Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016159.1 Corchorus olitorius cultivar O-4 contig16192, 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: 4777
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.35


Found at i:633 original size:45 final size:45

Alignment explanation


    Indices: 543--635  Score: 141
    Period size: 45  Copynumber: 2.1  Consensus size: 45

        533 ATTTTTCAAA

                                     *              *    
        543 GGAGTTGAAATTTTAAACGTATAATTATACTATAAGAACTGAACC
          1 GGAGTTGAAATTTTAAACGTATAATCATACTATAAGAACTAAACC

                     *                           **      
        588 GGAGTTGAATTTTTAAACGTATAATCATACTATAAGAGGTAAACC
          1 GGAGTTGAAATTTTAAACGTATAATCATACTATAAGAACTAAACC

               
        633 GGA
          1 GGA

        636 TTAGATTGCC


Statistics
Matches: 43,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  45   43  1.00

ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30


Consensus pattern (45 bp):   
GGAGTTGAAATTTTAAACGTATAATCATACTATAAGAACTAAACC

Found at i:1883 original size:18 final size:18

Alignment explanation


    Indices: 1862--1896  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       1852 GCTTGGGCCG

                   *          
       1862 GCCAGGCGTGGCCCAAGT
          1 GCCAGGCCTGGCCCAAGT

                        *    
       1880 GCCAGGCCTGGCGCAAG
          1 GCCAGGCCTGGCCCAAG

       1897 GGCCTGAGCT


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.17, C:0.34, G:0.40, T:0.09


Consensus pattern (18 bp):   
GCCAGGCCTGGCCCAAGT

Found at i:2059 original size:6 final size:6

Alignment explanation


    Indices: 2047--2080  Score: 59
    Period size: 6  Copynumber: 5.7  Consensus size: 6

       2037 AAAAGAAAGG

                     *                             
       2047 AAAAAT AATAAT AAAAAT AAAAAT AAAAAT AAAA
          1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA

       2081 GGGAAGGAAA


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

Matches are distributed among these distances:
   6   26  1.00

ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18


Consensus pattern (6 bp):   
AAAAAT

Found at i:3095 original size:28 final size:28

Alignment explanation


    Indices: 3035--3087  Score: 72
    Period size: 28  Copynumber: 1.9  Consensus size: 28

       3025 CCCTATCATG

                    *          *   *    
       3035 AAAATTACTATTTTGCCCTTTGTCGAAT
          1 AAAATTACCATTTTGCCCTCTGTAGAAT

                                      
       3063 AAAATTACCATTTTGCCC-CTGTAGA
          1 AAAATTACCATTTTGCCCTCTGTAGA

       3088 CCTAAAATAA


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  27    5  0.23
  28   17  0.77

ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38


Consensus pattern (28 bp):   
AAAATTACCATTTTGCCCTCTGTAGAAT
Done.