Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008323.1 Corchorus olitorius cultivar O-4 contig08350, 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: 2656
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:2006 original size:43 final size:42

Alignment explanation


    Indices: 1958--2286  Score: 466
    Period size: 43  Copynumber: 7.8  Consensus size: 42

       1948 CCAATAAGCA

                          *                            
       1958 AAAGTCCCCAAACAAATATATAACACAGGGGCATCTCTATCCC
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTAT-CC

                   *                    * *     *     
       2001 AAAGTCCTCAAACACATATATAACACAGAGACATCTATAT-C
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATCC

                                                       
       2042 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATCCC
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTAT-CC

                   *                   **       *     
       2085 AAAGTCCTCAAACACATATATAACACAAAGGCATCTATAT-C
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATCC

                    *                                  
       2126 AAAGTCCCAAAACACATATATAACACAGGGGCATCTCTATTCC
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTA-TCC

                   *                    * *     *     
       2169 AAAGTCCTCAAACACATATATAACACAGAGACATCTATAT-C
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATCC

                                                       
       2210 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTA-TCC

                   *                          
       2253 AAAGTCCTCAAACACATATATAACACAGGGGCAT
          1 AAAGTCCCCAAACACATATATAACACAGGGGCAT

       2287 TTCTCTTTAT


Statistics
Matches: 252,  Mismatches: 28, Indels: 12
        0.86            0.10        0.04

Matches are distributed among these distances:
  41  108  0.43
  42    3  0.01
  43  141  0.56

ACGTcount: A:0.42, C:0.27, G:0.10, T:0.20


Consensus pattern (42 bp):   
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATCC

Found at i:2315 original size:84 final size:84

Alignment explanation


    Indices: 1958--2280  Score: 592
    Period size: 84  Copynumber: 3.8  Consensus size: 84

       1948 CCAATAAGCA

                          *                                                  
       1958 AAAGTCCCCAAACAAATATATAACACAGGGGCATCTCTATCCCAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATCCCAAAGTCCTCAAACACATATATA

                               
       2023 ACACAGAGACATCTATATC
         66 ACACAGAGACATCTATATC

                                                                             
       2042 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATCCCAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATCCCAAAGTCCTCAAACACATATATA

                 *  *          
       2107 ACACAAAGGCATCTATATC
         66 ACACAGAGACATCTATATC

                    *                               *                        
       2126 AAAGTCCCAAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATCCCAAAGTCCTCAAACACATATATA

                               
       2191 ACACAGAGACATCTATATC
         66 ACACAGAGACATCTATATC

                                                    *                        
       2210 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATCCCAAAGTCCTCAAACACATATATA

                  
       2275 ACACAG
         66 ACACAG

       2281 GGGCATTTCT


Statistics
Matches: 231,  Mismatches: 8, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  84  231  1.00

ACGTcount: A:0.42, C:0.28, G:0.10, T:0.20


Consensus pattern (84 bp):   
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATCCCAAAGTCCTCAAACACATATATA
ACACAGAGACATCTATATC
Done.