Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013693.1 Corchorus olitorius cultivar O-4 contig13726, 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: 22381
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:4059 original size:6 final size:5

Alignment explanation


    Indices: 4028--4057  Score: 51
    Period size: 5  Copynumber: 5.8  Consensus size: 5

       4018 AGCCCCCCCA

                                               
       4028 AAAAG AAAAAG AAAAG AAAAG AAAAG AAAA
          1 AAAAG -AAAAG AAAAG AAAAG AAAAG AAAA

       4058 AGGAACTGCT


Statistics
Matches: 24,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   5   19  0.79
   6    5  0.21

ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00


Consensus pattern (5 bp):   
AAAAG

Found at i:5766 original size:24 final size:24

Alignment explanation


    Indices: 5739--5788  Score: 82
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       5729 ATGTTTCAAT

                                *   
       5739 TGTTGTTGTTGCTGCTGCTGTTGC
          1 TGTTGTTGTTGCTGCTGCTGCTGC

                       *            
       5763 TGTTGTTGTTGTTGCTGCTGCTGC
          1 TGTTGTTGTTGCTGCTGCTGCTGC

              
       5787 TG
          1 TG

       5789 CTGCTGCTGT


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.00, C:0.16, G:0.34, T:0.50


Consensus pattern (24 bp):   
TGTTGTTGTTGCTGCTGCTGCTGC

Found at i:5781 original size:3 final size:3

Alignment explanation


    Indices: 5748--5797  Score: 55
    Period size: 3  Copynumber: 16.7  Consensus size: 3

       5738 TTGTTGTTGT

                          *       *   *   *   *                            
       5748 TGC TGC TGC TGT TGC TGT TGT TGT TGT TGC TGC TGC TGC TGC TGC TGC
          1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC

              
       5796 TG
          1 TG

       5798 TTGGAGCTGT


Statistics
Matches: 43,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   3   43  1.00

ACGTcount: A:0.00, C:0.22, G:0.34, T:0.44


Consensus pattern (3 bp):   
TGC

Found at i:9333 original size:62 final size:62

Alignment explanation


    Indices: 9262--9384  Score: 237
    Period size: 62  Copynumber: 2.0  Consensus size: 62

       9252 TACCCAAAAA

                                  *                                       
       9262 AACGTGAACAAGTTTAAACACATATTTAGAAAGTTTAGTGACAATTTAAATCGGTACCAAAG
          1 AACGTGAACAAGTTTAAACACAAATTTAGAAAGTTTAGTGACAATTTAAATCGGTACCAAAG

                                                                         
       9324 AACGTGAACAAGTTTAAACACAAATTTAGAAAGTTTAGTGACAATTTAAATCGGTACCAAA
          1 AACGTGAACAAGTTTAAACACAAATTTAGAAAGTTTAGTGACAATTTAAATCGGTACCAAA

       9385 AAAAAGTCAC


Statistics
Matches: 60,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  62   60  1.00

ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27


Consensus pattern (62 bp):   
AACGTGAACAAGTTTAAACACAAATTTAGAAAGTTTAGTGACAATTTAAATCGGTACCAAAG

Found at i:14781 original size:25 final size:25

Alignment explanation


    Indices: 14753--14800  Score: 78
    Period size: 25  Copynumber: 1.9  Consensus size: 25

      14743 CTAATGTATC

                            *        
      14753 ACATATTCCCAACAAATCAATTAAA
          1 ACATATTCCCAACAAACCAATTAAA

                *                  
      14778 ACATTTTCCCAACAAACCAATTA
          1 ACATATTCCCAACAAACCAATTA

      14801 TACTAACTTC


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  25   21  1.00

ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25


Consensus pattern (25 bp):   
ACATATTCCCAACAAACCAATTAAA
Done.