Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011311.1 Corchorus olitorius cultivar O-4 contig11344, 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: 8802
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29


Found at i:1580 original size:19 final size:19

Alignment explanation


    Indices: 1556--1593  Score: 76
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       1546 TCAACTCGCC

                               
       1556 AATCCTATGTTTCTGGGAT
          1 AATCCTATGTTTCTGGGAT

                               
       1575 AATCCTATGTTTCTGGGAT
          1 AATCCTATGTTTCTGGGAT

       1594 TCGGTCTGTA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42


Consensus pattern (19 bp):   
AATCCTATGTTTCTGGGAT

Found at i:2125 original size:12 final size:13

Alignment explanation


    Indices: 2105--2133  Score: 51
    Period size: 12  Copynumber: 2.3  Consensus size: 13

       2095 GGACCCAATA

                         
       2105 AATTCTTAATTGG
          1 AATTCTTAATTGG

                         
       2118 AATT-TTAATTGG
          1 AATTCTTAATTGG

                
       2130 AATT
          1 AATT

       2134 AAAGGATCCT


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   12  0.75
  13    4  0.25

ACGTcount: A:0.34, C:0.03, G:0.14, T:0.48


Consensus pattern (13 bp):   
AATTCTTAATTGG

Found at i:5806 original size:15 final size:15

Alignment explanation


    Indices: 5776--5817  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       5766 TTACTTTGCT

                            
       5776 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
       5792 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
       5807 TTGCTTTCTGT
          1 TTGTTTTCTGT

       5818 CAATCTCTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:8749 original size:22 final size:21

Alignment explanation


    Indices: 8724--8791  Score: 73
    Period size: 22  Copynumber: 3.1  Consensus size: 21

       8714 CCAAGCCATT

                     *            
       8724 ACCGGCCATTCACCGTGCCACC
          1 ACCGGCCATGC-CCGTGCCACC

                 ** *            
       8746 ACCGGTTAAGCCCGTGCCACC
          1 ACCGGCCATGCCCGTGCCACC

                                * 
       8767 ACCGGCCAATGCCCGTGCCATC
          1 ACCGGCC-ATGCCCGTGCCACC

               
       8789 ACC
          1 ACC

       8792 ATTCCAAGCC


Statistics
Matches: 37,  Mismatches: 8, Indels: 2
        0.79            0.17        0.04

Matches are distributed among these distances:
  21   15  0.41
  22   22  0.59

ACGTcount: A:0.19, C:0.47, G:0.21, T:0.13


Consensus pattern (21 bp):   
ACCGGCCATGCCCGTGCCACC

Found at i:8762 original size:21 final size:22

Alignment explanation


    Indices: 8736--8791  Score: 78
    Period size: 21  Copynumber: 2.6  Consensus size: 22

       8726 CGGCCATTCA

                           **     
       8736 CCGTGCCACCACCGGTTAA-GC
          1 CCGTGCCACCACCGGCCAATGC

                                  
       8757 CCGTGCCACCACCGGCCAATGC
          1 CCGTGCCACCACCGGCCAATGC

                    *    
       8779 CCGTGCCATCACC
          1 CCGTGCCACCACC

       8792 ATTCCAAGCC


Statistics
Matches: 31,  Mismatches: 3, Indels: 1
        0.89            0.09        0.03

Matches are distributed among these distances:
  21   17  0.55
  22   14  0.45

ACGTcount: A:0.18, C:0.48, G:0.21, T:0.12


Consensus pattern (22 bp):   
CCGTGCCACCACCGGCCAATGC
Done.