Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013749.1 Corchorus olitorius cultivar O-4 contig13782, 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: 31615
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35


Found at i:7641 original size:2 final size:2

Alignment explanation


    Indices: 7612--7670  Score: 82
    Period size: 2  Copynumber: 29.5  Consensus size: 2

       7602 AATTGAAAGT

                      *        *     *     *                              
       7612 TC TC TC TA TC TC TG TC TG TC TG TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                                     
       7654 TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC T

       7671 ATATATATAT


Statistics
Matches: 49,  Mismatches: 8, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
   2   49  1.00

ACGTcount: A:0.02, C:0.42, G:0.05, T:0.51


Consensus pattern (2 bp):   
TC

Found at i:7675 original size:2 final size:2

Alignment explanation


    Indices: 7670--7695  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       7660 TCTCTCTCTC

                                                  
       7670 TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA

       7696 AAGTTCATTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:15273 original size:30 final size:30

Alignment explanation


    Indices: 15207--15289  Score: 78
    Period size: 30  Copynumber: 2.7  Consensus size: 30

      15197 ATTTGAAGGG

                            *      *       
      15207 TTTAGCAAATAAGGGTTAAACGTTTTCGAGT
          1 TTTA-CAAATAAGGGTAAAACGTATTCGAGT

            *        *                     
      15238 ATTACAAATGAGGGTAAAACGTATTCGTA-T
          1 TTTACAAATAAGGGTAAAACGTATTCG-AGT

                  **      *       
      15268 TTTACAGTTAAGGGCAAAACGT
          1 TTTACAAATAAGGGTAAAACGT

      15290 TTTAAAAGCC


Statistics
Matches: 42,  Mismatches: 9, Indels: 3
        0.78            0.17        0.06

Matches are distributed among these distances:
  30   38  0.90
  31    4  0.10

ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31


Consensus pattern (30 bp):   
TTTACAAATAAGGGTAAAACGTATTCGAGT

Found at i:16997 original size:13 final size:13

Alignment explanation


    Indices: 16979--17005  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

      16969 CATCAGTACC

                         
      16979 AAAAAAAAAAGAA
          1 AAAAAAAAAAGAA

                         
      16992 AAAAAAAAAAGAA
          1 AAAAAAAAAAGAA

             
      17005 A
          1 A

      17006 GAAAGAAATC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00


Consensus pattern (13 bp):   
AAAAAAAAAAGAA
Done.