Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012608.1 Corchorus olitorius cultivar O-4 contig12641, 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: 27647
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:8 original size:2 final size:2

Alignment explanation


    Indices: 2--42  Score: 64
    Period size: 2  Copynumber: 20.5  Consensus size: 2

          1 C

                                                          *     *        
          2 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         43 TTGTCCAACA


Statistics
Matches: 35,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:742 original size:14 final size:15

Alignment explanation


    Indices: 717--745  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

        707 GTTTCATTCA

                           
        717 CTTTTCTTTTTTATT
          1 CTTTTCTTTTTTATT

                           
        732 CTTTT-TTTTTTATT
          1 CTTTTCTTTTTTATT

        746 GAAGGTAAGT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14    9  0.64
  15    5  0.36

ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83


Consensus pattern (15 bp):   
CTTTTCTTTTTTATT

Found at i:15623 original size:22 final size:21

Alignment explanation


    Indices: 15585--15625  Score: 55
    Period size: 22  Copynumber: 1.9  Consensus size: 21

      15575 CATTGATAAA

                       **        
      15585 TGAAATTTCCATTTAAGTAGT
          1 TGAAATTTCCAGCTAAGTAGT

                                
      15606 TGAAATATTCCAGCTAAGTA
          1 TGAAAT-TTCCAGCTAAGTA

      15626 CCAATGAAGG


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21    6  0.35
  22   11  0.65

ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37


Consensus pattern (21 bp):   
TGAAATTTCCAGCTAAGTAGT

Found at i:26788 original size:39 final size:39

Alignment explanation


    Indices: 26729--26817  Score: 144
    Period size: 39  Copynumber: 2.3  Consensus size: 39

      26719 GGTGACAAAA

                                                    
      26729 TGAACCCGA-TCTGAGAAAAACTTGAATCCGAACCCAATT
          1 TGAACCCGATTC-GAGAAAAACTTGAATCCGAACCCAATT

                *                           *      
      26768 TGAATCCGATTCGAGAAAAACTTGAATCCGAATCCAATT
          1 TGAACCCGATTCGAGAAAAACTTGAATCCGAACCCAATT

                       
      26807 TGAACCCGATT
          1 TGAACCCGATT

      26818 GACTAAAGAA


Statistics
Matches: 46,  Mismatches: 3, Indels: 2
        0.90            0.06        0.04

Matches are distributed among these distances:
  39   44  0.96
  40    2  0.04

ACGTcount: A:0.37, C:0.24, G:0.16, T:0.24


Consensus pattern (39 bp):   
TGAACCCGATTCGAGAAAAACTTGAATCCGAACCCAATT

Found at i:26941 original size:20 final size:21

Alignment explanation


    Indices: 26902--26941  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      26892 TATGAAACCC

                           *     
      26902 GAAAAAACCGAACTTGAATAT
          1 GAAAAAACCGAACTTCAATAT

                  *             
      26923 GAAAAACCCGAA-TTCAATA
          1 GAAAAAACCGAACTTCAATA

      26942 CTAATAATTG


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  20    6  0.35
  21   11  0.65

ACGTcount: A:0.53, C:0.17, G:0.12, T:0.17


Consensus pattern (21 bp):   
GAAAAAACCGAACTTCAATAT

Found at i:27164 original size:32 final size:33

Alignment explanation


    Indices: 27123--27208  Score: 104
    Period size: 32  Copynumber: 2.7  Consensus size: 33

      27113 ACCCAGCCCA

                                             
      27123 AATCCGAATTAACCTGA-CCAAAAATTAACACG
          1 AATCCGAATTAACCTGATCCAAAAATTAACACG

                *       *           *     *  
      27155 AATCTGAATTAATCTGATCC-AAATTTAACCCG
          1 AATCCGAATTAACCTGATCCAAAAATTAACACG

              *      *            
      27187 AAACCGAATCAACCTGATCCAA
          1 AATCCGAATTAACCTGATCCAA

      27209 CTATAACCCG


Statistics
Matches: 44,  Mismatches: 8, Indels: 3
        0.80            0.15        0.05

Matches are distributed among these distances:
  32   41  0.93
  33    3  0.07

ACGTcount: A:0.43, C:0.26, G:0.09, T:0.22


Consensus pattern (33 bp):   
AATCCGAATTAACCTGATCCAAAAATTAACACG
Done.