Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022162.1 Corchorus olitorius cultivar O-4 contig22195, 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: 12114
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31


Found at i:605 original size:21 final size:21

Alignment explanation


    Indices: 581--714  Score: 200
    Period size: 21  Copynumber: 6.4  Consensus size: 21

        571 CTTAGGCAAT

                         *       
        581 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
        602 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
        623 TCCAATGAACTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
        644 TCCAATGAACTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
        665 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                                  
        686 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
        707 TCCAATGA
          1 TCCAATGA

        715 ACTTCTAGCA


Statistics
Matches: 108,  Mismatches: 4, Indels: 2
        0.95            0.04        0.02

Matches are distributed among these distances:
  20    3  0.03
  21  105  0.97

ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:4371 original size:38 final size:38

Alignment explanation


    Indices: 4320--4695  Score: 268
    Period size: 38  Copynumber: 9.8  Consensus size: 38

       4310 GATTCTAATG

                   *                              
       4320 AGAGACCGAAGCAGGTTTGATTAAACGAAACTCTAAGC
          1 AGAGACCTAAGCAGGTTTGATTAAACGAAACTCTAAGC

            *     * *                  *    *     * 
       4358 CGAGACTTGAGCAGGTTT-ACTTAAATGGAAATTCTAAAC
          1 AGAGACCTAAGCAGGTTTGA-TTAAA-CGAAACTCTAAGC

                              *           *       *
       4397 A-AGAACCTAAGCAGGTTCGATTAAACGAAGCTCTAAGA
          1 AGAG-ACCTAAGCAGGTTTGATTAAACGAAACTCTAAGC

                              *             *     **
       4435 AGAGACCTAAGCAGG-TTCATTTAAACGGAAATTCTAAAT
          1 AGAGACCTAAGCAGGTTTGA-TTAAAC-GAAACTCTAAGC

            * *                  *    *           
       4474 GGGGACCTAAGCAGGTTTGATCAAACAAAACTCTAAGC
          1 AGAGACCTAAGCAGGTTTGATTAAACGAAACTCTAAGC

                           *           *    *        
       4512 AGAGACCTAAGCAGGCTT-ACTTAAATGGAAATTCTGAA-C
          1 AGAGACCTAAGCAGGTTTGA-TTAAA-CGAAACTCT-AAGC

                      *                   *        
       4551 A-AGGACCTAGGCAGGTTTGATTAAACGAAGCTCTAAGC
          1 AGA-GACCTAAGCAGGTTTGATTAAACGAAACTCTAAGC

                                       *    *        
       4589 AGAGACCTAAGCAGGTTT-ACTTAAATGGAAATTCTGAA-C
          1 AGAGACCTAAGCAGGTTTGA-TTAAA-CGAAACTCT-AAGC

                          *        *      *       *
       4628 A-AGGACCTAAGCAAGTTTGATTGAACGAAGCTCTAAGT
          1 AGA-GACCTAAGCAGGTTTGATTAAACGAAACTCTAAGC

                    *   * *                
       4666 AGAGACCTGAGCCGCTTT-ACTTAAACGAAA
          1 AGAGACCTAAGCAGGTTTGA-TTAAACGAAA

       4696 ATTCTAAATG


Statistics
Matches: 257,  Mismatches: 58, Indels: 46
        0.71            0.16        0.13

Matches are distributed among these distances:
  37   10  0.04
  38  129  0.50
  39  108  0.42
  40   10  0.04

ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22


Consensus pattern (38 bp):   
AGAGACCTAAGCAGGTTTGATTAAACGAAACTCTAAGC

Found at i:4409 original size:77 final size:77

Alignment explanation


    Indices: 4323--4703  Score: 501
    Period size: 77  Copynumber: 4.9  Consensus size: 77

       4313 TCTAATGAGA

                *                     *        *     * *                     
       4323 GACCGAAGCAGGTTTGATTAAACGAAACTCTAAGCCGAGACTTGAGCAGGTTTACTTAAATGGAA
          1 GACCTAAGCAGGTTTGATTAAACGAAGCTCTAAGCAGAGACCTAAGCAGGTTTACTTAAATGGAA

