Cluster no. 169

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Cluster is part of supercluster: 77

Cluster characteristics:

size 577
size_real 577
ecount 4574
supercluster 77
annotations_summary 18.20% Class_I/LTR/Ty1_copia/Tork:Ty1-RT
13.52% Class_I/LTR/Ty1_copia/Tork:Ty1-INT
8.67% Class_I/LTR/Ty1_copia/Tork:Ty1-RH
7.97% Class_I/LTR/Ty1_copia/Tork:Ty1-GAG
5.72% Class_I/LTR/Ty1_copia/Tork:Ty1-PROT
2.77% organelle/mitochondria
0.52% Class_I/LTR/Ty1_copia/SIRE:Ty1-RT
0.17% Class_I/LTR/Ty1_copia/Ivana:Ty1-RH
0.17% Class_I/LTR/Ty1_copia/Ale:Ty1-RT
0.17% Class_I/LTR/Ty1_copia/Ikeros:Ty1-RT
pair_completeness 0.855305466237942
pbs_score 7.223622
TR_score 0.8098199809917814
TR_monomer_length 4218.0
loop_index 0.965337954939341
satellite_probability 0.767082439601018
consensus 
TCCACAATTTCAGGTCCTGTATCAGATGCACCTAGACTGTCTTTGTACATCATCTGTTCGTTGAAGAGAACATCCCGACT
GCGAATAATCTTCTTGTTCTGACTGTCCCAAAACCGATATCCGAAATCATCACCGCCGTATCCAATAAACGTGCACTTAA
CAGACTTTGCATCTAACTTGCTTCTCTCAAGGGGAGCAATATGAACATATGAATCACATCCAAATACTCGTAGAAAGGAC
AGATTTACCTGCTTGCCGCTCCAAGCTTCTTCAGGAATGCCATTCTGCAAAGGAGTCGACGGCCCTCTGTTGATCAAGAA
TGCTGCCGTGTTAACTGCTTCTGCCCAGAACATCTTCGGAAGTCCACACTTCAGCCTCATGCTTCTAGCACGCTCACACA
AAGTTCTGTTCATTCGTTCTGCAACTCCATTCTCCTGAGGAGTCCCTTTCAGAGTCTTCTCCATCCGAATTCCATTCTCA
GCACAGAATTCTTTGAATTCCTGAAGTTCATATTCCCCACCATTGTCTGACCTCAAGCATTTTACCTTCAGACCTGTCTC
ATTCTCAACAAGAGCCTTCCATTTTCGAAAAACATCAAAAGCATCAGATTTCTTTTTCAGAAAATAGATCCATACCTTCC
TAGTGGAGTCGTCAATAAGGGTCATGTAGTACGAAGCTCCACCAAGAGATTTCACAGGTGCAGGCCCCCATAGATCGCTG
TGAACTAGCTCCAACTTCTGCTTCTTCAAAGTTCTGCCACCCTTGGAGAAACTGACTCTTTTCTGCTTCCCGAAGATACA
ATCCTCACATAGCCCAAGATCAGCTGACTTCAAACCCGGTAACAGACCCTTCGAACACAGCACCTTCATCCCCTTTTCAC
TCATGTGACCAAGACGGCAGTGCCACAAATCTGCATTAACAATCTCTCTTGCTACATCAATGCTGTTACAGACGCTGTCT
GTAATATATAGTGACCCAACCTTCTCACCACGAGCTATCAACATAGATCCTTTTGTAATTTTCCAGACTTTACCTCCGAA
TACAACATGATATCCTTCATCATCCAATTGCCCAACTGACAACAGATTTCTCTTCAGGCCTGGAACATGCCTTACACTAG
ACAGCTTCACCACAGATCCATTTGGGGACTTGATCGAAACATCTCCCTTCCCCACAATCTCCAAAGGCTCATCATCAGCT
AGATAAACTTTTCCGAATTTCCCAGGGGTATAGTGCTCCATCAAATCTGCCCTACTACAAGAGTGAAACGAAGCTCCAGA
ATCTAACACCCAAGGCTCCAGAGAGCCTCTCACGTTCAAAGCTAATTCTTCTGTGGTTTCTGCAGTAGAATCACACAAAA
CCAACGCATCATCAAAATCCTCGGCAACTGCGTTTATGGATTTCTCCTTTGGCGGTTTTTTACATTGATTCCTATAATGA
CCCGTCTCATCACAATTCCAGCACTTGATGTGTCTCTTGTCCTTGACAACAGATTTCCCTCTTCCCTTTGACTTGGATCT
GCCACGATTCTGCTGGTTTGATTTCCAATCTGACCTACCCCGATTTTCTGTATTCAAGGCTGATCCAGACGTTGATCCTG
ATTCCTTCCTGCGAATCTCCTCGCTTACAATCAGATCTCTAACATCATCAACCTTAAGCTTTTCTTTTCCCGCTGATGCA
