Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014662.1 Corchorus olitorius cultivar O-4 contig14695, 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: 15694
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:2771 original size:41 final size:41

Alignment explanation


    Indices: 2714--2791  Score: 131
    Period size: 41  Copynumber: 1.9  Consensus size: 41

       2704 ATGAATTTCT

                                          *           
       2714 TTTCTTAACTAAATTTTCTTAAAA-ACACTTATAAAATTCCA
          1 TTTCTTAACTAAATTTTCTTAAAATA-ACTCATAAAATTCCA

                                                 
       2755 TTTCTTAACTAAATTTTCTTAAAATAACTCATAAAAT
          1 TTTCTTAACTAAATTTTCTTAAAATAACTCATAAAAT

       2792 AAAATAGGCA


Statistics
Matches: 35,  Mismatches: 1, Indels: 2
        0.92            0.03        0.05

Matches are distributed among these distances:
  41   34  0.97
  42    1  0.03

ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42


Consensus pattern (41 bp):   
TTTCTTAACTAAATTTTCTTAAAATAACTCATAAAATTCCA

Found at i:4089 original size:21 final size:19

Alignment explanation


    Indices: 4034--4092  Score: 66
    Period size: 19  Copynumber: 2.9  Consensus size: 19

       4024 TTGAAATTCA

                                
       4034 TCAATATTTGGTGTAATGAT
          1 TCAAT-TTTGGTGTAATGAT

               *                
       4054 TACCA-TTTGGTGTAATGAT
          1 T-CAATTTTGGTGTAATGAT

                                
       4073 GTCAATTTTGAGTGTAATGA
          1 -TCAATTTTG-GTGTAATGA

       4093 AAAATCTTTT


Statistics
Matches: 33,  Mismatches: 2, Indels: 7
        0.79            0.05        0.17

Matches are distributed among these distances:
  19   16  0.48
  20    6  0.18
  21   11  0.33

ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42


Consensus pattern (19 bp):   
TCAATTTTGGTGTAATGAT

Found at i:5156 original size:22 final size:22

Alignment explanation


    Indices: 5103--5159  Score: 60
    Period size: 22  Copynumber: 2.6  Consensus size: 22

       5093 TTTTAACCAT

                *       *         
       5103 ACTACGAAATTTCAATAAACTC
          1 ACTATGAAATTTTAATAAACTC

            *    *            *   
       5125 TCTATAAAATTTTAATAACCTC
          1 ACTATGAAATTTTAATAAACTC

             *           
       5147 AGTATGAAATTTT
          1 ACTATGAAATTTT

       5160 GTTTACCTCC


Statistics
Matches: 27,  Mismatches: 8, Indels: 0
        0.77            0.23        0.00

Matches are distributed among these distances:
  22   27  1.00

ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37


Consensus pattern (22 bp):   
ACTATGAAATTTTAATAAACTC

Found at i:8059 original size:20 final size:20

Alignment explanation


    Indices: 8036--8076  Score: 82
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       8026 TTTTTTTTTA

                                
       8036 AATTTAAATAAATCAAAAGG
          1 AATTTAAATAAATCAAAAGG

                                
       8056 AATTTAAATAAATCAAAAGG
          1 AATTTAAATAAATCAAAAGG

             
       8076 A
          1 A

       8077 TTTTTTATAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   21  1.00

ACGTcount: A:0.61, C:0.05, G:0.10, T:0.24


Consensus pattern (20 bp):   
AATTTAAATAAATCAAAAGG

Found at i:14749 original size:13 final size:13

Alignment explanation


    Indices: 14731--14756  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      14721 CATTAGCGGT

                         
      14731 AAAGAAGAGAGAG
          1 AAAGAAGAGAGAG

                         
      14744 AAAGAAGAGAGAG
          1 AAAGAAGAGAGAG

      14757 GACGGAGAAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00


Consensus pattern (13 bp):   
AAAGAAGAGAGAG

Found at i:15670 original size:2 final size:2

Alignment explanation


    Indices: 15663--15688  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      15653 ATTTGCCTTC

                                                  
      15663 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

      15689 TTATTA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
AT

Done.