Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015801.1 Corchorus capsularis cultivar CVL-1 contig15822, 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: 15773
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32


Found at i:721 original size:12 final size:12

Alignment explanation


    Indices: 704--773  Score: 59
    Period size: 12  Copynumber: 5.3  Consensus size: 12

        694 ACGGATGGGA

                        
        704 CATCGCACGGGC
          1 CATCGCACGGGC

                     *  
        716 CATCGCACGAGC
          1 CATCGCACGGGC

                              
        728 CATCCGGCCACAGCAGGC
          1 CAT-C-G-CAC-G--GGC

                       *
        746 CATCGCACGGGA
          1 CATCGCACGGGC

                    *   
        758 CATCGCACAGGC
          1 CATCGCACGGGC

                
        770 CATC
          1 CATC

        774 CGGCCACAAC


Statistics
Matches: 47,  Mismatches: 5, Indels: 12
        0.73            0.08        0.19

Matches are distributed among these distances:
  12   30  0.64
  13    1  0.02
  14    2  0.04
  15    6  0.13
  16    2  0.04
  17    1  0.02
  18    5  0.11

ACGTcount: A:0.23, C:0.41, G:0.27, T:0.09


Consensus pattern (12 bp):   
CATCGCACGGGC

Found at i:750 original size:42 final size:42

Alignment explanation


    Indices: 704--790  Score: 131
    Period size: 42  Copynumber: 2.1  Consensus size: 42

        694 ACGGATGGGA

                       *                         *     
        704 CATCGCACGGGCCATCGCAC-GAGCCATCCGGCCACAGCAGGC
          1 CATCGCACGGGACATCGCACAG-GCCATCCGGCCACAACAGGC

                                                  *   
        746 CATCGCACGGGACATCGCACAGGCCATCCGGCCACAACCGGC
          1 CATCGCACGGGACATCGCACAGGCCATCCGGCCACAACAGGC

               
        788 CAT
          1 CAT

        791 TCGACCCATT


Statistics
Matches: 41,  Mismatches: 3, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  42   40  0.98
  43    1  0.02

ACGTcount: A:0.23, C:0.43, G:0.26, T:0.08


Consensus pattern (42 bp):   
CATCGCACGGGACATCGCACAGGCCATCCGGCCACAACAGGC

Found at i:7263 original size:18 final size:18

Alignment explanation


    Indices: 7240--7292  Score: 55
    Period size: 18  Copynumber: 3.3  Consensus size: 18

       7230 CATCGCACGA

                              
       7240 GCCATCCGGCCACAACCG
          1 GCCATCCGGCCACAACCG

                            * 
       7258 GCCAT-C-G---C-ACGG
          1 GCCATCCGGCCACAACCG

                              
       7270 GCCATCCGGCCACAACCG
          1 GCCATCCGGCCACAACCG

                 
       7288 GCCAT
          1 GCCAT

       7293 TCGACCCATT


Statistics
Matches: 27,  Mismatches: 2, Indels: 12
        0.66            0.05        0.29

Matches are distributed among these distances:
  12    8  0.30
  13    2  0.07
  14    1  0.04
  16    1  0.04
  17    2  0.07
  18   13  0.48

ACGTcount: A:0.21, C:0.47, G:0.25, T:0.08


Consensus pattern (18 bp):   
GCCATCCGGCCACAACCG

Found at i:7263 original size:30 final size:30

Alignment explanation


    Indices: 7227--7292  Score: 123
    Period size: 30  Copynumber: 2.2  Consensus size: 30

       7217 ACATCGCACG

                                          
       7227 GGCCATCGCACGAGCCATCCGGCCACAACC
          1 GGCCATCGCACGAGCCATCCGGCCACAACC

                        *                 
       7257 GGCCATCGCACGGGCCATCCGGCCACAACC
          1 GGCCATCGCACGAGCCATCCGGCCACAACC

                  
       7287 GGCCAT
          1 GGCCAT

       7293 TCGACCCATT


Statistics
Matches: 35,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   35  1.00

ACGTcount: A:0.21, C:0.45, G:0.26, T:0.08


Consensus pattern (30 bp):   
GGCCATCGCACGAGCCATCCGGCCACAACC

Found at i:15554 original size:21 final size:21

Alignment explanation


    Indices: 15507--15546  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      15497 CCTTGTTCTT

                                 
      15507 GCCTCATCTCTTCTTGTGAAG
          1 GCCTCATCTCTTCTTGTGAAG

                   *           
      15528 GCCTCATTTCTTCTTGTGA
          1 GCCTCATCTCTTCTTGTGA

      15547 CTGTCTCAAT


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

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.12, C:0.28, G:0.17, T:0.42


Consensus pattern (21 bp):   
GCCTCATCTCTTCTTGTGAAG
Done.