Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017590.1 Corchorus olitorius cultivar O-4 contig17623, 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: 2891
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29


Found at i:717 original size:29 final size:29

Alignment explanation


    Indices: 668--723  Score: 94
    Period size: 29  Copynumber: 1.9  Consensus size: 29

        658 ACCCTTCACA

                        *   *            
        668 AAACAAGTCAATTAAATTAGTTAAATAGT
          1 AAACAAGTCAATCAAACTAGTTAAATAGT

                                       
        697 AAACAAGTCAATCAAACTAGTTAAATA
          1 AAACAAGTCAATCAAACTAGTTAAATA

        724 CTATATAAAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  29   25  1.00

ACGTcount: A:0.54, C:0.11, G:0.09, T:0.27


Consensus pattern (29 bp):   
AAACAAGTCAATCAAACTAGTTAAATAGT

Found at i:2195 original size:6 final size:6

Alignment explanation


    Indices: 2176--2232  Score: 51
    Period size: 6  Copynumber: 9.5  Consensus size: 6

       2166 CTCCAGCCTG

                      *               *    ***    *                
       2176 ACCTTC ACCATC ACCTTC ACCTTG ACCAGG ACCATC ACCTTC ACCTTC
          1 ACCTTC ACCTTC ACCTTC ACCTTC ACCTTC ACCTTC ACCTTC ACCTTC

             *        
       2224 ATCTTC ACC
          1 ACCTTC ACC

       2233 AGGACCATCA


Statistics
Matches: 41,  Mismatches: 10, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
   6   41  1.00

ACGTcount: A:0.23, C:0.46, G:0.05, T:0.26


Consensus pattern (6 bp):   
ACCTTC

Found at i:2197 original size:18 final size:18

Alignment explanation


    Indices: 2176--2232  Score: 60
    Period size: 18  Copynumber: 3.2  Consensus size: 18

       2166 CTCCAGCCTG

                              
       2176 ACCTTCACCATCACCTTC
          1 ACCTTCACCATCACCTTC

                 *    **   *  
       2194 ACCTTGACCAGGACCATC
          1 ACCTTCACCATCACCTTC

                     *   *    
       2212 ACCTTCACCTTCATCTTC
          1 ACCTTCACCATCACCTTC

               
       2230 ACC
          1 ACC

       2233 AGGACCATCA


Statistics
Matches: 29,  Mismatches: 10, Indels: 0
        0.74            0.26        0.00

Matches are distributed among these distances:
  18   29  1.00

ACGTcount: A:0.23, C:0.46, G:0.05, T:0.26


Consensus pattern (18 bp):   
ACCTTCACCATCACCTTC

Found at i:2201 original size:24 final size:24

Alignment explanation


    Indices: 2174--2233  Score: 75
    Period size: 24  Copynumber: 2.5  Consensus size: 24

       2164 ACCTCCAGCC

                                    
       2174 TGACCTTCACCATCACCTTCACCT
          1 TGACCTTCACCATCACCTTCACCT

                 ***                
       2198 TGACCAGGACCATCACCTTCACCT
          1 TGACCTTCACCATCACCTTCACCT

             * *        
       2222 TCATCTTCACCA
          1 TGACCTTCACCA

       2234 GGACCATCAT


Statistics
Matches: 28,  Mismatches: 8, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
  24   28  1.00

ACGTcount: A:0.23, C:0.43, G:0.07, T:0.27


Consensus pattern (24 bp):   
TGACCTTCACCATCACCTTCACCT

Found at i:2214 original size:30 final size:30

Alignment explanation


    Indices: 2175--2242  Score: 100
    Period size: 30  Copynumber: 2.3  Consensus size: 30

       2165 CCTCCAGCCT

                *                   *     
       2175 GACCTTCACCATCACCTTCACCTTGACCAG
          1 GACCATCACCATCACCTTCACCTTCACCAG

                      *         *         
       2205 GACCATCACCTTCACCTTCATCTTCACCAG
          1 GACCATCACCATCACCTTCACCTTCACCAG

                    
       2235 GACCATCA
          1 GACCATCA

       2243 TCACCACCAA


Statistics
Matches: 34,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  30   34  1.00

ACGTcount: A:0.25, C:0.43, G:0.09, T:0.24


Consensus pattern (30 bp):   
GACCATCACCATCACCTTCACCTTCACCAG
Done.