Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016498.1 Corchorus capsularis cultivar CVL-1 contig16519, 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: 14542
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:6400 original size:9 final size:9

Alignment explanation


    Indices: 6386--6410  Score: 50
    Period size: 9  Copynumber: 2.8  Consensus size: 9

       6376 CCACAATCTC

                     
       6386 TAAGAACGT
          1 TAAGAACGT

                     
       6395 TAAGAACGT
          1 TAAGAACGT

                   
       6404 TAAGAAC
          1 TAAGAAC

       6411 AGATTCGTCA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   16  1.00

ACGTcount: A:0.48, C:0.12, G:0.20, T:0.20


Consensus pattern (9 bp):   
TAAGAACGT

Found at i:8381 original size:18 final size:18

Alignment explanation


    Indices: 8358--8393  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       8348 AAATTTCAAA

                              
       8358 ATGCTCGACGCGCCCAAC
          1 ATGCTCGACGCGCCCAAC

                              
       8376 ATGCTCGACGCGCCCAAC
          1 ATGCTCGACGCGCCCAAC

       8394 GCGAGTTTCC


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.22, C:0.44, G:0.22, T:0.11


Consensus pattern (18 bp):   
ATGCTCGACGCGCCCAAC

Found at i:9399 original size:62 final size:63

Alignment explanation


    Indices: 9300--9425  Score: 236
    Period size: 62  Copynumber: 2.0  Consensus size: 63

       9290 GTCTTAATTT

                                            *                              
       9300 TTTATTTTCCTTAAGTAAAAATTCGGTATACCTATTTGAATAGGTATAAACTACCAAAAACTG
          1 TTTATTTTCCTTAAGTAAAAATTCGGTATACCAATTTGAATAGGTATAAACTACCAAAAACTG

                                                                           
       9363 TTTATTTT-CTTAAGTAAAAATTCGGTATACCAATTTGAATAGGTATAAACTACCAAAAACTG
          1 TTTATTTTCCTTAAGTAAAAATTCGGTATACCAATTTGAATAGGTATAAACTACCAAAAACTG

             
       9425 T
          1 T

       9426 CTTTTATCTG


Statistics
Matches: 62,  Mismatches: 1, Indels: 1
        0.97            0.02        0.02

Matches are distributed among these distances:
  62   54  0.87
  63    8  0.13

ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37


Consensus pattern (63 bp):   
TTTATTTTCCTTAAGTAAAAATTCGGTATACCAATTTGAATAGGTATAAACTACCAAAAACTG

Found at i:13104 original size:21 final size:23

Alignment explanation


    Indices: 13060--13107  Score: 64
    Period size: 22  Copynumber: 2.2  Consensus size: 23

      13050 TGAAGTTTGC

                     *             
      13060 TTTTTTATATAAAAAATAATAGA
          1 TTTTTTATACAAAAAATAATAGA

                             *     
      13083 TTTTTTAT-CAAAAAATTA-AGA
          1 TTTTTTATACAAAAAATAATAGA

                
      13104 TTTT
          1 TTTT

      13108 AATACCCTCT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  21    7  0.30
  22    8  0.35
  23    8  0.35

ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48


Consensus pattern (23 bp):   
TTTTTTATACAAAAAATAATAGA

Found at i:13654 original size:21 final size:21

Alignment explanation


    Indices: 13610--13667  Score: 91
    Period size: 21  Copynumber: 2.8  Consensus size: 21

      13600 GGGTTAAAAG

                                 
      13610 TGAAAATATAGATATA-TGGA
          1 TGAAAATATAGATATATTGGA

                              *  
      13630 TGAAAATATAGATATATTTGA
          1 TGAAAATATAGATATATTGGA

                      *      
      13651 TGAAAATATAAATATAT
          1 TGAAAATATAGATATAT

      13668 GATGAGTTAA


Statistics
Matches: 35,  Mismatches: 2, Indels: 1
        0.92            0.05        0.03

Matches are distributed among these distances:
  20   16  0.46
  21   19  0.54

ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34


Consensus pattern (21 bp):   
TGAAAATATAGATATATTGGA
Done.