Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016141.1 Corchorus olitorius cultivar O-4 contig16174, 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: 4449
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32


Found at i:1947 original size:13 final size:13

Alignment explanation


    Indices: 1929--1961  Score: 66
    Period size: 13  Copynumber: 2.5  Consensus size: 13

       1919 TTAGGTGCTT

                         
       1929 ATATCACATATGC
          1 ATATCACATATGC

                         
       1942 ATATCACATATGC
          1 ATATCACATATGC

                   
       1955 ATATCAC
          1 ATATCAC

       1962 TTGCATTGTA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   20  1.00

ACGTcount: A:0.39, C:0.24, G:0.06, T:0.30


Consensus pattern (13 bp):   
ATATCACATATGC

Found at i:3171 original size:5 final size:5

Alignment explanation


    Indices: 3163--3209  Score: 67
    Period size: 5  Copynumber: 9.2  Consensus size: 5

       3153 AAGAAAAATG

                        **                                          
       3163 AAGAA AAGAA TTGAAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
          1 AAGAA AAGAA AAG-AA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A

       3210 GAAGTTGAAA


Statistics
Matches: 37,  Mismatches: 4, Indels: 2
        0.86            0.09        0.05

Matches are distributed among these distances:
   5   34  0.92
   6    3  0.08

ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04


Consensus pattern (5 bp):   
AAGAA

Found at i:3178 original size:26 final size:26

Alignment explanation


    Indices: 3149--3198  Score: 75
    Period size: 26  Copynumber: 1.9  Consensus size: 26

       3139 AGAGGGAAAG

                          *            
       3149 GAAAAAGAAAA-ATGAAGAAAAGAATT
          1 GAAAAAGAAAAGA-AAAGAAAAGAATT

                                    
       3175 GAAAAAGAAAAGAAAAGAAAAGAA
          1 GAAAAAGAAAAGAAAAGAAAAGAA

       3199 AAGAAAAGAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  26   21  0.95
  27    1  0.05

ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06


Consensus pattern (26 bp):   
GAAAAAGAAAAGAAAAGAAAAGAATT

Found at i:3204 original size:26 final size:26

Alignment explanation


    Indices: 3144--3209  Score: 73
    Period size: 26  Copynumber: 2.6  Consensus size: 26

       3134 AAAACAGAGG

                *             *       
       3144 GAAAGGAAAAAGAAAAATGAAGAAAA
          1 GAAAAGAAAAAGAAAAATAAAGAAAA

               **                      
       3170 GAATTGAAAAAGAAAAGA-AAAGAAAA
          1 GAAAAGAAAAAGAAAA-ATAAAGAAAA

                           
       3196 GAAAAG-AAAAGAAA
          1 GAAAAGAAAAAGAAA

       3210 GAAGTTGAAA


Statistics
Matches: 34,  Mismatches: 5, Indels: 3
        0.81            0.12        0.07

Matches are distributed among these distances:
  25    8  0.24
  26   25  0.74
  27    1  0.03

ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05


Consensus pattern (26 bp):   
GAAAAGAAAAAGAAAAATAAAGAAAA
Done.