Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015437.1 Corchorus olitorius cultivar O-4 contig15470, 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: 5745
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34


Found at i:501 original size:21 final size:23

Alignment explanation


    Indices: 459--503  Score: 58
    Period size: 21  Copynumber: 2.0  Consensus size: 23

        449 CAACACACAA

                                   
        459 TTTATATATATATATATGTTAAT
          1 TTTATATATATATATATGTTAAT

                           * *     
        482 TTTA-ATAT-TATATGTTTTAAT
          1 TTTATATATATATATATGTTAAT

             
        503 T
          1 T

        504 AATTTATAAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  21   12  0.60
  22    4  0.20
  23    4  0.20

ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60


Consensus pattern (23 bp):   
TTTATATATATATATATGTTAAT

Found at i:1788 original size:5 final size:5

Alignment explanation


    Indices: 1772--1809  Score: 51
    Period size: 5  Copynumber: 7.6  Consensus size: 5

       1762 TTACCTATTC

                                                  *       
       1772 ATAAA A-AAA ATAAA ATAAAA ATAAA ATAAA AAAAA ATA
          1 ATAAA ATAAA ATAAA AT-AAA ATAAA ATAAA ATAAA ATA

       1810 TCAGCTCTTT


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
   4    4  0.14
   5   20  0.69
   6    5  0.17

ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16


Consensus pattern (5 bp):   
ATAAA

Found at i:1793 original size:11 final size:11

Alignment explanation


    Indices: 1777--1809  Score: 59
    Period size: 11  Copynumber: 3.1  Consensus size: 11

       1767 TATTCATAAA

                       
       1777 AAAAATAAAAT
          1 AAAAATAAAAT

                       
       1788 AAAAATAAAAT
          1 AAAAATAAAAT

                       
       1799 AAAAA-AAAAT
          1 AAAAATAAAAT

             
       1809 A
          1 A

       1810 TCAGCTCTTT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  10    6  0.27
  11   16  0.73

ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15


Consensus pattern (11 bp):   
AAAAATAAAAT
Done.