Cluster no. 111

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Cluster is part of supercluster: 48

Cluster characteristics:

size 3023
size_real 3023
ecount 38651
supercluster 48
annotations_summary 15.68% Class_I/LTR/Ty1_copia/TAR:Ty1-RT
13.93% Class_I/LTR/Ty1_copia/TAR:Ty1-INT
9.20% Class_I/LTR/Ty1_copia/TAR:Ty1-RH
3.11% Class_I/LTR/Ty1_copia/TAR:Ty1-PROT
3.01% Class_I/LTR/Ty1_copia/TAR:Ty1-GAG
0.60% Class_I/LTR/Ty1_copia/Ivana:Ty1-RH
0.13% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-INT
0.10% Class_I/LTR/Ty1_copia/Ale:Ty1-RT
0.03% Class_I/LTR/Ty1_copia/Ivana:Ty1-RT
pair_completeness 0.782429245283019
pbs_score 0.047337
TR_score 0.6123723496206507
TR_monomer_length 5417.0
loop_index 0.790274561693682
satellite_probability 0.0442745530792202
consensus 
GAATGAAATTTACTTGTCCCACATCGGCAAAAATAAAAGCTACTATGAGCTAATATATCCAAGTTTTACAAAGGCCAATG
GGCCCTTTGGGTCACTTGATTTTGTGAACGGGAGAGGACGCAGATGACCATGAACACACGCGCGCACCACCACCGCCCGC
CCGGCCCGGCTCGGCTCGGTTCGGTCCGGTCCGCGTCCGTGTTCGGGTTTCGGGTTCGGGCTTGGGCTTGGGCCCGGTCC
ACTGAGATATATTGATTTTGCTGAAAGAATGAATACTGTACATGAACAGTAGACACGGACGGGTGCAACCATTCAACAGT
AGACGCGACTGTTGACGAAGAGGTGCGGCCGGACGGGACGAGACATGACCGGACAGAAATTCAGAGGGTTAGGCGGACCG
GGCGCATTGTTTTTTGCGAACGGGTGCAACTATCTGAATGAACAGTTGCAACTCTAATAAAACGTTGTAAAAGCTATATG
AATAGCTGCAACATGAATGAAGTGTTGTAATTGCTGAATGAATGATTGCAACTTAATTAAAAGGTTGCAACTTTCTAAAA
TGAAGAGAAGCAATGTTTGATTGCCTATAAAAGGAAAGGGATGCTGATCACATTCCTCACTCAATTCAAGCAATCAAATC
ATTCTTCTTCTCTCTCATTCAAGCTTTCTGTCCTCCATTAATATATCACAAAATTAACGAGCATACTCGTTACAATCTCG
AGAAGCTATTCGCTGCTGTATCTTGGGAAACTTGCAAAATCAAGTTTTAAGGAAATTGCTAAGGCAAGCCCCAGCGAAGT
TCCTGAAATCCGTAAACTCAACATCTACATCTTAAAACTTTGCAGTTTTATTGATTCAGGAAATGGCAACAGTTGAATTA
TCAACTAAAACTGCGACCCACAACAGACCTGATCCATTCAAAGGTGATGGTGATGATTTTCAGACATGGCAGAGCCAAAT
GCTGTTCTATCTCACCACACTCGGTCTACAGAGGTACCTCGATGAGGAGGAACCTGTGCCTACAGCAGGCCAAACTCAAG
AAACACATAGAGATGCGTTTCTGGCGATTGATGCATGGAAACAAGGAGACTTCTTGTGCAGAAATTATATTCTTAATTGT
CTGAACAAGATGTTGTATAAAGTGTATCAGCCACTCAAGACAGCGAAGGCACTTTGGGCTGCACTTGCAAATAAGTACAA
GACACAAAATGTCAGCCTAAAGAAATTCATTGTCGACAAATTTATGGACTACAAGATGGTAGACTCCAAATCAGTGACTA