CTCAGAGCAGTAACCGTACCACTCCAGCTTTCTGGTAAAGAAGATAATAAAATTAGGGCTAATACCTCGTCGTCGAAATG
AATATCCACAGAGCTTAATTGAGAGATTGTCATATTAAACTCATTTAGATGCGTCGCCACTGCTGTGTTTTCTGTCATCC
GTAGATTAAACAGACGTCGCATCAGATGAACCTTGTTTGCTGCGGAAGGCTTCTCATACAATCCACTCAAAATCTCGAAC
ATCTCCTTCGTGGTCTTTGCCTTCACCGTGTGATGCGCCACGTTCCTAGACAGCGACAGTCGAATCACGCTCATCGCCTT
TCTGTCCAACAGATTCCACTCTTTATCATCCATGCCATCCGGCTGCTCATCCATAGGCTGGTACAGATCTTTACCATACA
GATAATCCTCGATCTGCATCTTCCAGAAACCATAATCCGAACCATCGAATTTCTCCACTGGTGATTTTCCGTCCATCGTA
ATTGCCAGCAAAACCTAGCTCTGATACCAATTGTTAGGAACAATATATGCAAATACGATAAATAAAATCAAACACAGAAT
TTGTTAACCCAGTATCCACTCAATGTGAGTGACTAATCTGGAGGCACTACCAAGCCAGGATTTCACTATGATTTCGAGAG
AGATACAGATCTTAGAATGGAATACGGCTAACAAATAATGAGGCTGTATTTATAGAGCCACACACTCAAACCCTAACCCT
AACGGGTCAAAAAAATTTGGGCCTCACGCTAGATTTGTCTCCAAAGCCCAACAATCTCCCACCTGGAGACAAGATCCATC
ATCTGCTGGTAGTGCCAAGCCTTTCAACTAGTTACCAAGGCCAACTGAAGCTTTGCAAAGCTTCAGCTTCTCTAAGGTTA
CAACCTTAGTCAACATGTCTGCAGGATTTTCTGTGCCAAGAATCTTCAACAACTGCAATGTCTTCCTTTCCAAGAGATGT
CGTATGTAGTGATACTTCAACTCTATGTGCTTCGTCCTTGAATGAAATGCGGGATTCTTTGCCAAATGAATTGCACTCTG
ACTGTCGCTGTACAGAATACGATCCTTCTGCTCTTTACCCAACTCACGCAAGAAATTCTGCAACCATACCATCTCCTTAC
TAGCCTCAGTCACTGCAACGTACTCCGCTTCTGCAGTAGACAAAGCTATAACCTTCTGCAACTTTGAAGCCCAAGAGACC
GCAGTACCACCCAATGTGAAGATATAACCGGTTGTACTTCTTCTCTTGTCAAGGTCACTTGATGCCAAATCTGCATCCAC
ATATCCTGTCAACATGATTTCCTTGCCCTCAAAACACAAACCTCGTTCAGTGGTACCCTTCAAGTACCTCAGAATCCACT
TTACTGCTTCCCAATGCTTCTCACCAGGGTCTCCCATGAAACGACTAACAACTCCCACAGCATGTGCAATATCCGGCCTT
GTGCACACCATTGCATACATCAAGCTGCCAATTGCTGAGGCATACGGGGTTCTCTCCATCTGAGCTCGCTCTTCTCTACT
CTTGGGTGAGTCCTGTCTAGATAGCTTGAAATGACTAGCCAAGGGAACCGTTGCTGGCTTGGCATCTTGCATGCCGAATC
TCTTCAAGACCTTCTTGATATACTCAGCTTGTGAAAGATACAATTTTCCAGCCTTCCTGTCTCTTTCAATCCGCATACCC
AGAATCTGCTTTGCTTCTCCAAGATCTTTCATAGCAAACCGCTCAGATAACTGCTGCTTCAGATTTCTCATCTCTCGAGC
ACTCGACCCTGTAATCAGCATATCATCAACATATAACAGCAAAATGATGTAGCCCTTATCCAGCTTCCTGAAGTAACAAC
AATGATCAGCTTCACTCCTCACGAACTTGATCTCATGCATGAAACTGTCAAATTTCTTGTACCACTGCTTCGGAGCTTGC
TTCAGGCCATACAAGCTCTTATTCAATTTGCACACAAGGTCGGCTTTTCCAGACTCATAGCCCTGAGGTTGTTTCATGTA
GATGTCCTCATCTAAGTCCCCATGAAGAAATGCCGTTTTTACATCCATCTGTTGCAGCTCCAAATCTTCTACAGCTACCA
TACTCAACACTAAACGAATAGTAGTCAACTTCACCACTGGAGTAAAAACATCAGTATAATCTATACCGTACCTCTGCTGA
AAGCCTTTCACAACTAGCCTTGCCTTGTAGCGTTTGCTACCATCTGCCTCCTCTTTGATTCTGAAGATCCACCTATTCTG
TAGAGCCTTCTTACCCTTTGGAAGCTTAACTAGCTCCCAAGTGCCATTAGTCATCAAAGAGTCCATCTCATCATCCATAG
CAGCCTTCCACTTGCTCGCTTCCTCTCCATGAGATGCTTCCAAGTAGCTTTCTGGTTCACCACTATCTGTCAGCAGCAAG
TGGTTGCTTGTGGGTGTGAACTTGTTAGGTGCTCTACGCTCTCTAGTGGATCTGCGTGTTGTAGCCTCTGGAGTTCTGGG
TTCTTGTTCTTCCTCAACAACTTCCTGCTTACTCCCACCAGAATTTGTAATGTCTAGG

