Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012860.1 Corchorus olitorius cultivar O-4 contig12893, 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: 6129
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:557 original size:31 final size:28

Alignment explanation


    Indices: 519--575  Score: 78
    Period size: 31  Copynumber: 1.9  Consensus size: 28

        509 GTCGTTTTGA

                        *                  
        519 AAAAAAAAAATTGTTTTGTGTTTTTGCGTCG
          1 AAAAAAAAAA-TCTTTT-TG-TTTTGCGTCG

                                      
        550 AAAAAAAAAATCTTTTTGTTTTGCGT
          1 AAAAAAAAAATCTTTTTGTTTTGCGT

        576 TTTTAATTTT


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  28    8  0.32
  29    2  0.08
  30    5  0.20
  31   10  0.40

ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42


Consensus pattern (28 bp):   
AAAAAAAAAATCTTTTTGTTTTGCGTCG

Found at i:642 original size:30 final size:30

Alignment explanation


    Indices: 604--673  Score: 90
    Period size: 29  Copynumber: 2.3  Consensus size: 30

        594 CCTGCGTCAC

                     *                    
        604 AAAAAAAAAGAGTTT-TTGCGT-TTTATAA
          1 AAAAAAAAAAAGTTTGTTGCGTATTTATAA

                                           *
        632 AAATAAAAAAAAGTTTGTTGCGTCATTTATAT
          1 AAA-AAAAAAAAGTTTGTTGCGT-ATTTATAA

                      
        664 AAAAAAAAAA
          1 AAAAAAAAAA

        674 TTCTGCGTCT


Statistics
Matches: 36,  Mismatches: 2, Indels: 5
        0.84            0.05        0.12

Matches are distributed among these distances:
  28    3  0.08
  29   11  0.31
  30    6  0.17
  31    7  0.19
  32    9  0.25

ACGTcount: A:0.53, C:0.04, G:0.11, T:0.31


Consensus pattern (30 bp):   
AAAAAAAAAAAGTTTGTTGCGTATTTATAA

Found at i:3078 original size:42 final size:42

Alignment explanation


    Indices: 3011--3101  Score: 119
    Period size: 42  Copynumber: 2.2  Consensus size: 42

       3001 CGAGTATCAC

                           *                * *   *   
       3011 GCCCGGCCATGCCCGGCACCACAAGCCTCAGCTGCGCCTCAT
          1 GCCCGGCCATGCCCGCCACCACAAGCCTCAGCCGAGCCACAT

                              * *         *           
       3053 GCCCGGCCATGCCCGCCATCTCAAGCCTCATCCGAGCCACAT
          1 GCCCGGCCATGCCCGCCACCACAAGCCTCAGCCGAGCCACAT

                   
       3095 GCCCGGC
          1 GCCCGGC

       3102 TAGGACCGGC


Statistics
Matches: 42,  Mismatches: 7, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  42   42  1.00

ACGTcount: A:0.16, C:0.48, G:0.23, T:0.12


Consensus pattern (42 bp):   
GCCCGGCCATGCCCGCCACCACAAGCCTCAGCCGAGCCACAT

Found at i:5074 original size:11 final size:11

Alignment explanation


    Indices: 5058--5105  Score: 50
    Period size: 11  Copynumber: 4.7  Consensus size: 11

       5048 GAAGTTCGTG

                       
       5058 TTTGAAGACCA
          1 TTTGAAGACCA

                    ** 
       5069 TTTGAAGATAA
          1 TTTGAAGACCA

                       
       5080 TTTGAAGA-C-
          1 TTTGAAGACCA

                       
       5089 -TTGAAGACCA
          1 TTTGAAGACCA

                    
       5099 -TTGAAGA
          1 TTTGAAGA

       5106 TTTATTTCAA


Statistics
Matches: 32,  Mismatches: 3, Indels: 5
        0.80            0.08        0.12

Matches are distributed among these distances:
   8    7  0.22
   9    1  0.03
  10    7  0.22
  11   17  0.53

ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29


Consensus pattern (11 bp):   
TTTGAAGACCA
Done.