Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019012.1 Corchorus olitorius cultivar O-4 contig19045, 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: 5428
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32


Found at i:1660 original size:21 final size:21

Alignment explanation


    Indices: 1634--1709  Score: 107
    Period size: 21  Copynumber: 3.6  Consensus size: 21

       1624 CGCCCATTCA

                                 
       1634 CCGTGCCACCACCGGTCAAGC
          1 CCGTGCCACCACCGGTCAAGC

             *              *    
       1655 CTGTGCCACCACCGGTTAAGC
          1 CCGTGCCACCACCGGTCAAGC

                           *  *  
       1676 CCGTGCCACCACCGGCCATGC
          1 CCGTGCCACCACCGGTCAAGC

                    *    
       1697 CCGTGCCATCACC
          1 CCGTGCCACCACC

       1710 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:3593 original size:19 final size:18

Alignment explanation


    Indices: 3569--3604  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       3559 TGAAGACCAT

                               
       3569 TTGAAGATAATTTGAAGAC
          1 TTGAAGAT-ATTTGAAGAC

                    *        
       3588 TTGAAGATTTTTGAAGA
          1 TTGAAGATATTTGAAGA

       3605 TTTATTTCAA


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

Matches are distributed among these distances:
  18    8  0.50
  19    8  0.50

ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36


Consensus pattern (18 bp):   
TTGAAGATATTTGAAGAC

Found at i:4735 original size:14 final size:14

Alignment explanation


    Indices: 4716--4748  Score: 57
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       4706 AACCTAGGAT

                          
       4716 ACACAAAGAGAGAC
          1 ACACAAAGAGAGAC

                         *
       4730 ACACAAAGAGAGAG
          1 ACACAAAGAGAGAC

                 
       4744 ACACA
          1 ACACA

       4749 GATACGTATT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  14   18  1.00

ACGTcount: A:0.58, C:0.21, G:0.21, T:0.00


Consensus pattern (14 bp):   
ACACAAAGAGAGAC
Done.