Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021697.1 Corchorus olitorius cultivar O-4 contig21730, 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: 5349
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.36


Found at i:1932 original size:2 final size:2

Alignment explanation


    Indices: 1925--1967  Score: 77
    Period size: 2  Copynumber: 21.0  Consensus size: 2

       1915 TTCGTACTTT

                                                                           
       1925 TA TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       1968 GATAATAAAA


Statistics
Matches: 40,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   2   38  0.95
   3    2  0.05

ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:2852 original size:2 final size:2

Alignment explanation


    Indices: 2847--2892  Score: 58
    Period size: 2  Copynumber: 22.5  Consensus size: 2

       2837 TGAAAAGATA

                                                             *              
       2847 AT AT AT ACT AT AT AT AT AT A- AT AT AT AT AT AT CT AT AT ACT AT
          1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT

                
       2890 AT A
          1 AT A

       2893 AGTCTAAACT


Statistics
Matches: 39,  Mismatches: 2, Indels: 6
        0.83            0.04        0.13

Matches are distributed among these distances:
   1    1  0.03
   2   34  0.87
   3    4  0.10

ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46


Consensus pattern (2 bp):   
AT

Found at i:2865 original size:13 final size:13

Alignment explanation


    Indices: 2847--2892  Score: 67
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       2837 TGAAAAGATA

                         
       2847 ATATATACTATAT
          1 ATATATACTATAT

                   *     
       2860 ATATATAATATAT
          1 ATATATACTATAT

                         
       2873 ATATAT-CTATAT
          1 ATATATACTATAT

                    
       2885 ACTATATA
          1 A-TATATA

       2893 AGTCTAAACT


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  12    6  0.21
  13   23  0.79

ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46


Consensus pattern (13 bp):   
ATATATACTATAT

Found at i:2898 original size:17 final size:16

Alignment explanation


    Indices: 2848--2898  Score: 52
    Period size: 17  Copynumber: 3.1  Consensus size: 16

       2838 GAAAAGATAA

                           *
       2848 TATATACTATAT-ATA
          1 TATATACTATATAATC

                              
       2863 TATAATA-TATATATATC
          1 TAT-ATACTATATA-ATC

                             
       2880 TATATACTATATAAGTC
          1 TATATACTATATAA-TC

              
       2897 TA
          1 TA

       2899 AACTTCAAAA


Statistics
Matches: 30,  Mismatches: 1, Indels: 8
        0.77            0.03        0.21

Matches are distributed among these distances:
  15    8  0.27
  16    7  0.23
  17   15  0.50

ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45


Consensus pattern (16 bp):   
TATATACTATATAATC

Found at i:4839 original size:14 final size:13

Alignment explanation


    Indices: 4802--4827  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       4792 TAGTAACTAG

                         
       4802 GAACCAATTTTGT
          1 GAACCAATTTTGT

                         
       4815 GAACCAATTTTGT
          1 GAACCAATTTTGT

       4828 ACACCTAATT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38


Consensus pattern (13 bp):   
GAACCAATTTTGT

Found at i:5235 original size:36 final size:36

Alignment explanation


    Indices: 5181--5250  Score: 104
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       5171 GAGATTTTGG

                         *      *               
       5181 AGAAATATAATAATCAAAATTACAAAAAATGTAATA
          1 AGAAATATAATAACCAAAATCACAAAAAATGTAATA

                    *                  *      
       5217 AGAAATATGATAACCAAAATCACAAAAGATGTAA
          1 AGAAATATAATAACCAAAATCACAAAAAATGTAA

       5251 GGTTATTGAA


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  36   30  1.00

ACGTcount: A:0.61, C:0.09, G:0.09, T:0.21


Consensus pattern (36 bp):   
AGAAATATAATAACCAAAATCACAAAAAATGTAATA
Done.