Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015048.1 Corchorus olitorius cultivar O-4 contig15081, 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: 9945
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:684 original size:19 final size:18

Alignment explanation


    Indices: 660--695  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

        650 TGAAGACTTA

                               
        660 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
        679 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

        696 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:5031 original size:14 final size:15

Alignment explanation


    Indices: 5003--5046  Score: 54
    Period size: 14  Copynumber: 2.9  Consensus size: 15

       4993 CCTCAGCGCC

                            
       5003 CCAGCAGCACCAGGCA
          1 CCAGC-GCACCAGGCA

                     *     
       5019 CCAG-GCACAAGGCA
          1 CCAGCGCACCAGGCA

            *             
       5033 GCAGCGCACCAGGC
          1 CCAGCGCACCAGGC

       5047 CGTGCCAACA


Statistics
Matches: 24,  Mismatches: 3, Indels: 3
        0.80            0.10        0.10

Matches are distributed among these distances:
  14   12  0.50
  15    8  0.33
  16    4  0.17

ACGTcount: A:0.30, C:0.41, G:0.30, T:0.00


Consensus pattern (15 bp):   
CCAGCGCACCAGGCA

Found at i:6242 original size:17 final size:18

Alignment explanation


    Indices: 6220--6255  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       6210 AAAGGGTAAT

                     *        
       6220 TAAAAA-AATTGTTTTCA
          1 TAAAAATAAGTGTTTTCA

                              
       6237 TAAAAATAAGTGTTTTCA
          1 TAAAAATAAGTGTTTTCA

             
       6255 T
          1 T

       6256 GATAGAGGAG


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  17    6  0.35
  18   11  0.65

ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42


Consensus pattern (18 bp):   
TAAAAATAAGTGTTTTCA

Found at i:7116 original size:19 final size:18

Alignment explanation


    Indices: 7092--7127  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       7082 TGAAGACTTA

                               
       7092 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
       7111 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

       7128 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:8725 original size:8 final size:8

Alignment explanation


    Indices: 8714--8743  Score: 51
    Period size: 8  Copynumber: 3.6  Consensus size: 8

       8704 AATTTTTAAG

                    
       8714 ATTCAAAA
          1 ATTCAAAA

                     
       8722 ATTCCAAAA
          1 ATT-CAAAA

                    
       8731 ATTCAAAA
          1 ATTCAAAA

                 
       8739 ATTCA
          1 ATTCA

       8744 TTGTGGTTTC


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
   8   13  0.62
   9    8  0.38

ACGTcount: A:0.57, C:0.17, G:0.00, T:0.27


Consensus pattern (8 bp):   
ATTCAAAA
Done.