Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013386.1 Corchorus olitorius cultivar O-4 contig13419, 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: 20455
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30


Found at i:2835 original size:21 final size:21

Alignment explanation


    Indices: 2781--2838  Score: 71
    Period size: 21  Copynumber: 2.7  Consensus size: 21

       2771 CCGGCCATAC

                    *             
       2781 CCGGCCATTCACCGTGCCACCA
          1 CCGGCCATGC-CCGTGCCACCA

                ** *             
       2803 CCGGTTAAGCCCGTGCCACCA
          1 CCGGCCATGCCCGTGCCACCA

                           
       2824 CCGGCCATGCCCGTG
          1 CCGGCCATGCCCGTG

       2839 GCCGCCACAT


Statistics
Matches: 29,  Mismatches: 7, Indels: 1
        0.78            0.19        0.03

Matches are distributed among these distances:
  21   23  0.79
  22    6  0.21

ACGTcount: A:0.16, C:0.47, G:0.24, T:0.14


Consensus pattern (21 bp):   
CCGGCCATGCCCGTGCCACCA

Found at i:9981 original size:19 final size:18

Alignment explanation


    Indices: 9957--9992  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       9947 TGAAGACTTA

                               
       9957 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
       9976 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

       9993 ATTATTTCCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:15848 original size:21 final size:21

Alignment explanation


    Indices: 15814--15853  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      15804 CTTTGCATAT

                 *               
      15814 TTAATTTTAATTTTAATTTTA
          1 TTAATATTAATTTTAATTTTA

                     *         
      15835 TTAATATTATTTTTAATTT
          1 TTAATATTAATTTTAATTT

      15854 ATGAACTAAT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68


Consensus pattern (21 bp):   
TTAATATTAATTTTAATTTTA

Found at i:17811 original size:30 final size:29

Alignment explanation


    Indices: 17768--17827  Score: 95
    Period size: 30  Copynumber: 2.0  Consensus size: 29

      17758 TTAGGATTAG

                                         
      17768 TTATTTATGCTTTAATTTTCAA-TTTCTT
          1 TTATTTATGCTTTAATTTTCAAGTTTCTT

                                           
      17796 TTATCTTATGTCTTTAATTTTCAAGTTTCTT
          1 TTAT-TTATG-CTTTAATTTTCAAGTTTCTT

             
      17827 T
          1 T

      17828 AATAAACTAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 3
        0.91            0.00        0.09

Matches are distributed among these distances:
  28    4  0.14
  29    5  0.17
  30   13  0.45
  31    7  0.24

ACGTcount: A:0.20, C:0.12, G:0.05, T:0.63


Consensus pattern (29 bp):   
TTATTTATGCTTTAATTTTCAAGTTTCTT

Found at i:17828 original size:17 final size:16

Alignment explanation


    Indices: 17777--17830  Score: 58
    Period size: 14  Copynumber: 3.4  Consensus size: 16

      17767 GTTATTTATG

                            
      17777 CTTTAATTTTCAATTT
          1 CTTTAATTTTCAATTT

                *  *      * 
      17793 CTTTTATCTT--ATGT
          1 CTTTAATTTTCAATTT

                             
      17807 CTTTAATTTTCAAGTTT
          1 CTTTAATTTTCAA-TTT

                   
      17824 CTTTAAT
          1 CTTTAAT

      17831 AAACTATCTA


Statistics
Matches: 29,  Mismatches: 6, Indels: 5
        0.73            0.15        0.12

Matches are distributed among these distances:
  14   11  0.38
  16    9  0.31
  17    9  0.31

ACGTcount: A:0.22, C:0.13, G:0.04, T:0.61


Consensus pattern (16 bp):   
CTTTAATTTTCAATTT
Done.