Cluster no. 257

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Cluster is part of supercluster: 150

Cluster characteristics:

size 2534
size_real 2534
ecount 29091
supercluster 150
annotations_summary 14.13% Class_I/LTR/Ty1_copia/Tork:Ty1-RT
9.87% Class_I/LTR/Ty1_copia/Tork:Ty1-INT
7.81% Class_I/LTR/Ty1_copia/Tork:Ty1-RH
4.85% Class_I/LTR/Ty1_copia/Tork:Ty1-GAG
2.96% Class_I/LTR/Ty1_copia/Tork:Ty1-PROT
2.92% organelle/mitochondria
0.39% Class_I/LTR/Ty1_copia/Ale:Ty1-RT
0.32% Class_I/LTR/Ty1_copia/Ivana:Ty1-RT
0.20% Class_I/LTR/Ty1_copia/Gymco-II:Ty1-INT
0.12% Class_I/LTR/Ty1_copia/Ikeros:Ty1-RT
0.08% Class_I/LTR/Ty1_copia/Ivana:Ty1-INT
0.08% Class_I/LTR/Ty1_copia/TAR:Ty1-RT
0.08% Class_I/LTR/Ty1_copia/Ivana:Ty1-RH
0.04% Class_I/LTR/Ty1_copia/TAR:Ty1-PROT
0.04% Class_I/LTR/Ty1_copia/Ikeros:Ty1-INT
0.04% Class_I/LTR/Ty1_copia/Gymco-I:Ty1-RT
0.04% Class_I/LTR/Ty1_copia/Ty1-outgroup:Ty1-RT
0.04% Class_I/LTR/Ty1_copia/Gymco-II:Ty1-RT
pair_completeness 0.823021582733813
pbs_score 5.1615792
TR_score 0.7653249144961848
TR_monomer_length 4819.0
loop_index 0.878058405682715
satellite_probability 0.0702409333848258
consensus 
GGCATGAATTTGATTGAAAATGGAGACAACAGTTACAGATATGGAGAAGTTGAGCGGGGCTAATTTTTCCCTATGGAAAT
CACAGATGGAGGATATACTGATTTTAAAGGATCAGTATTTGCCGATTGAGGGCACAACAAAGAAACCCTCATCGATGACA
AATGAAGAGTGGAATAAGCTAGATAGAAAGGCGATTGCAACAATCCGCCAATATTTAGCAAAGAATGTTTATTTCAATGT
GTCCGGAGAAAAGACGGCTGAAGGATTATGGAAGAAGCTCCATGATCTATATGAGAAGAACACGACATCAAACAAAGTGT
TCTTGATGAAGAAGCTTTATAATCTCAAAATGAAGGAGGGTGCTTCAGTTGCTGAGCACTTGAATGCATTTAATATTATT
ACTAATCAACTTGCCTCTGTTAAAATCATTTTAGATGATGAAATTAGAGCTATTTTGCTAATGTGTTCTATGCCAGACAG
CTGGGAAAATTTAATTGTAGCTATGAGCACTTCAACAACTATAGGGACCCTGAAGTTTGATGATGTCAGCAACAGTTTAA
TGAATGAGGAGCTGCGACGCAAGTCAATTGCGGAAAACCAGGGAGGAGAGGCTCTAGCTCTAGCTGATCGTGGTAGGAGA
ATGGATCGAGGCCGGCAAGGGCGATCAAGATCGAGAGGCCGATCAAAATCAAGGAGAGGAAGGATCATCTGCTTTCATTG
TGGCAAACCCGGGCACATGAAGAAAGAATGTCGATTCTGGAAGAAAGGACAAAAGGATCAGAGACCGTCTAGTACAAATC
ACAAGTCATCCAGCACAAATGAAGGTGAGACTACTGTTGTAGCCACAGATGGTGATGTGTTGTTTACTGTTTCAGTAGAG
