Cluster no. 50

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Cluster is part of supercluster: 22

Cluster characteristics:

size 5875
size_real 5875
ecount 1948964
supercluster 22
annotations_summary 0.80% Class_I/LTR/Ty1_copia/Ivana:Ty1-RT
0.02% Class_I/LTR/Ty1_copia/Ivana:Ty1-RH
0.02% organelle/plastid
0.02% Class_I/LINE:LINE-RT
0.02% Class_I/pararetrovirus:PARA-RT
0.02% Class_I/LTR/Ty1_copia/Ty1-outgroup:Ty1-RT
pair_completeness 0.866857324435971
pbs_score 0.0
TR_score 0.5862605542983673
TR_monomer_length 356.0
loop_index 0.923181740759666
satellite_probability 0.429075228287152
consensus 
GTCAATGGATAGTTTAATGCCCAAAAAAGACTATCCGAACCTCAATCGGGTCTCGGAAGTTTTTTACCCTTCGTTTTTTC
GACACGTGGATTTTTTCGGTAAAACGGGATTACCGTGGCTGGTCTTCGATTTACCATCGCTGGAGAGTGGTGCACCATGG
TACTGCACCGTTTCAAATCCATGCACGCATTTCTAAAAGTCGTACGGCACTGTTTCGTCATTTTGGACGGATGTTGCACC
CTGTGGATATCGATTATTCGGAGGGCCATAACTCTTGGCTCGTTTAGAGTTACGGGAGCCATAACCAGTCAAAACGAAGG
CCTCGGTGAGTTCTACAGCTTTGACAGCTTTCAGCC

  

  

    TAREAN_annotation
    Putative satellite (low confidence)
  

  

    orientation_score
    0.999998461353035
  

 


 
 comparative analysis:


  





 
 Comparative analysis - species read counts:



  

    Species
    Read count
  

   

    S8
       8
  

  

    S5
       7
  

  

    S4
       1
  

  

    S7
      14
  

  

    S9
       6
  

  

    S6
       7
  

  

    S2
    1950
  

  

    S1
    1830
  

  

    S3
    2050
  

 


 
 comparative analysis - number of edges between species:



  

    
    S8
    S5
    S4
    S7
    S9
    S6
    S2
    S1
    S3
  

   

    S8
      4.0
      4.5
     0.0
       6.0
      3
      3.0
       716
       698
       738.0
  

  

    S5
      4.5
      2.0
     0.0
       4.5
      1
      2.5
       629
       570
       642.0
  

  

    S4
      0.0
      0.0
     0.0
       0.0
      0
      0.0
         9
        10
         8.5
  

  

    S7
      6.0
      4.5
     0.0
       5.0
      5
      3.0
      1350
      1250
      1450.0
  

  

    S9
      3.0
      1.0
     0.0
       5.0
      1
      1.0
       642
       580
       644.0
  

  

    S6
      3.0
      2.5
     0.0
       3.0
      1
      1.0
       518
       487
       550.0
  

  

    S2
    716.0
    629.0
     9.0
    1350.0
    642
    518.0
    216000
    202000
    228000.0
  

  

    S1
    698.0
    570.0
    10.0
    1250.0
    580
    487.0
    202000
    188000
    212000.0
  

  

    S3
    738.0
    642.0
     8.5
    1450.0
    644
    550.0
    228000
    212000
    240000.0
  

 


 
 comparative analysis - observed/expected number of edges between species



  

    
    S8
    S5
    S4
    S7
    S9
    S6
    S2
    S1
    S3
  

   

    S8
    1.650
    2.180
    0.000
    1.320
    1.430
    1.720
    0.991
    1.030
    0.968
  

  

    S5
    2.180
    1.130
    0.000
    1.160
    0.559
    1.680
    1.020
    0.990
    0.986
  

  

    S4
    0.000
    0.000
    0.000
    0.000
    0.000
    0.000
    0.983
    1.170
    0.881
  

  

    S7
    1.320
    1.160
    0.000
    0.588
    1.280
    0.917
    0.997
    0.990
    1.010
  

  

    S9
    1.430
    0.559
    0.000
    1.280
    0.553
    0.663
    1.030
    0.996
    0.978
  

  

    S6
    1.720
    1.680
    0.000
    0.917
    0.663
    0.795
    0.995
    1.000
    1.000
  

  

    S2
    0.991
    1.020
    0.983
    0.997
    1.030
    0.995
    0.998
    1.000
    1.000
  

  

    S1
    1.030
    0.990
    1.170
    0.990
    0.996
    1.000
    1.000
    0.999
    1.000
  

  

    S3
    0.968
    0.986
    0.881
    1.010
    0.978
    1.000
    1.000
    1.000
    0.999
  

 


 
 protein domains:



protein domains:


  





 
 Reads annotation summary










	

	 
	
 
		   
		cl_string  
		domain  
		Freq  
		proportion 
	
 

 
plastid 

plastid



 1

0.00017


 

 
LINE LINE-RT

LINE

LINE-RT

 1

0.00017


 

 
pararetrovirus PARA-RT

pararetrovirus

PARA-RT

 1

0.00017


 

 
Ivana Ty1-RH

Ivana

Ty1-RH

 1

0.00017


 

 
Ivana Ty1-RT

Ivana

Ty1-RT

47

0.00800


 

 
Ty1-outgroup Ty1-RT

Ty1-outgroup

Ty1-RT

 1

0.00017


 
	


 

 


 
 clusters connected through mates:



  

    
      




 

    Cluster
    Number of shared
 read pairs		
    k
  

      

   		
 

 

   
     

       




  

    108
    20
    0.0323
  

  

    175
    11
    0.0271
  

  

    124
    6
    0.0139
  

  

    21
    3
    0.00437
  

  

    226
    3
    0.011
  

  

    9210
    3
    0.0142
  

  

    17100
    3
    0.0142
  

  

    19500
    3
    0.0142
  

  

    7
    2
    0.00121
  

  

    23
    2
    0.00149
  

  

    47500
    2
    0.0095
  

  

    13
    1
    0.000577
  

  

    30
    1
    0.000821
  

  

    42
    1
    0.00126
  

  

    77
    1
    0.00223
  

  

    100
    1
    0.00157
  

  

    113
    1
    0.00169
  

  

    127
    1
    0.00284
  

  

    168
    1
    0.00194
  

  

    180
    1
    0.00424
  

  

    189
    1
    0.00295
  

  

    196
    1
    0.00274
  

  

    200
    1
    0.00304
  

  

    275
    1
    0.00365
  

  

    294
    1
    0.00416
  

  

    362
    1
    0.00441
  

  

    6470
    1
    0.00472
  

  

    33200
    1
    0.00475
  

  

    49100
    1
    0.00475
  

       

     

  		
 





  
CL50 ----> CL108

       image
     
 No. of shared pairs: :20





  
CL50 ----> CL175

       image
     
 No. of shared pairs: :11