Cluster no. 43

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Cluster is part of supercluster: 4

Cluster characteristics:

size	4679
size_real	4679
ecount	197839
supercluster	4
annotations_summary	23.51% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT 14.21% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-GAG 6.24% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-PROT 0.51% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-PROT 0.41% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-GAG 0.21% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-GAG 0.13% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-INT 0.04% Class_I/pararetrovirus:PARA-PROT 0.04% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-RT 0.04% Class_I/LTR/Ty3_gypsy/chromovirus/Chlamyvir:Ty3-RT 0.02% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-CHDII 0.02% Class_I/LTR/Ty1_copia/Ale:Ty1-RT
pair_completeness	0.724023581429624
pbs_score	None
TR_score	None
TR_monomer_length	None
loop_index	0.000854883522120111
satellite_probability	1.17014641654426e-22
consensus	None
TAREAN_annotation	Other
orientation_score	1

comparative analysis:

Comparative analysis - species read counts:

Species	Read count
S2	1440
S1	1510
S3	1730

comparative analysis - number of edges between species:

	S2	S1	S3
S2	19000	19700	22600
S1	19700	20400	23500
S3	22600	23500	26800

comparative analysis - observed/expected number of edges between species

	S2	S1	S3
S2	1.000	0.999	1.000
S1	0.999	0.998	1.000
S3	1.000	1.000	0.997

protein domains:

Reads annotation summary

cl_string domain Freq proportion

pararetrovirus PARA-PROT pararetrovirus PARA-PROT 2 0.00043

Ale Ty1-RT Ale Ty1-RT 1 0.00021

Tekay Ty3-CHDII Tekay Ty3-CHDII 1 0.00021

CRM Ty3-GAG CRM Ty3-GAG 19 0.00406

Reina Ty3-GAG Reina Ty3-GAG 10 0.00214

Tekay Ty3-GAG Tekay Ty3-GAG 665 0.14212

TatV Ty3-INT TatV Ty3-INT 6 0.00128

Reina Ty3-PROT Reina Ty3-PROT 24 0.00513

Tekay Ty3-PROT Tekay Ty3-PROT 292 0.06241

Chlamyvir Ty3-RT Chlamyvir Ty3-RT 2 0.00043

Galadriel Ty3-RT Galadriel Ty3-RT 2 0.00043

Tekay Ty3-RT Tekay Ty3-RT 1100 0.23509

clusters with similarity:

Cluster	Number of similarity hits

55	1680
9	615
71	195
25	1
54	1

clusters connected through mates:

Cluster	Number of shared read pairs	k

9	279	0.174
55	220	0.321
71	65	0.102
54	3	0.00502
8	2	0.00211
25	2	0.00161
36	2	0.00231
75	2	0.0025
48300	2	0.00533
4	1	0.00038
11	1	0.000622
12	1	0.000482
16	1	0.000493
17	1	0.000627
18	1	0.000447
20	1	0.00154
21	1	0.000857
22	1	0.000741
23	1	0.000861
38	1	0.000764
39	1	0.000704
42	1	0.00072
46	1	0.00104
48	1	0.00113
51	1	0.00141
52	1	0.00181
59	1	0.00127
70	1	0.00146
72	1	0.0014
77	1	0.00186
80	1	0.000894
84	1	0.00149
1700	1	0.00264
2150	1	0.00264
3080	1	0.00265
3820	1	0.00265
8960	1	0.00266
19600	1	0.00266
20200	1	0.00266
25300	1	0.00266
31200	1	0.00266

CL43 ----> CL9

No. of shared pairs: :279

CL43 ----> CL55

No. of shared pairs: :220

CL43 ----> CL71

No. of shared pairs: :65