Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016640.1 Corchorus olitorius cultivar O-4 contig16673, 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: 3600
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31


Found at i:683 original size:12 final size:13

Alignment explanation


    Indices: 668--696  Score: 51
    Period size: 12  Copynumber: 2.3  Consensus size: 13

        658 TGAAAACGAA

                         
        668 AGAAGAAGAAG-G
          1 AGAAGAAGAAGAG

                         
        680 AGAAGAAGAAGAG
          1 AGAAGAAGAAGAG

                
        693 AGAA
          1 AGAA

        697 ACCAAACTTA


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


Consensus pattern (13 bp):   
AGAAGAAGAAGAG

Found at i:2822 original size:43 final size:42

Alignment explanation


    Indices: 2693--3021  Score: 431
    Period size: 43  Copynumber: 7.8  Consensus size: 42

       2683 CCAATAACCA

                   *                    *            * 
       2693 AAAGTCCCCAAACAC--ATATAACACAGGGGCATCTCTATTCC
          1 AAAGTCCTCAAACACATATATAACACAGAGGCAT-TCTATTAC

                                           *            
       2734 AAAAGTCCTCAAACACATATATAACACAGAGACA-TCTA-TATC
          1 -AAAGTCCTCAAACACATATATAACACAGAGGCATTCTATTA-C

                   *                    *              
       2776 AAAGTCCCCAAACACATATATAACACAGCGGCACTTCTATTAC
          1 AAAGTCCTCAAACACATATATAACACAGAGGCA-TTCTATTAC

                                                       
       2819 AAAGTCCTCAAACACATATATAACACAGAGGCA-TCTA-TATC
          1 AAAGTCCTCAAACACATATATAACACAGAGGCATTCTATTA-C

                  *                     *     *        
       2860 AAAGTCTTCAAACACATATATAACACAGGGGCAACTCTATTAC
          1 AAAGTCCTCAAACACATATATAACACAGAGGC-ATTCTATTAC

                                                       
       2903 AAAGTCCTCAAACACATATATAACACAGAGGCATT-TA-TATC
          1 AAAGTCCTCAAACACATATATAACACAGAGGCATTCTATTA-C

                   *                    *              
       2944 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
          1 AAAGTCCTCAAACACATATATAACACAGAGGCAT-TCTATTAC

                                               
       2987 AAAGTCCTCAAACACATATATAACACAGAGGCATT
          1 AAAGTCCTCAAACACATATATAACACAGAGGCATT

       3022 TTTCCCTATG


Statistics
Matches: 255,  Mismatches: 18, Indels: 28
        0.85            0.06        0.09

Matches are distributed among these distances:
  40    4  0.02
  41  101  0.40
  42   24  0.09
  43  106  0.42
  44   20  0.08

ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22


Consensus pattern (42 bp):   
AAAGTCCTCAAACACATATATAACACAGAGGCATTCTATTAC

Found at i:3022 original size:84 final size:84

Alignment explanation


    Indices: 2693--3020  Score: 554
    Period size: 84  Copynumber: 3.9  Consensus size: 84

       2683 CCAATAACCA

                                                     *                       
       2693 AAAGTCCCCAAACAC--ATATAACACAGGGGCATCTCTATTCCAAAAGTCCTCAAACACATATAT
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC-AAAGTCCTCAAACACATATAT

                     *          
       2756 AACACAGAGACATCTATATC
         65 AACACAGAGGCATCTATATC

                                        *                                    
       2776 AAAGTCCCCAAACACATATATAACACAGCGGCA-CTTCTATTACAAAGTCCTCAAACACATATAT
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATC-TCTATTACAAAGTCCTCAAACACATATAT

                                
       2840 AACACAGAGGCATCTATATC
         65 AACACAGAGGCATCTATATC

                  **                         *                               
       2860 AAAGTCTTCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA

                        *      
       2925 ACACAGAGGCATTTATATC
         66 ACACAGAGGCATCTATATC

                                                                             
       2944 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA

                        
       3009 ACACAGAGGCAT
         66 ACACAGAGGCAT

       3021 TTTTCCCTAT


Statistics
Matches: 231,  Mismatches: 10, Indels: 7
        0.93            0.04        0.03

Matches are distributed among these distances:
  83   15  0.06
  84  193  0.84
  85   23  0.10

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


Consensus pattern (84 bp):   
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC

Found at i:3139 original size:2 final size:2

Alignment explanation


    Indices: 3127--3160  Score: 52
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       3117 ACCAAATTCC

                                                      *         
       3127 TA TA T- TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       3161 GTGACAAAGG


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   28  0.97

ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.