Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004899.1 Corchorus capsularis cultivar CVL-1 contig04917, 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: 15114
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34


Found at i:4427 original size:20 final size:20

Alignment explanation


    Indices: 4399--4436  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       4389 AAATTGGTAT

                *               
       4399 AATGGGTAGCTTTTATTTAA
          1 AATGAGTAGCTTTTATTTAA

                     *        
       4419 AATGAGTAGTTTTTATTT
          1 AATGAGTAGCTTTTATTT

       4437 TATTTTGAAT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50


Consensus pattern (20 bp):   
AATGAGTAGCTTTTATTTAA

Found at i:4646 original size:16 final size:17

Alignment explanation


    Indices: 4619--4651  Score: 50
    Period size: 16  Copynumber: 2.0  Consensus size: 17

       4609 TGTAGTTTGT

                        *    
       4619 GGTAGTTTTTTTTAATG
          1 GGTAGTTTTTTTAAATG

                             
       4636 GGTAG-TTTTTTAAATG
          1 GGTAGTTTTTTTAAATG

       4652 ATATAAATTA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  16   10  0.67
  17    5  0.33

ACGTcount: A:0.21, C:0.00, G:0.24, T:0.55


Consensus pattern (17 bp):   
GGTAGTTTTTTTAAATG

Found at i:6721 original size:81 final size:81

Alignment explanation


    Indices: 6586--6747  Score: 315
    Period size: 81  Copynumber: 2.0  Consensus size: 81

       6576 TTTCTCTCTT

                                                                             
       6586 TGTCTTCTTCGAGGAAGCCTTCACTTCAAGTACAACAGCAAAAACTTCACTTCCGCTATTACCCA
          1 TGTCTTCTTCGAGGAAGCCTTCACTTCAAGTACAACAGCAAAAACTTCACTTCCGCTATTACCCA

                            
       6651 CAAAGCCCCAAATCTC
         66 CAAAGCCCCAAATCTC

                                                                             
       6667 TGTCTTCTTCGAGGAAGCCTTCACTTCAAGTACAACAGCAAAAACTTCACTTCCGCTATTACCCA
          1 TGTCTTCTTCGAGGAAGCCTTCACTTCAAGTACAACAGCAAAAACTTCACTTCCGCTATTACCCA

              *             
       6732 CAGAGCCCCAAATCTC
         66 CAAAGCCCCAAATCTC

       6748 CAACAGGTTG


Statistics
Matches: 80,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  81   80  1.00

ACGTcount: A:0.30, C:0.33, G:0.12, T:0.25


Consensus pattern (81 bp):   
TGTCTTCTTCGAGGAAGCCTTCACTTCAAGTACAACAGCAAAAACTTCACTTCCGCTATTACCCA
CAAAGCCCCAAATCTC

Found at i:13036 original size:14 final size:14

Alignment explanation


    Indices: 13017--13046  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

      13007 ACCTTCTCTC

                     *    
      13017 TTTTTTTTCCTTTT
          1 TTTTTTTTCATTTT

                          
      13031 TTTTTTTTCATTTT
          1 TTTTTTTTCATTTT

              
      13045 TT
          1 TT

      13047 CTATGATATG


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87


Consensus pattern (14 bp):   
TTTTTTTTCATTTT

Found at i:13056 original size:5 final size:5

Alignment explanation


    Indices: 13048--13080  Score: 59
    Period size: 5  Copynumber: 6.8  Consensus size: 5

      13038 TCATTTTTTC

                                                    
      13048 TATGA TATGA TATGA TATGA TATGA TA-GA TATG
          1 TATGA TATGA TATGA TATGA TATGA TATGA TATG

      13081 GTTTTGTGCC


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   4    4  0.15
   5   23  0.85

ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39


Consensus pattern (5 bp):   
TATGA

Done.