Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024623.1 Corchorus olitorius cultivar O-4 contig24656, 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: 11629
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:3879 original size:11 final size:10

Alignment explanation


    Indices: 3863--3909  Score: 53
    Period size: 11  Copynumber: 4.7  Consensus size: 10

       3853 AAGTTCGTGT

                       
       3863 TTGAAGACTCA
          1 TTGAAGA-TCA

                    * 
       3874 TTGAAGATAA
          1 TTGAAGATCA

                       
       3884 TTTGAAGAT--
          1 -TTGAAGATCA

                      
       3893 TTGAAGATCA
          1 TTGAAGATCA

                   
       3903 TTGAAGA
          1 TTGAAGA

       3910 ATTATCTCAA


Statistics
Matches: 32,  Mismatches: 1, Indels: 7
        0.80            0.03        0.17

Matches are distributed among these distances:
   8    8  0.25
  10    9  0.28
  11   15  0.47

ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32


Consensus pattern (10 bp):   
TTGAAGATCA

Found at i:3898 original size:19 final size:18

Alignment explanation


    Indices: 3874--3909  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       3864 TGAAGACTCA

                               
       3874 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
       3893 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

       3910 ATTATCTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT

Found at i:5230 original size:22 final size:22

Alignment explanation


    Indices: 5188--5230  Score: 52
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       5178 TTTTTAATTA

                           **     
       5188 ATTGTTTTCTTTAATTTTTTTG
          1 ATTGTTTTCTTTAATAATTTTG

                                  
       5210 ATTGTTTTC-TTAGATAATTTT
          1 ATTGTTTTCTTTA-ATAATTTT

       5231 AATTACTAGT


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  21    3  0.17
  22   15  0.83

ACGTcount: A:0.19, C:0.05, G:0.09, T:0.67


Consensus pattern (22 bp):   
ATTGTTTTCTTTAATAATTTTG

Found at i:10792 original size:18 final size:18

Alignment explanation


    Indices: 10769--10816  Score: 87
    Period size: 18  Copynumber: 2.7  Consensus size: 18

      10759 AGCGCACCAG

                              
      10769 GCACCAGGCAGCAGTAGT
          1 GCACCAGGCAGCAGTAGT

                    *         
      10787 GCACCAGGAAGCAGTAGT
          1 GCACCAGGCAGCAGTAGT

                        
      10805 GCACCAGGCAGC
          1 GCACCAGGCAGC

      10817 TCGAATAAGC


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  18   28  1.00

ACGTcount: A:0.29, C:0.29, G:0.33, T:0.08


Consensus pattern (18 bp):   
GCACCAGGCAGCAGTAGT
Done.