Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017043.1 Corchorus olitorius cultivar O-4 contig17076, 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: 32988
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35


Found at i:14137 original size:1 final size:1

Alignment explanation


    Indices: 14131--14175  Score: 90
    Period size: 1  Copynumber: 45.0  Consensus size: 1

      14121 CCAAGCAAAG

                                                         
      14131 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      14176 GCTGCCAAGA


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   44  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:14527 original size:18 final size:18

Alignment explanation


    Indices: 14501--14535  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

      14491 AACTTTTTCT

                *    *        
      14501 TCACTTAAATACAAAAAG
          1 TCACCTAAAAACAAAAAG

                             
      14519 TCACCTAAAAACAAAAA
          1 TCACCTAAAAACAAAAA

      14536 CAATTTAGAT


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17


Consensus pattern (18 bp):   
TCACCTAAAAACAAAAAG

Found at i:21060 original size:1 final size:1

Alignment explanation


    Indices: 21054--21100  Score: 94
    Period size: 1  Copynumber: 47.0  Consensus size: 1

      21044 CATACTAAAG

                                                           
      21054 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

      21101 CACAAGCTTC


Statistics
Matches: 46,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   46  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:23505 original size:63 final size:63

Alignment explanation


    Indices: 23382--23506  Score: 180
    Period size: 63  Copynumber: 2.0  Consensus size: 63

      23372 CTATGCGTTT

                          *               *         *           *          
      23382 CTGATGACAAAACCGGTAATGAAGTCCAAGGCAATGATGCCATTTCAAACAAGTCTGACACCA
          1 CTGATGACAAAACCAGTAATGAAGTCCAAGACAATGATGCAATTTCAAACAACTCTGACACCA

                                           **                              
      23445 CTGATGACAAAACCAGTAATGAAGTCCAAGATGATGATGCAATTTCAAACAAC-CTCGACACC
          1 CTGATGACAAAACCAGTAATGAAGTCCAAGACAATGATGCAATTTCAAACAACTCT-GACACC

      23507 TGTGTTAATG


Statistics
Matches: 55,  Mismatches: 6, Indels: 2
        0.87            0.10        0.03

Matches are distributed among these distances:
  62    2  0.04
  63   53  0.96

ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19


Consensus pattern (63 bp):   
CTGATGACAAAACCAGTAATGAAGTCCAAGACAATGATGCAATTTCAAACAACTCTGACACCA

Found at i:28108 original size:28 final size:28

Alignment explanation


    Indices: 28054--28108  Score: 76
    Period size: 28  Copynumber: 2.0  Consensus size: 28

      28044 GACTTTTAAT

                               **       
      28054 AAGTTTATGAAATATTTCACCAAAAAAA
          1 AAGTTTATGAAATATTTCAAAAAAAAAA

                                   *    
      28082 AAGTTTATGAAATATTT-AAAAAGAAAA
          1 AAGTTTATGAAATATTTCAAAAAAAAAA

      28109 TATGCCAATT


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  27    7  0.29
  28   17  0.71

ACGTcount: A:0.56, C:0.05, G:0.09, T:0.29


Consensus pattern (28 bp):   
AAGTTTATGAAATATTTCAAAAAAAAAA

Found at i:31440 original size:12 final size:13

Alignment explanation


    Indices: 31417--31445  Score: 51
    Period size: 12  Copynumber: 2.3  Consensus size: 13

      31407 TAAGTTTGGT

                         
      31417 TTCTCTCTTCTTC
          1 TTCTCTCTTCTTC

                         
      31430 TTCTC-CTTCTTC
          1 TTCTCTCTTCTTC

                
      31442 TTCT
          1 TTCT

      31446 TTCGTTTTCA


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   11  0.69
  13    5  0.31

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


Consensus pattern (13 bp):   
TTCTCTCTTCTTC
Done.