Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002439.1 Corchorus olitorius cultivar O-4 contig02439, 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, 657

Length: 1095
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29


Found at i:1012 original size:11 final size:11

Alignment explanation


    Indices: 996--1036  Score: 50
    Period size: 11  Copynumber: 3.7  Consensus size: 11

        986 ATGTCTTATA

                       
        996 TATATTAAGAT
          1 TATATTAAGAT

                       
       1007 TATATTAA-A-
          1 TATATTAAGAT

                         
       1016 TATATATATAGAT
          1 TATAT-TA-AGAT

                    
       1029 TATATTAA
          1 TATATTAA

       1037 AAAATGAAAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 8
        0.76            0.00        0.24

Matches are distributed among these distances:
   9    5  0.19
  10    3  0.12
  11   10  0.38
  12    3  0.12
  13    5  0.19

ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46


Consensus pattern (11 bp):   
TATATTAAGAT

Found at i:1021 original size:22 final size:22

Alignment explanation


    Indices: 992--1037  Score: 74
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        982 GAGGATGTCT

                                    
        992 TATATATATTAAGATTATATTAAA
          1 TATATATA-T-AGATTATATTAAA

                                  
       1016 TATATATATAGATTATATTAAA
          1 TATATATATAGATTATATTAAA

       1038 AAATGAAAAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  22   13  0.59
  23    1  0.05
  24    8  0.36

ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46


Consensus pattern (22 bp):   
TATATATATAGATTATATTAAA

Found at i:1050 original size:22 final size:22

Alignment explanation


    Indices: 1002--1050  Score: 55
    Period size: 22  Copynumber: 2.2  Consensus size: 22

        992 TATATATATT

                            *   * 
       1002 AAGATTATATTAAATATATATA
          1 AAGATTATATTAAATAAATAAA

            *                      
       1024 TAGATTATATTAAA-AAATGAAA
          1 AAGATTATATTAAATAAAT-AAA

                 
       1046 AAGAT
          1 AAGAT

       1051 GGACAATCAA


Statistics
Matches: 22,  Mismatches: 4, Indels: 2
        0.79            0.14        0.07

Matches are distributed among these distances:
  21    3  0.14
  22   19  0.86

ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35


Consensus pattern (22 bp):   
AAGATTATATTAAATAAATAAA
Done.