Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023936.1 Corchorus olitorius cultivar O-4 contig23969, 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: 4588
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33


Found at i:2366 original size:15 final size:15

Alignment explanation


    Indices: 2346--2382  Score: 56
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       2336 CAAGAGACGT

                        ** 
       2346 TTTTCAAGAAAATTG
          1 TTTTCAAGAAAAAGG

                           
       2361 TTTTCAAGAAAAAGG
          1 TTTTCAAGAAAAAGG

                   
       2376 TTTTCAA
          1 TTTTCAA

       2383 AAATGAGTTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  15   20  1.00

ACGTcount: A:0.41, C:0.08, G:0.14, T:0.38


Consensus pattern (15 bp):   
TTTTCAAGAAAAAGG

Found at i:3105 original size:21 final size:22

Alignment explanation


    Indices: 3079--3127  Score: 66
    Period size: 21  Copynumber: 2.3  Consensus size: 22

       3069 GAGCAACTAA

                           *    * 
       3079 AAAATGAATGAAAAATG-AATG
          1 AAAATGAATGAAAAAAGAAAAG

                                  
       3100 AAAATG-ATGAAAAAAGAAAAG
          1 AAAATGAATGAAAAAAGAAAAG

                   
       3121 AAAATGA
          1 AAAATGA

       3128 TAAAGTTCTA


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  20    9  0.38
  21   15  0.62

ACGTcount: A:0.67, C:0.00, G:0.18, T:0.14


Consensus pattern (22 bp):   
AAAATGAATGAAAAAAGAAAAG

Found at i:3114 original size:11 final size:11

Alignment explanation


    Indices: 3078--3113  Score: 58
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       3068 GGAGCAACTA

                       
       3078 AAAAATGAATG
          1 AAAAATGAATG

                       
       3089 AAAAATGAATG
          1 AAAAATGAATG

                       
       3100 -AAAATG-ATG
          1 AAAAATGAATG

                 
       3109 AAAAA
          1 AAAAA

       3114 AGAAAAGAAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
   9    3  0.12
  10   10  0.42
  11   11  0.46

ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17


Consensus pattern (11 bp):   
AAAAATGAATG

Done.