Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012007.1 Corchorus olitorius cultivar O-4 contig12040, 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: 24816
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30


Found at i:5450 original size:15 final size:14

Alignment explanation


    Indices: 5429--5472  Score: 52
    Period size: 15  Copynumber: 3.0  Consensus size: 14

       5419 TAGTAAACAC

                          
       5429 TTTCGGTGCCATCA
          1 TTTCGGTGCCATCA

                       *    
       5443 TCTTCGGTGCCGTCGA
          1 T-TTCGGTGCCATC-A

                *         
       5459 TTTCAGTGCCATCA
          1 TTTCGGTGCCATCA

       5473 GCTTTGTCCA


Statistics
Matches: 25,  Mismatches: 3, Indels: 4
        0.78            0.09        0.12

Matches are distributed among these distances:
  14    2  0.08
  15   21  0.84
  16    2  0.08

ACGTcount: A:0.14, C:0.30, G:0.23, T:0.34


Consensus pattern (14 bp):   
TTTCGGTGCCATCA

Found at i:6719 original size:18 final size:18

Alignment explanation


    Indices: 6696--6751  Score: 67
    Period size: 18  Copynumber: 3.1  Consensus size: 18

       6686 GAACAACTGT

                              
       6696 GGCAACTTGGTGCGGTGC
          1 GGCAACTTGGTGCGGTGC

                         *    
       6714 GGCAACTTGGTGCAGTGC
          1 GGCAACTTGGTGCGGTGC

            ** *        *     
       6732 AACCACTTGGTGTGGTGC
          1 GGCAACTTGGTGCGGTGC

              
       6750 GG
          1 GG

       6752 GATCTAGGTG


Statistics
Matches: 30,  Mismatches: 8, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  18   30  1.00

ACGTcount: A:0.14, C:0.21, G:0.41, T:0.23


Consensus pattern (18 bp):   
GGCAACTTGGTGCGGTGC

Found at i:7384 original size:49 final size:48

Alignment explanation


    Indices: 7303--7428  Score: 168
    Period size: 49  Copynumber: 2.6  Consensus size: 48

       7293 GAGCGTGCCA

                                   *                          
       7303 ATCAATTTTGTC-AAAAATTTGATAAAAA-GTGCAA-TAAAAAGTAAAAG
          1 ATCAATTTTGTCTAAAAA-TTGAGAAAAAGGTGCAAGTAAAAA-TAAAAG

                                                             
       7350 ATCAATTTTGTCTTAAAAATTGAGAAAAAGGTGCAAGTAAAAATAAAAG
          1 ATCAATTTTGTC-TAAAAATTGAGAAAAAGGTGCAAGTAAAAATAAAAG

            *           *                 
       7399 TTCAATTTTGTAGTAAAAATTGAGAAAAAG
          1 ATCAATTTTGT-CTAAAAATTGAGAAAAAG

       7429 TACAGGAAAT


Statistics
Matches: 71,  Mismatches: 3, Indels: 8
        0.87            0.04        0.10

Matches are distributed among these distances:
  47   12  0.17
  48    9  0.13
  49   44  0.62
  50    6  0.08

ACGTcount: A:0.51, C:0.06, G:0.15, T:0.29


Consensus pattern (48 bp):   
ATCAATTTTGTCTAAAAATTGAGAAAAAGGTGCAAGTAAAAATAAAAG

Found at i:18864 original size:2 final size:2

Alignment explanation


    Indices: 18857--18885  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      18847 TCTTTCTTCC

                                                       
      18857 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      18886 CTAGTTTAAG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.