CTCAAGTGCAAGAGCTGCAGATCATCATTCATGAACTTGAATCAGAAGGACATGAAGTTGGAGAGTCATTTCTGGTTGAA
GCAATAACAGGCAAATTGCCCCCGTCATGGAAAGACTACCGCAACTATCTGAAACACAAAAAGAAGGAGATTTCTTTACA
GGATCTCATTGTCAGATTGAAGATTGAGGCAGATAATCGTGGGGTAACACAGCCAAAAGGCGAGGAGGCTTATGCTGTGG
AAGGCTCGAAGAAAAATAAGCCATATGCCAACAAAAAGAAGAACCAGAACAACAAAAGAAAGGCACCAGACAACAGATTT
AAAGAGAAGAAGCAGGCCAAGAAGTTCAATGGTCAGTGTTGGGTATGCGGAAAAACTGGACATGCTGCTAAAGATTGTAG
GCACAAGAAGCAAGAAAATAACTCAGAAGCACACATGGTGAATAATATGGATATAGACGAATCATCCTTTTCTGCAGTTG
TTTCTGAATGCAATCTGGTCCAGAACCCTGCACAATGGTGGGTAGACACAGGGGCTACACGTCATGTTTGCTCGGATAAG
TCTATGTTTTCCACTTATACCAAATTCGATAAGGAGGAAAAACTATATATGGGAAATTCTGCAATTTCCATGATAGAAGG
CAGCGGCAATGTCATTCTCAAATTTACTTCGGGAAAGACTATTACTTTGAAAGAAGTGCTACACGTTCCAGAAATTCGTA
AGAACCTAATTTCAGGACCCGTGCTTTCAAAGAAAGGATTCCGAATGGTGTTTGAATCCGATAAAATGGTTCTGTCAAAA
GCTGGTGTGTATATAGGAAGGGGTTATTTATGTGATGGCCTATTTAAGGCAAATGTAGCCGTAATCGGCAATAACACTAT
GTATTCTGATTGTGAAATGAATAAAAATAATGTTTCTTATGTGGTTTTGCATGAAACTCTTTTATGGCATGATAGATTAG
GACACATAAACTTCCGAAAAATGAAAAAACTTGCAAACTTAGGATTAATTCCAAAATTTCAAGTAGATAAGAAATACAAA
TGTGAGACTTGTGTAGAAGCAAAAATGGTCAAAAAACCATTTAATATTGTTGATAGAAGTACTGAACCATTAGGGATGGT
ACATACTGACTTATGTGATTTTAAGTCATTACCTACAAGAGGTGGGAAAAAGTATTTTATTACTTTTATTGATGATTATA
CACGATATTGCTATGTATATCTTTTAAATAGTAAAGATGAAGCAATAACATCGTTCATAAAATATAAGGCTGAAGTAGAA
AATCAGCTTAATAAAAAGATCAAGATATTGAGATCTGATCGAGGTGGAGAATATGAATCACCATTTGAACAATTATGTGC
AGAAAATGGCATAATTCATCAAACAACAGCACCATATTCACCACAACAAAATGGTATTGCCGAGAGAAAGAATAGAACGT
TAAAAGATATGATTAACGCAATGCTATTAACTTCTGGCCTACCGACGAACTTGTGGGGGGAAGCCCTAAATATGTCTAAT
CATATATTGAACAGGGTTCCTCACAGTAAAACAGGAACAATTCCATATGAGTTATGGAAAGGACACCTACCAAGCTTCAA
ATACCTTAAAGTGTGGGGGTGTTTGGCAAAGGTTCCAGTTCCGCCTCCCAAGAAGGTCAAACTTGGACCAAAAACTGTAG
ATTGCTACTATTTAGGACCTGCCGAAAATAGTAGTGCATACAGATTTTTAGTATTTAAGTCTGATATAAATGATATCGGT
GTAAATACAATTATGGAGTCAAGAGATGCCTCATTCTTTGAAGATGTGTTTCCACATAAAAGGAATGAAGGAGTACATGT
TCCTAAAAGGACAAGAGAAGAAATTAGTGAGCCACATGAAGATGAAACTTATCGTGAAAATGATGAAGTTGAACCTAGAA
GGAGTGTAAGGCCACGAACATCTAAATCGTTTGGTTCAGATTTTATTACATATGTATTAGAACATGAACCTCAAACGTAT
AAAGAAGCAATGTCATCTTCTGAATCTTCATATTGGAAAGAAGCAGTCAAAAGTGAGATTGATTCAATACTAAGCAATCA
