Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019433.1 Corchorus olitorius cultivar O-4 contig19466, 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: 7949
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30


Found at i:2409 original size:77 final size:78

Alignment explanation


    Indices: 2274--2622  Score: 276
    Period size: 77  Copynumber: 4.6  Consensus size: 78

       2264 GAGGGACTTG

                                         *                       *   *       
       2274 AGCAGGTTTGATTGAAA-GAAA-TTCTAAGC-ATAGATCC-AAGCAGGTTCACTTAAGCGGGAAT
          1 AGCAGGTTTGATT-AAACGAAACTTCTAAACGA-AGA-CCTAAGCAGGTTCACCTAAACGGGAAT

                            
       2335 TCTAAACAAGAACCTA
         63 TCTAAACAAGAACCTA

                                         *          *      *            *    
       2351 AGCAGGTTTGATTAAACGAAACTTCTAAATGAAGACCTAAACAGGTTTACCT-AACGGGAGTTCT
          1 AGCAGGTTTGATTAAACGAAACTTCTAAACGAAGACCTAAGCAGGTTCACCTAAACGGGAATTCT

                   *  *  
       2415 AAACAAGGACTTA
         66 AAACAAGAACCTA

                *                                          *    **   *   *   
       2428 AGCAAGTTTGATTAAACGAAAC-TCTAAACGAAGACCTAAGCAGGTTTA-CTCGAC-TGAACTC-
          1 AGCAGGTTTGATTAAACGAAACTTCTAAACGAAGACCTAAGCAGGTTCACCTAAACGGGAATTCT

               *      *    
       2489 AGAGCATAGATCCTA
         66 A-AACA-AGAACCTA

                            *               *  *             *   *    *  *   
       2504 AGCAGGTTT-AGTT-ATCTGAAA-TTCTAAA-TATGGACCTAAGCAGGTGCACTTAAATGGAAAT
          1 AGCAGGTTTGA-TTAAAC-GAAACTTCTAAACGA-AGACCTAAGCAGGTTCACCTAAACGGGAAT

              *    *  *     
       2565 TCAAAACGAGGACCTA
         63 TCTAAACAAGAACCTA

                                      *                
       2581 AGCAGGTTTGATTAAACGAAACTT-TTAACGAAGACCTAAGCA
          1 AGCAGGTTTGATTAAACGAAACTTCTAAACGAAGACCTAAGCA

       2623 AGCTTACCTG


Statistics
Matches: 213,  Mismatches: 41, Indels: 36
        0.73            0.14        0.12

Matches are distributed among these distances:
  74    1  0.00
  75   13  0.06
  76   68  0.32
  77   97  0.46
  78   32  0.15
  79    2  0.01

ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24


Consensus pattern (78 bp):   
AGCAGGTTTGATTAAACGAAACTTCTAAACGAAGACCTAAGCAGGTTCACCTAAACGGGAATTCT
AAACAAGAACCTA

Found at i:2707 original size:31 final size:31

Alignment explanation


    Indices: 2672--2737  Score: 78
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       2662 CAGGTTCATC

                        *                  
       2672 TAAACAAAACAGCGACCTAAACAGGTTTACT
          1 TAAACAAAACAGAGACCTAAACAGGTTTACT

                 **   *         *       *  
       2703 TAAACGGAACGGAGACCTAAGCAGGTTTGCT
          1 TAAACAAAACAGAGACCTAAACAGGTTTACT

                
       2734 TAAA
          1 TAAA

       2738 TGGAAATTCT


Statistics
Matches: 29,  Mismatches: 6, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  31   29  1.00

ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20


Consensus pattern (31 bp):   
TAAACAAAACAGAGACCTAAACAGGTTTACT

Found at i:2961 original size:39 final size:38

Alignment explanation


    Indices: 2899--2985  Score: 111
    Period size: 39  Copynumber: 2.2  Consensus size: 38

       2889 AAACGGAACA

                              *       * *         
       2899 AAGACCTAAGCAGGCTTGCTTAAACGGACATTCTAAAC
          1 AAGACCTAAGCAGGCTTGATTAAACGAAAATTCTAAAC

                        *  *                       
       2937 AAGGACCTAAGCCGGTTTGATTAAACGAAAATTCTAAAC
          1 AA-GACCTAAGCAGGCTTGATTAAACGAAAATTCTAAAC

                      
       2976 ATAGACCTAA
          1 A-AGACCTAA

       2986 ACAAGTTTAC


Statistics
Matches: 42,  Mismatches: 5, Indels: 3
        0.84            0.10        0.06

Matches are distributed among these distances:
  38    2  0.05
  39   39  0.93
  40    1  0.02

ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22


Consensus pattern (38 bp):   
AAGACCTAAGCAGGCTTGATTAAACGAAAATTCTAAAC

Found at i:3000 original size:39 final size:40

Alignment explanation


    Indices: 2895--3000  Score: 94
    Period size: 39  Copynumber: 2.7  Consensus size: 40

       2885 ACTTAAACGG

                 *       *  * *            * *      
       2895 AACAAAGACCTAAGCAGGCTTG-CTTAAACGGACATTCTA
          1 AACAAGGACCTAAACAAGTTTGACTTAAACGAAAATTCTA

                         * **                       
       2934 AACAAGGACCTAAGCCGGTTTGA-TTAAACGAAAATTCTA
          1 AACAAGGACCTAAACAAGTTTGACTTAAACGAAAATTCTA

                                          
       2973 AACATA-GACCTAAACAAGTTT-ACTTAAA
          1 AACA-AGGACCTAAACAAGTTTGACTTAAA

       3001 TGGCAATTCT


Statistics
Matches: 56,  Mismatches: 8, Indels: 6
        0.80            0.11        0.09

Matches are distributed among these distances:
  38    1  0.02
  39   54  0.96
  40    1  0.02

ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23


Consensus pattern (40 bp):   
AACAAGGACCTAAACAAGTTTGACTTAAACGAAAATTCTA
Done.