Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009534.1 Corchorus olitorius cultivar O-4 contig09566, 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: 6474
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33


Found at i:2938 original size:19 final size:19

Alignment explanation


    Indices: 2914--2955  Score: 59
    Period size: 19  Copynumber: 2.2  Consensus size: 19

       2904 TTACTAATTA

                                
       2914 TTTATTT-TAATATTATAAT
          1 TTTATTTAT-ATATTATAAT

                             * 
       2933 TTTATTTATATATTATATT
          1 TTTATTTATATATTATAAT

                
       2952 TTTA
          1 TTTA

       2956 CTTAAAAATT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  19   20  0.95
  20    1  0.05

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (19 bp):   
TTTATTTATATATTATAAT

Found at i:3665 original size:27 final size:26

Alignment explanation


    Indices: 3614--3666  Score: 72
    Period size: 27  Copynumber: 2.0  Consensus size: 26

       3604 TCTCCCATCC

                                       
       3614 CGCTTCATTACCCTAAATAGATTTTTT
          1 CGCTTCATTACCCT-AATAGATTTTTT

                  *                    
       3641 CGCTTCTTTACCCT-ATAGAATTTTTT
          1 CGCTTCATTACCCTAATAG-ATTTTTT

       3667 GTTTTCTCCT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  25    4  0.17
  26    7  0.29
  27   13  0.54

ACGTcount: A:0.23, C:0.23, G:0.08, T:0.47


Consensus pattern (26 bp):   
CGCTTCATTACCCTAATAGATTTTTT

Found at i:5398 original size:2 final size:2

Alignment explanation


    Indices: 5345--5381  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       5335 TATCTCAAAT

                                                                   
       5345 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       5382 TAGGAATTGA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:5805 original size:45 final size:45

Alignment explanation


    Indices: 5741--5827  Score: 174
    Period size: 45  Copynumber: 1.9  Consensus size: 45

       5731 TGAAAGATGG

                                                         
       5741 CATCCAGGAGTTGAATCAATGATTCTCTAATTGGCCATTATTTGC
          1 CATCCAGGAGTTGAATCAATGATTCTCTAATTGGCCATTATTTGC

                                                      
       5786 CATCCAGGAGTTGAATCAATGATTCTCTAATTGGCCATTATT
          1 CATCCAGGAGTTGAATCAATGATTCTCTAATTGGCCATTATT

       5828 ACTTTTAATT


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  45   42  1.00

ACGTcount: A:0.28, C:0.20, G:0.17, T:0.36


Consensus pattern (45 bp):   
CATCCAGGAGTTGAATCAATGATTCTCTAATTGGCCATTATTTGC
Done.