Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012549.1 Corchorus olitorius cultivar O-4 contig12582, 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: 4262
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:249 original size:33 final size:33

Alignment explanation


    Indices: 80--230  Score: 293
    Period size: 33  Copynumber: 4.6  Consensus size: 33

         70 CTCCGGGGGT

                                             
         80 GGCACGCCCATGGTCGTGCTGTCCTCACAGGGC
          1 GGCACGCCCATGGTCGTGCTGTCCTCACAGGGC

                           *                 
        113 GGCACGCCCATGGTCATGCTGTCCTCACAGGGC
          1 GGCACGCCCATGGTCGTGCTGTCCTCACAGGGC

                                             
        146 GGCACGCCCATGGTCGTGCTGTCCTCACAGGGC
          1 GGCACGCCCATGGTCGTGCTGTCCTCACAGGGC

                                             
        179 GGCACGCCCATGGTCGTGCTGTCCTCACAGGGC
          1 GGCACGCCCATGGTCGTGCTGTCCTCACAGGGC

                               
        212 GGCACGCCCATGGTCGTGC
          1 GGCACGCCCATGGTCGTGC

        231 CATCCCCGGA


Statistics
Matches: 116,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  33  116  1.00

ACGTcount: A:0.13, C:0.36, G:0.33, T:0.18


Consensus pattern (33 bp):   
GGCACGCCCATGGTCGTGCTGTCCTCACAGGGC

Found at i:3861 original size:20 final size:21

Alignment explanation


    Indices: 3816--3873  Score: 73
    Period size: 21  Copynumber: 2.8  Consensus size: 21

       3806 TTGTATATGC

                        *        
       3816 ATGGTCAAACCCCAAATGATG
          1 ATGGTCAAACCCAAAATGATG

                              *  
       3837 ATGGTCAAACCCAAAAT-TTG
          1 ATGGTCAAACCCAAAATGATG

            *                
       3857 GTGGTCAAACCACAAAA
          1 ATGGTCAAACC-CAAAA

       3874 AATATCATTG


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

Matches are distributed among these distances:
  20   12  0.36
  21   21  0.64

ACGTcount: A:0.41, C:0.22, G:0.17, T:0.19


Consensus pattern (21 bp):   
ATGGTCAAACCCAAAATGATG

Found at i:3885 original size:75 final size:76

Alignment explanation


    Indices: 3761--4013  Score: 280
    Period size: 75  Copynumber: 3.3  Consensus size: 76

       3751 TTGTACATGC

                                       * *                                   
       3761 ATGGTCAAACCCCAAAGTTTGATAGTCCACCCACAAAAAATATCATTGTATATGCATGGTCAAAC
          1 ATGGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAAAATATCATTGTATATGCATGGTCAAAC

                        
       3826 CCCAAATGAT-G
         66 CCCAAA-GATCG

                            *    * *                          *      *      *
       3837 ATGGTCAAA-CCCAAAATTTGGTGGTCAAACCACAAAAAATATCATTGTACATGCATAGTCAAAT
          1 ATGGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAAAATATCATTGTATATGCATGGTCAAAC

                   *   
       3901 CCCAAAGTTCG
         66 CCCAAAGATCG

              *                *                       * *          *   *    
       3912 ATAGTCAAACCCCAAAGTTCGATAGTCAAACCACAAAAAACATTTTATTGTATATGTATGATCAA
          1 ATGGTCAAACCCCAAAGTTTGATAGTCAAACCAC-AAAAA-ATATCATTGTATATGCATGGTCAA

                        **
       3977 ACCCCAAA-ATTTA
         64 ACCCCAAAGA-TCG

                                     
       3990 ATAGG-CAAACCCCAAAGTTTGATA
          1 AT-GGTCAAACCCCAAAGTTTGATA

       4014 TTCATATTGT


Statistics
Matches: 145,  Mismatches: 26, Indels: 10
        0.80            0.14        0.06

Matches are distributed among these distances:
  74    2  0.01
  75   62  0.43
  76   29  0.20
  77    5  0.03
  78   46  0.32
  79    1  0.01

ACGTcount: A:0.41, C:0.22, G:0.13, T:0.25


Consensus pattern (76 bp):   
ATGGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAAAATATCATTGTATATGCATGGTCAAAC
CCCAAAGATCG

Found at i:3915 original size:21 final size:21

Alignment explanation


    Indices: 3891--3948  Score: 98
    Period size: 21  Copynumber: 2.8  Consensus size: 21

       3881 TTGTACATGC

                     *           
       3891 ATAGTCAAATCCCAAAGTTCG
          1 ATAGTCAAACCCCAAAGTTCG

                                 
       3912 ATAGTCAAACCCCAAAGTTCG
          1 ATAGTCAAACCCCAAAGTTCG

                       *    
       3933 ATAGTCAAACCACAAA
          1 ATAGTCAAACCCCAAA

       3949 AAACATTTTA


Statistics
Matches: 35,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   35  1.00

ACGTcount: A:0.43, C:0.26, G:0.12, T:0.19


Consensus pattern (21 bp):   
ATAGTCAAACCCCAAAGTTCG

Found at i:4065 original size:22 final size:22

Alignment explanation


    Indices: 4040--4084  Score: 63
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       4030 TTTAACTGAA

                      *           
       4040 TTGCTAAATATCGCCCCCCTTT
          1 TTGCTAAATACCGCCCCCCTTT

                  **              
       4062 TTGCTAGTTACCGCCCCCCTTT
          1 TTGCTAAATACCGCCCCCCTTT

             
       4084 T
          1 T

       4085 GACAATTTTG


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.13, C:0.38, G:0.11, T:0.38


Consensus pattern (22 bp):   
TTGCTAAATACCGCCCCCCTTT
Done.