Cluster no. 95

Go back to cluster table

Cluster is part of supercluster: 32

Cluster characteristics:

size 3450
size_real 3450
ecount 74241
supercluster 32
annotations_summary 16.09% Class_I/LTR/Ty1_copia/TAR:Ty1-RT
12.26% Class_I/LTR/Ty1_copia/TAR:Ty1-INT
9.51% Class_I/LTR/Ty1_copia/TAR:Ty1-RH
4.75% Class_I/LTR/Ty1_copia/TAR:Ty1-PROT
3.77% Class_I/LTR/Ty1_copia/TAR:Ty1-GAG
0.26% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-INT
0.03% Class_I/LTR/Ty3_gypsy/chromovirus/Tcn1:Ty3-INT
0.03% Class_I/LTR/Ty1_copia/Ale:Ty1-PROT
pair_completeness 0.808176100628931
pbs_score 0.0488199
TR_score 0.6832374941561468
TR_monomer_length 5419.0
loop_index 0.835942028985507
satellite_probability 0.0592276930416326
consensus 
CAAGTGTGAATGAAATTTACTTGTCCCACATCGGCAAAAATATAAGCTAATATGAGCTAATATATCCAAGTTTTACAAAG
GCCAATGGGCCCTTTGGGTCACTTGATTTTGTGAACGGGAGAGGACGCAGATGACCATGAACACACGCGCGCACCACCAC
CGCCCGCCCGGCCCGGCTCGGCTCGGTTCGGTCCGGTCCGCGTCCGTGTTCGGGTTTCGGGTTCGGGCTTGGGCTTGGGC
CCGGTCCACTGAGATATATTGATTTTGCTGAAAGAATGAATACTGTACATGAACAGTATTAAATTCAGGTGCAACCATTC
AACAGTAGACGCGACTGTTGACGAAGAGGTGCGGCCGGACGGGACGAGACATGACCGGACAGAAATTCAGAGGGTTAGGC
GGACCGGGCGCATTGTTTTTTGCGAACGGGTGCAACTATCTGAATGAACAGTTGCAACTCTAATAAAACGTTGTAAAAGC
TATATGAATAGCTGCAACATGAATGAAGTGTTGTAATTGCTGAATGAATGATTGCAACTTAATTAAAAGGTTGCAACTTT
CTAAAATGAAGAGAAGCAATGTTTGATTGCCTATAAAAGGAAAGGGATGCTGATCACATTCCTCACTCAATTCAAGCAAT
CAAATCATTCTTCTTCTCTCTCATTCAAGCTTTCTGTCCTCCATTAATATATCACAAAATTAACGAGCATACTCGTTACA
ATCTCGAGAAGCTATTCGCTGCTGTATCTTGGGAAACTTGCAAAATCAAGTTTTAAGGAAATTGCTAAGGCAAGCCCCAG
CGAAGTTCCTGAAATCCGTAAACTCAACATCTACATCTTAAAACTTTGCAGTTTTATTGATTCAGGAAATGGCAACAGTT
GAATTATCAACTAAAACTGCGACCCACAACAGACCTGATCCATTCAAAGGTGATGGTGATGATTTTCAGACATGGCAGAG
CCAAATGCTGTTCTATCTCACCACACTCGGTCTACAGAGGTACCTCGATGAGGAGGAACCTGTGCCTACAGCAGGCCAAA
CTCAAGAAACACATAGAGATGCGTTTCTGGCGATTGATGCATGGAAACAAGGAGACTTCTTGTGCAGAAATTATATTCTT
AATTGTCTGAACAAGATGTTGTATAAAGTGTATCAGCCACTCAAGACAGCGAAGGCACTTTGGGCTGCACTTGCAAATAA
GTACAAGACACAAAATGTCAGCCTAAAGAAATTCATTGTCGACAAATTTATGGACTACAAGATGGTAGACTCCAAATCAG
TGACTACTCAAGTGCAAGAGCTGCAGATCATCATTCATGAACTTGAATCAGAAGGACATGAAGTTGGAGAGTCATTTCTG
