Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018302.1 Corchorus olitorius cultivar O-4 contig18335, 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: 21294
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32


Found at i:854 original size:17 final size:17

Alignment explanation


    Indices: 828--889  Score: 50
    Period size: 17  Copynumber: 4.1  Consensus size: 17

        818 ATAGTAAAAG

                             
        828 AATT-AGAAACCCAAAT
          1 AATTAAGAAACCCAAAT

                             
        844 AATTAAGAAA--C--A-
          1 AATTAAGAAACCCAAAT

                              
        856 AA--AAGAAACCCAAAAT
          1 AATTAAGAAACCC-AAAT

                     *       
        872 AATTAAGAAGCCCAAAT
          1 AATTAAGAAACCCAAAT

             
        889 A
          1 A

        890 TTACCCAACT


Statistics
Matches: 36,  Mismatches: 1, Indels: 17
        0.67            0.02        0.31

Matches are distributed among these distances:
  10    6  0.17
  12    3  0.08
  13    1  0.03
  15    2  0.06
  16    6  0.17
  17   10  0.28
  18    8  0.22

ACGTcount: A:0.61, C:0.16, G:0.08, T:0.15


Consensus pattern (17 bp):   
AATTAAGAAACCCAAAT

Found at i:11867 original size:21 final size:20

Alignment explanation


    Indices: 11843--11885  Score: 77
    Period size: 21  Copynumber: 2.1  Consensus size: 20

      11833 CCTTAGGCAA

                                 
      11843 CTCCAATGAGCTTGAAACCTT
          1 CTCCAATGAGCTTGAAA-CTT

                                
      11864 CTCCAATGAGCTTGAAACTT
          1 CTCCAATGAGCTTGAAACTT

              
      11884 CT
          1 CT

      11886 TTGTGAGTAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  20    5  0.23
  21   17  0.77

ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30


Consensus pattern (20 bp):   
CTCCAATGAGCTTGAAACTT

Found at i:15393 original size:63 final size:63

Alignment explanation


    Indices: 15294--15507  Score: 340
    Period size: 63  Copynumber: 3.4  Consensus size: 63

      15284 TGGCGCATCA

                           *          *                       *   *        
      15294 CCAAAATACCCTTTCGGACAAAGGGTTAGCCTTGTCACATTTCTTGCATTGAGACTTAGTTTC
          1 CCAAAATACCCTTTCAGACAAAGGGTCAGCCTTGTCACATTTCTTGCATTTAGATTTAGTTTC

                           *      *                                    *   
      15357 CCAAAATACCCTTTCGGACAAAAGGTCAGCCTTGTCACATTTCTTGCATTTAGATTTAGCTTC
          1 CCAAAATACCCTTTCAGACAAAGGGTCAGCCTTGTCACATTTCTTGCATTTAGATTTAGTTTC

                                          *                                 
      15420 CCATAAA-ACCCTTTCAGACAAAGGGTCAGTCTTGTCACATTTCTTGCATTTAGATTTAGTTTC
          1 CCA-AAATACCCTTTCAGACAAAGGGTCAGCCTTGTCACATTTCTTGCATTTAGATTTAGTTTC

                                     
      15483 CCAAAATACCCTTTCAGACAAAGGG
          1 CCAAAATACCCTTTCAGACAAAGGG

      15508 AGGAATTTTG


Statistics
Matches: 140,  Mismatches: 9, Indels: 4
        0.92            0.06        0.03

Matches are distributed among these distances:
  62    3  0.02
  63  134  0.96
  64    3  0.02

ACGTcount: A:0.28, C:0.24, G:0.15, T:0.32


Consensus pattern (63 bp):   
CCAAAATACCCTTTCAGACAAAGGGTCAGCCTTGTCACATTTCTTGCATTTAGATTTAGTTTC

Found at i:16734 original size:22 final size:22

Alignment explanation


    Indices: 16692--16734  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      16682 TTTCCCGCAA

                          * *     
      16692 CAAGTCCTGGGCAGGAGTTGTC
          1 CAAGTCCTGGGCAGAAATTGTC

                                 
      16714 CAAGTCCTGGGCAGAAATTGT
          1 CAAGTCCTGGGCAGAAATTGT

      16735 TCTGAAATTC


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.23, C:0.21, G:0.33, T:0.23


Consensus pattern (22 bp):   
CAAGTCCTGGGCAGAAATTGTC
Done.