Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017461.1 Corchorus olitorius cultivar O-4 contig17494, 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: 9697
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:184 original size:42 final size:42

Alignment explanation


    Indices: 128--236  Score: 173
    Period size: 42  Copynumber: 2.6  Consensus size: 42

        118 ATTTTTGTTA

                                                      
        128 TTTAATTAAGGTGAAAGTAAATATAGAATGAATTAAAAGTTG
          1 TTTAATTAAGGTGAAAGTAAATATAGAATGAATTAAAAGTTG

                     *           *        *      *    
        170 TTTAATTAATGTGAAAGTAAACATAGAATGCATTAAATGTTG
          1 TTTAATTAAGGTGAAAGTAAATATAGAATGAATTAAAAGTTG

                        *            
        212 TTTAATTAAGGTAAAAGTAAATATA
          1 TTTAATTAAGGTGAAAGTAAATATA

        237 AAACAAATTG


Statistics
Matches: 60,  Mismatches: 7, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  42   60  1.00

ACGTcount: A:0.47, C:0.02, G:0.17, T:0.35


Consensus pattern (42 bp):   
TTTAATTAAGGTGAAAGTAAATATAGAATGAATTAAAAGTTG

Found at i:739 original size:52 final size:52

Alignment explanation


    Indices: 626--964  Score: 471
    Period size: 52  Copynumber: 6.4  Consensus size: 52

        616 AAATCAGAGC

                   *                           *  *               
        626 AATTAAATTAAAGAGTAAAAGAAGAAGTAAACAGATGCTAGTTTAATTCTGGGT
          1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACA-AAG-AAGTTTAATTCTGGGT

                        *                *                      
        680 AATTAAACTAAATAGTAAAAGAAGAAGTACACAAAGAAGTTTAATTCTGGGT
          1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAAAGAAGTTTAATTCTGGGT

                        *                                       
        732 AATTAAACTAAATAGTAAAAGAAGAAGTAAACAAAGAAGTTTAATTCTGGGT
          1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAAAGAAGTTTAATTCTGGGT

                        *                                       
        784 AATTAAACTAAATAGTAAAAGAAGAAGTAAACAAAGAAGTTTAATTCTGGGT
          1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAAAGAAGTTTAATTCTGGGT

                                *                       *       
        836 AATTAAACTAAAGAGTAAAAAAAGAAGTAAACAAAGAAGTTTAACTCTGGGT
          1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAAAGAAGTTTAATTCTGGGT

                   *            *         *  **      *       *    
        888 AATTAAATTAAAGAGTAAAAAAAGAAGTAAGCAGTGATTAGCTTAATTCCGGGT
          1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAAAGA--AGTTTAATTCTGGGT

                  **          *    
        942 AATTAAGTTAAAGAGTAAGAGAA
          1 AATTAAACTAAAGAGTAAAAGAA

        965 AGCAATAATT


Statistics
Matches: 264,  Mismatches: 19, Indels: 4
        0.92            0.07        0.01

Matches are distributed among these distances:
  52  200  0.76
  53    2  0.01
  54   62  0.23

ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25


Consensus pattern (52 bp):   
AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAAAGAAGTTTAATTCTGGGT

Found at i:3529 original size:19 final size:18

Alignment explanation


    Indices: 3505--3540  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       3495 TGAAGACCAT

                               
       3505 TTGAAGATAATTTGAAGAC
          1 TTGAAGAT-ATTTGAAGAC

                    *        
       3524 TTGAAGATTTTTGAAGA
          1 TTGAAGATATTTGAAGA

       3541 ATTATTTCAA


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

Matches are distributed among these distances:
  18    8  0.50
  19    8  0.50

ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36


Consensus pattern (18 bp):   
TTGAAGATATTTGAAGAC
Done.