Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022642.1 Corchorus olitorius cultivar O-4 contig22675, 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: 10146
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:2593 original size:25 final size:25

Alignment explanation


    Indices: 2559--2607  Score: 89
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       2549 AATTTGCATA

                         *           
       2559 GCATTGTTATACTTCATGGTAGATG
          1 GCATTGTTATACTACATGGTAGATG

                                    
       2584 GCATTGTTATACTACATGGTAGAT
          1 GCATTGTTATACTACATGGTAGAT

       2608 TAGAGATTTG


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

Matches are distributed among these distances:
  25   23  1.00

ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39


Consensus pattern (25 bp):   
GCATTGTTATACTACATGGTAGATG

Found at i:6772 original size:12 final size:12

Alignment explanation


    Indices: 6755--6779  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       6745 ACTTCCTGAA

                        
       6755 GGCCTGAAGCAT
          1 GGCCTGAAGCAT

                        
       6767 GGCCTGAAGCAT
          1 GGCCTGAAGCAT

             
       6779 G
          1 G

       6780 TTTTTCTTGG


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:0.24, G:0.36, T:0.16


Consensus pattern (12 bp):   
GGCCTGAAGCAT

Found at i:9737 original size:7 final size:7

Alignment explanation


    Indices: 9709--9751  Score: 54
    Period size: 7  Copynumber: 6.3  Consensus size: 7

       9699 GGCAACCCAA

                   
       9709 TTTTAAT
          1 TTTTAAT

               *   
       9716 TTTCAAT
          1 TTTTAAT

                   
       9723 TTTT--T
          1 TTTTAAT

                    
       9728 TTTTAATT
          1 TTTTAA-T

                   
       9736 TTTTAAT
          1 TTTTAAT

                   
       9743 TTTTAAT
          1 TTTTAAT

              
       9750 TT
          1 TT

       9752 CTAACTTGAT


Statistics
Matches: 31,  Mismatches: 2, Indels: 6
        0.79            0.05        0.15

Matches are distributed among these distances:
   5    5  0.16
   7   19  0.61
   8    7  0.23

ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74


Consensus pattern (7 bp):   
TTTTAAT

Found at i:10056 original size:17 final size:17

Alignment explanation


    Indices: 10034--10122  Score: 151
    Period size: 17  Copynumber: 5.2  Consensus size: 17

      10024 CAGGCCACTT

                        *    
      10034 CCGCGCCGAGCCTGTGC
          1 CCGCGCCGAGCCCGTGC

                             
      10051 CCGCGCCGAGCCCGTGC
          1 CCGCGCCGAGCCCGTGC

                *            
      10068 CCGCACCGAGCCCGTGC
          1 CCGCGCCGAGCCCGTGC

                             
      10085 CCGCGCCGAGCCCGTGC
          1 CCGCGCCGAGCCCGTGC

                *            
      10102 CCGCACCGAGCCCGTGC
          1 CCGCGCCGAGCCCGTGC

                
      10119 CCGC
          1 CCGC

      10123 ACAACACCAG


Statistics
Matches: 68,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   68  1.00

ACGTcount: A:0.08, C:0.53, G:0.33, T:0.07


Consensus pattern (17 bp):   
CCGCGCCGAGCCCGTGC

Done.