Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022852.1 Corchorus olitorius cultivar O-4 contig22885, 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: 10070
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31


Found at i:881 original size:21 final size:19

Alignment explanation


    Indices: 857--896  Score: 53
    Period size: 20  Copynumber: 2.0  Consensus size: 19

        847 TTTGGTAGTT

                     *           
        857 TTAGATTTGTATATGTCTAAG
          1 TTAGA-TTGGATAT-TCTAAG

                               
        878 TTAGATTGGATATTCTAAG
          1 TTAGATTGGATATTCTAAG

        897 GCCGGATTTG


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  19    6  0.33
  20    7  0.39
  21    5  0.28

ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45


Consensus pattern (19 bp):   
TTAGATTGGATATTCTAAG

Found at i:3643 original size:7 final size:7

Alignment explanation


    Indices: 3631--3723  Score: 150
    Period size: 7  Copynumber: 13.3  Consensus size: 7

       3621 AAGGTTGAAT

                   
       3631 ATTTGGC
          1 ATTTGGC

                   
       3638 ATTTGGC
          1 ATTTGGC

                   
       3645 ATTTGGC
          1 ATTTGGC

                   
       3652 ATTTGGC
          1 ATTTGGC

                   
       3659 ATTTGGC
          1 ATTTGGC

                   
       3666 ATTTGGC
          1 ATTTGGC

             *     
       3673 ACTTGGC
          1 ATTTGGC

                   
       3680 ATTTGGC
          1 ATTTGGC

             *     
       3687 ACTTGGC
          1 ATTTGGC

                   
       3694 ATTTGGC
          1 ATTTGGC

             *     
       3701 ACTTGGC
          1 ATTTGGC

                   
       3708 ATTTGGC
          1 ATTTGGC

             *     
       3715 ACTTGGC
          1 ATTTGGC

              
       3722 AT
          1 AT

       3724 AGTCATGTAT


Statistics
Matches: 78,  Mismatches: 8, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   7   78  1.00

ACGTcount: A:0.15, C:0.18, G:0.28, T:0.39


Consensus pattern (7 bp):   
ATTTGGC

Found at i:7757 original size:28 final size:27

Alignment explanation


    Indices: 7725--7796  Score: 99
    Period size: 28  Copynumber: 2.6  Consensus size: 27

       7715 ATAAGTGAAT

                 *                      
       7725 AATATACAATATAATTTTTTTGAGGGAA
          1 AATATTCAATATAATTTTTTTGA-GGAA

                                    **  
       7753 AATATTCAATATAATTTTTTTTGATTAA
          1 AATATTCAATATAA-TTTTTTTGAGGAA

                            
       7781 AATATTCAATATAATT
          1 AATATTCAATATAATT

       7797 AAGACTAGTA


Statistics
Matches: 40,  Mismatches: 3, Indels: 3
        0.87            0.07        0.07

Matches are distributed among these distances:
  27    2  0.05
  28   29  0.73
  29    9  0.22

ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46


Consensus pattern (27 bp):   
AATATTCAATATAATTTTTTTGAGGAA

Found at i:8342 original size:5 final size:5

Alignment explanation


    Indices: 8332--8373  Score: 84
    Period size: 5  Copynumber: 8.4  Consensus size: 5

       8322 CCCTTATCAT

                                                              
       8332 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA
          1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA

       8374 ATTTATATCA


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   37  1.00

ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60


Consensus pattern (5 bp):   
TATTA

Done.