Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018591.1 Corchorus olitorius cultivar O-4 contig18624, 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: 4568
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28


Found at i:499 original size:21 final size:21

Alignment explanation


    Indices: 469--508  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        459 CTAAAAACAA

                 *               
        469 GACAAGTCCTGCCCAGGACTT
          1 GACAACTCCTGCCCAGGACTT

                               
        490 GACAACTCCTGCCCAGGAC
          1 GACAACTCCTGCCCAGGAC

        509 CTGGTCTGCT


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:0.25, C:0.38, G:0.23, T:0.15


Consensus pattern (21 bp):   
GACAACTCCTGCCCAGGACTT

Found at i:567 original size:21 final size:21

Alignment explanation


    Indices: 541--582  Score: 84
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        531 AAAAATCAGA

                                 
        541 ACAACTCCTGCCCAGGACTTG
          1 ACAACTCCTGCCCAGGACTTG

                                 
        562 ACAACTCCTGCCCAGGACTTG
          1 ACAACTCCTGCCCAGGACTTG

        583 GTCTGTTGAA


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:0.24, C:0.38, G:0.19, T:0.19


Consensus pattern (21 bp):   
ACAACTCCTGCCCAGGACTTG

Found at i:593 original size:71 final size:71

Alignment explanation


    Indices: 470--654  Score: 298
    Period size: 71  Copynumber: 2.6  Consensus size: 71

        460 TAAAAACAAG

                                                   *             *           
        470 ACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCTGCTGAAAGACGGAAGAAAA
          1 ACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGCTGAAAAACGGAAGAAAA

                  
        535 ATCAGA
         66 ATCAGA

                *                                          *                 
        541 ACAACTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGGAAGAAAA
          1 ACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGCTGAAAAACGGAAGAAAA

            *     
        606 TTCAGA
         66 ATCAGA

                      * *                              
        612 ACAAGTCCTGTCAAGGACTTGGACAACTCCTGCCCAGGACTTG
          1 ACAAGTCCTGCCCAGGACTT-GACAACTCCTGCCCAGGACTTG

        655 TTGCGGAAAA


Statistics
Matches: 105,  Mismatches: 8, Indels: 1
        0.92            0.07        0.01

Matches are distributed among these distances:
  71   83  0.79
  72   22  0.21

ACGTcount: A:0.31, C:0.28, G:0.23, T:0.18


Consensus pattern (71 bp):   
ACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGCTGAAAAACGGAAGAAAA
ATCAGA

Found at i:642 original size:22 final size:22

Alignment explanation


    Indices: 612--654  Score: 59
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        602 AAAATTCAGA

                *     *           
        612 ACAAGTCCTGTCAAGGACTTGG
          1 ACAACTCCTGCCAAGGACTTGG

                        *        
        634 ACAACTCCTGCCCAGGACTTG
          1 ACAACTCCTGCCAAGGACTTG

        655 TTGCGGAAAA


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21


Consensus pattern (22 bp):   
ACAACTCCTGCCAAGGACTTGG

Found at i:2925 original size:15 final size:16

Alignment explanation


    Indices: 2901--2940  Score: 64
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       2891 AGAGGTTGAA

                 *          
       2901 AGAAAGCAATTAAAC-
          1 AGAAAACAATTAAACT

                            
       2916 AGAAAACAATTAAACT
          1 AGAAAACAATTAAACT

                     
       2932 AGAAAACAA
          1 AGAAAACAA

       2941 AGCAAAGTAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  15   14  0.61
  16    9  0.39

ACGTcount: A:0.65, C:0.12, G:0.10, T:0.12


Consensus pattern (16 bp):   
AGAAAACAATTAAACT

Done.