Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016249.1 Corchorus olitorius cultivar O-4 contig16282, 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: 23839
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33


Found at i:4331 original size:3 final size:3

Alignment explanation


    Indices: 4323--4360  Score: 76
    Period size: 3  Copynumber: 12.7  Consensus size: 3

       4313 GTCCATTGCT

                                                              
       4323 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
          1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT

       4361 TTTTTCTTTA


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

Matches are distributed among these distances:
   3   35  1.00

ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68


Consensus pattern (3 bp):   
TTC

Found at i:12268 original size:3 final size:3

Alignment explanation


    Indices: 12260--12297  Score: 76
    Period size: 3  Copynumber: 12.7  Consensus size: 3

      12250 AGATATGCAT

                                                              
      12260 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
          1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT

      12298 TTTGGCAAAA


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

Matches are distributed among these distances:
   3   35  1.00

ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68


Consensus pattern (3 bp):   
TTG

Found at i:14174 original size:42 final size:42

Alignment explanation


    Indices: 14123--14206  Score: 150
    Period size: 42  Copynumber: 2.0  Consensus size: 42

      14113 TCTGTAATCG

                      *                               
      14123 TTTCATCACCGTTTTGAGTCAAACGGAGCTTAAGTGTAAACT
          1 TTTCATCACCATTTTGAGTCAAACGGAGCTTAAGTGTAAACT

                            *                         
      14165 TTTCATCACCATTTTGGGTCAAACGGAGCTTAAGTGTAAACT
          1 TTTCATCACCATTTTGAGTCAAACGGAGCTTAAGTGTAAACT

      14207 CCGTTTCAAT


Statistics
Matches: 40,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  42   40  1.00

ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33


Consensus pattern (42 bp):   
TTTCATCACCATTTTGAGTCAAACGGAGCTTAAGTGTAAACT

Found at i:17346 original size:14 final size:14

Alignment explanation


    Indices: 17320--17356  Score: 56
    Period size: 14  Copynumber: 2.6  Consensus size: 14

      17310 CGTTTTTCTT

                    *     
      17320 AAAAAAGAGAAAGA
          1 AAAAAAGAAAAAGA

              *           
      17334 AAGAAAGAAAAAGA
          1 AAAAAAGAAAAAGA

                     
      17348 AAAAAAGAA
          1 AAAAAAGAA

      17357 TTATCCAAAA


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  14   20  1.00

ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00


Consensus pattern (14 bp):   
AAAAAAGAAAAAGA

Found at i:22935 original size:16 final size:16

Alignment explanation


    Indices: 22916--22946  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      22906 AAATCATTGA

                     *      
      22916 TTTATATTTTTTTCAT
          1 TTTATATTTGTTTCAT

                           
      22932 TTTATATTTGTTTCA
          1 TTTATATTTGTTTCA

      22947 AAGGTTTTTT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.19, C:0.06, G:0.03, T:0.71


Consensus pattern (16 bp):   
TTTATATTTGTTTCAT

Found at i:23725 original size:25 final size:25

Alignment explanation


    Indices: 23697--23835  Score: 199
    Period size: 25  Copynumber: 5.6  Consensus size: 25

      23687 CGCTCATGTT

                *                    
      23697 CTTGTGTTTGGAAAACGAGCCTGTG
          1 CTTGCGTTTGGAAAACGAGCCTGTG

                                     
      23722 CTTGCGTTTGGAAAACGAGCCTGTG
          1 CTTGCGTTTGGAAAACGAGCCTGTG

                              *      
      23747 CTTGCGTTTGGAAAACGAACCTGTG
          1 CTTGCGTTTGGAAAACGAGCCTGTG

                              **     
      23772 CTTGCGTTTGGAAAACGAATCTGTG
          1 CTTGCGTTTGGAAAACGAGCCTGTG

                       *  *           
      23797 CTTGCGTTTGGCAAGCGAGCCT-TAG
          1 CTTGCGTTTGGAAAACGAGCCTGT-G

                     *    
      23822 CTTGCGTTTAGAAA
          1 CTTGCGTTTGGAAA

      23836 CGAA


Statistics
Matches: 104,  Mismatches: 9, Indels: 2
        0.90            0.08        0.02

Matches are distributed among these distances:
  24    1  0.01
  25  103  0.99

ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30


Consensus pattern (25 bp):   
CTTGCGTTTGGAAAACGAGCCTGTG

Done.