Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000370.1 Corchorus olitorius cultivar O-4 contig00370, 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: 4969
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:1169 original size:3 final size:3

Alignment explanation


    Indices: 1161--1185  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

       1151 TGGTGGCGGT

                                             
       1161 GGA GGA GGA GGA GGA GGA GGA GGA G
          1 GGA GGA GGA GGA GGA GGA GGA GGA G

       1186 TAAAATGGTG


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00


Consensus pattern (3 bp):   
GGA

Found at i:4857 original size:33 final size:34

Alignment explanation


    Indices: 4802--4869  Score: 120
    Period size: 33  Copynumber: 2.0  Consensus size: 34

       4792 TAGGCGCGGA

                                       *      
       4802 GATGGGTGCCGTCCCCCGGAGGACGGCCCACCAC
          1 GATGGGTGCCGTCCCCCGGAGGACGGCACACCAC

                                              
       4836 GATGGGTGCCGT-CCCCGGAGGACGGCACACCAC
          1 GATGGGTGCCGTCCCCCGGAGGACGGCACACCAC

             
       4869 G
          1 G

       4870 GTGAGAGCCG


Statistics
Matches: 33,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  33   21  0.64
  34   12  0.36

ACGTcount: A:0.16, C:0.38, G:0.37, T:0.09


Consensus pattern (34 bp):   
GATGGGTGCCGTCCCCCGGAGGACGGCACACCAC

Found at i:4880 original size:33 final size:33

Alignment explanation


    Indices: 4809--4881  Score: 101
    Period size: 33  Copynumber: 2.2  Consensus size: 33

       4799 GGAGATGGGT

                                *          * *
       4809 GCCGTCCCCCGGAGGACGGCCCACCACGATGGGT
          1 GCCGT-CCCCGGAGGACGGCACACCACGATGAGA

                                       *     
       4843 GCCGTCCCCGGAGGACGGCACACCACGGTGAGA
          1 GCCGTCCCCGGAGGACGGCACACCACGATGAGA

                  
       4876 GCCGTC
          1 GCCGTC

       4882 ACGGTGTGTG


Statistics
Matches: 35,  Mismatches: 4, Indels: 1
        0.88            0.10        0.03

Matches are distributed among these distances:
  33   30  0.86
  34    5  0.14

ACGTcount: A:0.16, C:0.40, G:0.36, T:0.08


Consensus pattern (33 bp):   
GCCGTCCCCGGAGGACGGCACACCACGATGAGA

Found at i:4966 original size:33 final size:33

Alignment explanation


    Indices: 4881--4958  Score: 120
    Period size: 33  Copynumber: 2.4  Consensus size: 33

       4871 TGAGAGCCGT

                   *                         
       4881 CACGGTGTGTGCAATCCCCGAAGGACGGCCCAC
          1 CACGGTGGGTGCAATCCCCGAAGGACGGCCCAC

                        *           **       
       4914 CACGGTGGGTGCCATCCCCGAAGGGTGGCCCAC
          1 CACGGTGGGTGCAATCCCCGAAGGACGGCCCAC

                        
       4947 CACGGTGGGTGC
          1 CACGGTGGGTGC

       4959 TGTCCCCGGA


Statistics
Matches: 41,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  33   41  1.00

ACGTcount: A:0.17, C:0.35, G:0.36, T:0.13


Consensus pattern (33 bp):   
CACGGTGGGTGCAATCCCCGAAGGACGGCCCAC
Done.