Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016126.1 Corchorus olitorius cultivar O-4 contig16159, 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: 16049
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:7134 original size:32 final size:34

Alignment explanation


    Indices: 7093--7166  Score: 98
    Period size: 32  Copynumber: 2.2  Consensus size: 34

       7083 ACAAAGTTTA

                *       *       *  *          
       7093 TTTAACATGCATGATCT-CTTCTTCTACCTTT-T
          1 TTTATCATGCATAATCTCCTCCTACTACCTTTCT

                                              
       7125 TTTATCATGCATAATCTCCTCCTACTACCTTTCT
          1 TTTATCATGCATAATCTCCTCCTACTACCTTTCT

                    
       7159 TTTATCAT
          1 TTTATCAT

       7167 TAAAAATTAT


Statistics
Matches: 36,  Mismatches: 4, Indels: 2
        0.86            0.10        0.05

Matches are distributed among these distances:
  32   15  0.42
  33   12  0.33
  34    9  0.25

ACGTcount: A:0.20, C:0.27, G:0.04, T:0.49


Consensus pattern (34 bp):   
TTTATCATGCATAATCTCCTCCTACTACCTTTCT

Found at i:7231 original size:20 final size:20

Alignment explanation


    Indices: 7206--7245  Score: 80
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       7196 TTGAATATTA

                                
       7206 GTGGCACCTGAAGTTGTCAC
          1 GTGGCACCTGAAGTTGTCAC

                                
       7226 GTGGCACCTGAAGTTGTCAC
          1 GTGGCACCTGAAGTTGTCAC

       7246 ATCAAAAATA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.20, C:0.25, G:0.30, T:0.25


Consensus pattern (20 bp):   
GTGGCACCTGAAGTTGTCAC

Found at i:7288 original size:29 final size:29

Alignment explanation


    Indices: 7255--7315  Score: 95
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       7245 CATCAAAAAT

                               *         
       7255 ATAGTATCACCTTGACACCCGAAGTTGTC
          1 ATAGTATCACCTTGACACCAGAAGTTGTC

                     **                  
       7284 ATAGTATCATTTTGACACCAGAAGTTGTC
          1 ATAGTATCACCTTGACACCAGAAGTTGTC

               
       7313 ATA
          1 ATA

       7316 TTAAGGATGG


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  29   29  1.00

ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31


Consensus pattern (29 bp):   
ATAGTATCACCTTGACACCAGAAGTTGTC

Found at i:8421 original size:2 final size:2

Alignment explanation


    Indices: 8414--8443  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       8404 TTGATATTGA

                                                        
       8414 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

       8444 TTCGTTCTAT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:8714 original size:35 final size:35

Alignment explanation


    Indices: 8667--8736  Score: 104
    Period size: 35  Copynumber: 2.0  Consensus size: 35

       8657 TCGGGTAGTG

                   *                           
       8667 CAAATTTGATTGAAGACTCCAGAAGAGCAAGTATT
          1 CAAATTTCATTGAAGACTCCAGAAGAGCAAGTATT

                           *    *       *      
       8702 CAAATTTCATTGAAGGCTCCGGAAGAGCTAGTATT
          1 CAAATTTCATTGAAGACTCCAGAAGAGCAAGTATT

       8737 GTTTTATCTG


Statistics
Matches: 31,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  35   31  1.00

ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27


Consensus pattern (35 bp):   
CAAATTTCATTGAAGACTCCAGAAGAGCAAGTATT

Found at i:12640 original size:20 final size:19

Alignment explanation


    Indices: 12612--12650  Score: 69
    Period size: 19  Copynumber: 2.1  Consensus size: 19

      12602 AATTCAAAAC

                *              
      12612 AAAATAAAAACTACCCATT
          1 AAAAAAAAAACTACCCATT

                               
      12631 AAAAAAAAAACTACCCATT
          1 AAAAAAAAAACTACCCATT

             
      12650 A
          1 A

      12651 GAGGATAAAT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.62, C:0.21, G:0.00, T:0.18


Consensus pattern (19 bp):   
AAAAAAAAAACTACCCATT

Found at i:13779 original size:2 final size:2

Alignment explanation


    Indices: 13772--13798  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      13762 CCAATTTACC

                                                    
      13772 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

      13799 ATGTTCCAAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:15143 original size:22 final size:22

Alignment explanation


    Indices: 15115--15156  Score: 84
    Period size: 22  Copynumber: 1.9  Consensus size: 22

      15105 AAGATAATCA

                                  
      15115 TCACAACCATAAATACATTGGC
          1 TCACAACCATAAATACATTGGC

                                
      15137 TCACAACCATAAATACATTG
          1 TCACAACCATAAATACATTG

      15157 TCAAGACAAG


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24


Consensus pattern (22 bp):   
TCACAACCATAAATACATTGGC
Done.