Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020224.1 Corchorus olitorius cultivar O-4 contig20257, 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: 19184
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:4551 original size:22 final size:22

Alignment explanation


    Indices: 4521--4565  Score: 72
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       4511 ACTGTATCCC

                *             *   
       4521 TATGGCAGCAATAAATCTGACT
          1 TATGACAGCAATAAATCTAACT

                                  
       4543 TATGACAGCAATAAATCTAACT
          1 TATGACAGCAATAAATCTAACT

             
       4565 T
          1 T

       4566 CTAGCAGCAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29


Consensus pattern (22 bp):   
TATGACAGCAATAAATCTAACT

Found at i:4573 original size:22 final size:21

Alignment explanation


    Indices: 4525--4575  Score: 66
    Period size: 22  Copynumber: 2.3  Consensus size: 21

       4515 TATCCCTATG

                          *      
       4525 GCAGCAATAAATCTGACTTAT
          1 GCAGCAATAAATCTAACTTAT

                                * 
       4546 GACAGCAATAAATCTAACTTCT
          1 G-CAGCAATAAATCTAACTTAT

                    
       4568 AGCAGCAA
          1 -GCAGCAA

       4576 GAAAAATTGA


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  21    1  0.04
  22   24  0.92
  23    1  0.04

ACGTcount: A:0.41, C:0.22, G:0.14, T:0.24


Consensus pattern (21 bp):   
GCAGCAATAAATCTAACTTAT

Found at i:7542 original size:21 final size:21

Alignment explanation


    Indices: 7518--7559  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       7508 TCAGATAAAA

                                 
       7518 GCTTTACACCTTCAAAGGATG
          1 GCTTTACACCTTCAAAGGATG

                  *              
       7539 GCTTTAGACCTTCAAAGGATG
          1 GCTTTACACCTTCAAAGGATG

       7560 ATATAGGCAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29


Consensus pattern (21 bp):   
GCTTTACACCTTCAAAGGATG

Found at i:7966 original size:64 final size:63

Alignment explanation


    Indices: 7893--8015  Score: 221
    Period size: 64  Copynumber: 1.9  Consensus size: 63

       7883 TATCATTGGC

                                                                             
       7893 AGGTTTAATTAGTGTTTGATTTAATTAAAGTTTTTTTTTTA-ATCAAATAATCACTTTCACATCA
          1 AGGTTTAATTAGTGTTTGATTTAATTAAAG--TTTTTTTTAGATCAAATAATCACTTTCACATCA

                                                                       
       7957 AGGTTTAATTAGTGTTTGATTTAATTAAAGTTTTTTTTAGATCAAATAATCACTTTCAC
          1 AGGTTTAATTAGTGTTTGATTTAATTAAAGTTTTTTTTAGATCAAATAATCACTTTCAC

       8016 TAATCAATAA


Statistics
Matches: 58,  Mismatches: 0, Indels: 3
        0.95            0.00        0.05

Matches are distributed among these distances:
  62    9  0.16
  63   19  0.33
  64   30  0.52

ACGTcount: A:0.33, C:0.09, G:0.11, T:0.48


Consensus pattern (63 bp):   
AGGTTTAATTAGTGTTTGATTTAATTAAAGTTTTTTTTAGATCAAATAATCACTTTCACATCA
Done.