Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024397.1 Corchorus olitorius cultivar O-4 contig24430, 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: 9683
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:688 original size:12 final size:11

Alignment explanation


    Indices: 671--718  Score: 78
    Period size: 12  Copynumber: 4.2  Consensus size: 11

        661 TTAATTCACT

                       
        671 TTTGATTTGAA
          1 TTTGATTTGAA

                        
        682 CTTTGATTTGAA
          1 -TTTGATTTGAA

                        
        694 TTTCGATTTGAA
          1 TTT-GATTTGAA

                       
        706 TTTGATTTGAA
          1 TTTGATTTGAA

              
        717 TT
          1 TT

        719 ACTTAACGAA


Statistics
Matches: 35,  Mismatches: 0, Indels: 3
        0.92            0.00        0.08

Matches are distributed among these distances:
  11   13  0.37
  12   22  0.63

ACGTcount: A:0.25, C:0.04, G:0.17, T:0.54


Consensus pattern (11 bp):   
TTTGATTTGAA

Found at i:713 original size:23 final size:24

Alignment explanation


    Indices: 674--718  Score: 83
    Period size: 23  Copynumber: 1.9  Consensus size: 24

        664 ATTCACTTTT

                                    
        674 GATTTGAACTTTGATTTGAATTTC
          1 GATTTGAACTTTGATTTGAATTTC

                                  
        698 GATTTGAA-TTTGATTTGAATT
          1 GATTTGAACTTTGATTTGAATT

        719 ACTTAACGAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  23   13  0.62
  24    8  0.38

ACGTcount: A:0.27, C:0.04, G:0.18, T:0.51


Consensus pattern (24 bp):   
GATTTGAACTTTGATTTGAATTTC

Found at i:4830 original size:7 final size:7

Alignment explanation


    Indices: 4818--4847  Score: 51
    Period size: 7  Copynumber: 4.1  Consensus size: 7

       4808 TTAATCTAAC

                   
       4818 TTTCTTT
          1 TTTCTTT

                    
       4825 TTTCTTCT
          1 TTTCTT-T

                   
       4833 TTTCTTT
          1 TTTCTTT

                   
       4840 TTTCTTT
          1 TTTCTTT

             
       4847 T
          1 T

       4848 ATTACTCTAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
   7   15  0.68
   8    7  0.32

ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83


Consensus pattern (7 bp):   
TTTCTTT

Found at i:7050 original size:13 final size:13

Alignment explanation


    Indices: 7032--7057  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       7022 GTTATATAGA

                         
       7032 CTGTAAAACAAAG
          1 CTGTAAAACAAAG

                         
       7045 CTGTAAAACAAAG
          1 CTGTAAAACAAAG

       7058 ACAAATGTTA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15


Consensus pattern (13 bp):   
CTGTAAAACAAAG

Found at i:8675 original size:41 final size:41

Alignment explanation


    Indices: 8629--8716  Score: 113
    Period size: 41  Copynumber: 2.1  Consensus size: 41

       8619 TAGAGACGAA

                          *   *  * *                 
       8629 ATTGAATCAATAAATAAATATTACCCTAAATCAGGGACAAT
          1 ATTGAATCAATAAACAAACATAAACCTAAATCAGGGACAAT

                       * *                        *  
       8670 ATTGAATCAATTACCAAACATAAACCTAAATCAGGGACTAT
          1 ATTGAATCAATAAACAAACATAAACCTAAATCAGGGACAAT

                  
       8711 ATTGAA
          1 ATTGAA

       8717 AATGGGAAAA


Statistics
Matches: 40,  Mismatches: 7, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  41   40  1.00

ACGTcount: A:0.48, C:0.16, G:0.10, T:0.26


Consensus pattern (41 bp):   
ATTGAATCAATAAACAAACATAAACCTAAATCAGGGACAAT
Done.