Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015845.1 Corchorus capsularis cultivar CVL-1 contig15866, 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: 12035
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34


Found at i:5826 original size:22 final size:21

Alignment explanation


    Indices: 5801--5847  Score: 78
    Period size: 20  Copynumber: 2.3  Consensus size: 21

       5791 GTCACTTACG

                *                
       5801 TTTTCCCATTTCTCTCTGCAT
          1 TTTTTCCATTTCTCTCTGCAT

                                 
       5822 TTTTT-CATTTCTCTCTGCAT
          1 TTTTTCCATTTCTCTCTGCAT

                  
       5842 TTTTTC
          1 TTTTTC

       5848 TTCAAGGAAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  20   20  0.83
  21    4  0.17

ACGTcount: A:0.09, C:0.28, G:0.04, T:0.60


Consensus pattern (21 bp):   
TTTTTCCATTTCTCTCTGCAT

Found at i:5845 original size:20 final size:20

Alignment explanation


    Indices: 5807--5847  Score: 82
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       5797 TACGTTTTCC

                                
       5807 CATTTCTCTCTGCATTTTTT
          1 CATTTCTCTCTGCATTTTTT

                                
       5827 CATTTCTCTCTGCATTTTTT
          1 CATTTCTCTCTGCATTTTTT

             
       5847 C
          1 C

       5848 TTCAAGGAAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   21  1.00

ACGTcount: A:0.10, C:0.27, G:0.05, T:0.59


Consensus pattern (20 bp):   
CATTTCTCTCTGCATTTTTT

Found at i:6172 original size:21 final size:21

Alignment explanation


    Indices: 6143--6191  Score: 73
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       6133 CCTACCTCTG

                                 
       6143 TCCA-GCCTGCAAATTCAACC
          1 TCCAGGCCTGCAAATTCAACC

                         *       
       6163 TCCAGGCCTGCAAGTTCAACC
          1 TCCAGGCCTGCAAATTCAACC

              *     
       6184 TCTAGGCC
          1 TCCAGGCC

       6192 GCTCCCTTCA


Statistics
Matches: 26,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  20    4  0.15
  21   22  0.85

ACGTcount: A:0.24, C:0.39, G:0.16, T:0.20


Consensus pattern (21 bp):   
TCCAGGCCTGCAAATTCAACC

Found at i:8655 original size:46 final size:46

Alignment explanation


    Indices: 8596--8688  Score: 186
    Period size: 46  Copynumber: 2.0  Consensus size: 46

       8586 ATAATTGTTC

                                                          
       8596 TTAATGCTTTGTTCTTGACAATTTTTAAACTGGATCAGTAATTAAT
          1 TTAATGCTTTGTTCTTGACAATTTTTAAACTGGATCAGTAATTAAT

                                                          
       8642 TTAATGCTTTGTTCTTGACAATTTTTAAACTGGATCAGTAATTAAT
          1 TTAATGCTTTGTTCTTGACAATTTTTAAACTGGATCAGTAATTAAT

             
       8688 T
          1 T

       8689 GTTTAAGAAT


Statistics
Matches: 47,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  46   47  1.00

ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46


Consensus pattern (46 bp):   
TTAATGCTTTGTTCTTGACAATTTTTAAACTGGATCAGTAATTAAT
Done.