Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008820.1 Corchorus capsularis cultivar CVL-1 contig08841, 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: 27062
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:21773 original size:19 final size:19

Alignment explanation


    Indices: 21745--21792  Score: 71
    Period size: 19  Copynumber: 2.5  Consensus size: 19

      21735 AATTAATTGT

                               
      21745 TTTAATATTATATTTTTA-
          1 TTTAATATTATATTTTTAC

                                
      21763 TTTATATATTATATTTTTAC
          1 TTTA-ATATTATATTTTTAC

                 *    
      21783 TTTAAAATTA
          1 TTTAATATTA

      21793 CTCATAATCA


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  18    4  0.15
  19   19  0.70
  20    4  0.15

ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62


Consensus pattern (19 bp):   
TTTAATATTATATTTTTAC

Found at i:22904 original size:31 final size:31

Alignment explanation


    Indices: 22866--22929  Score: 110
    Period size: 31  Copynumber: 2.1  Consensus size: 31

      22856 TCTTTATCAT

                             *             
      22866 GGTTTCCTTTCTAAGCAGTTTACGCTTTGGA
          1 GGTTTCCTTTCTAAGCAATTTACGCTTTGGA

                           *               
      22897 GGTTTCCTTTCTAAGTAATTTACGCTTTGGA
          1 GGTTTCCTTTCTAAGCAATTTACGCTTTGGA

              
      22928 GG
          1 GG

      22930 AGATATCGGT


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  31   31  1.00

ACGTcount: A:0.17, C:0.17, G:0.23, T:0.42


Consensus pattern (31 bp):   
GGTTTCCTTTCTAAGCAATTTACGCTTTGGA

Found at i:23058 original size:41 final size:41

Alignment explanation


    Indices: 22990--23076  Score: 120
    Period size: 41  Copynumber: 2.1  Consensus size: 41

      22980 CTCAAACTTG

                *                 *                  
      22990 ACCCTCCTAATAATTAAGAAAATAAATTAAATTCAGGTTTA
          1 ACCCCCCTAATAATTAAGAAAAGAAATTAAATTCAGGTTTA

            *                 **                *    
      23031 GCCCCCCTAATAATTAAGGTAAGAAATTAAATTCAGTTTTA
          1 ACCCCCCTAATAATTAAGAAAAGAAATTAAATTCAGGTTTA

                 
      23072 ACCCC
          1 ACCCC

      23077 TAGTTATAAA


Statistics
Matches: 39,  Mismatches: 7, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  41   39  1.00

ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30


Consensus pattern (41 bp):   
ACCCCCCTAATAATTAAGAAAAGAAATTAAATTCAGGTTTA

Found at i:25538 original size:20 final size:21

Alignment explanation


    Indices: 25505--25543  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 21

      25495 AAAAAAAACT

                 *               
      25505 CATAATTAAATAAA-TAAAGA
          1 CATAAATAAATAAACTAAAGA

                     *         
      25525 CATAAATAATTAAACTAAA
          1 CATAAATAAATAAACTAAA

      25544 ATCTATTAAG


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  20   12  0.75
  21    4  0.25

ACGTcount: A:0.64, C:0.08, G:0.03, T:0.26


Consensus pattern (21 bp):   
CATAAATAAATAAACTAAAGA

Found at i:27054 original size:33 final size:33

Alignment explanation


    Indices: 26982--27054  Score: 85
    Period size: 33  Copynumber: 2.2  Consensus size: 33

      26972 AAAATTGCTC

                     * *   *                 
      26982 ATGCCGCCCTAGGGGGGCGGCTGAGCCATGGTA
          1 ATGCCGCCCCAAGGGAGCGGCTGAGCCATGGTA

            **                                
      27015 GGGCCGCCCCAAGGGAGCGGCCTG-GCCATGGTA
          1 ATGCCGCCCCAAGGGAGCGG-CTGAGCCATGGTA

                   
      27048 ATGCCGC
          1 ATGCCGC

      27055 ACCAGGGG


Statistics
Matches: 32,  Mismatches: 7, Indels: 2
        0.78            0.17        0.05

Matches are distributed among these distances:
  33   29  0.91
  34    3  0.09

ACGTcount: A:0.15, C:0.32, G:0.41, T:0.12


Consensus pattern (33 bp):   
ATGCCGCCCCAAGGGAGCGGCTGAGCCATGGTA
Done.