Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014750.1 Corchorus olitorius cultivar O-4 contig14783, 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: 6741
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30


Found at i:290 original size:12 final size:12

Alignment explanation


    Indices: 271--300  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

        261 ATACCCGAAC

                        
        271 CAACAACCATAG
          1 CAACAACCATAG

             *          
        283 CGACAACCATAG
          1 CAACAACCATAG

                  
        295 CAACAA
          1 CAACAA

        301 AATAAAACAG


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  12   16  1.00

ACGTcount: A:0.50, C:0.33, G:0.10, T:0.07


Consensus pattern (12 bp):   
CAACAACCATAG

Found at i:4019 original size:15 final size:16

Alignment explanation


    Indices: 3999--4034  Score: 56
    Period size: 15  Copynumber: 2.3  Consensus size: 16

       3989 TCTATTTTAC

                         *  
       3999 TATTTATTTA-TTTGT
          1 TATTTATTTACTTAGT

                            
       4014 TATTTATTTACTTAGT
          1 TATTTATTTACTTAGT

                 
       4030 TATTT
          1 TATTT

       4035 GTTTGACTAT


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  15   10  0.53
  16    9  0.47

ACGTcount: A:0.22, C:0.03, G:0.06, T:0.69


Consensus pattern (16 bp):   
TATTTATTTACTTAGT

Found at i:5557 original size:34 final size:32

Alignment explanation


    Indices: 5519--5654  Score: 152
    Period size: 34  Copynumber: 4.1  Consensus size: 32

       5509 AAGAATTTCG

                                              
       5519 TCAGGTTTAAGTTTTCAAATTGGGAAAGTTCCCA
          1 TCAGGTTT-AG-TTTCAAATTGGGAAAGTTCCCA

                                            * 
       5553 TCAGGGTTTAGTTTTCAAATTGGGAAAGTTCCTA
          1 TCA-GGTTTAG-TTTCAAATTGGGAAAGTTCCCA

                 *                            
       5587 TCGAGTTTTAAGTTTCAAATTGGGAAAGTT-CCA
          1 TC-AGGTTT-AGTTTCAAATTGGGAAAGTTCCCA

              *                               
       5620 -CCGAGTTTAGTTTC-AATTAGGGAAAGTTCCCA
          1 TCAG-GTTTAGTTTCAAATT-GGGAAAGTTCCCA

               
       5652 TCA
          1 TCA

       5655 TTTTCAGCTT


Statistics
Matches: 89,  Mismatches: 6, Indels: 15
        0.81            0.05        0.14

Matches are distributed among these distances:
  30    4  0.04
  31   16  0.18
  32    7  0.08
  33    3  0.03
  34   51  0.57
  35    8  0.09

ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35


Consensus pattern (32 bp):   
TCAGGTTTAGTTTCAAATTGGGAAAGTTCCCA

Found at i:5608 original size:68 final size:66

Alignment explanation


    Indices: 5524--5649  Score: 184
    Period size: 68  Copynumber: 1.9  Consensus size: 66

       5514 TTTCGTCAGG

                                             *                               
       5524 TTTAAGTTTTCAAATTGGGAAAGTTCCCATCAGGGTTTAGTTTTCAAATT-GGGAAAGTTCCTAT
          1 TTTAAGTTTTCAAATTGGGAAAGTT-CCA-CAGAGTTTAG-TTTC-AATTAGGGAAAGTTCCTAT

                 
       5588 CGAGT
         62 CGAGT

                                         *                            
       5593 TTTAAG-TTTCAAATTGGGAAAGTTCCACCGAGTTTAGTTTCAATTAGGGAAAGTTCC
          1 TTTAAGTTTTCAAATTGGGAAAGTTCCACAGAGTTTAGTTTCAATTAGGGAAAGTTCC

       5650 CATCATTTTC


Statistics
Matches: 54,  Mismatches: 2, Indels: 6
        0.87            0.03        0.10

Matches are distributed among these distances:
  64    4  0.07
  65   15  0.28
  66    8  0.15
  67    3  0.06
  68   18  0.33
  69    6  0.11

ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37


Consensus pattern (66 bp):   
TTTAAGTTTTCAAATTGGGAAAGTTCCACAGAGTTTAGTTTCAATTAGGGAAAGTTCCTATCGAG
T
Done.