AACTTGGGAATTGGTTAATATTCCACCTGGAATAAAACCAATTGGCTGCAAATGGATATTCAAGAAGAAAATGAAACCAG
ATGGTTCCATTGACAAATACAAAGCTAGATTAGTAGCTAAAGGATATCGTCAGAAGGAAGGTATAGACTTCTTTGATACA
TATTCACCGGTTACACGAATAACCTCTATAAGAATGCTAATTGCAATCGCATCTATATATAATTTAGAAATTCATCAAAT
GGATGTAAAAACAACATTCTTAAATGGAGATCTCGATGAGGAGATATACATGGAGCAACCTGAAGGTTTTATATCCAAAG
GAAATGAAAACAAAGTCTGTAGATTAGTAAAATCATTATACGGACTAAAACAAGCTCCAAAACAATGGCATGAAAAATTT
GACAGTGTCATGATGAAAAATGGTTTTCGTATAAATGAATGTGATAAATGTGTTTATTACAAAAGACTTGGTGAATCATA
TGTGATTATTTGTCTATATGTGGACGATATGCTAATCTTTGGTCCTAACACTAAGGTTATAGAAACCATAAAGAAGATGT
TAATAAATCATTTCGATATGAAAGATTTAGGCATAGCAGATGTTATGTTAGGAATAAAAATAATAAAAACATCTGATGGG
ATTGAATTATCACAATCACATTATGTAGAGAAGGTGATTGAAAGATTCAAAGATCTTGGGATCAAAGGTGCAAGAACACC
GTTCAATCCATCTGAAGTTCTGCATAAAAACACTAATGAGAGTGTAATGCAACTGGAATATTCTCGTGTAATAGGATGTC
TCATGTATATCATGAATTGCACAAGACCAGATATAGCTTATGCAGTAAATAGACTAAGCAGGTATACAAGTAACCCAGGA
AAAGAACATTGGGCAGCACTAATGAGAGTGTTGGGGTATTTAAAGAACACCACAAATTTTTCCTTACATTATGGAAAATA
TCCTGCAGTTCTAGAAGGATATAGTGATGCAAACTGGATATCAGATTCAGAAGAATCAAAATCCACAAGTGGTTATGTCT
TTACCCTTGCAGGAGCAGCAGTGTCTTGGAAATCTAATAAACAAACATGCATAGCTCGATCCACCATGGAATCTGAGTTT
ATTGCATTAGATAAAGCAGGCGAAGAAGCAGAATGGCTTCGTCAATTTTTAGAAGATATTCCATTTTGGCCAAAACCTGT
ACCGGCCATATGTATTCACTGCGATAATCAAGCAGCGCTAAGTAGAGCGCAAAACTTTGTGTATAATGGAAAGTCACGAC
ATATTCGTCGGCGCCATAATACAGTAAGGCAGTTACTCTCACATGGAATTATTTCCATTGATTATGTAAGATCAAAAGAT
AACCTAGCGGATCCATTTACTAAAGGTTTATCTAGAGAGAAAATTGACTGCGCATCGAGGGGAATGGGCTTAAAAGCCTA
AAATAACAATGAGTTACCTTATACGGAAACCTATCCTAGCGACTGGAGATCCCACGGACTAGGATCAATAGGCAAACCAG
TTATGAGTAATTCAAGAAGTAATGCATTTTTCTACTCATTCCTATGATGCAAAATAAATGCATACCTACAGAAGTATTAA
AAGGATAAGCTATGCTTTTAATGATGTCCATATCTTGTAAAAGAACAAGTGGGGTATACGTAGGATACTCTTGATGGAAG
CGATCACCTATGTTAGTGTGAGCTGGGTCGGCTCTATGAGAATTTTCAAAGGCTTAAAATTCTCTAATACACTCGCAGAA
CCAAATATGTTCAGGACCAAAATGAACAAAACCAAGAGATTGGATGAGAAGGGAAATAATGTTTTGTAAAACTTATTGTC
TGGTTATACAATAACGGCTGACGGTTCAAGATGAAATATTTCACCGATTAGCCAAGTATATCCGATAAGTTTTAACTAGG
GAAGGTTCAAAGTGAAATATCTACCTATCCACGATACAACATTATTCCATATGTATTCTGTGATATTCCCCTTTGTGTGG
GGGAAAAGTATATTATCATTCATGTGGGGGATTGTTGGAGACTATCTCTTGCAAAGT

