Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016241.1 Corchorus olitorius cultivar O-4 contig16274, 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: 17324
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:439 original size:199 final size:199

Alignment explanation


    Indices: 1--567  Score: 816
    Period size: 203  Copynumber: 2.8  Consensus size: 199

                    *       *    *                                           
          1 AGTCCAAAGTTTACACCGACATTGTATTGTATAATAATCCCTATAAGAAAAATTATACAATACAC
          1 AGTCCAAAATTTACACTGACAATGTATTGTATAATAATCCCTATAAGAAAAATTATACAATACAC

               *                                   *               *         
         66 CGTTAGTGGA-TCTTAGCAGACTGCACGTGTGGGGTTTATGGGTTGACATGTGTCCCCTTAGGGA
         66 CGTCAGTGGAGT-TTAGCAGACTGCACGTGTGGGGTTTAAGGGTTGACATGTGTCTCCTTAGGGA

                                                                             
        130 ATATGTCTTAATTAATATTAAATATTTAATTAATTATGAAATGGGTATGTGTCAACCTCTTAACC
        130 ATATG---T-ATTAATATTAAATATTTAATTAATTATGAAATGGGTATGTGTCAACCTCTTAACC

                     
        195 CACTTATGG
        191 CACTTATGG

                                 *       *                           *       
        204 AGTCCAAAATTTACACTGACAGTGTATTGCATAATAATCCCTATAAGAAAAATTATATAATACAC
          1 AGTCCAAAATTTACACTGACAATGTATTGTATAATAATCCCTATAAGAAAAATTATACAATACAC

                                                         *   *               
        269 CGTCAGTGGAGTTTAGCAGACTGCACGTGTGGGGTTTAAGGGTTGGCATATGTCTCCTTAGGGAA
         66 CGTCAGTGGAGTTTAGCAGACTGCACGTGTGGGGTTTAAGGGTTGACATGTGTCTCCTTAGGGAA

                                                                 *       **  
        334 TATGTATTAATATTAAATATTTAATTAATTATGAAATGGGTATGTGTCAACCTTTTAACCCGTTT
        131 TATGTATTAATATTAAATATTTAATTAATTATGAAATGGGTATGTGTCAACCTCTTAACCCACTT

                
        399 ATGG
        196 ATGG

                  **         *                      *                *       
        403 AGTCCAGGATTTACACTTACAATGTATTGTATAATAAT-CATATAAGAAAAATTATAGAATACAC
          1 AGTCCAAAATTTACACTGACAATGTATTGTATAATAATCCCTATAAGAAAAATTATACAATACAC

                   *                   * * **  *                             
        467 CGTCAGTAGAGTTTAGCAGACTGCACGGGCGATGTGTAAGGGTTGACATGTGT-TGCCTTAGGGA
         66 CGTCAGTGGAGTTTAGCAGACTGCACGTGTGGGGTTTAAGGGTTGACATGTGTCT-CCTTAGGGA

                  *        *                     
        531 ATATGTGTTAATATTTAATATTTAATTAATTATGAAA
        130 ATATGTATTAATATTAAATATTTAATTAATTATGAAA

        568 AAGCTCAGTT


Statistics
Matches: 332,  Mismatches: 30, Indels: 9
        0.89            0.08        0.02

Matches are distributed among these distances:
 197    1  0.00
 198  113  0.34
 199   94  0.28
 200    1  0.00
 203  122  0.37
 204    1  0.00

ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34


Consensus pattern (199 bp):   
AGTCCAAAATTTACACTGACAATGTATTGTATAATAATCCCTATAAGAAAAATTATACAATACAC
CGTCAGTGGAGTTTAGCAGACTGCACGTGTGGGGTTTAAGGGTTGACATGTGTCTCCTTAGGGAA
TATGTATTAATATTAAATATTTAATTAATTATGAAATGGGTATGTGTCAACCTCTTAACCCACTT
ATGG

Found at i:597 original size:16 final size:16

Alignment explanation


    Indices: 576--606  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

        566 AAAAGCTCAG

                    *       
        576 TTAATAAGGTTACTAA
          1 TTAATAAGATTACTAA

                           
        592 TTAATAAGATTACTA
          1 TTAATAAGATTACTA

        607 TACAACTTGA


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:0.45, C:0.06, G:0.10, T:0.39


Consensus pattern (16 bp):   
TTAATAAGATTACTAA

Found at i:649 original size:20 final size:21

Alignment explanation


    Indices: 620--661  Score: 59
    Period size: 20  Copynumber: 2.0  Consensus size: 21

        610 AACTTGATAC

                        *        
        620 GGTTACTAAAAAGATTT-TAA
          1 GGTTACTAAAAAAATTTATAA

                 *               
        640 GGTTATTAAAAAAATTTATAA
          1 GGTTACTAAAAAAATTTATAA

             
        661 G
          1 G

        662 ATAACTAATA


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

Matches are distributed among these distances:
  20   15  0.79
  21    4  0.21

ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36


Consensus pattern (21 bp):   
GGTTACTAAAAAAATTTATAA

Found at i:2200 original size:20 final size:20

Alignment explanation


    Indices: 2175--2217  Score: 86
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       2165 TACAAGGTAG

                                
       2175 AAAACAAATTTTCAACTTGT
          1 AAAACAAATTTTCAACTTGT

                                
       2195 AAAACAAATTTTCAACTTGT
          1 AAAACAAATTTTCAACTTGT

               
       2215 AAA
          1 AAA

       2218 TCATTCCAAG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   23  1.00

ACGTcount: A:0.49, C:0.14, G:0.05, T:0.33


Consensus pattern (20 bp):   
AAAACAAATTTTCAACTTGT

Found at i:7033 original size:27 final size:27

Alignment explanation


    Indices: 6995--7110  Score: 178
    Period size: 27  Copynumber: 4.3  Consensus size: 27

       6985 ATTTACTTCT

                             **        
       6995 CATTTTGGTCATTTGCATGTCCAGGGG
          1 CATTTTGGTCATTTGCACCTCCAGGGG

                                       
       7022 CATTTTGGTCATTTGCACCTCCAGGGG
          1 CATTTTGGTCATTTGCACCTCCAGGGG

                                *  *   
       7049 CATTTTGGTCATTTGCACCTTCAAGGG
          1 CATTTTGGTCATTTGCACCTCCAGGGG

                              *   *    
       7076 CATTTTGGTCATTTGCACGTCCGGGGG
          1 CATTTTGGTCATTTGCACCTCCAGGGG

                    
       7103 CATTTTGG
          1 CATTTTGG

       7111 GTCACTTCAA


Statistics
Matches: 81,  Mismatches: 8, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  27   81  1.00

ACGTcount: A:0.15, C:0.22, G:0.28, T:0.36


Consensus pattern (27 bp):   
CATTTTGGTCATTTGCACCTCCAGGGG

Found at i:16731 original size:2 final size:2

Alignment explanation


    Indices: 16724--16763  Score: 73
    Period size: 2  Copynumber: 20.5  Consensus size: 2

      16714 TTATGTTCTT

                                                                         
      16724 TA TA TA TA -A 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 TA TA T

      16764 GCCACGTGTT


Statistics
Matches: 37,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   36  0.97

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


Consensus pattern (2 bp):   
TA

Done.