Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023649.1 Corchorus olitorius cultivar O-4 contig23682, 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: 20426
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30


Found at i:1906 original size:16 final size:17

Alignment explanation


    Indices: 1880--1911  Score: 57
    Period size: 16  Copynumber: 1.9  Consensus size: 17

       1870 AGTGCAAATT

                             
       1880 AAAATAGAAAAATAAAG
          1 AAAATAGAAAAATAAAG

                            
       1897 AAAA-AGAAAAATAAA
          1 AAAATAGAAAAATAAA

       1912 ACGCAAGTTC


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

Matches are distributed among these distances:
  16   11  0.73
  17    4  0.27

ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09


Consensus pattern (17 bp):   
AAAATAGAAAAATAAAG

Found at i:2144 original size:12 final size:13

Alignment explanation


    Indices: 2122--2151  Score: 53
    Period size: 12  Copynumber: 2.4  Consensus size: 13

       2112 ACTAACAATT

                         
       2122 AAAATCAATCAAG
          1 AAAATCAATCAAG

                         
       2135 AAAA-CAATCAAG
          1 AAAATCAATCAAG

                 
       2147 AAAAT
          1 AAAAT

       2152 TAAAGAAAAC


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

Matches are distributed among these distances:
  12   12  0.75
  13    4  0.25

ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13


Consensus pattern (13 bp):   
AAAATCAATCAAG

Found at i:8899 original size:2 final size:2

Alignment explanation


    Indices: 8892--8926  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       8882 ACATACGTAC

                                                                
       8892 AT AT AT 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 AT AT AT A

       8927 AGATAGGAAT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:9048 original size:83 final size:84

Alignment explanation


    Indices: 8961--9142  Score: 212
    Period size: 83  Copynumber: 2.2  Consensus size: 84

       8951 CAAGTATATA

                           *                                                 
       8961 TATATCATGAGCTTTTGCCA-TAAAGAGA-A-ATGCCTCTGTGTTATATATGTGTTTGAGGACTT
          1 TATAT-ATGAG-TTTGGCCACT-AAGAGATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTT

                                   
       9023 TGGA-ATAGAGATAC-CCTGTGT
         63 T-GATATAGAGATACTCCTGTGT

                    *      **   **  *                                        
       9044 TATATATGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGA
          1 TATATATGAGTTTGGCCACTAAGAGATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGA

                     *         
       9109 TATAGAGATGCTCCTGTGT
         66 TATAGAGATACTCCTGTGT

                    *      
       9128 TATATATGTGTTTGG
          1 TATATATGAGTTTGG

       9143 GGACTTTTGG


Statistics
Matches: 86,  Mismatches: 8, Indels: 9
        0.83            0.08        0.09

Matches are distributed among these distances:
  81    8  0.09
  82    8  0.09
  83   48  0.56
  84   22  0.26

ACGTcount: A:0.24, C:0.10, G:0.25, T:0.41


Consensus pattern (84 bp):   
TATATATGAGTTTGGCCACTAAGAGATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGA
TATAGAGATACTCCTGTGT

Found at i:9119 original size:43 final size:43

Alignment explanation


    Indices: 8990--9149  Score: 240
    Period size: 43  Copynumber: 3.8  Consensus size: 43

       8980 ATAAAGAGAA

                                                        
       8990 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGGA-ATAGAG
          1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTT-GATATAGAG

              *                       *                
       9033 ATACC-CTGTGTTATATATGTGTTTGGGGACTTTGATAT--AG
          1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGATATAGAG

                                                       
       9073 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGATATAGAG
          1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGATATAGAG

                                       *       
       9116 ATG-CTCCTGTGTTATATATGTGTTTGGGGACTTT
          1 ATGCCT-CTGTGTTATATATGTGTTTGAGGACTTT

       9150 TGGTTATTGG


Statistics
Matches: 107,  Mismatches: 5, Indels: 10
        0.88            0.04        0.08

Matches are distributed among these distances:
  40    6  0.06
  41   34  0.32
  42   31  0.29
  43   36  0.34

ACGTcount: A:0.21, C:0.10, G:0.26, T:0.42


Consensus pattern (43 bp):   
ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGATATAGAG

Found at i:12296 original size:28 final size:28

Alignment explanation


    Indices: 12242--12306  Score: 96
    Period size: 28  Copynumber: 2.3  Consensus size: 28

      12232 AATCTCAATC

                                         
      12242 TTAATTATTAAGATTTCAACACTTTTTTT
          1 TTAA-TATTAAGATTTCAACACTTTTTTT

               *                         
      12271 TTAGTATTAAGATTTCTAACAC-TTTTTT
          1 TTAATATTAAGATTTC-AACACTTTTTTT

                    
      12299 TTAATATT
          1 TTAATATT

      12307 TATTAGGGAT


Statistics
Matches: 33,  Mismatches: 2, Indels: 3
        0.87            0.05        0.08

Matches are distributed among these distances:
  28   25  0.76
  29    8  0.24

ACGTcount: A:0.31, C:0.09, G:0.05, T:0.55


Consensus pattern (28 bp):   
TTAATATTAAGATTTCAACACTTTTTTT
Done.