  

  

    TAREAN_annotation
    Putative LTR element
  

  

    orientation_score
    1
  

 


 
 comparative analysis:


  





 
 Comparative analysis - species read counts:



  

    Species
    Read count
  

   

    S8
     53
  

  

    S5
    703
  

  

    S4
    687
  

  

    S7
     36
  

  

    S9
     43
  

  

    S6
    692
  

  

    S2
    275
  

  

    S1
    256
  

  

    S3
    278
  

 


 
 comparative analysis - number of edges between species:



  

    
    S8
    S5
    S4
    S7
    S9
    S6
    S2
    S1
    S3
  

   

    S8
    17.0
      58.5
      49.5
    16.0
    16.5
      54.0
     57
     64.5
     61.0
  

  

    S5
    58.5
    3190.0
    3180.0
    44.0
    42.0
    3250.0
    154
    264.0
    201.0
  

  

    S4
    49.5
    3180.0
    3120.0
    32.0
    31.0
    3070.0
    154
    246.0
    162.0
  

  

    S7
    16.0
      44.0
      32.0
     8.0
    11.5
      38.5
     33
     55.5
     46.5
  

  

    S9
    16.5
      42.0
      31.0
    11.5
    15.0
      34.0
     54
     53.0
     62.0
  

  

    S6
    54.0
    3250.0
    3070.0
    38.5
    34.0
    3300.0
    173
    246.0
    208.0
  

  

    S2
    57.0
     154.0
     154.0
    33.0
    54.0
     173.0
    492
    504.0
    508.0
  

  

    S1
    64.5
     264.0
     246.0
    55.5
    53.0
     246.0
    504
    498.0
    512.0
  

  

    S3
    61.0
     201.0
     162.0
    46.5
    62.0
     208.0
    508
    512.0
    518.0
  

 


 
 comparative analysis - observed/expected number of edges between species



  

    
    S8
    S5
    S4
    S7
    S9
    S6
    S2
    S1
    S3
  

   

    S8
    4.230
    0.553
    0.484
    5.510
    5.070
    0.511
    2.630
    2.590
    2.630
  

  

    S5
    0.553
    1.140
    1.180
    0.575
    0.490
    1.170
    0.268
    0.403
    0.328
  

  

    S4
    0.484
    1.180
    1.190
    0.432
    0.374
    1.140
    0.279
    0.387
    0.274
  

  

    S7
    5.510
    0.575
    0.432
    3.810
    4.890
    0.503
    2.100
    3.080
    2.770
  

  

    S9
    5.070
    0.490
    0.374
    4.890
    5.700
    0.397
    3.070
    2.630
    3.300
  

  

    S6
    0.511
    1.170
    1.140
    0.503
    0.397
    1.190
    0.303
    0.375
    0.340
  

  

    S2
    2.630
    0.268
    0.279
    2.100
    3.070
    0.303
    4.190
    3.750
    4.050
  

  

    S1
    2.590
    0.403
    0.387
    3.080
    2.630
    0.375
    3.750
    3.220
    3.550
  

  

    S3
    2.630
    0.328
    0.274
    2.770
    3.300
    0.340
    4.050
    3.550
    3.860
  

 


 
 protein domains:



protein domains:


  





 
 Reads annotation summary










	

	 
	
 
		   
		cl_string  
		domain  
		Freq  
		proportion 
	
 

 
TAR Ty1-GAG

TAR

Ty1-GAG

 91

0.03010


 

