Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005874.1 Corchorus capsularis cultivar CVL-1 contig05892, 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: 4933
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:864 original size:11 final size:11

Alignment explanation


    Indices: 848--907  Score: 56
    Period size: 11  Copynumber: 5.7  Consensus size: 11

        838 GAAGTTCGTG

                       
        848 TTTGAAGATTA
          1 TTTGAAGATTA

                     * 
        859 TTTGAAGATAA
          1 TTTGAAGATTA

                       
        870 TTTGAAG---A
          1 TTTGAAGATTA

                     * 
        878 TTTGAAGATCA
          1 TTTGAAGATTA

                        
        889 -TTGAAGAATTA
          1 TTTGAAG-ATTA

               *    
        900 TTTCAAGA
          1 TTTGAAGA

        908 AGTAAGAATT


Statistics
Matches: 41,  Mismatches: 3, Indels: 10
        0.76            0.06        0.19

Matches are distributed among these distances:
   8    8  0.20
  10    6  0.15
  11   22  0.54
  12    5  0.12

ACGTcount: A:0.40, C:0.03, G:0.18, T:0.38


Consensus pattern (11 bp):   
TTTGAAGATTA

Found at i:876 original size:22 final size:22

Alignment explanation


    Indices: 848--907  Score: 65
    Period size: 22  Copynumber: 2.9  Consensus size: 22

        838 GAAGTTCGTG

                                  
        848 TTTGAAGATTATTTGAAGATAA
          1 TTTGAAGATTATTTGAAGATAA

                                * 
        870 TTTGAAG---ATTTGAAGATCA
          1 TTTGAAGATTATTTGAAGATAA

                           *    
        889 -TTGAAGAATTATTTCAAGA
          1 TTTGAAG-ATTATTTGAAGA

        908 AGTAAGAATT


Statistics
Matches: 32,  Mismatches: 2, Indels: 8
        0.76            0.05        0.19

Matches are distributed among these distances:
  18    6  0.19
  19   11  0.34
  22   15  0.47

ACGTcount: A:0.40, C:0.03, G:0.18, T:0.38


Consensus pattern (22 bp):   
TTTGAAGATTATTTGAAGATAA

Found at i:882 original size:19 final size:18

Alignment explanation


    Indices: 858--895  Score: 58
    Period size: 19  Copynumber: 2.1  Consensus size: 18

        848 TTTGAAGATT

                               
        858 ATTTGAAGATAATTTGAAG
          1 ATTTGAAGATAA-TTGAAG

                      *       
        877 ATTTGAAGATCATTGAAG
          1 ATTTGAAGATAATTGAAG

             
        895 A
          1 A

        896 ATTATTTCAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18    7  0.39
  19   11  0.61

ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34


Consensus pattern (18 bp):   
ATTTGAAGATAATTGAAG

Found at i:2269 original size:21 final size:20

Alignment explanation


    Indices: 2245--2291  Score: 51
    Period size: 20  Copynumber: 2.3  Consensus size: 20

       2235 TAGATTTAGA

                      *           
       2245 TTTAATTTACTTTGCTTAT-TT
          1 TTTAATTTA-ATTGCTT-TCTT

                *               
       2266 TTTAGTTTAATTGCTTTCTT
          1 TTTAATTTAATTGCTTTCTT

                  
       2286 TTTAAT
          1 TTTAAT

       2292 CCCTTGTTTC


Statistics
Matches: 22,  Mismatches: 3, Indels: 3
        0.79            0.11        0.11

Matches are distributed among these distances:
  19    1  0.05
  20   13  0.59
  21    8  0.36

ACGTcount: A:0.19, C:0.09, G:0.06, T:0.66


Consensus pattern (20 bp):   
TTTAATTTAATTGCTTTCTT

Found at i:2559 original size:23 final size:22

Alignment explanation


    Indices: 2533--2588  Score: 76
    Period size: 22  Copynumber: 2.5  Consensus size: 22

       2523 TTTTTTTTCA

                                   
       2533 AAAAAAAAATTGCGTTTTCCCTT
          1 AAAAAAAAATTGC-TTTTCCCTT

                    *        **   
       2556 AAAAAAAATTTGCTTTTTGCTT
          1 AAAAAAAAATTGCTTTTCCCTT

                       
       2578 AAAAAAAAATT
          1 AAAAAAAAATT

       2589 TTGAAAAAAA


Statistics
Matches: 29,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  22   17  0.59
  23   12  0.41

ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36


Consensus pattern (22 bp):   
AAAAAAAAATTGCTTTTCCCTT

Found at i:2589 original size:23 final size:24

Alignment explanation


    Indices: 2532--2589  Score: 75
    Period size: 23  Copynumber: 2.5  Consensus size: 24

       2522 TTTTTTTTTC

                     *              
       2532 AAAAAAAAAATTGCGTTTTCCCTT
          1 AAAAAAAAATTTGCGTTTTCCCTT

                               **   
       2556 -AAAAAAAATTTGC-TTTTTGCTT
          1 AAAAAAAAATTTGCGTTTTCCCTT

                        
       2578 AAAAAAAAATTT
          1 AAAAAAAAATTT

       2590 TGAAAAAAAA


Statistics
Matches: 30,  Mismatches: 3, Indels: 3
        0.83            0.08        0.08

Matches are distributed among these distances:
  22    7  0.23
  23   23  0.77

ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36


Consensus pattern (24 bp):   
AAAAAAAAATTTGCGTTTTCCCTT

Found at i:3665 original size:15 final size:15

Alignment explanation


    Indices: 3645--3687  Score: 59
    Period size: 15  Copynumber: 2.9  Consensus size: 15

       3635 CCTTGCCAAG

                       *   
       3645 CCAGAAGATGAGCCA
          1 CCAGAAGATGAACCA

                          *
       3660 CCAGAAGATGAACCG
          1 CCAGAAGATGAACCA

             *           
       3675 CAAGAAGATGAAC
          1 CCAGAAGATGAAC

       3688 AACTTGAACT


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  15   25  1.00

ACGTcount: A:0.44, C:0.23, G:0.26, T:0.07


Consensus pattern (15 bp):   
CCAGAAGATGAACCA
Done.