GATGCATGTGTATATACATCTAGCAGTAGCTTTGATTGGATCCTTGACTCTGGGGCATCTCACCATGTAACCCCATGCAA
AGATAGTTTTGTTTCATATAATCCTGGTGATTATGGTAGAGTGCATTTGGGGAATAATCATTTTTGCAGTATTGTTGGAG
TGGGAGATGTCCAGATCAAGATGAAAGATGGACAAGATATATTGTTGAAACAGGTCAGGCATGTACCAGAAATGCGCATG
AGTTTAATCTCTATGGGACGACTGGATGATGAAGGCTATTCGACAAGCTTTGGAAAAGGAGGCTGGAAAATTAGCAAAGG
AGCATTGGTCGTGGCCAAAGGACCCAAGACAGGAACATTATACACATTGAAGACACTGATAGGAAAATCAGATTTGGCTG
CTGTCACAAAAGAAGGAAATTCAGCAGATCTGTGGCATAAGCGTTTGGGTCACATGAGCGAGAAGGGCTTAAAAATCCTT
GTTGGTAAAAATTTATTGCCAGGTTTGAAATCCTACAATCTTGATCTTTGTGAGCATTGTATATATGGTAGACAAAGAAG
GGTTTCATTCCTTAGAGGTGGCCATGACAGAAAGAAAAATGTGTTAGAATTGGTACACTCAGATGTGTTTGGGCCTGTTA
ACATCAAATCATTAGGAGGAGCATCATATTTTGTAACATTTATAGATGATGCATCCAGGAAGGTTTGGGCATATCCTATG
AAAAATAAAAGTGAAGTGTTTGGAATATTTCAAAAATTCCATGTTGTTGTTGAAAGAGAGACTAACAAATTGCTGAAGTG
TTTAAGAACAGATAATGGTGGAGAATATTGCTCAAATGCATTTAAGGAATATTGTAACAGGTTTGGCATAAAGCATGAGA
AGACTGTGCCTGGTACTCCTCAACAGAATGGTGTCGCAGAAAGGATGAATCGCACCATTATGGAAAAGGTGCGAAGTATG
TTGTCCAATTCCGGTTTGGAGAAGAATTTTTGGGCTGAAGCAGTCAGGACCGCTTGCTACCTCATAAATAGATCTCCAAC
TACAGCCTTGGATGGCGGTATCCCTGAAGAAGTTTGGACTGGTAAGAATTTGAATTATTCTCACTTGAAAATCTTTGGAT
GTGAAGCATTTGTACATATTCCCAAAGAAAATAGAACTAAGCTAGATGATAAATCTATGAAATGCATTTTTTTGGGATAT
GCGGATGAAGATTTTGGTTATCGTCTATGGGATCCAGTCAAACATAAAATTATTAGAAGCAGGGATGTTATATTTAATGA
GTCAGAAATGTTCAAGAGGACTGTAGGTGAGTTGGAGGTCAAGAAGGTTATTGACAGGTTTGAAGAGCAGCAGGAAAACA
TACCACCAATACAAGAAAATGAACAACAAATTCAGGAGCATGAAGAACAACAAGTGGAAAATGATGAACAACAAGAAGAA
GGAATCTTGCAGGAACCTTTACAGGAGATTCAACCTGATAATGCACCACCACAGTTGGTTCGCAGATCTTCTAGGCCTCA
TAAGCCTTCACAAAGGTATCCTCCTTCAAACTATATTTTGTTGACTGATGAAGGTGAGCCTAATTGTTTTCAAGAAGCTT
GTAAAGTTGAGCACAGTAAAGAATGGAAGAAAGCAATGGAAGAAGAAATGAACTCTTTGCTGGAAAATAAAACTTGGGAG
TTGGTAAACCTCCCAAAAGGTAGAAAGGCTCTACAAAACAAATGGGTGTACAGGATTAAGCATGAAGGTGACGAAAAGAA
GGAGAGGTATAAAGCAAGGCTGGTGGTGAAAGGTTTTGCCCAAAAAGAAGGTATTGACTTCACTGAAATTTTCTCACCTG
TTGTTAAAATGTCATCCATTAGAGTCATTCTTGGTCTAGTTGCTGCTTTAGACCTAGAATGTGAACAGTTAGATGTAAAA