 
TAR Ty1-INT

TAR

Ty1-INT

421

0.13927


 

 
TAR Ty1-PROT

TAR

Ty1-PROT

 94

0.03109


 

 
Ivana Ty1-RH

Ivana

Ty1-RH

 18

0.00595


 

 
TAR Ty1-RH

TAR

Ty1-RH

278

0.09196


 

 
Ale Ty1-RT

Ale

Ty1-RT

  3

0.00099


 

 
Ivana Ty1-RT

Ivana

Ty1-RT

  1

0.00033


 

 
TAR Ty1-RT

TAR

Ty1-RT

474

0.15680


 

 
Reina Ty3-INT

Reina

Ty3-INT

  4

0.00132


 
	


 

 


 
 clusters with similarity:



  

    
      



 

    Cluster
    Number of similarity hits
  

      

   		
 

 

   
     

       



  

    81
    1
  

       

     

  		
 




 
 clusters connected through mates:



  

    
      




 

    Cluster
    Number of shared
 read pairs		
    k
  

      

   		
 

 

   
     

       




  

    779
    9
    0.0466
  

  

    1400
    7
    0.0364
  

  

    2930
    6
    0.0319
  

  

    6
    5
    0.00177
  

  

    4670
    5
    0.0267
  

  

    6590
    5
    0.0267
  

  

    3
    3
    0.000998
  

  

    81
    3
    0.00542
  

  

    126
    3
    0.00505
  

  

    1
    2
    0.00105
  

  

    34
    2
    0.00147
  

  

    46
    2
    0.00183
  

  

    61
    2
    0.00196
  

  

    88
    2
    0.00239
  

  

    2070
    2
    0.0106
  

  

    4510
    2
    0.0107
  

  

    6550
    2
    0.0108
  

  

    9000
    2
    0.0107
  

  

    9510
    2
    0.0107
  

  

    9630
    2
    0.0107
  

  

    17400
    2
    0.0108
  

  

    33500
    2
    0.0108
  

  

    35300
    2
    0.0108
  

  

    47200
    2
    0.0108
  

  

    47800
    2
    0.0108
  

  

    53800
    2
    0.0108
  

  

    59300
    2
    0.0108
  

  

    66900
    2
    0.0108
  

  

    9
    1
    0.00113
  

  

    14
    1
    0.000558
  

  

    28
    1
    0.00082
  

  

    33
    1
    0.000515
  

  

    52
    1
    0.00136
  

  

    55
    1
    0.00111
  

  

    67
    1
    0.000962
  

  

    87
    1
    0.00124
  

  

    95
    1
    0.00137
  

  

    105
    1
    0.00141
  

  

    128
    1
    0.00124
  

  

    130
    1
    0.00169
  

  

    140
    1
    0.00159
  

  

    148
    1
    0.0018
  

  

    186
    1
    0.00345
  

  

    810
    1
    0.00514
  

  

    1270
    1
    0.00521
  

  

    1480
    1
    0.00526
  

  

    1960
    1
    0.00525
  

  

    2740
    1
    0.00538
  

  

    3720
    1
    0.00532
  

  

    8220
    1
    0.00536
  

  

    12000
    1
    0.00538
  

  

    13000
    1
    0.00538
  

  

    14900
    1
    0.00538
  

  

    15700
    1
    0.00538
  

  

    16300
    1
    0.00538
  

  

    18300
    1
    0.00538
  

  

    19200
    1
    0.00541
  

  

    20400
    1
    0.00539
  

  

    21500
    1
    0.00539
  

  

    25800
    1
    0.00539
  

  

    30400
    1
    0.00539
  

  

    33200
    1
    0.00539
  

  

    37500
    1
    0.00539
  

  

    37500
    1
    0.00539
  

  

    38400
    1
    0.00539
  

  

    56400
    1
    0.00539
  

  

    57900
    1
    0.00539
  

  

    59000
    1
    0.00539
  

  

    62200
    1
    0.00539
  

  

    63000
    1
    0.00539
  

  

    63900
    1
    0.00539