Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017328.1 Corchorus olitorius cultivar O-4 contig17361, 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: 31901
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30


Found at i:7744 original size:19 final size:19

Alignment explanation


    Indices: 7722--7765  Score: 88
    Period size: 19  Copynumber: 2.3  Consensus size: 19

       7712 GGCAGAACTT

                               
       7722 AAACCCAGAGGCTGAACCC
          1 AAACCCAGAGGCTGAACCC

                               
       7741 AAACCCAGAGGCTGAACCC
          1 AAACCCAGAGGCTGAACCC

                  
       7760 AAACCC
          1 AAACCC

       7766 GCCTTACAAG


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   25  1.00

ACGTcount: A:0.39, C:0.39, G:0.18, T:0.05


Consensus pattern (19 bp):   
AAACCCAGAGGCTGAACCC

Found at i:10449 original size:19 final size:18

Alignment explanation


    Indices: 10425--10460  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      10415 TGAAGATTTA

                               
      10425 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
      10444 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

      10461 ATAATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:13808 original size:16 final size:16

Alignment explanation


    Indices: 13787--13830  Score: 52
    Period size: 16  Copynumber: 2.7  Consensus size: 16

      13777 AAAGAAAAGA

                      *     
      13787 AAAAATTAAACGAAAT
          1 AAAAATTAAAAGAAAT

                  *      *  
      13803 AAAAATAAAAAGATAT
          1 AAAAATTAAAAGAAAT

                        
      13819 AACAAATTAAAA
          1 AA-AAATTAAAA

      13831 TAGAAATTAA


Statistics
Matches: 23,  Mismatches: 4, Indels: 1
        0.82            0.14        0.04

Matches are distributed among these distances:
  16   15  0.65
  17    8  0.35

ACGTcount: A:0.73, C:0.05, G:0.05, T:0.18


Consensus pattern (16 bp):   
AAAAATTAAAAGAAAT

Found at i:16323 original size:25 final size:24

Alignment explanation


    Indices: 16272--16327  Score: 64
    Period size: 24  Copynumber: 2.4  Consensus size: 24

      16262 GGAGTTGGGT

                                   *
      16272 AGAGAGAA--AAAAGAAAGAAGAG
          1 AGAGAGAAGGAAAAGAAAGAAGAA

                                *    
      16294 A-AGAGAAGGAAAAGGAAAGGAGAA
          1 AGAGAGAAGGAAAA-GAAAGAAGAA

                      
      16318 AGAGAGAAGG
          1 AGAGAGAAGG

      16328 GAGAGAGGAA


Statistics
Matches: 28,  Mismatches: 2, Indels: 5
        0.80            0.06        0.14

Matches are distributed among these distances:
  21    6  0.21
  22    1  0.04
  23    4  0.14
  24    9  0.32
  25    8  0.29

ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00


Consensus pattern (24 bp):   
AGAGAGAAGGAAAAGAAAGAAGAA

Found at i:17513 original size:2 final size:2

Alignment explanation


    Indices: 17506--17533  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      17496 ACATACATAC

                                                     
      17506 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      17534 TAATATGGAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:17733 original size:33 final size:33

Alignment explanation


    Indices: 17696--17761  Score: 114
    Period size: 33  Copynumber: 2.0  Consensus size: 33

      17686 TCTGATTTCA

                                  *          
      17696 ATTAATAGTGTTCCCACCTTTTTAAATTGCATG
          1 ATTAATAGTGTTCCCACCTTTTCAAATTGCATG

                  *                          
      17729 ATTAATGGTGTTCCCACCTTTTCAAATTGCATG
          1 ATTAATAGTGTTCCCACCTTTTCAAATTGCATG

      17762 CCGTTTATGT


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  33   31  1.00

ACGTcount: A:0.26, C:0.20, G:0.14, T:0.41


Consensus pattern (33 bp):   
ATTAATAGTGTTCCCACCTTTTCAAATTGCATG

Found at i:31474 original size:27 final size:29

Alignment explanation


    Indices: 31427--31481  Score: 87
    Period size: 27  Copynumber: 2.0  Consensus size: 29

      31417 GCGACCCGCA

                                 *       
      31427 TTTCCTTTTTTTTTTTCAATCCTTATAGG
          1 TTTCCTTTTTTTTTTTCAATCATTATAGG

                                        
      31456 TTTCC-TTTTTTTTTT-AATCATTATAG
          1 TTTCCTTTTTTTTTTTCAATCATTATAG

      31482 ATTCTTCTTT


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  27   10  0.40
  28   10  0.40
  29    5  0.20

ACGTcount: A:0.16, C:0.15, G:0.05, T:0.64


Consensus pattern (29 bp):   
TTTCCTTTTTTTTTTTCAATCATTATAGG
Done.