GTTGAAGCAATAACAGGCAAATTGCCCCCGTCATGGAAAGACTACCGCAACTATCTGAAACACAAAAAGAAGGAGATTTC
TTTACAGGATCTCATTGTCAGATTGAAGATTGAGGCAGATAATCGTGGGGTAACACAGCCAAAAGGCGAGGAGGCTTATG
CTGTGGAAGGCTCGAAGAAAAATAAGCCATATGCCAACAAAAAGAAGAACCAGAACAACAAAAGAAAGGCACCAGACAAC
AGATTTAAAGAGCAGAAACAGGCCAAGAAGTTCAATGGTCAGTGTTGGGTATGCGGAAAAACTGGACATGCTGCTAAAGA
TTGTAGGCACAAGAAGCAAGAGAATAACTCAGAAGCACACATGGTGAATAATATGGATATAGACGAATCATCCTTTTCTG
CAGTTGTTTCTGAATGCAATCTGGTCCAGAACCCTGCACAATGGTGGGTAGACACAGGGGCTACACGTCATGTTTGCTCG
GATAAGTCTATGTTTTCCACTTATACCAAATTCGATAAGGAGGAAAAACTATATATGGGAAATTCTGCAATTTCCATGAT
AGAAGGCAGCGGCAATGTCATTCTCAAATTTACTTCGGGAAAGACTATTACTTTGAAAGAAGTGCTACACGTTCCAGAAA
TTCGTAAGAACCTAATTTCAGGACCCGTGCTTTCAAAGAAAGGATTCCGAATGGTGTTTGAATCCGATAAAATGGTTCTG
TCAAAAGCTGGTGTGTATATAGGAAGGGGTTATTTATGTGATGGCCTATTTAAGGCAAATGTAGCCGTAGTCGGCAATAA
CACTATGTATTCTAATTGTGAAATGAATAAAAATAATGTTTCTTATGTGGTTTTGCATGAAACTCTTTTATGGCATGATA
GATTAGGACACATAAACTTCCGAAAAATGAAAAAACTTGCAAATCTAGGATTAATTCCAAAATTTCAAGTAGATAAGAAA
TTCAAATGTGAGACTTGTGTAGAAGCAAAAATGGTCAAAAAGCCATTTAATATTGTTGATAGAAGTACTGAACCTTTAGG
GATGGTACATACTGACTTATGTGATTTTAAGTCATTACCTACAAGAGGTGGGAAAAAGTATTTCATTACTTTTATTGATG
ATTATACACGATATTGCTATGTATATCTTTTAAATAGTAAAGATGAAGCAATCACATCGTTCATCAAATATAAGGCTGAA
GTAGAAAATCAGCTTAACAGAAAGATCAAGATATTGAGATCTGATCGAGGAGGAGAATATGAGTCACCATTTGAACAAAT
ATGTGCAGAAAATGGCATAATTCATCAAAGAACAGCACCATATTCACCACAACAAAATGGTATTGCAGAAAGAAAGAATA
GAACGTTAAAAGATATGATTAACGCAATGCTATTAACTTCTGGCCTACCAACGAACTTGTGGGGGGAAGCCCTGATTATG
TCTAATCATATATTGAATAGGGTTCCTCATAGTAAAACAGGAACAATTCCATATGAGTTATGGAAAGGACATCTACCAAG
CTTCAAATACCTTAAAGTGTGGGGGTGTTTGGCAAAGGTTCCAGTTCCGCCACCCAAGAAGGTCAAACTTGGACCAAAAA
CTGTAGATTGCTACTATTTAGGACCTGCCGAAAATAGTAGTGCATACAGATTTTTAGTATTTAAGTCTGATATAAATGAT
ATCGGAGTAAATACAATTATGGAGTCAAGAGATGCCTCATTCTTTGAAGATGTGTTTCCACATAAAAGAAATGAAGGAGT
ACATGTTCCTAAAAGGACAAGAGAAGAAATTAGTGAGCCACATGAAGATGAAACTTATCGTGAAAATGATGAAGTTGAAC
CTAGAAGGAGTGTAAGGCCACGAACATCTAAATCGTTTGGTTCAGATTATATTACATATGTATTAGAACATGAACCTCAA
ACGTATAAAGAAGCAATGTCATCTTCTGAATCTTCATATTGGAAAGAAGCAGTCAAAAGTGAGATTGACTCAATACTAAG
