Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024721.1 Corchorus olitorius cultivar O-4 contig24754, 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: 8948
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32


Found at i:3584 original size:39 final size:39

Alignment explanation


    Indices: 3508--3586  Score: 158
    Period size: 39  Copynumber: 2.0  Consensus size: 39

       3498 CATGAATAAA

                                                   
       3508 CTCCATTTTCATTAAAAATTCAATCTTTAACCTAAATCC
          1 CTCCATTTTCATTAAAAATTCAATCTTTAACCTAAATCC

                                                   
       3547 CTCCATTTTCATTAAAAATTCAATCTTTAACCTAAATCC
          1 CTCCATTTTCATTAAAAATTCAATCTTTAACCTAAATCC

             
       3586 C
          1 C

       3587 AATTTCCATA


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  39   40  1.00

ACGTcount: A:0.35, C:0.27, G:0.00, T:0.38


Consensus pattern (39 bp):   
CTCCATTTTCATTAAAAATTCAATCTTTAACCTAAATCC

Found at i:4451 original size:36 final size:36

Alignment explanation


    Indices: 4411--4482  Score: 99
    Period size: 36  Copynumber: 2.0  Consensus size: 36

       4401 CTTCAACTAC

                      * *                       
       4411 AAGATTGAGCTCTTACCCAAGACTTTGAGAGCGTTT
          1 AAGATTGAGCCCCTACCCAAGACTTTGAGAGCGTTT

                              *  **             
       4447 AAGATTGAGCCCCTACCCGAGGTTTTGAGAGCGTTT
          1 AAGATTGAGCCCCTACCCAAGACTTTGAGAGCGTTT

       4483 CCGGTTGGCC


Statistics
Matches: 31,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29


Consensus pattern (36 bp):   
AAGATTGAGCCCCTACCCAAGACTTTGAGAGCGTTT

Found at i:6093 original size:27 final size:28

Alignment explanation


    Indices: 6061--6134  Score: 114
    Period size: 27  Copynumber: 2.7  Consensus size: 28

       6051 AAATGAACCT

                                       *
       6061 AAAATGACCAAAATGCCCCTGAATAT-C
          1 AAAATGACCAAAATGCCCCTGAATATGA

             *                      *   
       6088 ATAATGACCAAAATGCCCCTGAATGTGA
          1 AAAATGACCAAAATGCCCCTGAATATGA

                               
       6116 AAAATGACCAAAATGCCCC
          1 AAAATGACCAAAATGCCCC

       6135 CTAAATGATT


Statistics
Matches: 42,  Mismatches: 4, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  27   24  0.57
  28   18  0.43

ACGTcount: A:0.43, C:0.26, G:0.14, T:0.18


Consensus pattern (28 bp):   
AAAATGACCAAAATGCCCCTGAATATGA

Found at i:8223 original size:21 final size:21

Alignment explanation


    Indices: 8199--8238  Score: 64
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       8189 GTAGAGACTA

                                  
       8199 ATGAAATTTGG-TGAAAAAGTG
          1 ATGAAATTTGGCT-AAAAAGTG

                               
       8220 ATGAAATTTGGCTAAAAAG
          1 ATGAAATTTGGCTAAAAAG

       8239 GGGCTGGAAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  21   17  0.94
  22    1  0.06

ACGTcount: A:0.45, C:0.03, G:0.25, T:0.28


Consensus pattern (21 bp):   
ATGAAATTTGGCTAAAAAGTG
Done.