Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008303.1 Corchorus capsularis cultivar CVL-1 contig08324, 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: 32524
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:2536 original size:22 final size:23

Alignment explanation


    Indices: 2505--2558  Score: 74
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       2495 TTATGCTTGT

                                  **
       2505 TTTAGAATTATTCA-ATTAACATG
          1 TTTA-AATTATTCATATTAACACA

                                   
       2528 TTTAAATTATTCATATTAACACA
          1 TTTAAATTATTCATATTAACACA

                    
       2551 TTTAAATT
          1 TTTAAATT

       2559 GTGTTAGTCA


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  22    9  0.32
  23   19  0.68

ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46


Consensus pattern (23 bp):   
TTTAAATTATTCATATTAACACA

Found at i:7161 original size:19 final size:18

Alignment explanation


    Indices: 7133--7174  Score: 57
    Period size: 19  Copynumber: 2.3  Consensus size: 18

       7123 AATTAATTGT

                              
       7133 TTTAATATTAAATTTTTA
          1 TTTAATATTAAATTTTTA

                       *       
       7151 TTTATATATTATATTTTTA
          1 TTTA-ATATTAAATTTTTA

            *    
       7170 CTTAA
          1 TTTAA

       7175 AAAATTACTC


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  18    5  0.24
  19   16  0.76

ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62


Consensus pattern (18 bp):   
TTTAATATTAAATTTTTA

Found at i:7902 original size:12 final size:12

Alignment explanation


    Indices: 7881--7910  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

       7871 AAAAAATTTT

                 *      
       7881 AAAAATTCAACA
          1 AAAAAATCAACA

                        
       7893 AAAAAATCAACA
          1 AAAAAATCAACA

                  
       7905 AAAAAA
          1 AAAAAA

       7911 CAAGCTGCTT


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

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.77, C:0.13, G:0.00, T:0.10


Consensus pattern (12 bp):   
AAAAAATCAACA

Found at i:16779 original size:2 final size:2

Alignment explanation


    Indices: 16772--16803  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      16762 GGTAAAAGGT

                                                           
      16772 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      16804 ATCCTCACAA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:18489 original size:17 final size:17

Alignment explanation


    Indices: 18467--18515  Score: 89
    Period size: 17  Copynumber: 2.9  Consensus size: 17

      18457 GATACAGCAG

                             
      18467 ATGCTACCTAGTACCTC
          1 ATGCTACCTAGTACCTC

                             
      18484 ATGCTACCTAGTACCTC
          1 ATGCTACCTAGTACCTC

                     *     
      18501 ATGCTACCTGGTACC
          1 ATGCTACCTAGTACC

      18516 ATGAGGGGGA


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  17   31  1.00

ACGTcount: A:0.22, C:0.35, G:0.14, T:0.29


Consensus pattern (17 bp):   
ATGCTACCTAGTACCTC

Found at i:27804 original size:31 final size:31

Alignment explanation


    Indices: 27766--27830  Score: 121
    Period size: 31  Copynumber: 2.1  Consensus size: 31

      27756 TTGGGTTATC

                         *                 
      27766 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
          1 AGTCTCCAGATCTCTAGATCTTGGATGTTTG

                                           
      27797 AGTCTCCAGATCTCTAGATCTTGGATGTTTG
          1 AGTCTCCAGATCTCTAGATCTTGGATGTTTG

               
      27828 AGT
          1 AGT

      27831 TAGTTCAGTT


Statistics
Matches: 33,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  31   33  1.00

ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40


Consensus pattern (31 bp):   
AGTCTCCAGATCTCTAGATCTTGGATGTTTG

Found at i:32112 original size:13 final size:13

Alignment explanation


    Indices: 32094--32126  Score: 57
    Period size: 13  Copynumber: 2.5  Consensus size: 13

      32084 AATTATTGTT

                         
      32094 TGCTTTATTAATC
          1 TGCTTTATTAATC

                        *
      32107 TGCTTTATTAATT
          1 TGCTTTATTAATC

                   
      32120 TGCTTTA
          1 TGCTTTA

      32127 GATTTAGATT


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

Matches are distributed among these distances:
  13   19  1.00

ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58


Consensus pattern (13 bp):   
TGCTTTATTAATC

Found at i:32134 original size:6 final size:6

Alignment explanation


    Indices: 32123--32161  Score: 78
    Period size: 6  Copynumber: 6.5  Consensus size: 6

      32113 ATTAATTTGC

                                                         
      32123 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT

      32162 GCTTTGCTTT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   33  1.00

ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54


Consensus pattern (6 bp):   
TTTAGA

Done.