Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017508.1 Corchorus olitorius cultivar O-4 contig17541, 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: 21579
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--33  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

                                                             
          1 AT AT AT 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 AT AT AT A

         34 ATCAAACAAA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:1748 original size:60 final size:60

Alignment explanation


    Indices: 1629--1748  Score: 172
    Period size: 60  Copynumber: 2.0  Consensus size: 60

       1619 TCTTTCCGAC

                      *   *                                     *       
       1629 AAAATTAGTAGTATGTTCAAGATTTTAATTTTCAATAATTTAAACATATTGGTTGCACGT
          1 AAAATTAGTAATATCTTCAAGATTTTAATTTTCAATAATTTAAACATATTGGGTGCACGT

                                                *                         
       1689 AAAATTAGTAATATACTT-AAGATTTTAATTTTCATTTAATTTAAACATATTGGGT-CACGT
          1 AAAATTAGTAATAT-CTTCAAGATTTTAATTTTCA-ATAATTTAAACATATTGGGTGCACGT

       1749 TCAACGCAGG


Statistics
Matches: 54,  Mismatches: 4, Indels: 4
        0.87            0.06        0.06

Matches are distributed among these distances:
  60   34  0.63
  61   20  0.37

ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42


Consensus pattern (60 bp):   
AAAATTAGTAATATCTTCAAGATTTTAATTTTCAATAATTTAAACATATTGGGTGCACGT

Found at i:4646 original size:22 final size:22

Alignment explanation


    Indices: 4621--4666  Score: 92
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       4611 TGACTTCTTC

                                  
       4621 TTGTTTCCTCTTGTATTAACAA
          1 TTGTTTCCTCTTGTATTAACAA

                                  
       4643 TTGTTTCCTCTTGTATTAACAA
          1 TTGTTTCCTCTTGTATTAACAA

              
       4665 TT
          1 TT

       4667 ATTATGGCTG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   24  1.00

ACGTcount: A:0.22, C:0.17, G:0.09, T:0.52


Consensus pattern (22 bp):   
TTGTTTCCTCTTGTATTAACAA

Found at i:11896 original size:18 final size:19

Alignment explanation


    Indices: 11857--11896  Score: 55
    Period size: 21  Copynumber: 2.1  Consensus size: 19

      11847 GTGCTCTCGT

                                 
      11857 TGTGATGCTCCCACTTTTCAA
          1 TGTGATGCTCCCA--TTTCAA

                               
      11878 TGTGATGCTCCCA-TTCAA
          1 TGTGATGCTCCCATTTCAA

             
      11896 T
          1 T

      11897 TCTGACCATT


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  18    6  0.32
  21   13  0.68

ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38


Consensus pattern (19 bp):   
TGTGATGCTCCCATTTCAA

Found at i:13187 original size:31 final size:31

Alignment explanation


    Indices: 13146--13250  Score: 83
    Period size: 31  Copynumber: 3.5  Consensus size: 31

      13136 AAAGGCTGAT

                *          *               
      13146 TGCTCAAATAAGGGCCCAACATTTGCGAAAA
          1 TGCTTAAATAAGGGCACAACATTTGCGAAAA

                                   * **    
      13177 TGCTTAAATAAGGGCACAA-A--GGAAAAAA
          1 TGCTTAAATAAGGGCACAACATTTGCGAAAA

                       *  *  *    *          
      13205 TTG-TTCAAATCAGAGCTCAACGTTTGCGAAAA
          1 -TGCTT-AAATAAGGGCACAACATTTGCGAAAA

                          
      13237 TGCTTAAATAAGGG
          1 TGCTTAAATAAGGG

      13251 TCCAGAATAG


Statistics
Matches: 54,  Mismatches: 14, Indels: 12
        0.68            0.17        0.15

Matches are distributed among these distances:
  28    7  0.13
  29   13  0.24
  30    1  0.02
  31   26  0.48
  32    7  0.13

ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22


Consensus pattern (31 bp):   
TGCTTAAATAAGGGCACAACATTTGCGAAAA

Found at i:15350 original size:14 final size:14

Alignment explanation


    Indices: 15313--15355  Score: 52
    Period size: 14  Copynumber: 3.1  Consensus size: 14

      15303 TTTGAGTTTG

                          
      15313 TTTTCGAGTCAGTT
          1 TTTTCGAGTCAGTT

              **           
      15327 TGAGTC-AGTCAGTT
          1 T-TTTCGAGTCAGTT

                          
      15341 TTTTCGAGTCAGTT
          1 TTTTCGAGTCAGTT

             
      15355 T
          1 T

      15356 CGAGTCTAGT


Statistics
Matches: 23,  Mismatches: 4, Indels: 4
        0.74            0.13        0.13

Matches are distributed among these distances:
  13    2  0.09
  14   19  0.83
  15    2  0.09

ACGTcount: A:0.16, C:0.14, G:0.23, T:0.47


Consensus pattern (14 bp):   
TTTTCGAGTCAGTT

Found at i:19603 original size:28 final size:28

Alignment explanation


    Indices: 19555--19629  Score: 73
    Period size: 28  Copynumber: 2.7  Consensus size: 28

      19545 TCCGGCATTT

                 *     *                 
      19555 AAGGGAAAAACTGTAA-TTTAG-TCAACC
          1 AAGGGTAAAACAGTAATTTTAGCT-AACC

             *        **            *   
      19582 AGGGGTAAAATGGTAATTTTAGCTGACC
          1 AAGGGTAAAACAGTAATTTTAGCTAACC

                                
      19610 AAGGGTAAAACAGTAATTTT
          1 AAGGGTAAAACAGTAATTTT

      19630 GACATCTTAA


Statistics
Matches: 38,  Mismatches: 8, Indels: 3
        0.78            0.16        0.06

Matches are distributed among these distances:
  27   12  0.32
  28   25  0.66
  29    1  0.03

ACGTcount: A:0.40, C:0.11, G:0.23, T:0.27


Consensus pattern (28 bp):   
AAGGGTAAAACAGTAATTTTAGCTAACC
Done.