Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022313.1 Corchorus olitorius cultivar O-4 contig22346, 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: 4931
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:235 original size:15 final size:15

Alignment explanation


    Indices: 205--246  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        195 TTACTTTGCT

                            
        205 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
        221 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

                       
        236 TTGTTTTCTGT
          1 TTGTTTTCTGT

        247 CAACCTCTGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:3500 original size:21 final size:21

Alignment explanation


    Indices: 3476--3524  Score: 62
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       3466 TCGATTGCCA

                     **          
       3476 CACCACCGGTTAAGCCCGTGC
          1 CACCACCGGCCAAGCCCGTGC

                        *        
       3497 CACCACCGGCCATGCCCGTGC
          1 CACCACCGGCCAAGCCCGTGC

              *    
       3518 CATCACC
          1 CACCACC

       3525 ATTCCAAGCC


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.18, C:0.49, G:0.20, T:0.12


Consensus pattern (21 bp):   
CACCACCGGCCAAGCCCGTGC

Found at i:3897 original size:15 final size:14

Alignment explanation


    Indices: 3877--3906  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       3867 ATCTCTTTAA

                           
       3877 TTTTCCTTGCATTAT
          1 TTTTCCTTG-ATTAT

                          
       3892 TTTTCCTTGATTAT
          1 TTTTCCTTGATTAT

             
       3906 T
          1 T

       3907 GCTTTAATTG


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.