Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020978.1 Corchorus olitorius cultivar O-4 contig21011, 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: 7218
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32


Found at i:650 original size:34 final size:34

Alignment explanation


    Indices: 561--656  Score: 104
    Period size: 33  Copynumber: 2.9  Consensus size: 34

        551 GAGTAATTCT

                *        *         *     *    
        561 AAATCTGTTTTAGATGTTGTTTGCGATGATACTA
          1 AAATTTGTTTTAGGTGTTGTTTGTGATGACACTA

              ** **   *                       
        595 AACCTAATTTGA-GTGTTGTTTGTGATGACACTA
          1 AAATTTGTTTTAGGTGTTGTTTGTGATGACACTA

                                         
        628 AAATTTGTTTTAGGTGTTGTTTGTGATGA
          1 AAATTTGTTTTAGGTGTTGTTTGTGATGA

        657 AACAAATTCT


Statistics
Matches: 47,  Mismatches: 14, Indels: 2
        0.75            0.22        0.03

Matches are distributed among these distances:
  33   25  0.53
  34   22  0.47

ACGTcount: A:0.25, C:0.07, G:0.23, T:0.45


Consensus pattern (34 bp):   
AAATTTGTTTTAGGTGTTGTTTGTGATGACACTA

Found at i:2540 original size:21 final size:21

Alignment explanation


    Indices: 2514--2555  Score: 84
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2504 TAAGGAAGAA

                                 
       2514 GTTTCAAGCTCATCGGAGTTG
          1 GTTTCAAGCTCATCGGAGTTG

                                 
       2535 GTTTCAAGCTCATCGGAGTTG
          1 GTTTCAAGCTCATCGGAGTTG

       2556 CCTAAGATGC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33


Consensus pattern (21 bp):   
GTTTCAAGCTCATCGGAGTTG

Found at i:4381 original size:11 final size:11

Alignment explanation


    Indices: 4367--4400  Score: 68
    Period size: 11  Copynumber: 3.1  Consensus size: 11

       4357 TAAAGGAAAA

                       
       4367 AGCTAGGAAGG
          1 AGCTAGGAAGG

                       
       4378 AGCTAGGAAGG
          1 AGCTAGGAAGG

                       
       4389 AGCTAGGAAGG
          1 AGCTAGGAAGG

             
       4400 A
          1 A

       4401 TCCTACTCCT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   23  1.00

ACGTcount: A:0.38, C:0.09, G:0.44, T:0.09


Consensus pattern (11 bp):   
AGCTAGGAAGG

Found at i:4794 original size:21 final size:21

Alignment explanation


    Indices: 4770--4903  Score: 200
    Period size: 21  Copynumber: 6.4  Consensus size: 21

       4760 CTTAGTCATT

                         *        
       4770 TCCAATGAGCTTGAAACCTT-C
          1 TCCAATGAGCTTGGAA-CTTGC

                    *             
       4791 TCCAATGATCTTGGAACCTT-C
          1 TCCAATGAGCTTGGAA-CTTGC

                    *        *   
       4812 TCCAATGAACTTGGAACCTGC
          1 TCCAATGAGCTTGGAACTTGC

                                 
       4833 TCCAATGAGCTTGGAACTTGC
          1 TCCAATGAGCTTGGAACTTGC

                                 
       4854 TCCAATGAGCTTGGAACTTGC
          1 TCCAATGAGCTTGGAACTTGC

                                 
       4875 TCCAATGAGCTTGGAACTTGC
          1 TCCAATGAGCTTGGAACTTGC

                    
       4896 TCCAATGA
          1 TCCAATGA

       4904 ACTTCTAGCA


Statistics
Matches: 106,  Mismatches: 6, Indels: 2
        0.93            0.05        0.02

Matches are distributed among these distances:
  20    2  0.02
  21  104  0.98

ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACTTGC

Done.