Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001917.1 Corchorus olitorius cultivar O-4 contig01917, 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: 6015
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34


Found at i:1969 original size:21 final size:20

Alignment explanation


    Indices: 1939--1977  Score: 60
    Period size: 21  Copynumber: 1.9  Consensus size: 20

       1929 CACGTCAGCA

                 *               
       1939 TTGATTGTTGACTGTTGACTT
          1 TTGATAGTTGACT-TTGACTT

                              
       1960 TTGATAGTTGACTTTGAC
          1 TTGATAGTTGACTTTGAC

       1978 CTCTGAGAGT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20    5  0.29
  21   12  0.71

ACGTcount: A:0.18, C:0.10, G:0.23, T:0.49


Consensus pattern (20 bp):   
TTGATAGTTGACTTTGACTT

Found at i:2235 original size:14 final size:14

Alignment explanation


    Indices: 2216--2249  Score: 59
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       2206 TATCCGTGAT

                          
       2216 TCCGTTGTCGGCTG
          1 TCCGTTGTCGGCTG

                     *    
       2230 TCCGTTGTCTGCTG
          1 TCCGTTGTCGGCTG

                  
       2244 TCCGTT
          1 TCCGTT

       2250 TTTCGCTCCG


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  14   19  1.00

ACGTcount: A:0.00, C:0.29, G:0.29, T:0.41


Consensus pattern (14 bp):   
TCCGTTGTCGGCTG

Found at i:5338 original size:24 final size:24

Alignment explanation


    Indices: 5311--5362  Score: 86
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       5301 TGACCAAGAG

                   *   *            
       5311 ATTGATGGCAGGAAAATAAAAGGA
          1 ATTGATGACAGCAAAATAAAAGGA

                                    
       5335 ATTGATGACAGCAAAATAAAAGGA
          1 ATTGATGACAGCAAAATAAAAGGA

                
       5359 ATTG
          1 ATTG

       5363 GTCAATACCA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  24   26  1.00

ACGTcount: A:0.50, C:0.06, G:0.25, T:0.19


Consensus pattern (24 bp):   
ATTGATGACAGCAAAATAAAAGGA
Done.