Cluster no. 165

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Cluster is part of supercluster: 73

Cluster characteristics:

size	652
size_real	652
ecount	2387
supercluster	73
annotations_summary	40.49% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT 7.21% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-PROT 4.91% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RH 0.92% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RT 0.77% Class_I/LTR/Ty3_gypsy/chromovirus/Chlamyvir:Ty3-PROT 0.61% Class_I/LTR/Ty3_gypsy/chromovirus/Chlamyvir:Ty3-RT 0.46% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-PROT 0.15% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RH 0.15% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-RT 0.15% Class_I/LTR/Ty1_copia/Gymco-II:Ty1-INT 0.15% Class_I/LTR/Ty1_copia/Ivana:Ty1-RT 0.15% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-RH 0.15% Class_I/LTR/Ty3_gypsy/non-chromovirus/Selgy:Ty3-RH 0.15% Class_I/pararetrovirus:PARA-RT
pair_completeness	0.468468468468468
pbs_score	None
TR_score	None
TR_monomer_length	None
loop_index	0.00153374233128834
satellite_probability	3.54668226065428e-21
consensus	None
TAREAN_annotation	Other
orientation_score	1

comparative analysis:

Comparative analysis - species read counts:

Species	Read count
S5	237
S4	211
S6	204

comparative analysis - number of edges between species:

	S5	S4	S6
S5	330	314	246
S4	314	310	224
S6	246	224	179

comparative analysis - observed/expected number of edges between species

	S5	S4	S6
S5	0.993	0.994	1.02
S4	0.994	1.030	0.97
S6	1.020	0.970	1.02

protein domains:

Reads annotation summary

cl_string domain Freq proportion

pararetrovirus PARA-RT pararetrovirus PARA-RT 1 0.0015

Gymco-II Ty1-INT Gymco-II Ty1-INT 1 0.0015

Ivana Ty1-RT Ivana Ty1-RT 1 0.0015

Chlamyvir Ty3-PROT Chlamyvir Ty3-PROT 5 0.0077

Reina Ty3-PROT Reina Ty3-PROT 3 0.0046

Tekay Ty3-PROT Tekay Ty3-PROT 47 0.0721

Reina Ty3-RH Reina Ty3-RH 1 0.0015

Selgy Ty3-RH Selgy Ty3-RH 1 0.0015

TatV Ty3-RH TatV Ty3-RH 1 0.0015

Tekay Ty3-RH Tekay Ty3-RH 32 0.0491

Chlamyvir Ty3-RT Chlamyvir Ty3-RT 4 0.0061

Galadriel Ty3-RT Galadriel Ty3-RT 1 0.0015

Reina Ty3-RT Reina Ty3-RT 6 0.0092

Tekay Ty3-RT Tekay Ty3-RT 264 0.4049

clusters with similarity:

Cluster	Number of similarity hits

70	25
67	12
27	2
97	1
100	1

clusters connected through mates:

Cluster	Number of shared read pairs	k

67	46	0.0858
70	16	0.0267
181	9	0.0458
7	2	0.000883
1250	2	0.0163
3180	2	0.0165
10600	2	0.0167
25800	2	0.0168
27600	2	0.0168
36600	2	0.0168
41100	2	0.0168
44800	2	0.0168
2	1	0.000312
13	1	0.000641
30	1	0.000577
35	1	0.000866
56	1	0.000791
58	1	0.000765
62	1	0.00161
63	1	0.000795
77	1	0.00108
97	1	0.00177
5370	1	0.00833
6660	1	0.00833
8090	1	0.00837
11400	1	0.00844
19100	1	0.0084
30200	1	0.0084
30400	1	0.0084
31100	1	0.0084
32500	1	0.0084
43400	1	0.0084
46900	1	0.0084

CL165 ----> CL67

No. of shared pairs: :46

CL165 ----> CL70

No. of shared pairs: :16