CAATCAAACTTGGGAATTGGTTAATATTCCACCTGGAATAAAACCAATTGGCTGTAAATGGATATTCAAGAAGAAAATGA
AACCAGATGGTTCCATTGACAAATACAAAGCTAGATTAGTAGCTAAAGGATATCGTCAGAAGGAAGGTATAGACTTCTTT
GATACATATTCACCGGTTACACGAATAACCTCTATAAGAATGCTAATTGCAATCGCATCTATATATAATTTAGAAATTCA
TCAAATGGATGTGAAAACAACATTCTTAAATGGAGATCTCGATGAGGAGATATACATGGAGCAACCTGAAGGTTTCATAT
CCAAAGGAAATGAAAACAAAGTCTGTAGATTAGTAAAATCATTATACGGACTAAAACAAGCTCCAAAACAATGGCATGAA
AAATTTGACAGTGTCATGATGAAAAATGGTTTTCGTATAAATGAATGTGATAAATGTGTTTATTACAAAAGACTTGGTGA
ATCATATGTGATTATTTGTCTATATGTGGATGATATGCTAATCTTTGGTCCTAACACAAAGGTTATAGAAACCATAAAGA
AGATGCTAATAAATCATTTCGACATGAAAGATTTAGGCATAGCAGATGTTATGTTAGGAATAAAAATCATAAAAACATCT
GATGGGATTGAATTATCACAATCACACTATGTAGAGAAGGTGATTGAAAGATTCAAAGATCTTGGGATCAAAGGTGCAAG
AACACCATTCAATCCATCTGAAGTTCTGCATAAAAACACTAATGAGAGTGTCATGCAACTGGAATATTCTCGTGTAATAG
GATGTCTCATGTATATCATGAATTGCACCAGACCAGATATAGCTTATGCAGTAAATAGACTAAGCAGGTATACAAGTAAC
CCAGGAAAAGAACATTGGGCAGCACTAATGAGAGTGTTGGGGTATTTAAAGAACACCACAAATTTTTCCTTACATTATGG
AAAATATCCTGCAGTTCTAGAAGGATATAGTGATGCAAACTGGATATCAGATTCAGAAGAATCAAAATCCACAAGTGGTT
ATGTCTTTACCCTTGCAGGAGCAGCAGTGTCTTGGAAATCTAATAAACAAACATGCATAGCTCGATCCACCATGGAATCT
GAGTTTATTGCATTAGATAAAGCAGGCGAAGAAGCAGAATGGCTTCGTCAATTTTTAGAAGATATTCCATTTTGGCCCAA
ACCTGTACCGGCCATATGTATTCACTGCGATAATCAAGCAGCGTTAAGTAGAGCGCAAAACTTTGTGTATAATGGAAAGT
CACGACATATTCGTCGGCGCCATAATACAGTAAGGCAGTTACTCTCACATGGAATTATTACCATTGATTATGTAAGATCA
ATAGATAACCTAGCGGATCCATTTACTAAAGGTTTATCTAGAGAGAAAATTGACTGCGCATCGAGGGGAATGGGCTTAAA
AGCCTAAAATAACAATGAGTTACCTTATACGGAAACCTATCCTAGCGACTGGAGATCCCACGGACTAGGATCAATAGGCA
AACCAGTTATGAGTAATTCAAGAAGTAATGCATTTTTCTACTCATTCCTATGATGCAAAATAAATGCATACCTACAGAAG
TATTAAAAGGATAAGCTATGCTTTTAATGATGTCCATATCTTGTAAAAGAACAAGTGGGGTATACGTAGGATACTCTTGA
TGGAAGCGATCACCTATGTTAGTGTGAGCTGGGTCGGCTCTATGAGAATTTTCAAAGGCTTAAAATTCTCTAATACACTC
GCAGAACCAAATATGTTCAGGACCAAAATGAACAAAACCAAGAGATTGGATGAGAAGGGAAATAATGTTTTGTAAAACTT
ATTGTCTGGTTATACAATAACGGCTGACGGTTCAAGATGAAATATTTCACCGATTAGCCAAGTATATCCGATAAGTTTTA
ACTAGGGAAGGTTCAAAGTGAAATATCTACCTATCCACGATACAACGTTATTCCATATGTATTCTGTGATATTCCCCTTT
GTGTGGGGGAAAAGTATATTATCATTCATGTGGGGGATTGTTGGAGACTAACCTAAAAA

