Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011154.1 Corchorus olitorius cultivar O-4 contig11187, 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: 6860
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32


Found at i:560 original size:9 final size:9

Alignment explanation


    Indices: 546--587  Score: 66
    Period size: 9  Copynumber: 4.6  Consensus size: 9

        536 ACCTCCTATA

                     
        546 ACATACCTC
          1 ACATACCTC

                     
        555 ACATACCTC
          1 ACATACCTC

                  *  
        564 ACATACTTC
          1 ACATACCTC

                      
        573 ACATACCTTC
          1 ACATACC-TC

                 
        583 ACATA
          1 ACATA

        588 ATTCTCTTTA


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
   9   23  0.77
  10    7  0.23

ACGTcount: A:0.36, C:0.38, G:0.00, T:0.26


Consensus pattern (9 bp):   
ACATACCTC

Found at i:1408 original size:15 final size:16

Alignment explanation


    Indices: 1375--1414  Score: 64
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       1365 TTACTTTGCT

                            
       1375 TTGTTTTCTAGTATAA
          1 TTGTTTTCTAGTATAA

                        *   
       1391 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTATAA

                     
       1406 TTGTTTTCT
          1 TTGTTTTCT

       1415 TTCAACCTCT


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  15   14  0.61
  16    9  0.39

ACGTcount: A:0.15, C:0.07, G:0.12, T:0.65


Consensus pattern (16 bp):   
TTGTTTTCTAGTATAA

Found at i:5123 original size:21 final size:21

Alignment explanation


    Indices: 5068--5126  Score: 64
    Period size: 21  Copynumber: 2.8  Consensus size: 21

       5058 CAAAGCCATT

                     *      *     
       5068 ACCGGCCATTCACCGTACCACC
          1 ACCGGCCATGC-CCGTGCCACC

                 ** *            
       5090 ACCGGTTAAGCCCGTGCCACC
          1 ACCGGCCATGCCCGTGCCACC

                            
       5111 ACCGGCCATGCCCGTG
          1 ACCGGCCATGCCCGTG

       5127 TCATCACCAT


Statistics
Matches: 29,  Mismatches: 8, Indels: 1
        0.76            0.21        0.03

Matches are distributed among these distances:
  21   22  0.76
  22    7  0.24

ACGTcount: A:0.19, C:0.46, G:0.22, T:0.14


Consensus pattern (21 bp):   
ACCGGCCATGCCCGTGCCACC
Done.