Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007507.1 Corchorus capsularis cultivar CVL-1 contig07528, 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: 18971
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33


Found at i:5568 original size:2 final size:2

Alignment explanation


    Indices: 5561--5595  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       5551 TGACGTCCAT

                                                                
       5561 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       5596 GCTCAAAGCC


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:7157 original size:60 final size:61

Alignment explanation


    Indices: 7082--7230  Score: 212
    Period size: 60  Copynumber: 2.5  Consensus size: 61

       7072 AATAAGGATG

                                          * *                             
       7082 TAACGTTTGTC-AAAATGCTCAAATAAGGGTCTGATCTATTAATTTGGCCAAA-TAAGAGCC
          1 TAACG-TTGTCGAAAATGCTCAAATAAGGGCCCGATCTATTAATTTGGCCAAATTAAGAGCC

                                             *   *                   *   
       7142 TAACGTTGTCGAAAATGCTCAAATAAGGGCCCGGTCTTTTAATTTGGCCAAATTAAGGGCC
          1 TAACGTTGTCGAAAATGCTCAAATAAGGGCCCGATCTATTAATTTGGCCAAATTAAGAGCC

                   *   *                
       7203 TAACGTTATCGGAAATGCTCAAATAAGG
          1 TAACGTTGTCGAAAATGCTCAAATAAGG

       7231 ACTAGGTGTC


Statistics
Matches: 80,  Mismatches: 7, Indels: 3
        0.89            0.08        0.03

Matches are distributed among these distances:
  59    5  0.06
  60   42  0.52
  61   33  0.41

ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28


Consensus pattern (61 bp):   
TAACGTTGTCGAAAATGCTCAAATAAGGGCCCGATCTATTAATTTGGCCAAATTAAGAGCC

Found at i:7401 original size:60 final size:60

Alignment explanation


    Indices: 7275--7405  Score: 156
    Period size: 60  Copynumber: 2.2  Consensus size: 60

       7265 TCGACACCAG

                      * *              * *              *              *
       7275 GCCCTTATTTGGTCAAATTAAAAGATCGGGCCCTTATTTGAGCATTTTCGATAACGTTAG
          1 GCCCTTATTTAGCCAAATTAAAAGATCAGACCCTTATTTGAGCAATTTCGATAACGTTAC

             *                            *           *            *     
       7335 GTCCTTATTTAGCCAAATTAAAAGATCAGATCCTTATTTGAGTAATTT-GATAAATGTTAC
          1 GCCCTTATTTAGCCAAATTAAAAGATCAGACCCTTATTTGAGCAATTTCGAT-AACGTTAC

                       
       7395 GCCCTTATTTA
          1 GCCCTTATTTA

       7406 AGCAATTAGC


Statistics
Matches: 59,  Mismatches: 11, Indels: 2
        0.82            0.15        0.03

Matches are distributed among these distances:
  59    3  0.05
  60   56  0.95

ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37


Consensus pattern (60 bp):   
GCCCTTATTTAGCCAAATTAAAAGATCAGACCCTTATTTGAGCAATTTCGATAACGTTAC

Found at i:10611 original size:2 final size:2

Alignment explanation


    Indices: 10553--10592  Score: 64
    Period size: 2  Copynumber: 20.0  Consensus size: 2

      10543 ATGACACATA

                                                                        
      10553 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT ACT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT

      10593 TATTTTTGTC


Statistics
Matches: 36,  Mismatches: 0, Indels: 4
        0.90            0.00        0.10

Matches are distributed among these distances:
   1    1  0.03
   2   33  0.92
   3    2  0.06

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT
Done.