Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016181.1 Corchorus olitorius cultivar O-4 contig16214, 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: 14702
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:267 original size:15 final size:15

Alignment explanation


    Indices: 247--277  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

        237 GAGCACACAG

                           
        247 TTCATAGAGTCTAAC
          1 TTCATAGAGTCTAAC

                           
        262 TTCATAGAGTCTAAC
          1 TTCATAGAGTCTAAC

             
        277 T
          1 T

        278 GTATATTCCA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35


Consensus pattern (15 bp):   
TTCATAGAGTCTAAC

Found at i:4917 original size:3 final size:3

Alignment explanation


    Indices: 4905--4987  Score: 159
    Period size: 3  Copynumber: 28.0  Consensus size: 3

       4895 AATTGTCACG

                                                                           
       4905 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

                                                           
       4952 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

       4988 AATTTCGAAA


Statistics
Matches: 79,  Mismatches: 0, Indels: 2
        0.98            0.00        0.02

Matches are distributed among these distances:
   2    2  0.03
   3   77  0.97

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TAT

Found at i:5313 original size:43 final size:43

Alignment explanation


    Indices: 5265--5358  Score: 170
    Period size: 43  Copynumber: 2.2  Consensus size: 43

       5255 TTTGATTGAT

                                      *                
       5265 CATTTTGACTTAATTAATAGTAATCTCTTTAAGAAAAACCGGC
          1 CATTTTGACTTAATTAATAGTAATCTATTTAAGAAAAACCGGC

                                  *                    
       5308 CATTTTGACTTAATTAATAGTAGTCTATTTAAGAAAAACCGGC
          1 CATTTTGACTTAATTAATAGTAATCTATTTAAGAAAAACCGGC

                    
       5351 CATTTTGA
          1 CATTTTGA

       5359 AAAATTGGTT


Statistics
Matches: 49,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  43   49  1.00

ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36


Consensus pattern (43 bp):   
CATTTTGACTTAATTAATAGTAATCTATTTAAGAAAAACCGGC
Done.