Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014516.1 Corchorus olitorius cultivar O-4 contig14549, 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: 17315
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31


Found at i:4840 original size:16 final size:17

Alignment explanation


    Indices: 4814--4845  Score: 57
    Period size: 16  Copynumber: 1.9  Consensus size: 17

       4804 AGTGCAAATT

                             
       4814 AAAATAGAAAAATAAAG
          1 AAAATAGAAAAATAAAG

                            
       4831 AAAA-AGAAAAATAAA
          1 AAAATAGAAAAATAAA

       4846 ACGCAATCTC


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16   11  0.73
  17    4  0.27

ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09


Consensus pattern (17 bp):   
AAAATAGAAAAATAAAG

Found at i:9976 original size:19 final size:19

Alignment explanation


    Indices: 9936--9972  Score: 58
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       9926 AATTTTTAAG

                    *          
       9936 TAAAAATTTAATATATAAA
          1 TAAAAATTAAATATATAAA

                               
       9955 TAAAAATTAAATAT-TAAA
          1 TAAAAATTAAATATATAAA

       9973 ATAATTAATT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18    4  0.24
  19   13  0.76

ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35


Consensus pattern (19 bp):   
TAAAAATTAAATATATAAA

Found at i:10391 original size:119 final size:118

Alignment explanation


    Indices: 10185--10550  Score: 421
    Period size: 119  Copynumber: 3.0  Consensus size: 118

      10175 CTCAAACTTG

                     *    *                   *            *  *    ***       
      10185 TCAAATTCATTTAAGGATTCACTTAAATCTTAAAAGAATTATGAAAGTTTCCCAAAGCTTATTAA
          1 TCAAATTCAATTAAAGATTCACTTAAATCTT-AATGAATTATGAAA-ATTACCAACTTTTATTAA

                             *                   *                  
      10250 CTAAAGGTTATAATCACATAATTAAACCTTAAGTTTTGGGTCACTTAACCTTAATA
         64 CTAAAGGTTATAATCACTTAATTAAACC-TAAGTTTTAGGTCACTTAACCTTAATA

                                           *                                 
      10306 TCAAATTCAATTAAAGATTCACTTAAATCTTGATGAATTATGAAAATTACCAACTTTTATTAACT
          1 TCAAATTCAATTAAAGATTCACTTAAATCTTAATGAATTATGAAAATTACCAACTTTTATTAACT

              *                        *           *             *
      10371 AACGGTTATAATCACTTAATTAAACCAAAAGTTTTAGGTTACTTAACCTTAATT
         66 AAAGGTTATAATCACTTAATTAAACC-TAAGTTTTAGGTCACTTAACCTTAATA

                                   *                                         
      10425 TCAAATTCAATTAAAGATTCACTCAAATCTTAATGAATTATTATGAAAATTACCAAAAAAAGCTT
          1 TCAAATTCAATTAAAGATTCACTTAAATCTTAATG-A--ATTATGAAAATTACC-----AA-CTT

                            *                                  *           
      10490 TTA--AACTAAAGGTTTTAATCACTTAATTAAACCTAGAGTTTTAAGGTCAGTTAACCTTAAT
         57 TTATTAACTAAAGGTTATAATCACTTAATTAAACCTA-AGTTTT-AGGTCACTTAACCTTAAT

      10551 CTTAAGGCTT


Statistics
Matches: 211,  Mismatches: 23, Indels: 16
        0.84            0.09        0.06

Matches are distributed among these distances:
 119   95  0.45
 120   13  0.06
 121   29  0.14
 122   15  0.07
 125    1  0.00
 126   34  0.16
 127   18  0.09
 128    6  0.03

ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36


Consensus pattern (118 bp):   
TCAAATTCAATTAAAGATTCACTTAAATCTTAATGAATTATGAAAATTACCAACTTTTATTAACT
AAAGGTTATAATCACTTAATTAAACCTAAGTTTTAGGTCACTTAACCTTAATA

Found at i:14966 original size:21 final size:21

Alignment explanation


    Indices: 14942--15054  Score: 149
    Period size: 21  Copynumber: 5.4  Consensus size: 21

      14932 CTTAGGCAAT

                    *    *       
      14942 TCCAATGATCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
      14963 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *   *        
      14984 TCCAATGAACTTAGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
      15005 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                                  
      15026 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
      15047 TCCAATGA
          1 TCCAATGA

      15055 ACTTCTAGCA


Statistics
Matches: 86,  Mismatches: 5, Indels: 2
        0.92            0.05        0.02

Matches are distributed among these distances:
  20    3  0.03
  21   83  0.97

ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:16930 original size:33 final size:31

Alignment explanation


    Indices: 16857--17002  Score: 123
    Period size: 33  Copynumber: 4.5  Consensus size: 31

      16847 GCTATGATCA

                                       ** * 
      16857 ACCAAAACAGATTTGTTTTCATCACAATTAGC
          1 ACCAAAACAGATTTG-TTTCATCACAAACAAC

                                             
      16889 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
          1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC

                              *              
      16922 ACCTAAAACAGATTTAGTGTCATCACAAACAAC
          1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC

                   **  *             *        
      16955 ACTCAAATTAGGTTTAGTATT-ATCGCAAACAAC
          1 AC-CAAAACAGATTT-GT-TTCATCACAAACAAC

               *           
      16988 ATCTAAAACAGATTT
          1 A-CCAAAACAGATTT

      17003 AGAATTACTC


Statistics
Matches: 94,  Mismatches: 13, Indels: 13
        0.78            0.11        0.11

Matches are distributed among these distances:
  32    7  0.07
  33   79  0.84
  34    8  0.09

ACGTcount: A:0.42, C:0.21, G:0.09, T:0.27


Consensus pattern (31 bp):   
ACCAAAACAGATTTGTTTCATCACAAACAAC

Done.