Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002157.1 Corchorus capsularis cultivar CVL-1 contig02161, 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, 685

Length: 1143
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27


Found at i:437 original size:18 final size:18

Alignment explanation


    Indices: 414--449  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

        404 AAAACTCAAA

                              
        414 AAGAATACTTGCCTAAAC
          1 AAGAATACTTGCCTAAAC

                              
        432 AAGAATACTTGCCTAAAC
          1 AAGAATACTTGCCTAAAC

        450 TATATGATCC


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


Consensus pattern (18 bp):   
AAGAATACTTGCCTAAAC

Found at i:958 original size:27 final size:27

Alignment explanation


    Indices: 928--1037  Score: 139
    Period size: 27  Copynumber: 4.0  Consensus size: 27

        918 TAGTGATTTT

                      * * *            
        928 TACTTATACTCATAGCGATGATACCGA
          1 TACTTATACTAAAACCGATGATACCGA

                *       *   * * *      
        955 TACTAATACTAATACCAAGGGTACCGA
          1 TACTTATACTAAAACCGATGATACCGA

                                       
        982 TACTTATACTAAAACCGATGATACCGA
          1 TACTTATACTAAAACCGATGATACCGA

                                        
       1009 TACTTATACTAAAAACCGATGATACCGA
          1 TACTTATACT-AAAACCGATGATACCGA

             
       1037 T
          1 T

       1038 GAGACCGATG


Statistics
Matches: 71,  Mismatches: 11, Indels: 1
        0.86            0.13        0.01

Matches are distributed among these distances:
  27   53  0.75
  28   18  0.25

ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26


Consensus pattern (27 bp):   
TACTTATACTAAAACCGATGATACCGA

Found at i:1037 original size:9 final size:9

Alignment explanation


    Indices: 1023--1067  Score: 63
    Period size: 9  Copynumber: 4.9  Consensus size: 9

       1013 TATACTAAAA

                     
       1023 ACCGATGAT
          1 ACCGATGAT

                    *
       1032 ACCGATGAG
          1 ACCGATGAT

                     
       1041 ACCGATGAT
          1 ACCGATGAT

                      
       1050 ACCGATGAAT
          1 ACCGATG-AT

               *    
       1060 ACCAATGA
          1 ACCGATGA

       1068 GCCTAAGGAC


Statistics
Matches: 32,  Mismatches: 3, Indels: 2
        0.86            0.08        0.05

Matches are distributed among these distances:
   9   24  0.75
  10    8  0.25

ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18


Consensus pattern (9 bp):   
ACCGATGAT

Found at i:1046 original size:18 final size:18

Alignment explanation


    Indices: 1023--1057  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       1013 TATACTAAAA

                              
       1023 ACCGATGATACCGATGAG
          1 ACCGATGATACCGATGAG

                             
       1041 ACCGATGATACCGATGA
          1 ACCGATGATACCGATGA

       1058 ATACCAATGA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17


Consensus pattern (18 bp):   
ACCGATGATACCGATGAG
Done.