Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020180.1 Corchorus olitorius cultivar O-4 contig20213, 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: 10654
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34


Found at i:832 original size:60 final size:61

Alignment explanation


    Indices: 768--887  Score: 170
    Period size: 61  Copynumber: 2.0  Consensus size: 61

        758 ATTTCTAAAA

                      *                                  * *             
        768 GTTGGATCCTTATTTGAGC-TTTTTTTTTCTTTGGACACTTATTTGAGCACTTTCGCAAAT
          1 GTTGGATCCTGATTTGAGCATTTTTTTTTCTTTGGACACTTATTTAAACACTTTCGCAAAT

                 *                             * *            *         
        828 GTTGGGTCCTGATTTGAGCATTTTTTTTTCTTTGGGCCCTTATTTAAACATTTTCGCAAA
          1 GTTGGATCCTGATTTGAGCATTTTTTTTTCTTTGGACACTTATTTAAACACTTTCGCAAA

        888 GGGCACTTTT


Statistics
Matches: 52,  Mismatches: 7, Indels: 1
        0.87            0.12        0.02

Matches are distributed among these distances:
  60   17  0.33
  61   35  0.67

ACGTcount: A:0.18, C:0.17, G:0.17, T:0.47


Consensus pattern (61 bp):   
GTTGGATCCTGATTTGAGCATTTTTTTTTCTTTGGACACTTATTTAAACACTTTCGCAAAT

Found at i:2665 original size:73 final size:73

Alignment explanation


    Indices: 2577--2713  Score: 202
    Period size: 73  Copynumber: 1.9  Consensus size: 73

       2567 ACAGCAGGGG

                *                                                  *         
       2577 CAAGGATTCTTTTATATACATGCACTTCAAATGAAAAAAAAGGAAAATTTATAATTTGGCCCCCC
          1 CAAGAATTCTTTTATATACATGCACTTCAAATGAAAAAAAAGGAAAATTTATAATATGGCCCCCC

                    
       2642 CAAATTGC
         66 CAAATTGC

                              *     *     *        **                  *    
       2650 CAAGAATTCTTTTATATATATGCATTTCAACTGAAAAAACTGGAAAATTTATAATATGGTCCCC
          1 CAAGAATTCTTTTATATACATGCACTTCAAATGAAAAAAAAGGAAAATTTATAATATGGCCCCC

       2714 TAAAAATTTA


Statistics
Matches: 56,  Mismatches: 8, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  73   56  1.00

ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31


Consensus pattern (73 bp):   
CAAGAATTCTTTTATATACATGCACTTCAAATGAAAAAAAAGGAAAATTTATAATATGGCCCCCC
CAAATTGC

Found at i:4914 original size:15 final size:15

Alignment explanation


    Indices: 4895--4932  Score: 53
    Period size: 14  Copynumber: 2.7  Consensus size: 15

       4885 TCAAAACATA

                           
       4895 ATTTTT-TAAAATTT
          1 ATTTTTATAAAATTT

                     *     
       4909 ATTTTTATATAATTT
          1 ATTTTTATAAAATTT

                      
       4924 A-TTTTATAA
          1 ATTTTTATAA

       4933 TTAAAGATCA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  14   13  0.62
  15    8  0.38

ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63


Consensus pattern (15 bp):   
ATTTTTATAAAATTT
Done.