Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009828.1 Corchorus olitorius cultivar O-4 contig09860, 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: 2540
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33


Found at i:289 original size:40 final size:39

Alignment explanation


    Indices: 172--290  Score: 175
    Period size: 40  Copynumber: 3.0  Consensus size: 39

        162 TTGATCCTCT

                   *    *                        *  
        172 TAATAATCAAGGAAATAAATTAAATTCAGGTTTAGCCTCC
          1 TAATAATTAAGGTAATAAATTAAA-TCAGGTTTAGCCCCC

                                                    
        212 TAATAATTAAGGTAATAAATTAAATCTAGGTTTAGCCCCC
          1 TAATAATTAAGGTAATAAATTAAATC-AGGTTTAGCCCCC

                       *                           
        252 TAATAATTAAGTTAATAAATTAAATGCAGGTTTAGCCCC
          1 TAATAATTAAGGTAATAAATTAAAT-CAGGTTTAGCCCC

        291 AAGGTATAAA


Statistics
Matches: 73,  Mismatches: 4, Indels: 4
        0.90            0.05        0.05

Matches are distributed among these distances:
  39    2  0.03
  40   70  0.96
  41    1  0.01

ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32


Consensus pattern (39 bp):   
TAATAATTAAGGTAATAAATTAAATCAGGTTTAGCCCCC

Found at i:1815 original size:19 final size:20

Alignment explanation


    Indices: 1770--1817  Score: 59
    Period size: 19  Copynumber: 2.6  Consensus size: 20

       1760 TTTAATGTGG

                    *           
       1770 GTATACTTTTTTATGCATGT
          1 GTATACTTGTTTATGCATGT

                                
       1790 -TAT--TTGTTT-TGCATGT
          1 GTATACTTGTTTATGCATGT

                        
       1806 GTATACTTGTTT
          1 GTATACTTGTTT

       1818 CCACACCTAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 7
        0.75            0.03        0.22

Matches are distributed among these distances:
  16    7  0.29
  17    8  0.33
  19    9  0.38

ACGTcount: A:0.17, C:0.08, G:0.17, T:0.58


Consensus pattern (20 bp):   
GTATACTTGTTTATGCATGT
Done.