Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010737.1 Corchorus olitorius cultivar O-4 contig10769, 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: 5034
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30


Found at i:2254 original size:13 final size:13

Alignment explanation


    Indices: 2236--2262  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       2226 CTCTATAACC

                         
       2236 TCATAAATCATAT
          1 TCATAAATCATAT

                         
       2249 TCATAAATCATAT
          1 TCATAAATCATAT

             
       2262 T
          1 T

       2263 TATTATATTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41


Consensus pattern (13 bp):   
TCATAAATCATAT

Found at i:2411 original size:19 final size:18

Alignment explanation


    Indices: 2383--2418  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       2373 TTTTTAAGTA

                 *             
       2383 AAAATGTAATATATAAATT
          1 AAAATATAATAT-TAAATT

                             
       2402 AAAATATAATATTAAAT
          1 AAAATATAATATTAAAT

       2419 AATTAATAAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36


Consensus pattern (18 bp):   
AAAATATAATATTAAATT

Found at i:3164 original size:16 final size:16

Alignment explanation


    Indices: 3126--3158  Score: 50
    Period size: 15  Copynumber: 2.1  Consensus size: 16

       3116 ATACCTACCT

                             
       3126 ACAAACCAAATATACAA
          1 ACAAA-CAAATATACAA

                            
       3143 ACAAACAAAT-TACAA
          1 ACAAACAAATATACAA

             
       3158 A
          1 A

       3159 TTAAACTCAC


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  15    6  0.38
  16    5  0.31
  17    5  0.31

ACGTcount: A:0.67, C:0.21, G:0.00, T:0.12


Consensus pattern (16 bp):   
ACAAACAAATATACAA
Done.