                        
       4388 ATTCTAAACAAG
         66 ATTCTAAACAAG

            *             *                   *                 * *     *    
       4400 AACCTAAGCAGGTTCGATTAAACGAAGCTCTAAGAAGAGACCTAAGCAGGTTCATTTAAACGGAA
          1 GACCTAAGCAGGTTTGATTAAACGAAGCTCTAAGCAGAGACCTAAGCAGGTTTACTTAAATGGAA

                    *** 
       4465 ATTCTAAATGGG
         66 ATTCTAAACAAG

                              *    *  *                       *              
       4477 GACCTAAGCAGGTTTGATCAAACAAAACTCTAAGCAGAGACCTAAGCAGGCTTACTTAAATGGAA
          1 GACCTAAGCAGGTTTGATTAAACGAAGCTCTAAGCAGAGACCTAAGCAGGTTTACTTAAATGGAA

                 *      
       4542 ATTCTGAACAAG
         66 ATTCTAAACAAG

                  *                                                          
       4554 GACCTAGGCAGGTTTGATTAAACGAAGCTCTAAGCAGAGACCTAAGCAGGTTTACTTAAATGGAA
          1 GACCTAAGCAGGTTTGATTAAACGAAGCTCTAAGCAGAGACCTAAGCAGGTTTACTTAAATGGAA

                 *      
       4619 ATTCTGAACAAG
         66 ATTCTAAACAAG

                      *        *              *        *   * *          * *  
       4631 GACCTAAGCAAGTTTGATTGAACGAAGCTCTAAGTAGAGACCTGAGCCGCTTTACTTAAACGAAA
          1 GACCTAAGCAGGTTTGATTAAACGAAGCTCTAAGCAGAGACCTAAGCAGGTTTACTTAAATGGAA

                    
       4696 ATTCTAAA
         66 ATTCTAAA

       4704 TGGAGACCTA


Statistics
Matches: 261,  Mismatches: 43, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  77  261  1.00

ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23


Consensus pattern (77 bp):   
GACCTAAGCAGGTTTGATTAAACGAAGCTCTAAGCAGAGACCTAAGCAGGTTTACTTAAATGGAA
ATTCTAAACAAG

Found at i:4410 original size:39 final size:37

Alignment explanation


    Indices: 4367--4645  Score: 177
    Period size: 39  Copynumber: 7.2  Consensus size: 37

       4357 CCGAGACTTG

                                                   
       4367 AGCAGGTTTACTTAAATGGAAATTCTAAACAAGAACCTA
          1 AGCAGGTTTA-TTAAA-GGAAATTCTAAACAAGAACCTA

                     *      *   **      *          
       4406 AGCAGGTTCGATTAAACGAAGCTCT-AAGAAGAGACCTA
          1 AGCAGGTT-TATTAAAGGAAATTCTAAACAAGA-ACCTA

                    *                    *** *     
       4444 AGCAGGTTCATTTAAACGGAAATTCTAAATGGGGACCTA
          1 AGCAGGTTTA-TTAAA-GGAAATTCTAAACAAGAACCTA

                        *   **   *     *           
       4483 AGCAGGTTTGATCAAACAAAACTCTAAGC-AGAGACCTA
          1 AGCAGGTTT-ATTAAAGGAAATTCTAAACAAGA-ACCTA

                  *                   *      *     
       4521 AGCAGGCTTACTTAAATGGAAATTCTGAACAAGGACCTA
          1 AGCAGGTTTA-TTAAA-GGAAATTCTAAACAAGAACCTA

            *               *   **     *           
       4560 GGCAGGTTTGATTAAACGAAGCTCTAAGC-AGAGACCTA
          1 AGCAGGTTT-ATTAAAGGAAATTCTAAACAAGA-ACCTA

                                      *      *     
       4598 AGCAGGTTTACTTAAATGGAAATTCTGAACAAGGACCTA
          1 AGCAGGTTTA-TTAAA-GGAAATTCTAAACAAGAACCTA

                *    
       4637 AGCAAGTTT
          1 AGCAGGTTT

       4646 GATTGAACGA


Statistics
Matches: 179,  Mismatches: 46, Indels: 30
        0.70            0.18        0.12

Matches are distributed among these distances:
  37   12  0.07
  38   75  0.42
  39   82  0.46
  40   10  0.06

ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23


Consensus pattern (37 bp):   
AGCAGGTTTATTAAAGGAAATTCTAAACAAGAACCTA

Done.