Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004928.1 Corchorus capsularis cultivar CVL-1 contig04946, 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: 17004
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32


Found at i:3490 original size:49 final size:49

Alignment explanation


    Indices: 3305--3476  Score: 299
    Period size: 49  Copynumber: 3.5  Consensus size: 49

       3295 ACTTGCCTTT

                   *  *   *                                  
       3305 CGTCTGGAAAAGGCATTTTGGGAAATAGCAAGTAAAGATGAATGGCTTC
          1 CGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAGATGAATGGCTTC

                           *                                 
       3354 CGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAGATGAATGGCTTC
          1 CGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAGATGAATGGCTTC

                                      *                      
       3403 CGTCTGGGAAGGGCGTTTTGGGAAATGGCAAGTAAAGATGAATGGCTTC
          1 CGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAGATGAATGGCTTC

                                     
       3452 CGTCTGGGAAGGGCGTTTTGGGAAA
          1 CGTCTGGGAAGGGCGTTTTGGGAAA

       3477 AAGTAGATAA


Statistics
Matches: 117,  Mismatches: 6, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  49  117  1.00

ACGTcount: A:0.28, C:0.13, G:0.35, T:0.24


Consensus pattern (49 bp):   
CGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAGATGAATGGCTTC

Found at i:5091 original size:20 final size:20

Alignment explanation


    Indices: 5062--5104  Score: 59
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       5052 TTTTCTTTTC

                 *            * 
       5062 TTTTCTTTTTTTGTTTTTGT
          1 TTTTCGTTTTTTGTTTTTAT

                        *       
       5082 TTTTCGTTTTTTTTTTTTAT
          1 TTTTCGTTTTTTGTTTTTAT

               
       5102 TTT
          1 TTT

       5105 CTGTAGGAGA


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.02, C:0.05, G:0.07, T:0.86


Consensus pattern (20 bp):   
TTTTCGTTTTTTGTTTTTAT

Found at i:5497 original size:22 final size:22

Alignment explanation


    Indices: 5472--5540  Score: 111
    Period size: 22  Copynumber: 3.1  Consensus size: 22

       5462 TTGACCTCTT

                      *           
       5472 GCAGGAAAGCTTTGGTGACATG
          1 GCAGGAAAGCCTTGGTGACATG

                                  
       5494 GCAGGAAAGCCTTGGTGACATG
          1 GCAGGAAAGCCTTGGTGACATG

                  *    *          
       5516 GCAGGAGAGCCCTGGTGACATG
          1 GCAGGAAAGCCTTGGTGACATG

               
       5538 GCA
          1 GCA

       5541 TGTACAGATG


Statistics
Matches: 44,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  22   44  1.00

ACGTcount: A:0.26, C:0.19, G:0.38, T:0.17


Consensus pattern (22 bp):   
GCAGGAAAGCCTTGGTGACATG

Found at i:16472 original size:16 final size:16

Alignment explanation


    Indices: 16411--16476  Score: 62
    Period size: 16  Copynumber: 4.1  Consensus size: 16

      16401 CCCAACCCAA

                             *
      16411 AAATGACACTCGAACCCA
          1 AAATGAC-C-CGAACCCG

                *       *   
      16429 AAATTACCCGAATCC-
          1 AAATGACCCGAACCCG

               *  *         
      16444 AAACGATCCGAACCCG
          1 AAATGACCCGAACCCG

                            
      16460 AAATGACCCGAACCCG
          1 AAATGACCCGAACCCG

             
      16476 A
          1 A

      16477 TCAACCCGAC


Statistics
Matches: 39,  Mismatches: 8, Indels: 4
        0.76            0.16        0.08

Matches are distributed among these distances:
  15   11  0.28
  16   21  0.54
  17    1  0.03
  18    6  0.15

ACGTcount: A:0.41, C:0.35, G:0.14, T:0.11


Consensus pattern (16 bp):   
AAATGACCCGAACCCG
Done.