 TGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGG
          1 TGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGG

                
       3484 CTTG
         66 CTTG

                                                                             
       3488 TGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGG
          1 TGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGG

                
       3553 CTTG
         66 CTTG

                        
       3557 TGGAAAAGCCTA
          1 TGGAAAAGCCTA

       3569 CGTTGCTAAT


Statistics
Matches: 393,  Mismatches: 32, Indels: 2
        0.92            0.07        0.00

Matches are distributed among these distances:
  69  392  1.00
  70    1  0.00

ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27


Consensus pattern (69 bp):   
TGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGG
CTTG

Found at i:4850 original size:31 final size:31

Alignment explanation


    Indices: 4812--4874  Score: 126
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       4802 CGGACTGGAC

                                           
       4812 ATAGTGGGGACCTTTCTGCACATCAAGTAAA
          1 ATAGTGGGGACCTTTCTGCACATCAAGTAAA

                                           
       4843 ATAGTGGGGACCTTTCTGCACATCAAGTAAA
          1 ATAGTGGGGACCTTTCTGCACATCAAGTAAA

             
       4874 A
          1 A

       4875 GATTAGCAAC


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

Matches are distributed among these distances:
  31   32  1.00

ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25


Consensus pattern (31 bp):   
ATAGTGGGGACCTTTCTGCACATCAAGTAAA
Done.