  

  

    TAREAN_annotation
    Putative LTR element
  

  

    orientation_score
    1
  

 


 
 comparative analysis:


  





 
 Comparative analysis - species read counts:



  

    Species
    Read count
  

   

    S5
    1180
  

  

    S4
    1150
  

  

    S6
    1110
  

 


 
 comparative analysis - number of edges between species:



  

    
    S5
    S4
    S6
  

   

    S5
    9280
    8470
    8430
  

  

    S4
    8470
    7620
    7730
  

  

    S6
    8430
    7730
    8100
  

 


 
 comparative analysis - observed/expected number of edges between species



  

    
    S5
    S4
    S6
  

   

    S5
    1.010
    1.010
    0.985
  

  

    S4
    1.010
    0.998
    0.993
  

  

    S6
    0.985
    0.993
    1.020
  

 


 
 protein domains:



protein domains:


  





 
 Reads annotation summary










	

	 
	
 
		   
		cl_string  
		domain  
		Freq  
		proportion 
	
 

 
TAR Ty1-GAG

TAR

Ty1-GAG

130

0.03768


 

 
TAR Ty1-INT

TAR

Ty1-INT

423

0.12261


 

 
Ale Ty1-PROT

Ale

Ty1-PROT

  1

0.00029


 

 
TAR Ty1-PROT

TAR

Ty1-PROT

164

0.04754


 

 
TAR Ty1-RH

TAR

Ty1-RH

328

0.09507


 

 
TAR Ty1-RT

TAR

Ty1-RT

555

0.16087


 

 
Reina Ty3-INT

Reina

Ty3-INT

  9

0.00261


 

 
Tcn1 Ty3-INT

Tcn1

Ty3-INT

  1

0.00029


 
	


 

 


 
 clusters with similarity:



  

    
      



 

    Cluster
    Number of similarity hits
  

      

   		
 

 

   
     

       



  

    38
    1
  

       

     

  		
 




 
 clusters connected through mates:



  

    
      




 

    Cluster
    Number of shared
 read pairs		
    k
  

      

   		
 

 

   
     

       




  

    935
    6
    0.0316
  

  

    1910
    6
    0.0322
  

  

    1
    5
    0.00143
  

  

    58
    5
    0.00364
  

  

    928
    4
    0.0211
  

  

    2080
    4
    0.0214
  

  

    2130
    4
    0.0215
  

  

    33
    3
    0.00298
  

  

    83
    3
    0.00235
  

  

    113
    3
    0.00485
  

  

    1520
    3
    0.016
  

  

    5050
    3
    0.0162
  

  

    5
    2
    0.000835
  

  

    32
    2
    0.00133
  

  

    80
    2
    0.00545
  

  

    142
    2
    0.00362
  

  

    3460
    2
    0.0108
  

  

    5420
    2
    0.0108
  

  

    5430
    2
    0.0108
  

  

    15000
    2
    0.0109
  

  

    18100
    2
    0.0109
  

  

    7
    1
    0.000429
  

  

    10
    1
    0.000415
  

  

    11
    1
    0.000433
  

  

    12
    1
    0.000341
  

  

    19
    1
    0.000591
  

  

    22
    1
    0.00101
  

  

    30
    1
    0.000556
  

  

    35
    1
    0.00082
  

  

    38
    1
    0.00142
  

  

    42
    1
    0.00091
  

  

    45
    1
    0.000838
  

  

    49
    1
    0.000761
  

  

    54
    1
    0.000841
  

  

    57
    1
    0.000769
  

  

    60
    1
    0.00222
  

  

    61
    1
    0.000728
  

  

    65
    1
    0.00128
  

  

    77
    1
    0.00101
  

  

    90
    1
    0.00149
  

  

    127
    1
    0.00285
  

  

    137
    1
    0.00182
  

  

    150
    1
    0.00226
  

  

    171
    1
    0.00311
  

  

    1000
    1
    0.00533
  

  

    1030
    1
    0.00539
  

  

    2510
    1
    0.00536
  

  

    6500
    1
    0.00541
  

  

    6960
    1
    0.00541
  

  

    8340
    1
    0.00542
  

  

    8370
    1
    0.00542
  

  

    8620
    1
    0.00542
  

  

    16400
    1
    0.00543
  

  

    17800
    1
    0.00543
  

  

    18200
    1
    0.00543
  

  

    18500
    1
    0.00543
  

  

    20000
    1
    0.00543
  

  

    20100
    1
    0.00543
  

  

    24400
    1
    0.00543
  

  

    25100
    1
    0.00543
  

  

    29100
    1
    0.00543
  

  

    31500
    1
    0.00543
  

  

    33500
    1
    0.00543
  

  

    34800
    1
    0.00543
  

  

    40700
    1
    0.00543
  

  

    45500
    1
    0.00543
  

  

    46400
    1
    0.00543