Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001990.1 Corchorus olitorius cultivar O-4 contig01990, 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: 3130
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:1978 original size:3 final size:3

Alignment explanation


    Indices: 1963--2018  Score: 51
    Period size: 3  Copynumber: 17.7  Consensus size: 3

       1953 TGGCTTTTAG

                                       *   *                              
       1963 ATT ATT ATAT ATT ATT ATAT AAT AAT ATT ATT ATAT ATT ATT A-T ATT
          1 ATT ATT AT-T ATT ATT AT-T ATT ATT ATT ATT AT-T ATT ATT ATT ATT

                       
       2010 ATAT ATT AT
          1 AT-T ATT AT

       2019 ATAATATATA


Statistics
Matches: 46,  Mismatches: 2, Indels: 10
        0.79            0.03        0.17

Matches are distributed among these distances:
   2    2  0.04
   3   33  0.72
   4   11  0.24

ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57


Consensus pattern (3 bp):   
ATT

Found at i:1978 original size:10 final size:10

Alignment explanation


    Indices: 1963--2030  Score: 74
    Period size: 10  Copynumber: 7.1  Consensus size: 10

       1953 TGGCTTTTAG

                      
       1963 ATTATTATAT
          1 ATTATTATAT

                      
       1973 ATTATTATAT
          1 ATTATTATAT

                      
       1983 A--A-TA-AT
          1 ATTATTATAT

                      
       1989 ATTATTATAT
          1 ATTATTATAT

                       
       1999 ATTATTATATT
          1 ATTATTATA-T

                       
       2010 ATATATTATAT
          1 AT-TATTATAT

             *        
       2021 AATA-TATAT
          1 ATTATTATAT

             
       2030 A
          1 A

       2031 ATTAATTAGG


Statistics
Matches: 51,  Mismatches: 1, Indels: 13
        0.78            0.02        0.20

Matches are distributed among these distances:
   6    3  0.06
   7    2  0.04
   8    2  0.04
   9    8  0.16
  10   24  0.47
  11    5  0.10
  12    7  0.14

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (10 bp):   
ATTATTATAT

Found at i:1998 original size:26 final size:25

Alignment explanation


    Indices: 1963--2032  Score: 94
    Period size: 26  Copynumber: 2.9  Consensus size: 25

       1953 TGGCTTTTAG

                                      
       1963 ATTATTATATATTATTATATAATAAT
          1 ATTATTATATATTATTATATAAT-AT

                                     
       1989 ATTATTATATATTATTATAT--TAT
          1 ATTATTATATATTATTATATAATAT

                       *           
       2012 A-TATTATATAATA-TATATAAT
          1 ATTATTATATATTATTATATAAT

       2033 TAATTAGGAT


Statistics
Matches: 41,  Mismatches: 1, Indels: 7
        0.84            0.02        0.14

Matches are distributed among these distances:
  21    5  0.12
  22   11  0.27
  23    4  0.10
  24    1  0.02
  26   20  0.49

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (25 bp):   
ATTATTATATATTATTATATAATAT

Found at i:2270 original size:2 final size:2

Alignment explanation


    Indices: 2263--2289  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       2253 ACCAGGCTTT

                                                    
       2263 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

       2290 TAGCTTGGTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.