Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012774.1 Corchorus olitorius cultivar O-4 contig12807, 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: 19541
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34


Found at i:4519 original size:22 final size:22

Alignment explanation


    Indices: 4494--4542  Score: 64
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       4484 TAAAAAAATT

                                   
       4494 ATAGGGAGAT-TAACAAAATCTC
          1 ATAGGGA-ATGTAACAAAATCTC

                       *       *  
       4516 ATAGGGAATGTTACAAAATTTC
          1 ATAGGGAATGTAACAAAATCTC

                 
       4538 ATAGG
          1 ATAGG

       4543 AAGGTTTATT


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  21    2  0.08
  22   22  0.92

ACGTcount: A:0.43, C:0.10, G:0.20, T:0.27


Consensus pattern (22 bp):   
ATAGGGAATGTAACAAAATCTC

Found at i:4614 original size:22 final size:21

Alignment explanation


    Indices: 4507--4670  Score: 82
    Period size: 22  Copynumber: 7.4  Consensus size: 21

       4497 GGGAGATTAA

                  *                
       4507 CAAAATCTCATAGGGAATGTTA-
          1 CAAAATTTCATA-GGAAT-TTAT

                                   
       4529 CAAAATTTCATAGGAAGGTTTAT
          1 CAAAATTTCATAGGAA--TTTAT

            *   *        **  *    
       4552 TAAACTTTCATAATTAAGTTAT
          1 CAAAATTTCAT-AGGAATTTAT

                    *             
       4574 CAAAATTTTATATGGAATTTAT
          1 CAAAATTTCATA-GGAATTTAT

              *                   
       4596 CACAATTTCATAGGTAA-TTAT
          1 CAAAATTTCATAGG-AATTTAT

                       *    *        
       4617 CAAAAATTTTCGTA-GCATGGTTAT
          1 C-AAAA-TTTCATAGGAAT--TTAT

                    *      * *    
       4641 CAAAATTTAATAGGGTAGTTAT
          1 CAAAATTTCATA-GGAATTTAT

                    
       4663 CAAAATTT
          1 CAAAATTT

       4671 TATAAAAATA


Statistics
Matches: 108,  Mismatches: 21, Indels: 26
        0.70            0.14        0.17

Matches are distributed among these distances:
  21   13  0.12
  22   65  0.60
  23   20  0.19
  24   10  0.09

ACGTcount: A:0.40, C:0.10, G:0.13, T:0.38


Consensus pattern (21 bp):   
CAAAATTTCATAGGAATTTAT

Found at i:14717 original size:20 final size:19

Alignment explanation


    Indices: 14683--14721  Score: 51
    Period size: 20  Copynumber: 2.0  Consensus size: 19

      14673 CATACCTTAC

                   *            
      14683 CTTAATCGATATGAAGCATA
          1 CTTAATCCATATGAA-CATA

                      *        
      14703 CTTAATCCATGTGAACATA
          1 CTTAATCCATATGAACATA

      14722 GAATCTGAGA


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  19    4  0.24
  20   13  0.76

ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31


Consensus pattern (19 bp):   
CTTAATCCATATGAACATA

Found at i:16316 original size:56 final size:56

Alignment explanation


    Indices: 16220--16329  Score: 159
    Period size: 56  Copynumber: 1.9  Consensus size: 56

      16210 AATATTTAAA

                       *                  *                 *        
      16220 AAAAAAAAGAAGTAAAACTTCCTCCTTAGGTTAGGTACAAGGACTCATTGAGCTTGG
          1 AAAAAAAAGAAATAAAACTTCCTCCTTA-GATAGGTACAAGGACTCATGGAGCTTGG

                    *                                             
      16277 AAAAAAAATAAATCAAAACTTCCTCCTTA-ATAGGTACAAGGACTCATGGAGCT
          1 AAAAAAAAGAAAT-AAAACTTCCTCCTTAGATAGGTACAAGGACTCATGGAGCT

      16330 CGGCTTCATT


Statistics
Matches: 48,  Mismatches: 4, Indels: 3
        0.87            0.07        0.05

Matches are distributed among these distances:
  56   22  0.46
  57   11  0.23
  58   15  0.31

ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24


Consensus pattern (56 bp):   
AAAAAAAAGAAATAAAACTTCCTCCTTAGATAGGTACAAGGACTCATGGAGCTTGG

Found at i:19375 original size:39 final size:40

Alignment explanation


    Indices: 19296--19376  Score: 103
    Period size: 39  Copynumber: 2.0  Consensus size: 40

      19286 TTTAATTCCT

                                          *  *      
      19296 ATGTAATATATATAATAACTAAAATACTTATATCGATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATAGATTAA

                     *          *                    
      19336 ATGTAATA-CTATAATAACTGAAATACTTACATTAG-TTAA
          1 ATGTAATATATATAATAACTAAAATACTTACA-TAGATTAA

              
      19375 AT
          1 AT

      19377 TCTTAGGTAT


Statistics
Matches: 36,  Mismatches: 4, Indels: 3
        0.84            0.09        0.07

Matches are distributed among these distances:
  39   26  0.72
  40   10  0.28

ACGTcount: A:0.48, C:0.09, G:0.06, T:0.37


Consensus pattern (40 bp):   
ATGTAATATATATAATAACTAAAATACTTACATAGATTAA
Done.