  

  

    TAREAN_annotation
    Putative LTR element
  

  

    orientation_score
    1
  

 


 
 comparative analysis:


  





 
 Comparative analysis - species read counts:



  

    Species
    Read count
  

   

    S5
    171
  

  

    S4
    182
  

  

    S6
    224
  

 


 
 comparative analysis - number of edges between species:



  

    
    S5
    S4
    S6
  

   

    S5
    431
    436
    532
  

  

    S4
    436
    413
    560
  

  

    S6
    532
    560
    673
  

 


 
 comparative analysis - observed/expected number of edges between species



  

    
    S5
    S4
    S6
  

   

    S5
    1.010
    1.01
    0.985
  

  

    S4
    1.010
    0.95
    1.030
  

  

    S6
    0.985
    1.03
    0.988
  

 


 
 protein domains:



protein domains:


  





 
 Reads annotation summary










	

	 
	
 
		   
		cl_string  
		domain  
		Freq  
		proportion 
	
 

 
mitochondria 

mitochondria



 16

0.0277


 

 
Tork Ty1-GAG

Tork

Ty1-GAG

 46

0.0797


 

 
Tork Ty1-INT

Tork

Ty1-INT

 78

0.1352


 

 
Tork Ty1-PROT

Tork

Ty1-PROT

 33

0.0572


 

 
Ivana Ty1-RH

Ivana

Ty1-RH

  1

0.0017


 

 
Tork Ty1-RH

Tork

Ty1-RH

 50

0.0867


 

 
Ale Ty1-RT

Ale

Ty1-RT

  1

0.0017


 

 
Ikeros Ty1-RT

Ikeros

Ty1-RT

  1

0.0017


 

 
SIRE Ty1-RT

SIRE

Ty1-RT

  3

0.0052


 

 
Tork Ty1-RT

Tork

Ty1-RT

105

0.1820


 
	


 

 


 
 clusters connected through mates:



  

    
      




 

    Cluster
    Number of shared
 read pairs		
    k
  

      

   		
 

 

   
     

       




  

    15
    1
    0.00101
  

  

    40
    1
    0.00114
  

  

    58
    1
    0.000825
  

  

    59
    1
    0.00106
  

  

    73
    1
    0.0011
  

  

    84
    1
    0.00138
  

  

    9120
    1
    0.0435
  

  

    20100
    1
    0.0426