ACTGCTTTCCTTCATGGTGAATTGGAGGAAGAAATTTATATGGAGCAGCCAGAAGGCTTCATAGAAAAAGGCAAAGAAGA
CCTTGTTTGTAGGTTGAAGAAGAGTCTCTATGGGTTGAAACAGGCACCTCGACAATGGTACAAGAAATTTGATTCATTCA
TGTTGGAACATGGTTTTCAGAGGTTGGAAGCTGACCATTGTGTCTATATCAAGAGGTATGATCAAGGAAAGTATATCATA
TTATTGTTATATGTGGATGACATGTTGATTGTTGGGCATGATAAGAATAAGATCAATAGGTTGAAGAAAGATTTGGGTAG
CAAATTTGCAATGAAGGATTTGGGACCAGCACAACAGATATTGGGCATGCGGATTATGCGTGACAGGAAAAACAAAAGGT
TGTGGTTGTCACAAGAAAAATATATCAAGAAGGTGCTTGACAGGTTTAATATGAAGGATGCCAAGCCAGTTGGTACACCC
CTTGCAGCCCACTTCAAGCTGAGTACTGAATTATGTCCTAGTGATGACAAGGAGAAAGAAGAGATGAGCAAGATTCCTTA
TGCTTCAGCAGTTGGCAGCTTGATGTATGCCATGGTATGCACACGACCAGACATTGCATATTCAGTGGGAGTAGTGAGTA
GGTTCCTTGCCAATCCAGGCAAACAACATTGGCAAGCAGTAAAATGGATTTTGAGGTATCTCAAGGGTACTAGTCATTAT
TGTTTATGTTTTGGTCATGATGAGACTGTGCTTGAAGGATTTACAGATGCAGATATGGCTGGAGATATGGACACCAGAAA
GTCCACTACAGGTTATTTGTATACATTTGCAGGTGCAGCAGTATCTTGGGTGTCAAGGCTACAAAGAATAGTAGCCCTCT
CTACAACAGAAGCAGAGTACATAGCTGCAACAGAAGCTTGTAAAGAGATGTTGTGGATGCAGCGATTCCTAGGAGAGATA
GGAATAAAGCAGGACAAGTATGTGTTATATTGTGATAGTCAGAGTGCCATTCACTTGGCGAAAAACCCAGCATTTCATTC
AAAAACCAAGCACATTGACTTAAGGTACCATTGGATCCGGCATGTGTTGGAGGAAGAACAATTATCCTTGGAAAAGATCC
ATACAGATAGGAACCCTGCTGATATGCTCACTAAGATTCTACCACGAAATAAACATGAGTTATGTAGAGGCATGGTAGGA
CTCGGTGTGACTTGATGACTCTTATTTGGCTTCAAGTGGGAGAATGTTAAGTGTGAAGCCAAATTCATGCAGGATTCTAG
ATCCTTCTTCTGCCTCTATAAATTTGTAATTTCTCTGGCCAAGGAAAGCAAGCCAAGGCCCAAGCCTGTTATGTAATGCA
AAGTGATTTCTGTTCTCCAGTGATTGTTTTATCTATTCCGCTGTTTCTGATTGAGTAATCTTGTTGTTTCTCCATTTGTC
TGTCTCTGAGTATAAATCCGTTGTGTGTTATGTATGCTCTGGTCTAACAACTGGTATCAAAGCTAGGGTCGAATATCCAC
TGTGCAAGCCGCTTAGTGCCATCGCCTTACTCTGGCAGCGTTCGTTAAAACGTTGGTTGTTACCCCTGGAGCTGTTGAAG
GATCTGTCCAGGAAATAGCTGAGGAACGCTGGAACTAAAAGACAGTTGCTGCAAGAAAAACAAGGTCGTGGACCTATGTT
GAAACATGTTGCTGGAGTTTGAAACGTGGAGATCCGTGGAGATTGGAGTTGAAACGTGGTGTTCGTAAGTTTTTTTTACA
TCAAGCTTGCACGTATACGTCAAGTTTTTTCTCAAACCAACATATGTATGTGTGAAATGTGAAAAGGTTAAAACATTATA
TATGTTTTTATATTTATTATGAAACATATATAATTATATGTTGGAATTTTGAAAAGTATATTTTAAAAAGGAGCAGGAAT
TTTGAAAAGGGTATTTTAAAAGGAGGAAGGTCATTATTACTAAATTTTAAAGAGTAATAATTAAAGTTTTATTTTTAAGT
GGAGTTTTTTGTGTTTTGG

