Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024826.1 Corchorus olitorius cultivar O-4 contig24859, 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: 11744
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31


Found at i:2139 original size:33 final size:31

Alignment explanation


    Indices: 2066--2211  Score: 123
    Period size: 33  Copynumber: 4.5  Consensus size: 31

       2056 GCTATGATCA

                                       ** * 
       2066 ACCAAAACAGATTTGTTTTCATCACAATTAGC
          1 ACCAAAACAGATTTG-TTTCATCACAAACAAC

                                             
       2098 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
          1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC

                              *              
       2131 ACCTAAAACAGATTTAGTGTCATCACAAACAAC
          1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC

                   **  *             *        
       2164 ACTCAAATTAGGTTTAGTATT-ATCGCAAACAAC
          1 AC-CAAAACAGATTT-GT-TTCATCACAAACAAC

               *           
       2197 ATCTAAAACAGATTT
          1 A-CCAAAACAGATTT

       2212 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

Found at i:5129 original size:14 final size:15

Alignment explanation


    Indices: 5110--5139  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       5100 AACTAGAAAA

                           
       5110 AATAAAT-AACAAGG
          1 AATAAATAAACAAGG

                           
       5124 AATAAATAAACAAGG
          1 AATAAATAAACAAGG

             
       5139 A
          1 A

       5140 TTGGACTTAG


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

Matches are distributed among these distances:
  14    7  0.47
  15    8  0.53

ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13


Consensus pattern (15 bp):   
AATAAATAAACAAGG

Found at i:10624 original size:21 final size:21

Alignment explanation


    Indices: 10598--10710  Score: 158
    Period size: 21  Copynumber: 5.4  Consensus size: 21

      10588 TGCTAGAAGT

                                 
      10598 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                                 
      10619 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                       *        *
      10640 TCATTGGAGCAGGTTCCAAGT
          1 TCATTGGAGCAAGTTCCAAGC

                                 *
      10661 TCATTGGAG-AAGGTTCCAAGA
          1 TCATTGGAGCAA-GTTCCAAGC

                            *     
      10682 TCATTGGAG-AAGGTTTCAAGC
          1 TCATTGGAGCAA-GTTCCAAGC

                    
      10703 TCATTGGA
          1 TCATTGGA

      10711 AATGCCTAAG


Statistics
Matches: 85,  Mismatches: 6, Indels: 2
        0.91            0.06        0.02

Matches are distributed among these distances:
  20    1  0.01
  21   84  0.99

ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGCAAGTTCCAAGC

Done.