Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019653.1 Corchorus olitorius cultivar O-4 contig19686, 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: 5691
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:43 original size:12 final size:12

Alignment explanation


    Indices: 26--50  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

         16 CTACAAAATC

                        
         26 CGACATGATTTT
          1 CGACATGATTTT

                        
         38 CGACATGATTTT
          1 CGACATGATTTT

             
         50 C
          1 C

         51 TTCAAGATTG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40


Consensus pattern (12 bp):   
CGACATGATTTT

Found at i:420 original size:6 final size:6

Alignment explanation


    Indices: 402--458  Score: 78
    Period size: 6  Copynumber: 9.0  Consensus size: 6

        392 GTTTAGACTT

                                         *                            
        402 ATATAG TATATAG ATATAG ATATAAAT ATATAG ATATAG ATATAG ATATAG
          1 ATATAG -ATATAG ATATAG ATAT--AG ATATAG ATATAG ATATAG ATATAG

                  
        453 ATATAG
          1 ATATAG

        459 CTACTTGGGT


Statistics
Matches: 46,  Mismatches: 2, Indels: 5
        0.87            0.04        0.09

Matches are distributed among these distances:
   6   35  0.76
   7    6  0.13
   8    5  0.11

ACGTcount: A:0.51, C:0.00, G:0.14, T:0.35


Consensus pattern (6 bp):   
ATATAG

Found at i:433 original size:20 final size:20

Alignment explanation


    Indices: 408--451  Score: 79
    Period size: 20  Copynumber: 2.2  Consensus size: 20

        398 ACTTATATAG

                                
        408 TATATAGATATAGATATAAA
          1 TATATAGATATAGATATAAA

                              * 
        428 TATATAGATATAGATATAGA
          1 TATATAGATATAGATATAAA

                
        448 TATA
          1 TATA

        452 GATATAGCTA


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  20   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.11, T:0.36


Consensus pattern (20 bp):   
TATATAGATATAGATATAAA

Found at i:5544 original size:31 final size:31

Alignment explanation


    Indices: 5458--5545  Score: 104
    Period size: 31  Copynumber: 2.8  Consensus size: 31

       5448 TGTATTGCTG

                       *           *      * 
       5458 ACGTGGCAATGTCACGTCGGACAAAAAATGTC
          1 ACGTGGCAATGCCACGTCGGAC-CAAAATGAC

                 *           *             
       5490 ACGTGACAATGCCACGTTGGACCAAAATGAC
          1 ACGTGGCAATGCCACGTCGGACCAAAATGAC

                     *        *      
       5521 ACGTGGCAAGGCCACGTCAGACCAA
          1 ACGTGGCAATGCCACGTCGGACCAA

       5546 GGCGTTGATA


Statistics
Matches: 47,  Mismatches: 9, Indels: 1
        0.82            0.16        0.02

Matches are distributed among these distances:
  31   28  0.60
  32   19  0.40

ACGTcount: A:0.34, C:0.26, G:0.25, T:0.15


Consensus pattern (31 bp):   
ACGTGGCAATGCCACGTCGGACCAAAATGAC
Done.