  

  

    TAREAN_annotation
    Putative LTR element
  

  

    orientation_score
    1
  

 


 
 protein domains:



protein domains:


  





 
 Reads annotation summary










	

	 
	
 
		   
		cl_string  
		domain  
		Freq  
		proportion 
	
 

 
mitochondria 

mitochondria



 74

0.02920


 

 
Tork Ty1-GAG

Tork

Ty1-GAG

123

0.04854


 

 
Gymco-II Ty1-INT

Gymco-II

Ty1-INT

  5

0.00197


 

 
Ikeros Ty1-INT

Ikeros

Ty1-INT

  1

0.00039


 

 
Ivana Ty1-INT

Ivana

Ty1-INT

  2

0.00079


 

 
Tork Ty1-INT

Tork

Ty1-INT

250

0.09866


 

 
TAR Ty1-PROT

TAR

Ty1-PROT

  1

0.00039


 

 
Tork Ty1-PROT

Tork

Ty1-PROT

 75

0.02960


 

 
Ivana Ty1-RH

Ivana

Ty1-RH

  2

0.00079


 

 
Tork Ty1-RH

Tork

Ty1-RH

198

0.07814


 

 
Ale Ty1-RT

Ale

Ty1-RT

 10

0.00395


 

 
Gymco-I Ty1-RT

Gymco-I

Ty1-RT

  1

0.00039


 

 
Gymco-II Ty1-RT

Gymco-II

Ty1-RT

  1

0.00039


 

 
Ikeros Ty1-RT

Ikeros

Ty1-RT

  3

0.00118


 

 
Ivana Ty1-RT

Ivana

Ty1-RT

  8

0.00316


 

 
TAR Ty1-RT

TAR

Ty1-RT

  2

0.00079


 

 
Tork Ty1-RT

Tork

Ty1-RT

358

0.14128


 

 
Ty1-outgroup Ty1-RT

Ty1-outgroup

Ty1-RT

  1

0.00039


 
	


 

 


 
 clusters with similarity:



  

    
      



 

    Cluster
    Number of similarity hits
  

      

   		
 

 

   
     

       



  

    127
    4
  

  

    17
    1
  

       

     

  		
 




 
 clusters connected through mates:



  

    
      




 

    Cluster
    Number of shared
 read pairs		
    k
  

      

   		
 

 

   
     

       




  

    17
    4
    0.000694
  

  

    219
    4
    0.00952
  

  

    30
    2
    0.000549
  

  

    52
    2
    0.00105
  

  

    144
    2
    0.00325
  

  

    40700
    2
    0.0161
  

  

    109000
    2
    0.0161
  

  

    157000
    2
    0.0161
  

  

    340000
    2
    0.0161
  

  

    1
    1
    0.000282
  

  

    3
    1
    0.000273
  

  

    6
    1
    0.000262
  

  

    20
    1
    0.000288
  

  

    21
    1
    0.000421
  

  

    24
    1
    0.000323
  

  

    36
    1
    0.000618
  

  

    40
    1
    0.000279
  

  

    44
    1
    0.000329
  

  

    47
    1
    0.000394
  

  

    48
    1
    0.000306
  

  

    54
    1
    0.00092
  

  

    56
    1
    0.0029
  

  

    59
    1
    0.000849
  

  

    60
    1
    0.000865
  

  

    62
    1
    0.000367
  

  

    66
    1
    0.00035
  

  

    72
    1
    0.000739
  

  

    77
    1
    0.000743
  

  

    85
    1
    0.000708
  

  

    86
    1
    0.000397
  

  

    91
    1
    0.00129
  

  

    95
    1
    0.000953
  

  

    96
    1
    0.000916
  

  

    121
    1
    0.00161
  

  

    125
    1
    0.00117
  

  

    126
    1
    0.000813
  

  

    128
    1
    0.00123
  

  

    129
    1
    0.00143
  

  

    132
    1
    0.00117
  

  

    139
    1
    0.000835
  

  

    163
    1
    0.000725
  

  

    164
    1
    0.003
  

  

    174
    1
    0.000856
  

  

    175
    1
    0.00144
  

  

    198
    1
    0.0019
  

  

    206
    1
    0.00175
  

  

    208
    1
    0.00194
  

  

    232
    1
    0.00195
  

  

    242
    1
    0.00172
  

  

    243
    1
    0.0014
  

  

    250
    1
    0.00362
  

  

    299
    1
    0.00581
  

  

    302
    1
    0.00437
  

  

    303
    1
    0.00449
  

  

    379
    1
    0.00641
  

  

    712
    1
    0.00683
  

  

    11400
    1
    0.00794
  

  

    18300
    1
    0.008
  

  

    36400
    1
    0.00806
  

  

    49400
    1
    0.00803
  

  

    49500
    1
    0.00803
  

  

    59800
    1
    0.00803
  

  

    69400
    1
    0.00803
  

  

    78200
    1
    0.0081
  

  

    78800
    1
    0.00803
  

  

    79400
    1
    0.0081
  

  

    90100
    1
    0.00806
  

  

    162000
    1
    0.00806
  

  

    163000
    1
    0.00806
  

  

    228000
    1
    0.00806
  

  

    240000
    1
    0.00806