Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018186.1 Corchorus olitorius cultivar O-4 contig18219, 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: 17383
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30


Found at i:11 original size:2 final size:2

Alignment explanation


    Indices: 5--40  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

          1 GTAA

                                                                 
          5 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

         41 GCTTGTTCAA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:1363 original size:19 final size:18

Alignment explanation


    Indices: 1336--1377  Score: 57
    Period size: 19  Copynumber: 2.3  Consensus size: 18

       1326 TGAGTAATTT

                *             
       1336 TTAAGTAAAAATATAATA
          1 TTAAATAAAAATATAATA

                         *     
       1354 TATAAATAAAAATTTAATA
          1 T-TAAATAAAAATATAATA

                 
       1373 TTAAA
          1 TTAAA

       1378 ATAATTAATT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  18    5  0.24
  19   16  0.76

ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36


Consensus pattern (18 bp):   
TTAAATAAAAATATAATA

Found at i:1381 original size:19 final size:19

Alignment explanation


    Indices: 1341--1377  Score: 58
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       1331 AATTTTTAAG

                               
       1341 TAAAAATATAATATATAAA
          1 TAAAAATATAATATATAAA

                   *           
       1360 TAAAAATTTAATAT-TAAA
          1 TAAAAATATAATATATAAA

       1378 ATAATTAATT


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

Matches are distributed among these distances:
  18    4  0.24
  19   13  0.76

ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35


Consensus pattern (19 bp):   
TAAAAATATAATATATAAA

Found at i:5023 original size:18 final size:18

Alignment explanation


    Indices: 5000--5035  Score: 54
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       4990 CATCCCCACG

                    *         
       5000 ATACCCAGGTTCACTCCC
          1 ATACCCAGATTCACTCCC

                         *    
       5018 ATACCCAGATTCATTCCC
          1 ATACCCAGATTCACTCCC

       5036 TTGAGCATCA


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

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.25, C:0.42, G:0.08, T:0.25


Consensus pattern (18 bp):   
ATACCCAGATTCACTCCC

Found at i:6118 original size:20 final size:20

Alignment explanation


    Indices: 6090--6131  Score: 66
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       6080 AATTTAGTAG

                *           *   
       6090 ATGATATTGGAGATTTGACA
          1 ATGAAATTGGAGATTTCACA

                                
       6110 ATGAAATTGGAGATTTCACA
          1 ATGAAATTGGAGATTTCACA

              
       6130 AT
          1 AT

       6132 TTATGAATCA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.38, C:0.07, G:0.21, T:0.33


Consensus pattern (20 bp):   
ATGAAATTGGAGATTTCACA

Found at i:15716 original size:48 final size:48

Alignment explanation


    Indices: 15645--15741  Score: 194
    Period size: 48  Copynumber: 2.0  Consensus size: 48

      15635 CTATTGACAA

                                                            
      15645 TGGAGCTTGTTTGATGCTTCTCTATAACCCCCGCCCCAATTGCATATC
          1 TGGAGCTTGTTTGATGCTTCTCTATAACCCCCGCCCCAATTGCATATC

                                                            
      15693 TGGAGCTTGTTTGATGCTTCTCTATAACCCCCGCCCCAATTGCATATC
          1 TGGAGCTTGTTTGATGCTTCTCTATAACCCCCGCCCCAATTGCATATC

             
      15741 T
          1 T

      15742 CATATTCAAT


Statistics
Matches: 49,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  48   49  1.00

ACGTcount: A:0.19, C:0.31, G:0.16, T:0.34


Consensus pattern (48 bp):   
TGGAGCTTGTTTGATGCTTCTCTATAACCCCCGCCCCAATTGCATATC
Done.