Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017048.1 Corchorus olitorius cultivar O-4 contig17081, 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: 33644
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:7856 original size:45 final size:46

Alignment explanation


    Indices: 7792--7882  Score: 166
    Period size: 45  Copynumber: 2.0  Consensus size: 46

       7782 TAGACAAAAA

                                                   *      
       7792 TCAAAGTATGAAACCCTTCTAACATAGTTAT-AAAACCCGACACAG
          1 TCAAAGTATGAAACCCTTCTAACATAGTTATAAAAACCCCACACAG

                                                          
       7837 TCAAAGTATGAAACCCTTCTAACATAGTTATAAAAACCCCACACAG
          1 TCAAAGTATGAAACCCTTCTAACATAGTTATAAAAACCCCACACAG

       7883 AAGGCAATCT


Statistics
Matches: 44,  Mismatches: 1, Indels: 1
        0.96            0.02        0.02

Matches are distributed among these distances:
  45   31  0.70
  46   13  0.30

ACGTcount: A:0.43, C:0.25, G:0.10, T:0.22


Consensus pattern (46 bp):   
TCAAAGTATGAAACCCTTCTAACATAGTTATAAAAACCCCACACAG

Found at i:25526 original size:71 final size:68

Alignment explanation


    Indices: 25387--25532  Score: 170
    Period size: 71  Copynumber: 2.1  Consensus size: 68

      25377 CAATTAATCA

                                                        *                  * 
      25387 AAGACTAAAATTGAAATTAAAACATGTAGACAGAGATAATTGAGTAGGCATTGATGTGACATATG
          1 AAGACTAAAATTGAAATTAAAACATGTAGACAGAGATAATTGAGGAGGCA-T-A-GTGACATAAG

                  
      25452 TAAGTC
         63 TAAGTC

                   *                                                     *   
      25458 AAGACTAGAATTGAAATTAAAACATGTAGACAGAGCTAATATAATTGAGGAGGCA-A-TGATATA
          1 AAGACTAAAATTGAAATTAAAACATGTAGACAGAG-----ATAATTGAGGAGGCATAGTGACATA

                    
      25521 AGTAAGTC
         61 AGTAAGTC

                
      25529 AAGA
          1 AAGA

      25533 TCTATTAAAA


Statistics
Matches: 66,  Mismatches: 4, Indels: 10
        0.82            0.05        0.12

Matches are distributed among these distances:
  71   51  0.77
  73    1  0.02
  76   14  0.21

ACGTcount: A:0.46, C:0.08, G:0.21, T:0.25


Consensus pattern (68 bp):   
AAGACTAAAATTGAAATTAAAACATGTAGACAGAGATAATTGAGGAGGCATAGTGACATAAGTAA
GTC

Found at i:32666 original size:20 final size:21

Alignment explanation


    Indices: 32621--32666  Score: 51
    Period size: 19  Copynumber: 2.3  Consensus size: 21

      32611 AATTTATAAA

                          *      
      32621 ACATATAAAAAATATTAAAAT
          1 ACATATAAAAAATAATAAAAT

                      *        * 
      32642 A-ATAT-AAATATAATAAATT
          1 ACATATAAAAAATAATAAAAT

                  
      32661 ACATAT
          1 ACATAT

      32667 TAATTTGTAA


Statistics
Matches: 21,  Mismatches: 3, Indels: 3
        0.78            0.11        0.11

Matches are distributed among these distances:
  19   12  0.57
  20    8  0.38
  21    1  0.05

ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33


Consensus pattern (21 bp):   
ACATATAAAAAATAATAAAAT
Done.