Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015143.1 Corchorus olitorius cultivar O-4 contig15176, 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: 17917
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33


Found at i:4878 original size:25 final size:25

Alignment explanation


    Indices: 4845--4894  Score: 100
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       4835 CCCAAACAAT

                                     
       4845 TTTGAGCACTCTCGCTCGGTCTCTA
          1 TTTGAGCACTCTCGCTCGGTCTCTA

                                     
       4870 TTTGAGCACTCTCGCTCGGTCTCTA
          1 TTTGAGCACTCTCGCTCGGTCTCTA

       4895 CAAATCAATC


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   25  1.00

ACGTcount: A:0.12, C:0.32, G:0.20, T:0.36


Consensus pattern (25 bp):   
TTTGAGCACTCTCGCTCGGTCTCTA

Found at i:5883 original size:29 final size:28

Alignment explanation


    Indices: 5799--5886  Score: 70
    Period size: 29  Copynumber: 3.0  Consensus size: 28

       5789 TTAATGTCCC

                                  *   *   *
       5799 TTTTGCCCCCTGAACATGTACAGTTTTGACG
          1 TTTTGCCCCCTGAAC-T-T-CAATTTGGACA

                  *           *           
       5830 TTTTGCTCCCT-AGACTTTAATTTTGGACA
          1 TTTTGCCCCCTGA-ACTTCAA-TTTGGACA

                                        
       5859 TTTTGCCCCCTGAACTCTCAATTTGGAC
          1 TTTTGCCCCCTGAACT-TCAATTTGGAC

       5887 CCTTTTTAGT


Statistics
Matches: 46,  Mismatches: 7, Indels: 10
        0.73            0.11        0.16

Matches are distributed among these distances:
  28    1  0.02
  29   27  0.59
  30    6  0.13
  31   12  0.26

ACGTcount: A:0.19, C:0.26, G:0.16, T:0.39


Consensus pattern (28 bp):   
TTTTGCCCCCTGAACTTCAATTTGGACA

Found at i:10864 original size:6 final size:6

Alignment explanation


    Indices: 10850--10897  Score: 62
    Period size: 6  Copynumber: 8.2  Consensus size: 6

      10840 TGCAATGTTT

                *                                 *      *         
      10850 TCTAAA TCTATA TCTATA TCTATA TCTATA TCTCTA TCTTTA T-TATA
          1 TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA

             
      10897 T
          1 T

      10898 TAGTCTAAAC


Statistics
Matches: 38,  Mismatches: 4, Indels: 1
        0.88            0.09        0.02

Matches are distributed among these distances:
   5    4  0.11
   6   34  0.89

ACGTcount: A:0.31, C:0.17, G:0.00, T:0.52


Consensus pattern (6 bp):   
TCTATA

Found at i:12708 original size:23 final size:22

Alignment explanation


    Indices: 12660--12708  Score: 73
    Period size: 22  Copynumber: 2.2  Consensus size: 22

      12650 AATAATATTG

                               *  
      12660 TTTTTAGAATAATCACTTATAC
          1 TTTTTAGAATAATCACTTAAAC

                                   
      12682 TTTTTAGAATAATCA-TTGAAAC
          1 TTTTTAGAATAATCACTT-AAAC

                 
      12704 TTTTT
          1 TTTTT

      12709 TAGTAACTTT


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  21    2  0.08
  22   23  0.92

ACGTcount: A:0.35, C:0.10, G:0.06, T:0.49


Consensus pattern (22 bp):   
TTTTTAGAATAATCACTTAAAC
Done.