Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020954.1 Corchorus olitorius cultivar O-4 contig20987, 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: 11833
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33


Found at i:2203 original size:21 final size:21

Alignment explanation


    Indices: 2164--2212  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       2154 TCAATGCTTT

                         **       
       2164 AGGAATGCAAGAGGGATTTCAA
          1 AGGAA-GCAAGAGCCATTTCAA

                               * 
       2186 AGGAAGCAAGAGCCATTTCCA
          1 AGGAAGCAAGAGCCATTTCAA

                   
       2207 A-GAAGC
          1 AGGAAGC

       2213 TACAATTCTT


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

Matches are distributed among these distances:
  20    5  0.21
  21   14  0.58
  22    5  0.21

ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14


Consensus pattern (21 bp):   
AGGAAGCAAGAGCCATTTCAA

Found at i:7116 original size:4 final size:4

Alignment explanation


    Indices: 7109--7139  Score: 62
    Period size: 4  Copynumber: 7.8  Consensus size: 4

       7099 AAAAAAAAAA

                                                  
       7109 AATT AATT AATT AATT AATT AATT AATT AAT
          1 AATT AATT AATT AATT AATT AATT AATT AAT

       7140 AAAAGAAAAG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   27  1.00

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


Consensus pattern (4 bp):   
AATT

Found at i:7246 original size:26 final size:25

Alignment explanation


    Indices: 7200--7250  Score: 66
    Period size: 26  Copynumber: 2.0  Consensus size: 25

       7190 AAGTATTGTC

                *           *        
       7200 CCTCTAAAAAAAAGAGTGTTAGTAA
          1 CCTCAAAAAAAAAGAGAGTTAGTAA

                           *          
       7225 CCTCAAAAGAAAAAGGGAGTTAGTAA
          1 CCTCAAAA-AAAAAGAGAGTTAGTAA

       7251 ACCCTAAATC


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  25    7  0.32
  26   15  0.68

ACGTcount: A:0.49, C:0.12, G:0.20, T:0.20


Consensus pattern (25 bp):   
CCTCAAAAAAAAAGAGAGTTAGTAA
Done.