Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016667.1 Corchorus olitorius cultivar O-4 contig16700, 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: 7208
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31


Found at i:1268 original size:21 final size:21

Alignment explanation


    Indices: 1229--1277  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       1219 TCAATGCTTT

                         **       
       1229 AGGAATGCAAGAGGGATTTCAA
          1 AGGAA-GCAAGAGCCATTTCAA

                               * 
       1251 AGGAAGCAAGAGCCATTTCCA
          1 AGGAAGCAAGAGCCATTTCAA

                   
       1272 A-GAAGC
          1 AGGAAGC

       1278 TACAATTCTC


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:3946 original size:8 final size:8

Alignment explanation


    Indices: 3924--3957  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

       3914 ACCTTTTCCA

                    
       3924 TCAAATTT
          1 TCAAATTT

                     
       3932 CTCAAATTT
          1 -TCAAATTT

                    
       3941 TCAAATTT
          1 TCAAATTT

                *   
       3949 TCAAGTTT
          1 TCAAATTT

             
       3957 T
          1 T

       3958 GGAGAATTTG


Statistics
Matches: 24,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
   8   16  0.67
   9    8  0.33

ACGTcount: A:0.32, C:0.15, G:0.03, T:0.50


Consensus pattern (8 bp):   
TCAAATTT

Found at i:5402 original size:22 final size:21

Alignment explanation


    Indices: 5355--5402  Score: 53
    Period size: 22  Copynumber: 2.2  Consensus size: 21

       5345 TTGCATGCAT

                         *       
       5355 TTTTGTTTTATTTGTGTTTTA
          1 TTTTGTTTTATTTATGTTTTA

            *                      
       5376 ATTTGTATTTATCTTATG-TTTA
          1 TTTTGT-TTTAT-TTATGTTTTA

                 
       5398 TTTTG
          1 TTTTG

       5403 GATCTTATAT


Statistics
Matches: 22,  Mismatches: 3, Indels: 3
        0.79            0.11        0.11

Matches are distributed among these distances:
  21    5  0.23
  22   13  0.59
  23    4  0.18

ACGTcount: A:0.15, C:0.02, G:0.12, T:0.71


Consensus pattern (21 bp):   
TTTTGTTTTATTTATGTTTTA
Done.