Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012897.1 Corchorus olitorius cultivar O-4 contig12930, 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: 32361
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:3612 original size:28 final size:27

Alignment explanation


    Indices: 3567--3652  Score: 120
    Period size: 28  Copynumber: 3.1  Consensus size: 27

       3557 ATGATATTTA

                         *              
       3567 GGTCCTTGTACATGTTTTATGTGTAGTT
          1 GGTCCTTGT-CATATTTTATGTGTAGTT

                                        
       3595 GGTCCTTGTCCATATTTTATGTGTAGTT
          1 GGTCCTTGT-CATATTTTATGTGTAGTT

                             *          
       3623 GGTCCTTGTCA-ATGTTCATGTGTAGTT
          1 GGTCCTTGTCATAT-TTTATGTGTAGTT

               
       3650 GGT
          1 GGT

       3653 AGCTTAATAT


Statistics
Matches: 54,  Mismatches: 3, Indels: 3
        0.90            0.05        0.05

Matches are distributed among these distances:
  26    2  0.04
  27   17  0.31
  28   35  0.65

ACGTcount: A:0.14, C:0.13, G:0.26, T:0.48


Consensus pattern (27 bp):   
GGTCCTTGTCATATTTTATGTGTAGTT

Found at i:5197 original size:2 final size:2

Alignment explanation


    Indices: 5190--5217  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       5180 ATTGAAGCAG

                                                     
       5190 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT

       5218 TATATATATA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
CT

Found at i:8080 original size:32 final size:32

Alignment explanation


    Indices: 8038--8116  Score: 131
    Period size: 32  Copynumber: 2.5  Consensus size: 32

       8028 TGAGACATGA

                 *                          
       8038 ACACGGGACCTGTTTTTAAACGTATACACGGG
          1 ACACGAGACCTGTTTTTAAACGTATACACGGG

                       *           *        
       8070 ACACGAGACCTATTTTTAAACGTGTACACGGG
          1 ACACGAGACCTGTTTTTAAACGTATACACGGG

                           
       8102 ACACGAGACCTGTTT
          1 ACACGAGACCTGTTT

       8117 ACACGAGTAA


Statistics
Matches: 43,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  32   43  1.00

ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25


Consensus pattern (32 bp):   
ACACGAGACCTGTTTTTAAACGTATACACGGG

Found at i:8396 original size:20 final size:21

Alignment explanation


    Indices: 8359--8397  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 21

       8349 ACCCGAAAAC

                        **       
       8359 TAAAGCGTGTTATTCGTGTTT
          1 TAAAGCGTGTTAAACGTGTTT

                               
       8380 TAAA-CGTGTTAAACGTGT
          1 TAAAGCGTGTTAAACGTGT

       8398 CTTTGACACG


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  20   12  0.75
  21    4  0.25

ACGTcount: A:0.26, C:0.10, G:0.23, T:0.41


Consensus pattern (21 bp):   
TAAAGCGTGTTAAACGTGTTT

Found at i:13381 original size:13 final size:13

Alignment explanation


    Indices: 13363--13387  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      13353 TCTCATAAAT

                         
      13363 ATTTTTATTTATA
          1 ATTTTTATTTATA

                        
      13376 ATTTTTATTTAT
          1 ATTTTTATTTAT

      13388 TTATTTATTT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72


Consensus pattern (13 bp):   
ATTTTTATTTATA

Found at i:23827 original size:16 final size:16

Alignment explanation


    Indices: 23806--23837  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

      23796 TCTTTAAACC

                            
      23806 ATTCAATTATAATTTT
          1 ATTCAATTATAATTTT

                      *     
      23822 ATTCAATTATTATTTT
          1 ATTCAATTATAATTTT

      23838 TTAGCCTTTT


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59


Consensus pattern (16 bp):   
ATTCAATTATAATTTT

Found at i:26311 original size:21 final size:22

Alignment explanation


    Indices: 26282--26324  Score: 61
    Period size: 21  Copynumber: 2.0  Consensus size: 22

      26272 TAAAAGTGCA

                     *            
      26282 AAAGACAGGGAGGCGACTCCTG
          1 AAAGACAGGAAGGCGACTCCTG

                           *      
      26304 AAAG-CAGGAAGGCGCCTCCTG
          1 AAAGACAGGAAGGCGACTCCTG

      26325 GGCTAGAGGA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  21   15  0.79
  22    4  0.21

ACGTcount: A:0.30, C:0.26, G:0.35, T:0.09


Consensus pattern (22 bp):   
AAAGACAGGAAGGCGACTCCTG
Done.