Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015732.1 Corchorus capsularis cultivar CVL-1 contig15753, 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: 17645
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:431 original size:20 final size:21

Alignment explanation


    Indices: 399--437  Score: 62
    Period size: 20  Copynumber: 1.9  Consensus size: 21

        389 GCGAGGCAAA

                                 
        399 CCACATGGGGTGCCAAGCATG
          1 CCACATGGGGTGCCAAGCATG

                          *    
        420 CCACAT-GGGTGCCCAGCA
          1 CCACATGGGGTGCCAAGCA

        438 CTAGTCGACA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20   11  0.65
  21    6  0.35

ACGTcount: A:0.23, C:0.33, G:0.31, T:0.13


Consensus pattern (21 bp):   
CCACATGGGGTGCCAAGCATG

Found at i:2312 original size:33 final size:33

Alignment explanation


    Indices: 2270--2338  Score: 138
    Period size: 33  Copynumber: 2.1  Consensus size: 33

       2260 GAGCAAGGAG

                                             
       2270 GAGGTAAACCTAACACAAAGTCCATACTAATAT
          1 GAGGTAAACCTAACACAAAGTCCATACTAATAT

                                             
       2303 GAGGTAAACCTAACACAAAGTCCATACTAATAT
          1 GAGGTAAACCTAACACAAAGTCCATACTAATAT

               
       2336 GAG
          1 GAG

       2339 TCCATGGTTC


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  33   36  1.00

ACGTcount: A:0.45, C:0.20, G:0.14, T:0.20


Consensus pattern (33 bp):   
GAGGTAAACCTAACACAAAGTCCATACTAATAT

Found at i:4973 original size:13 final size:14

Alignment explanation


    Indices: 4955--4984  Score: 53
    Period size: 13  Copynumber: 2.2  Consensus size: 14

       4945 TAAATATTTG

                          
       4955 TTTTCCTTTTTA-T
          1 TTTTCCTTTTTACT

                          
       4968 TTTTCCTTTTTACT
          1 TTTTCCTTTTTACT

               
       4982 TTT
          1 TTT

       4985 ACACTTGATC


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

Matches are distributed among these distances:
  13   12  0.75
  14    4  0.25

ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77


Consensus pattern (14 bp):   
TTTTCCTTTTTACT
Done.