Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015897.1 Corchorus capsularis cultivar CVL-1 contig15918, 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: 6176
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31


Found at i:5730 original size:12 final size:12

Alignment explanation


    Indices: 5713--5737  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       5703 AAAAAGTCAT

                        
       5713 GGTTTTCAAAAA
          1 GGTTTTCAAAAA

                        
       5725 GGTTTTCAAAAA
          1 GGTTTTCAAAAA

             
       5737 G
          1 G

       5738 AGTCATGGTT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32


Consensus pattern (12 bp):   
GGTTTTCAAAAA

Found at i:5732 original size:31 final size:31

Alignment explanation


    Indices: 5694--5761  Score: 111
    Period size: 31  Copynumber: 2.2  Consensus size: 31

       5684 AAGCAACGAT

                                            
       5694 GGTTTTCAAAAAAAGTCATGGTTTT-CAAAAA
          1 GGTTTTCAAAAAAAGTCATGGTTTTGC-AAAA

                        *                  
       5725 GGTTTTCAAAAAGAGTCATGGTTTTGCAAAA
          1 GGTTTTCAAAAAAAGTCATGGTTTTGCAAAA

                  
       5756 GGTTTT
          1 GGTTTT

       5762 GATAAAATGG


Statistics
Matches: 35,  Mismatches: 1, Indels: 2
        0.92            0.03        0.05

Matches are distributed among these distances:
  31   34  0.97
  32    1  0.03

ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35


Consensus pattern (31 bp):   
GGTTTTCAAAAAAAGTCATGGTTTTGCAAAA

Found at i:5749 original size:19 final size:18

Alignment explanation


    Indices: 5692--5755  Score: 59
    Period size: 19  Copynumber: 3.7  Consensus size: 18

       5682 AAAAGCAACG

                               
       5692 ATGGTTTTCAAAAAAAGTC
          1 ATGGTTTTC-AAAAAAGTC

                              
       5711 ATGGTTTTC--AAAA---
          1 ATGGTTTTCAAAAAAGTC

                               
       5724 A-GGTTTTCAAAAAGAGTC
          1 ATGGTTTTCAAAAA-AGTC

                          
       5742 ATGGTTTTGCAAAA
          1 ATGGTTTT-CAAAA

       5756 GGTTTTGATA


Statistics
Matches: 37,  Mismatches: 0, Indels: 15
        0.71            0.00        0.29

Matches are distributed among these distances:
  12    7  0.19
  13    1  0.03
  14    3  0.08
  15    1  0.03
  16    4  0.11
  18    1  0.03
  19   15  0.41
  20    5  0.14

ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33


Consensus pattern (18 bp):   
ATGGTTTTCAAAAAAGTC

Found at i:5806 original size:45 final size:45

Alignment explanation


    Indices: 5727--5872  Score: 256
    Period size: 45  Copynumber: 3.2  Consensus size: 45

       5717 TTCAAAAAGG

                                                          
       5727 TTTTCAAAAAGAGTCATGGTTTTGCAAAAGGTTTTGATAAAATGGT
          1 TTTTCAAAAAGAGTCATGGTTTT-CAAAAGGTTTTGATAAAATGGT

                                       *                 
       5773 TTTTCAAAAAGAGTCATGGTTTTCAAAGGGTTTTGATAAAATGGT
          1 TTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGGT

                                                       * 
       5818 TTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGAT
          1 TTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGGT

               *      
       5863 TTTCCAAAAA
          1 TTTTCAAAAA

       5873 TGATTTCAAA


Statistics
Matches: 96,  Mismatches: 4, Indels: 1
        0.95            0.04        0.01

Matches are distributed among these distances:
  45   73  0.76
  46   23  0.24

ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37


Consensus pattern (45 bp):   
TTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGGT
Done.