Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017322.1 Corchorus olitorius cultivar O-4 contig17355, 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: 12712
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33


Found at i:4422 original size:18 final size:18

Alignment explanation


    Indices: 4399--4435  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       4389 AAAGGGTAGT

                     *        
       4399 TAAAAAAAATTGTTTTCA
          1 TAAAAAAAAGTGTTTTCA

                  *           
       4417 TAAAAACAAGTGTTTTCA
          1 TAAAAAAAAGTGTTTTCA

             
       4435 T
          1 T

       4436 GCAAGAGGAG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38


Consensus pattern (18 bp):   
TAAAAAAAAGTGTTTTCA

Found at i:5360 original size:8 final size:10

Alignment explanation


    Indices: 5335--5371  Score: 51
    Period size: 11  Copynumber: 3.8  Consensus size: 10

       5325 AAAGTTCGTG

                       
       5335 ATTGAAGACTT
          1 ATTGAAGAC-T

                      
       5346 ATTGAAGA-T
          1 ATTGAAGACT

                      
       5355 -TTGAAGACT
          1 ATTGAAGACT

                    
       5364 ATTGAAGA
          1 ATTGAAGA

       5372 ATTATCTCAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 5
        0.83            0.00        0.17

Matches are distributed among these distances:
   8    7  0.29
   9    2  0.08
  10    7  0.29
  11    8  0.33

ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32


Consensus pattern (10 bp):   
ATTGAAGACT

Found at i:5366 original size:18 final size:19

Alignment explanation


    Indices: 5336--5371  Score: 65
    Period size: 18  Copynumber: 1.9  Consensus size: 19

       5326 AAGTTCGTGA

                               
       5336 TTGAAGACTTATTGAAGAT
          1 TTGAAGACTTATTGAAGAT

                              
       5355 TTGAAGAC-TATTGAAGA
          1 TTGAAGACTTATTGAAGA

       5372 ATTATCTCAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  18    9  0.53
  19    8  0.47

ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33


Consensus pattern (19 bp):   
TTGAAGACTTATTGAAGAT

Found at i:8117 original size:27 final size:27

Alignment explanation


    Indices: 8087--8165  Score: 95
    Period size: 27  Copynumber: 2.9  Consensus size: 27

       8077 AGTGAACTTA

                          * *       *  
       8087 AAATGACCAAAATGTCTCTAAATGTGC
          1 AAATGACCAAAATGCCCCTAAATGAGC

                *              **      
       8114 AAATAACCAAAATGCCCCTGGATGAGC
          1 AAATGACCAAAATGCCCCTAAATGAGC

                                *    
       8141 AAATGACCAAAATGCCCCTAGATGA
          1 AAATGACCAAAATGCCCCTAAATGA

       8166 CCCTAATGCC


Statistics
Matches: 44,  Mismatches: 8, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  27   44  1.00

ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19


Consensus pattern (27 bp):   
AAATGACCAAAATGCCCCTAAATGAGC

Found at i:8658 original size:35 final size:35

Alignment explanation


    Indices: 8601--9007  Score: 618
    Period size: 35  Copynumber: 11.6  Consensus size: 35

       8591 CCGAATCATC

                *                               
       8601 CTTTAAAGATGCTACACCGAGTCATCTG-ATTCTAA
          1 CTTTGAAGATGCTACACCGAGTCATCTGAATTC-AA

               *    * *      *       *      *  
       8636 CTTCGAAGGTACTACACTGAGTCATTTGAATTAAA
          1 CTTTGAAGATGCTACACCGAGTCATCTGAATTCAA

                   *                           
       8671 CTTTGAATATGCTACACCGAGTCATCTGAATTCAA
          1 CTTTGAAGATGCTACACCGAGTCATCTGAATTCAA

                                       *       
       8706 CTTTGAAGATGCTACACCGAGTCATCTAAATTCAA
          1 CTTTGAAGATGCTACACCGAGTCATCTGAATTCAA

                *                      *       
       8741 CTTTAAAGATGCTACACCGAGTCATCTAAATTCAA
          1 CTTTGAAGATGCTACACCGAGTCATCTGAATTCAA

                                *     *        
       8776 CTTTGAAGATGCTACACCGAATCATCCGAATTCAA
          1 CTTTGAAGATGCTACACCGAGTCATCTGAATTCAA

                                      *        
       8811 CTTTGAAGATGCTACACCGAGTCATCCGAATTCAA
          1 CTTTGAAGATGCTACACCGAGTCATCTGAATTCAA

                                       *       
       8846 CTTTGAAGATGCTACACCGAGTCATCTAAATTCAA
          1 CTTTGAAGATGCTACACCGAGTCATCTGAATTCAA

                                              *
       8881 CTTTGAAGATGCTACACCGAGTCATCTGAATTCAT
          1 CTTTGAAGATGCTACACCGAGTCATCTGAATTCAA

                                               
       8916 CTTTGAAGATGCTACACCGAGTCATCTGAATTCAA
          1 CTTTGAAGATGCTACACCGAGTCATCTGAATTCAA

                  *         *              *   
       8951 CTTTGAGGATGCTACAACGAGTCATCTGAATCCAA
          1 CTTTGAAGATGCTACACCGAGTCATCTGAATTCAA

                           *      
       8986 CTTTGAAGATGCTACGCCGAGT
          1 CTTTGAAGATGCTACACCGAGT

       9008 TACCTGGCTC


Statistics
Matches: 338,  Mismatches: 33, Indels: 2
        0.91            0.09        0.01

Matches are distributed among these distances:
  35  335  0.99
  36    3  0.01

ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29


Consensus pattern (35 bp):   
CTTTGAAGATGCTACACCGAGTCATCTGAATTCAA

Done.