Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015184.1 Corchorus olitorius cultivar O-4 contig15217, 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: 19567
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29


Found at i:13082 original size:16 final size:17

Alignment explanation


    Indices: 13061--13106  Score: 53
    Period size: 16  Copynumber: 2.9  Consensus size: 17

      13051 AATTGCAAAT

                             
      13061 AAATAAATATTCAAGA-
          1 AAATAAATATTCAAGAG

                     *       
      13077 AAAT-AATAATCAAGAG
          1 AAATAAATATTCAAGAG

               *           
      13093 AAACAAATA-TCAAG
          1 AAATAAATATTCAAG

      13107 TGATGGAAAT


Statistics
Matches: 26,  Mismatches: 2, Indels: 4
        0.81            0.06        0.12

Matches are distributed among these distances:
  15   10  0.38
  16   12  0.46
  17    4  0.15

ACGTcount: A:0.63, C:0.09, G:0.09, T:0.20


Consensus pattern (17 bp):   
AAATAAATATTCAAGAG

Found at i:13895 original size:2 final size:2

Alignment explanation


    Indices: 13888--13920  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      13878 TGCGGCTAAA

                                                             
      13888 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      13921 ATCCTATTTT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:15933 original size:14 final size:15

Alignment explanation


    Indices: 15909--15937  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

      15899 AACTAAATGC

                           
      15909 TAAACGAAAAAGAAA
          1 TAAACGAAAAAGAAA

                           
      15924 TAAA-GAAAAAGAAA
          1 TAAACGAAAAAGAAA

      15938 GACTAACTAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14   10  0.71
  15    4  0.29

ACGTcount: A:0.76, C:0.03, G:0.14, T:0.07


Consensus pattern (15 bp):   
TAAACGAAAAAGAAA

Found at i:18253 original size:16 final size:16

Alignment explanation


    Indices: 18232--18264  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 16

      18222 AGATAGATTC

                            
      18232 GGGGTTGACGGGGCTG
          1 GGGGTTGACGGGGCTG

                   *        
      18248 GGGGTTGTCGGGGCTG
          1 GGGGTTGACGGGGCTG

             
      18264 G
          1 G

      18265 TTTGGTAGGG


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.03, C:0.12, G:0.64, T:0.21


Consensus pattern (16 bp):   
GGGGTTGACGGGGCTG

Found at i:18719 original size:15 final size:15

Alignment explanation


    Indices: 18699--18729  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      18689 GTTAGAAAAA

                           
      18699 TGGAGAGCAAAATTT
          1 TGGAGAGCAAAATTT

                           
      18714 TGGAGAGCAAAATTT
          1 TGGAGAGCAAAATTT

             
      18729 T
          1 T

      18730 ATTGTTGAAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29


Consensus pattern (15 bp):   
TGGAGAGCAAAATTT
Done.