Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023132.1 Corchorus olitorius cultivar O-4 contig23165, 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: 4691
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29


Found at i:382 original size:15 final size:16

Alignment explanation


    Indices: 351--390  Score: 73
    Period size: 15  Copynumber: 2.6  Consensus size: 16

        341 TTACTCTGCT

                            
        351 TTGTTTTCTAGTTTAA
          1 TTGTTTTCTAGTTTAA

                            
        367 TTGTTTTCTA-TTTAA
          1 TTGTTTTCTAGTTTAA

                     
        382 TTGTTTTCT
          1 TTGTTTTCT

        391 GTGAATCTCT


Statistics
Matches: 24,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   14  0.58
  16   10  0.42

ACGTcount: A:0.15, C:0.07, G:0.10, T:0.68


Consensus pattern (16 bp):   
TTGTTTTCTAGTTTAA

Found at i:3295 original size:24 final size:21

Alignment explanation


    Indices: 3242--3317  Score: 107
    Period size: 21  Copynumber: 3.6  Consensus size: 21

       3232 CGCCCATTCA

                                 
       3242 CCGTGCCACCACCGGTCAAGC
          1 CCGTGCCACCACCGGTCAAGC

                            *    
       3263 CCGTGCCACCACCGGTTAAGC
          1 CCGTGCCACCACCGGTCAAGC

            *              *  *  
       3284 TCGTGCCACCACCGGCCATGC
          1 CCGTGCCACCACCGGTCAAGC

                    *    
       3305 CCGTGCCATCACC
          1 CCGTGCCACCACC

       3318 ATTCCAAGCC


Statistics
Matches: 48,  Mismatches: 7, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  21   48  1.00

ACGTcount: A:0.17, C:0.47, G:0.22, T:0.13


Consensus pattern (21 bp):   
CCGTGCCACCACCGGTCAAGC

Found at i:3690 original size:15 final size:14

Alignment explanation


    Indices: 3670--3699  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       3660 ATCTCTTTAA

                           
       3670 TTTTCCTTGCATTAT
          1 TTTTCCTTG-ATTAT

                          
       3685 TTTTCCTTGATTAT
          1 TTTTCCTTGATTAT

             
       3699 T
          1 T

       3700 GCTTTGATTG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63


Consensus pattern (14 bp):   
TTTTCCTTGATTAT
Done.