Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021977.1 Corchorus olitorius cultivar O-4 contig22010, 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: 5588
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28


Found at i:288 original size:23 final size:22

Alignment explanation


    Indices: 262--381  Score: 117
    Period size: 23  Copynumber: 5.6  Consensus size: 22

        252 TGCTTGGCGC

                     *             
        262 CCGACCACTCCCAAACCTGGCAA
          1 CCGACCACTTCCAAACCTGGC-A

                         * *      
        285 CCGACCACTTCCATAGC--GC-
          1 CCGACCACTTCCAAACCTGGCA

                                 * 
        304 CCGACCACTTCCAAACCTGGTGA
          1 CCGACCACTTCCAAACCTGG-CA

                         * *      
        327 CCGACCACTTCCATAGC--GC-
          1 CCGACCACTTCCAAACCTGGCA

                                   
        346 CCGACCACTTCCAAACCTGGCGA
          1 CCGACCACTTCCAAACCTGGC-A

                         
        369 CCGACCACTTCCA
          1 CCGACCACTTCCA

        382 TATCGCGGCG


Statistics
Matches: 78,  Mismatches: 11, Indels: 16
        0.74            0.10        0.15

Matches are distributed among these distances:
  19   30  0.38
  21    6  0.08
  23   42  0.54

ACGTcount: A:0.25, C:0.46, G:0.15, T:0.14


Consensus pattern (22 bp):   
CCGACCACTTCCAAACCTGGCA

Found at i:309 original size:19 final size:19

Alignment explanation


    Indices: 285--358  Score: 85
    Period size: 19  Copynumber: 3.7  Consensus size: 19

        275 AACCTGGCAA

                               
        285 CCGACCACTTCCATAGCGC
          1 CCGACCACTTCCATAGCGC

                              * * *
        304 CCGACCACTTCCAAACCTGGTGA
          1 CCGACCACTTCC--A--TAGCGC

                               
        327 CCGACCACTTCCATAGCGC
          1 CCGACCACTTCCATAGCGC

                         
        346 CCGACCACTTCCA
          1 CCGACCACTTCCA

        359 AACCTGGCGA


Statistics
Matches: 45,  Mismatches: 6, Indels: 8
        0.76            0.10        0.14

Matches are distributed among these distances:
  19   28  0.62
  21    2  0.04
  23   15  0.33

ACGTcount: A:0.23, C:0.46, G:0.15, T:0.16


Consensus pattern (19 bp):   
CCGACCACTTCCATAGCGC

Found at i:318 original size:42 final size:42

Alignment explanation


    Indices: 258--383  Score: 225
    Period size: 42  Copynumber: 3.0  Consensus size: 42

        248 CAATTGCTTG

                         *           *                
        258 GCGCCCGACCACTCCCAAACCTGGCAACCGACCACTTCCATA
          1 GCGCCCGACCACTTCCAAACCTGGCGACCGACCACTTCCATA

                                    *                 
        300 GCGCCCGACCACTTCCAAACCTGGTGACCGACCACTTCCATA
          1 GCGCCCGACCACTTCCAAACCTGGCGACCGACCACTTCCATA

                                                      
        342 GCGCCCGACCACTTCCAAACCTGGCGACCGACCACTTCCATA
          1 GCGCCCGACCACTTCCAAACCTGGCGACCGACCACTTCCATA

        384 TCGCGGCGCT


Statistics
Matches: 80,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  42   80  1.00

ACGTcount: A:0.25, C:0.45, G:0.16, T:0.14


Consensus pattern (42 bp):   
GCGCCCGACCACTTCCAAACCTGGCGACCGACCACTTCCATA

Found at i:1100 original size:14 final size:14

Alignment explanation


    Indices: 1081--1113  Score: 57
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       1071 TTATATATTA

                          
       1081 AAATAATCCAAATG
          1 AAATAATCCAAATG

                       *  
       1095 AAATAATCCAAGTG
          1 AAATAATCCAAATG

                 
       1109 AAATA
          1 AAATA

       1114 GTCTTTGAAA


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:0.12, G:0.09, T:0.21


Consensus pattern (14 bp):   
AAATAATCCAAATG

Found at i:5558 original size:2 final size:2

Alignment explanation


    Indices: 5551--5588  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

       5541 AAGAGGAAGA

                                                                    
       5551 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00


Consensus pattern (2 bp):   
AG

Done.