Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018526.1 Corchorus olitorius cultivar O-4 contig18559, 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: 22196
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33


Found at i:6034 original size:6 final size:6

Alignment explanation


    Indices: 6023--6056  Score: 68
    Period size: 6  Copynumber: 5.7  Consensus size: 6

       6013 AATCTAATAT

                                                   
       6023 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAA
          1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAA

       6057 TACACAATCT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   28  1.00

ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00


Consensus pattern (6 bp):   
AGAAAA

Found at i:13607 original size:16 final size:16

Alignment explanation


    Indices: 13586--13625  Score: 73
    Period size: 15  Copynumber: 2.6  Consensus size: 16

      13576 TGTATGAAAA

                            
      13586 AAAAAAAACCTAAAGT
          1 AAAAAAAACCTAAAGT

                            
      13602 AAAAAAAA-CTAAAGT
          1 AAAAAAAACCTAAAGT

                     
      13617 AAAAAAAAC
          1 AAAAAAAAC

      13626 GAGAAAAAGT


Statistics
Matches: 23,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  15   15  0.65
  16    8  0.35

ACGTcount: A:0.75, C:0.10, G:0.05, T:0.10


Consensus pattern (16 bp):   
AAAAAAAACCTAAAGT

Found at i:17886 original size:17 final size:17

Alignment explanation


    Indices: 17866--17904  Score: 51
    Period size: 17  Copynumber: 2.3  Consensus size: 17

      17856 TTAGTAATAT

                             
      17866 TTATTGAATAATAATTA
          1 TTATTGAATAATAATTA

                 **     *    
      17883 TTATTTTATAATTATTA
          1 TTATTGAATAATAATTA

                 
      17900 TTATT
          1 TTATT

      17905 TTAGTAAATA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  17   19  1.00

ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59


Consensus pattern (17 bp):   
TTATTGAATAATAATTA

Found at i:17905 original size:17 final size:17

Alignment explanation


    Indices: 17873--17907  Score: 61
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      17863 TATTTATTGA

                             
      17873 ATAATAATTATTATTTT
          1 ATAATAATTATTATTTT

                 *           
      17890 ATAATTATTATTATTTT
          1 ATAATAATTATTATTTT

             
      17907 A
          1 A

      17908 GTAAATAATG


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60


Consensus pattern (17 bp):   
ATAATAATTATTATTTT

Found at i:20195 original size:2 final size:2

Alignment explanation


    Indices: 20188--20224  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

      20178 TACTATTTAG

                                                                   
      20188 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      20225 GCCTTTGTGA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:21083 original size:45 final size:45

Alignment explanation


    Indices: 21032--21161  Score: 242
    Period size: 45  Copynumber: 2.9  Consensus size: 45

      21022 CTAAATTCTA

                                                *        
      21032 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATGTTATACTC
          1 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTC

                                                         
      21077 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTC
          1 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTC

              *                                     
      21122 CTTCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
          1 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA

      21162 GTTGTTGCTT


Statistics
Matches: 83,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  45   83  1.00

ACGTcount: A:0.38, C:0.21, G:0.08, T:0.34


Consensus pattern (45 bp):   
CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTC

Found at i:22175 original size:1 final size:1

Alignment explanation


    Indices: 22171--22196  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

      22161 AGAAATTCAG

                                      
      22171 AAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Done.