Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019004.1 Corchorus olitorius cultivar O-4 contig19037, 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: 5478
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29


Found at i:88 original size:46 final size:46

Alignment explanation


    Indices: 27--236  Score: 189
    Period size: 46  Copynumber: 4.7  Consensus size: 46

         17 ATTGAAAACT

                      *                                   
         27 GGGACCTTCCGACTAGGAAGGGGCATTTTTTGTATAAAAGAAAATA
          1 GGGACCTTCCAACTAGGAAGGGGCATTTTTTGTATAAAAGAAAATA

                    **      *                 *   *     * 
         73 GGGACCTTTTAACTAGAAAGGGGCA-TTTTTG--GAAATGAAAACA
          1 GGGACCTTCCAACTAGGAAGGGGCATTTTTTGTATAAAAGAAAATA

             *               *              * *             
        116 GTGACCTTCCAACTAGGGAGGGGCA-TTTTTGGAAAGAAAGAAAACT-
          1 GGGACCTTCCAACTAGGAAGGGGCATTTTTTGTATA-AAAGAAAA-TA

                      *  **               *       *     * 
        162 GGGACCTTCCTACCGGGAAGGGGCATTTTTGGTATAAATGAAAAGA
          1 GGGACCTTCCAACTAGGAAGGGGCATTTTTTGTATAAAAGAAAATA

            *            *                
        208 AGGACCTTCCAACCAGGAA-GGGCATTTTT
          1 GGGACCTTCCAACTAGGAAGGGGCATTTTT

        237 GGTAGGAGAG


Statistics
Matches: 130,  Mismatches: 28, Indels: 13
        0.76            0.16        0.08

Matches are distributed among these distances:
  43   35  0.27
  45   17  0.13
  46   71  0.55
  47    7  0.05

ACGTcount: A:0.33, C:0.15, G:0.27, T:0.24


Consensus pattern (46 bp):   
GGGACCTTCCAACTAGGAAGGGGCATTTTTTGTATAAAAGAAAATA

Found at i:183 original size:89 final size:88

Alignment explanation


    Indices: 19--238  Score: 223
    Period size: 89  Copynumber: 2.4  Consensus size: 88

          9 AAAGAGATAT

                    *         *      *              * *                   *  
         19 TGAAAACTGGGACCTTCCGACTAGGAAGGGGCATTTTTTGTATAAAAGAAAATAGGGACCTTTTA
          1 TGAAAAC-AGGACCTTCCAACTAGGGAGGGGCA-TTTTTGGAAAAAAGAAAATAGGGACCTTCTA

              *                      
         84 ACTAGAAAGGGGCATTTTTGG-AAA
         64 ACCAGAAAGGGGCATTTTTGGTAAA

                                                                             
        108 TGAAAACAGTGACCTTCCAACTAGGGAGGGGCATTTTTGGAAAGAAAGAAAACT-GGGACCTTCC
          1 TGAAAACAG-GACCTTCCAACTAGGGAGGGGCATTTTTGGAAA-AAAGAAAA-TAGGGACCTT-C

                 * *                     
        172 T-ACCGGGAAGGGGCATTTTTGGTATAAA
         62 TAACCAGAAAGGGGCATTTTTGG--TAAA

                   *             *     *            
        200 TGAAAAGAAGGACCTTCCAACCA-GGAAGGGCATTTTTGG
          1 TGAAAA-CAGGACCTTCCAACTAGGGAGGGGCATTTTTGG

        239 TAGGAGAGAA


Statistics
Matches: 111,  Mismatches: 12, Indels: 14
        0.81            0.09        0.10

Matches are distributed among these distances:
  88    9  0.08
  89   62  0.56
  90    2  0.02
  91   15  0.14
  92   21  0.19
  93    2  0.02

ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24


Consensus pattern (88 bp):   
TGAAAACAGGACCTTCCAACTAGGGAGGGGCATTTTTGGAAAAAAGAAAATAGGGACCTTCTAAC
CAGAAAGGGGCATTTTTGGTAAA

Found at i:983 original size:12 final size:12

Alignment explanation


    Indices: 962--990  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

        952 ATCAATTTCT

                        
        962 TTTC-AAGTTAG
          1 TTTCAAAGTTAG

                        
        973 TTTCAAAGTTAG
          1 TTTCAAAGTTAG

                  
        985 TTTCAA
          1 TTTCAA

        991 TTTGAAAAGT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  11    4  0.24
  12   13  0.76

ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45


Consensus pattern (12 bp):   
TTTCAAAGTTAG

Found at i:1294 original size:50 final size:50

Alignment explanation


    Indices: 1240--1357  Score: 141
    Period size: 49  Copynumber: 2.4  Consensus size: 50

       1230 ATCTTTACTC

                               *       **         *            
       1240 ACAAATTACTTAAAAATTCTATCTT-TTCCTCAAAGATTACACTTTTATTT
          1 ACAAATTACTTAAAAATTCAAT-TTCTAACTCAAAGATGACACTTTTATTT

                             *                 *     *        
       1290 ACAAATTACTTAAAAA-ACAATTTCTAACTCAAAGGTGACATTTTTATTT
          1 ACAAATTACTTAAAAATTCAATTTCTAACTCAAAGATGACACTTTTATTT

                     *         
       1339 ACAAATTACCTAAAAATTC
          1 ACAAATTACTTAAAAATTC

       1358 CATCCTTTAA


Statistics
Matches: 57,  Mismatches: 9, Indels: 4
        0.81            0.13        0.06

Matches are distributed among these distances:
  48    2  0.04
  49   38  0.67
  50   17  0.30

ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38


Consensus pattern (50 bp):   
ACAAATTACTTAAAAATTCAATTTCTAACTCAAAGATGACACTTTTATTT
Done.