Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010506.1 Corchorus olitorius cultivar O-4 contig10538, 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: 10457
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34


Found at i:428 original size:19 final size:19

Alignment explanation


    Indices: 406--444  Score: 69
    Period size: 19  Copynumber: 2.1  Consensus size: 19

        396 AAGAAGACCC

                          *    
        406 TAGATTAGTTTCTAGCCAA
          1 TAGATTAGTTTCTAACCAA

                               
        425 TAGATTAGTTTCTAACCAA
          1 TAGATTAGTTTCTAACCAA

             
        444 T
          1 T

        445 TCTTGCCCTT


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:0.33, C:0.15, G:0.13, T:0.38


Consensus pattern (19 bp):   
TAGATTAGTTTCTAACCAA

Found at i:550 original size:56 final size:56

Alignment explanation


    Indices: 482--595  Score: 183
    Period size: 56  Copynumber: 2.0  Consensus size: 56

        472 TATTAGTTTC

                   *                    **       *      *           
        482 CTTTCACCCAATAAATGTTATAATAAATTTTATCCCCTTATCTCTACTTAATTATT
          1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCAACTTAATTATT

                                                                    
        538 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCAACTTAATTATT
          1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCAACTTAATTATT

              
        594 CT
          1 CT

        596 ACAAAATAAA


Statistics
Matches: 53,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  56   53  1.00

ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41


Consensus pattern (56 bp):   
CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCAACTTAATTATT

Found at i:720 original size:42 final size:42

Alignment explanation


    Indices: 661--741  Score: 144
    Period size: 42  Copynumber: 1.9  Consensus size: 42

        651 TAAGGATCAG

                                           *          
        661 GATTTGAGTTGAGTATTTCTTAATTTACAAATAATTTTCTAT
          1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT

                                         *         
        703 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
          1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC

        742 AAGACTTTAG


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

Matches are distributed among these distances:
  42   37  1.00

ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48


Consensus pattern (42 bp):   
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT

Found at i:3186 original size:23 final size:23

Alignment explanation


    Indices: 3155--3284  Score: 95
    Period size: 23  Copynumber: 5.5  Consensus size: 23

       3145 CTCTTGTTTG

                *    *             
       3155 ATCAACCTTATCTTTTACTTTTC
          1 ATCACCCTTGTCTTTTACTTTTC

                                   * *
       3178 ATCACCCTTGT-TTTTACAAGTTGTG
          1 ATCACCCTTGTCTTTTAC---TTTTC

                      *             
       3203 ATCAACCC-TATCTTTTACTTTTC
          1 ATC-ACCCTTGTCTTTTACTTTTC

                                   * *
       3226 ATCACCCTTGT-TTTTACAAGTTGTG
          1 ATCACCCTTGTCTTTTAC---TTTTC

                *       *          
       3251 ATCAACCTTGTCATTTACTTTTC
          1 ATCACCCTTGTCTTTTACTTTTC

                       
       3274 ATCACCCTTGT
          1 ATCACCCTTGT

       3285 TGTTACAAGG


Statistics
Matches: 82,  Mismatches: 15, Indels: 20
        0.70            0.13        0.17

Matches are distributed among these distances:
  22   16  0.20
  23   30  0.37
  25   21  0.26
  26   15  0.18

ACGTcount: A:0.21, C:0.25, G:0.08, T:0.46


Consensus pattern (23 bp):   
ATCACCCTTGTCTTTTACTTTTC

Found at i:3208 original size:48 final size:48

Alignment explanation


    Indices: 3153--3293  Score: 246
    Period size: 48  Copynumber: 2.9  Consensus size: 48

       3143 AACTCTTGTT

                                                            
       3153 TGATCAACCTTATCTTTTACTTTTCATCACCCTTGTTTTTACAAGTTG
          1 TGATCAACCTTATCTTTTACTTTTCATCACCCTTGTTTTTACAAGTTG

                     *                                      
       3201 TGATCAACCCTATCTTTTACTTTTCATCACCCTTGTTTTTACAAGTTG
          1 TGATCAACCTTATCTTTTACTTTTCATCACCCTTGTTTTTACAAGTTG

                       *  *                      *       
       3249 TGATCAACCTTGTCATTTACTTTTCATCACCCTTGTTGTTACAAG
          1 TGATCAACCTTATCTTTTACTTTTCATCACCCTTGTTTTTACAAG

       3294 GTGTAATCTT


Statistics
Matches: 88,  Mismatches: 5, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  48   88  1.00

ACGTcount: A:0.21, C:0.24, G:0.09, T:0.45


Consensus pattern (48 bp):   
TGATCAACCTTATCTTTTACTTTTCATCACCCTTGTTTTTACAAGTTG

Found at i:3259 original size:25 final size:25

Alignment explanation


    Indices: 3178--3261  Score: 84
    Period size: 25  Copynumber: 3.4  Consensus size: 25

       3168 TTTACTTTTC

                *                    
       3178 ATCACCCTTGTTTTTACAAGTTGTG
          1 ATCAACCTTGTTTTTACAAGTTGTG

                   * *             * *
       3203 ATCAACCCTATCTTTTAC---TTTTC
          1 ATCAACCTTGT-TTTTACAAGTTGTG

                *                    
       3226 ATCACCCTTGTTTTTACAAGTTGTG
          1 ATCAACCTTGTTTTTACAAGTTGTG

                       
       3251 ATCAACCTTGT
          1 ATCAACCTTGT

       3262 CATTTACTTT


Statistics
Matches: 44,  Mismatches: 11, Indels: 8
        0.70            0.17        0.13

Matches are distributed among these distances:
  22    6  0.14
  23   11  0.25
  25   21  0.48
  26    6  0.14

ACGTcount: A:0.21, C:0.24, G:0.11, T:0.44


Consensus pattern (25 bp):   
ATCAACCTTGTTTTTACAAGTTGTG
Done.