Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013579.1 Corchorus capsularis cultivar CVL-1 contig13600, 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: 12037
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24


Found at i:121 original size:38 final size:38

Alignment explanation


    Indices: 43--124  Score: 107
    Period size: 38  Copynumber: 2.2  Consensus size: 38

         33 TTCAAATCGC

                                      *         * 
         43 AAAACT-TTTTTTTTTTGAGAAAAAATCGGAAAAAGGA
          1 AAAACTATTTTTTTTTTGAGAAAAAAACGGAAAAAGCA

                                                    
         80 AAAACTATTTTTTTTTT-AGAAAAGAAAACGGAAAAA-CA
          1 AAAACTATTTTTTTTTTGAG-AAA-AAAACGGAAAAAGCA

                   
        118 AAAACTA
          1 AAAACTA

        125 ATTCTTGGAT


Statistics
Matches: 40,  Mismatches: 2, Indels: 5
        0.85            0.04        0.11

Matches are distributed among these distances:
  37    8  0.20
  38   21  0.52
  39   11  0.28

ACGTcount: A:0.51, C:0.07, G:0.12, T:0.29


Consensus pattern (38 bp):   
AAAACTATTTTTTTTTTGAGAAAAAAACGGAAAAAGCA

Found at i:3687 original size:75 final size:75

Alignment explanation


    Indices: 3559--3822  Score: 429
    Period size: 75  Copynumber: 3.5  Consensus size: 75

       3549 TCCTGAGCAA

                       *                             *      *            *   
       3559 AACTCTAAGCGTGGTCGAACGTCCAAGCAGACGTCACCCGCGGACGGCCGAGCACCTAGACCGGT
          1 AACTCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCACCTAGACTGGT

                      
       3624 GCCCCCGTAT
         66 GCCCCCGTAT

                                                                             
       3634 AACTCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCACCTAGACTGGT
          1 AACTCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCACCTAGACTGGT

                      
       3699 GCCCCCGTAT
         66 GCCCCCGTAT

                          *                   *               *              
       3709 AACTCTAAGCGAGGCCGAACGTCCAAGCAGACGTAACCCGCAGACGGCTGTGCACCTAGACTGGT
          1 AACTCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCACCTAGACTGGT

                      
       3774 GCCCCCGTAT
         66 GCCCCCGTAT

                 *      *             *       *    
       3784 AACTCCAAGCGAAGTCGAACGTCCAAACAGACGTTACCC
          1 AACTCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCC

       3823 ACAGGAGTCC


Statistics
Matches: 177,  Mismatches: 12, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  75  177  1.00

ACGTcount: A:0.26, C:0.34, G:0.26, T:0.14


Consensus pattern (75 bp):   
AACTCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCACCTAGACTGGT
GCCCCCGTAT

Found at i:4529 original size:26 final size:25

Alignment explanation


    Indices: 4486--4535  Score: 75
    Period size: 26  Copynumber: 2.0  Consensus size: 25

       4476 AAAAACAATT

                                     
       4486 ATAAAGAAAACAATTAAA-CTAAAA
          1 ATAAAGAAAACAATTAAATCTAAAA

                                      
       4510 ATAAAGCAAAACAAATTAAATCTAAA
          1 ATAAAG-AAAAC-AATTAAATCTAAA

       4536 TCTAAATCTA


Statistics
Matches: 23,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  24    6  0.26
  25    5  0.22
  26    7  0.30
  27    5  0.22

ACGTcount: A:0.68, C:0.10, G:0.04, T:0.18


Consensus pattern (25 bp):   
ATAAAGAAAACAATTAAATCTAAAA

Found at i:11954 original size:2 final size:2

Alignment explanation


    Indices: 11947--11985  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      11937 CAACACAACC

                                                                      
      11947 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      11986 CAATAAGATA


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

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


Consensus pattern (2 bp):   
AT

Done.