Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024183.1 Corchorus olitorius cultivar O-4 contig24216, 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: 8510
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32


Found at i:6248 original size:2 final size:2

Alignment explanation


    Indices: 6243--6279  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       6233 GCTCTCTACT

                                                                   
       6243 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

       6280 TAGTATTACT


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:7125 original size:5 final size:5

Alignment explanation


    Indices: 7076--7104  Score: 58
    Period size: 5  Copynumber: 5.8  Consensus size: 5

       7066 GCAAAAGAGC

                                              
       7076 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
          1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT

       7105 TGTTAGAACT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   24  1.00

ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83


Consensus pattern (5 bp):   
TTTTA

Found at i:7277 original size:19 final size:19

Alignment explanation


    Indices: 7235--7282  Score: 55
    Period size: 19  Copynumber: 2.6  Consensus size: 19

       7225 CATATAGGAG

                       * *     
       7235 TATATCATA-ATCGTAACA
          1 TATATCATATAACATAACA

                                
       7253 TCATATCATATAACATAACA
          1 T-ATATCATATAACATAACA

                       
       7273 TATAT-ATATA
          1 TATATCATATA

       7283 TATATATATA


Statistics
Matches: 26,  Mismatches: 2, Indels: 4
        0.81            0.06        0.12

Matches are distributed among these distances:
  18    6  0.23
  19   12  0.46
  20    8  0.31

ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35


Consensus pattern (19 bp):   
TATATCATATAACATAACA

Found at i:7332 original size:2 final size:2

Alignment explanation


    Indices: 7272--7322  Score: 50
    Period size: 2  Copynumber: 25.5  Consensus size: 2

       7262 ATAACATAAC

                                                *  *       *  *            
       7272 AT AT AT AT AT AT AT AT AT AT AT AT TT CT -T CAA AA AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT

                         
       7314 AT AT AT AT A
          1 AT AT AT AT A

       7323 ACAGATATAT


Statistics
Matches: 43,  Mismatches: 4, Indels: 4
        0.84            0.08        0.08

Matches are distributed among these distances:
   1    1  0.02
   2   42  0.98

ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:8426 original size:11 final size:11

Alignment explanation


    Indices: 8410--8435  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       8400 GCTGTCTATC

                       
       8410 TTATTATTATA
          1 TTATTATTATA

                       
       8421 TTATTATTATA
          1 TTATTATTATA

                
       8432 TTAT
          1 TTAT

       8436 CATATAGGGC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

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


Consensus pattern (11 bp):   
TTATTATTATA
Done.