Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017414.1 Corchorus olitorius cultivar O-4 contig17447, 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: 16490
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35


Found at i:733 original size:28 final size:28

Alignment explanation


    Indices: 693--747  Score: 92
    Period size: 28  Copynumber: 2.0  Consensus size: 28

        683 CAACTACACC

                                        
        693 AAATGATAATCAAGTCCAAACCAATTAG
          1 AAATGATAATCAAGTCCAAACCAATTAG

                         *    *        
        721 AAATGATAATCAATTCCATACCAATTA
          1 AAATGATAATCAAGTCCAAACCAATTA

        748 AACCACAACA


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  28   25  1.00

ACGTcount: A:0.49, C:0.18, G:0.07, T:0.25


Consensus pattern (28 bp):   
AAATGATAATCAAGTCCAAACCAATTAG

Found at i:2546 original size:24 final size:24

Alignment explanation


    Indices: 2502--2547  Score: 58
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       2492 GATTTATATT

                *           *       
       2502 CCATGCACTGTCAGTGTATAGAGG
          1 CCATACACTGTCAGTGCATAGAGG

                                   
       2526 CCATACACTGTCAG-GCCATAGA
          1 CCATACACTGTCAGTG-CATAGA

       2548 ATTATGCCAC


Statistics
Matches: 19,  Mismatches: 2, Indels: 2
        0.83            0.09        0.09

Matches are distributed among these distances:
  23    1  0.05
  24   18  0.95

ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22


Consensus pattern (24 bp):   
CCATACACTGTCAGTGCATAGAGG

Found at i:4748 original size:49 final size:49

Alignment explanation


    Indices: 4684--4788  Score: 192
    Period size: 49  Copynumber: 2.1  Consensus size: 49

       4674 CCCATGTTGT

                                    *                        
       4684 AGATGAAAACATATGAATCAAAATTAAAGTGCAAACTGTTAACCCAAGA
          1 AGATGAAAACATATGAATCAAAATAAAAGTGCAAACTGTTAACCCAAGA

                                                             
       4733 AGATGAAAACATATGAATCAAAATAAAAGTGCAAACTGTTAACCCAAGA
          1 AGATGAAAACATATGAATCAAAATAAAAGTGCAAACTGTTAACCCAAGA

              *    
       4782 AGCTGAA
          1 AGATGAA

       4789 GCTAACAAAA


Statistics
Matches: 54,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  49   54  1.00

ACGTcount: A:0.51, C:0.14, G:0.15, T:0.19


Consensus pattern (49 bp):   
AGATGAAAACATATGAATCAAAATAAAAGTGCAAACTGTTAACCCAAGA

Found at i:10192 original size:66 final size:69

Alignment explanation


    Indices: 10023--10192  Score: 190
    Period size: 69  Copynumber: 2.5  Consensus size: 69

      10013 ATCTCATCTC

                    *          *        *                     *      *   *   
      10023 CAAGGTCAGGACAAGCCGCAAATTCTTAGGAATTTTCAAAGTTTAAGACATGATTCCTTATCTCA
          1 CAAGGTCAAGACAAGCCGCTAATTCTTAAGAATTTTCAAAGTTTAAGACAGGATTCCCTATATCA

                
      10088 TTCT
         66 TTCT

                  *       *     *                                            
      10092 CAAGGTTAAGACAAACCGCTGATTCTT-AGAAATTTTCAAAGTTTAAGAGCAAGGA-TCCCTA-A
          1 CAAGGTCAAGACAAGCCGCTAATTCTTAAG-AATTTTCAAAGTTTAAGA-C-AGGATTCCCTATA

                   
      10154 TC-TT-T
         63 TCATTCT

                                               
      10159 -AAGGTCAAGACAAGCCGCTAATTCTTAAGAATTT
          1 CAAGGTCAAGACAAGCCGCTAATTCTTAAGAATTT

      10193 AGGATTCATT


Statistics
Matches: 85,  Mismatches: 12, Indels: 11
        0.79            0.11        0.10

Matches are distributed among these distances:
  66   28  0.33
  67    3  0.04
  68    3  0.04
  69   42  0.49
  70    6  0.07
  71    3  0.04

ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30


Consensus pattern (69 bp):   
CAAGGTCAAGACAAGCCGCTAATTCTTAAGAATTTTCAAAGTTTAAGACAGGATTCCCTATATCA
TTCT
Done.