Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020686.1 Corchorus olitorius cultivar O-4 contig20719, 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: 13780
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--35  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

                                                                
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T

         36 ATATATATAT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

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


Consensus pattern (2 bp):   
TC

Found at i:40 original size:2 final size:2

Alignment explanation


    Indices: 35--65  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

         25 TCTCTCTCTC

                                                          
         35 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 T

         66 TAATCATGCA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:4217 original size:38 final size:38

Alignment explanation


    Indices: 4166--4245  Score: 137
    Period size: 38  Copynumber: 2.1  Consensus size: 38

       4156 TCAAAATTTT

                                                   
       4166 CAAAACCTGGAATCAAAATTCTT-AGAGGAGAAAGAATA
          1 CAAAACCTGGAATCAAAATT-TTCAGAGGAGAAAGAATA

                                                  
       4204 CAAAACCTGGAATCAAAATTTTCAGAGGAGAAAGAATA
          1 CAAAACCTGGAATCAAAATTTTCAGAGGAGAAAGAATA

                 
       4242 -AAAA
          1 CAAAA

       4246 TTCAGAAACA


Statistics
Matches: 41,  Mismatches: 0, Indels: 3
        0.93            0.00        0.07

Matches are distributed among these distances:
  37    6  0.15
  38   35  0.85

ACGTcount: A:0.53, C:0.12, G:0.17, T:0.17


Consensus pattern (38 bp):   
CAAAACCTGGAATCAAAATTTTCAGAGGAGAAAGAATA

Found at i:6634 original size:31 final size:30

Alignment explanation


    Indices: 6559--6634  Score: 102
    Period size: 31  Copynumber: 2.5  Consensus size: 30

       6549 TTTAAATCAC

                                           
       6559 GACATTTTGA-CCCTAAACTTCCAAATTCAA
          1 GACATTTT-ACCCCTAAACTTCCAAATTCAA

                                             
       6589 GACA-TTTAGCCCCCTAAACTTCTCAAATTCAA
          1 GACATTTTA--CCCCTAAACTTC-CAAATTCAA

                          
       6621 GACATTTTACCCCT
          1 GACATTTTACCCCT

       6635 TGACAGAGGA


Statistics
Matches: 41,  Mismatches: 0, Indels: 9
        0.82            0.00        0.18

Matches are distributed among these distances:
  28    1  0.02
  29    3  0.07
  30    4  0.10
  31   16  0.39
  32   13  0.32
  33    4  0.10

ACGTcount: A:0.33, C:0.30, G:0.07, T:0.30


Consensus pattern (30 bp):   
GACATTTTACCCCTAAACTTCCAAATTCAA
Done.