Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009520.1 Corchorus olitorius cultivar O-4 contig09552, 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, 716

Length: 1194
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:475 original size:21 final size:21

Alignment explanation


    Indices: 445--484  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        435 CTAAAAACAG

                                 
        445 GACAAATCCTGCCCAGGACTT
          1 GACAAATCCTGCCCAGGACTT

                 *             
        466 GACAACTCCTGCCCAGGAC
          1 GACAAATCCTGCCCAGGAC

        485 CTGGTCTGTT


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:0.28, C:0.38, G:0.20, T:0.15


Consensus pattern (21 bp):   
GACAAATCCTGCCCAGGACTT

Found at i:543 original size:21 final size:21

Alignment explanation


    Indices: 517--558  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        507 AAAATACAGA

                                 
        517 ACAACTCCTGCCCAGAACTTG
          1 ACAACTCCTGCCCAGAACTTG

                           *     
        538 ACAACTCCTGCCCAGGACTTG
          1 ACAACTCCTGCCCAGAACTTG

        559 GTCAGTTGAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.26, C:0.38, G:0.17, T:0.19


Consensus pattern (21 bp):   
ACAACTCCTGCCCAGAACTTG

Found at i:567 original size:71 final size:71

Alignment explanation


    Indices: 437--630  Score: 266
    Period size: 71  Copynumber: 2.7  Consensus size: 71

        427 ATTGAAGCCT

                     *                                       *     *        *
        437 AAAA-ACAGGACAAATCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCTGTTG-AAAG
          1 AAAATACAGAACAAATCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCAGTTGAAAAA

                   
        500 ACGGAAG
         66 ACGG-AG

                          *          *                                       
        507 AAAATACAGAACAACTCCTGCCCAGAACTTGACAACTCCTGCCCAGGACTTGGTCAGTTGAAAAA
          1 AAAATACAGAACAAATCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCAGTTGAAAAA

                  
        572 ACGGAG
         66 ACGGAG

                 *  *     *     *                                
        578 AAAATTCAAAACAAGTCCTGTCCAGGACTTGGACAACTCCTGCCCAGGACTTG
          1 AAAATACAGAACAAATCCTGCCCAGGACTT-GACAACTCCTGCCCAGGACTTG

        631 TTGCGGAAAA


Statistics
Matches: 110,  Mismatches: 11, Indels: 4
        0.88            0.09        0.03

Matches are distributed among these distances:
  70    4  0.04
  71   77  0.70
  72   29  0.26

ACGTcount: A:0.34, C:0.27, G:0.21, T:0.18


Consensus pattern (71 bp):   
AAAATACAGAACAAATCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCAGTTGAAAAA
ACGGAG

Found at i:618 original size:22 final size:22

Alignment explanation


    Indices: 588--630  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        578 AAAATTCAAA

                *     *           
        588 ACAAGTCCTGTCCAGGACTTGG
          1 ACAACTCCTGCCCAGGACTTGG

                                 
        610 ACAACTCCTGCCCAGGACTTG
          1 ACAACTCCTGCCCAGGACTTG

        631 TTGCGGAAAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.23, C:0.33, G:0.23, T:0.21


Consensus pattern (22 bp):   
ACAACTCCTGCCCAGGACTTGG

Done.