Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020708.1 Corchorus olitorius cultivar O-4 contig20741, 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: 32142
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33


Found at i:11668 original size:15 final size:16

Alignment explanation


    Indices: 11639--11671  Score: 50
    Period size: 15  Copynumber: 2.1  Consensus size: 16

      11629 ACCGTATGGC

                      *     
      11639 TCTTACAAGTTATCAA
          1 TCTTACAAGTCATCAA

                            
      11655 TCTT-CAAGTCATCAA
          1 TCTTACAAGTCATCAA

              
      11670 TC
          1 TC

      11672 GTATTTTTTG


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  15   12  0.75
  16    4  0.25

ACGTcount: A:0.33, C:0.24, G:0.06, T:0.36


Consensus pattern (16 bp):   
TCTTACAAGTCATCAA

Found at i:12817 original size:22 final size:22

Alignment explanation


    Indices: 12785--12841  Score: 105
    Period size: 22  Copynumber: 2.6  Consensus size: 22

      12775 GAGCGAAAGC

                                  
      12785 AAGAGATTGAAGATGAAGAACA
          1 AAGAGATTGAAGATGAAGAACA

               *                  
      12807 AAGTGATTGAAGATGAAGAACA
          1 AAGAGATTGAAGATGAAGAACA

                         
      12829 AAGAGATTGAAGA
          1 AAGAGATTGAAGA

      12842 AAGAGTAAAA


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  22   33  1.00

ACGTcount: A:0.53, C:0.04, G:0.28, T:0.16


Consensus pattern (22 bp):   
AAGAGATTGAAGATGAAGAACA

Found at i:13587 original size:161 final size:161

Alignment explanation


    Indices: 13378--13721  Score: 548
    Period size: 161  Copynumber: 2.1  Consensus size: 161

      13368 CCCACTATAT

                                       *                                     
      13378 TTGA-TAATCCATCA-CCACAAATGACTATAGCCTTAGTTTAAGAAAAATAGGCTAAATATTTGG
          1 TTGATTAATCCAT-AGCCACAAATGACCATAGCCTTAGTTTAAGAAAAATAGGCTAAATATTTGG

                                                         *                   
      13441 AAATATAGCAATTCGGCTTTAATTATGAAAATCAAAGCCAAATTGGCATTTGAATGAAATCCAAC
         65 AAATATAGCAATTCGGCTTTAATTATGAAAATCAAAGCCAAATTGACATTTGAATGAAATCCAAC

                             *              
      13506 ACCACATATACATAATCTAATGCCATATTTAA
        130 ACCACATATACATAATCCAATGCCATATTTAA

                              *          *                                   
      13538 TTGATTAATCCATAGCCATAAATGACCATCGCCTTAGTTTAAGAAAAATAGGCTAAATATTTGGA
          1 TTGATTAATCCATAGCCACAAATGACCATAGCCTTAGTTTAAGAAAAATAGGCTAAATATTTGGA

                    *   *            **                   *               *  
      13603 AATATAGCCATTTGGCTTTAATTATTCAAATCAAAGCCAAATTGACTTTTGAATGAAATCCATCA
         66 AATATAGCAATTCGGCTTTAATTATGAAAATCAAAGCCAAATTGACATTTGAATGAAATCCAACA

                                *          
      13668 CCACATATACATAATCCAATTCCATATTTAA
        131 CCACATATACATAATCCAATGCCATATTTAA

                         *         
      13699 TTGATTAATCCATTGCCACAAAT
          1 TTGATTAATCCATAGCCACAAAT

      13722 TAAAAACTAG


Statistics
Matches: 168,  Mismatches: 14, Indels: 3
        0.91            0.08        0.02

Matches are distributed among these distances:
 160    5  0.03
 161  163  0.97

ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31


Consensus pattern (161 bp):   
TTGATTAATCCATAGCCACAAATGACCATAGCCTTAGTTTAAGAAAAATAGGCTAAATATTTGGA
AATATAGCAATTCGGCTTTAATTATGAAAATCAAAGCCAAATTGACATTTGAATGAAATCCAACA
CCACATATACATAATCCAATGCCATATTTAA

Found at i:24731 original size:96 final size:96

Alignment explanation


    Indices: 24553--24755  Score: 338
    Period size: 96  Copynumber: 2.1  Consensus size: 96

      24543 TCTAAAGTAA

                                                              *  *           
      24553 ACGCCGCT--ATATTTAATCTTCTACAAACAATAGAAATTCGGTGAAACTGAACACACCATTTAT
          1 ACGCCGCTAAATATTTAATCTTCTACAAACAATAGAAATTCGGTGAAACTAAAAACACCATTTAT

                        *                  
      24616 TTGTTATGAATAGCAGCGTTTTTCATGACAG
         66 TTGTTATGAATAACAGCGTTTTTCATGACAG

                *                                   *                        
      24647 ACGCTGCTAAATATTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTAT
          1 ACGCCGCTAAATATTTAATCTTCTACAAACAATAGAAATTCGGTGAAACTAAAAACACCATTTAT

                          *                
      24712 TTGTTATGAATAACGGCGTTTTTCATGACAG
         66 TTGTTATGAATAACAGCGTTTTTCATGACAG

                         
      24743 ACGCCGCTAAATA
          1 ACGCCGCTAAATA

      24756 GTGGCGCTTT


Statistics
Matches: 100,  Mismatches: 7, Indels: 2
        0.92            0.06        0.02

Matches are distributed among these distances:
  94    7  0.07
  96   93  0.93

ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32


Consensus pattern (96 bp):   
ACGCCGCTAAATATTTAATCTTCTACAAACAATAGAAATTCGGTGAAACTAAAAACACCATTTAT
TTGTTATGAATAACAGCGTTTTTCATGACAG
Done.