Cluster no. 42

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Cluster is part of supercluster: 5

Cluster characteristics:

size	4182
size_real	4182
ecount	154219
supercluster	5
annotations_summary	25.80% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT 9.21% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-GAG 5.98% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-PROT 1.34% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RT 0.96% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-GAG 0.62% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-RT 0.36% Class_I/LTR/Ty3_gypsy/chromovirus/Chlamyvir:Ty3-RT 0.26% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-GAG 0.22% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RH 0.10% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RH 0.07% Class_I/LTR/Ty3_gypsy/chromovirus/Tcn1:Ty3-RT 0.07% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-PROT 0.02% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-RT 0.02% Class_I/LTR/Ty1_copia/Ivana:Ty1-INT 0.02% Class_I/LTR/Ty1_copia/Ale:Ty1-PROT 0.02% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-RH 0.02% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-INT 0.02% Class_I/pararetrovirus:PARA-RT
pair_completeness	0.73167701863354
pbs_score	None
TR_score	None
TR_monomer_length	None
loop_index	0.00143472022955524
satellite_probability	9.81425038973844e-23
consensus	None
TAREAN_annotation	Other
orientation_score	1

comparative analysis:

Comparative analysis - species read counts:

Species	Read count
S8	1400
S9	1440
S7	1350

comparative analysis - number of edges between species:

	S8	S9	S7
S8	18300	18100	16800
S9	18100	18000	16500
S7	16800	16500	15100

comparative analysis - observed/expected number of edges between species

	S8	S9	S7
S8	0.995	0.998	1.010
S9	0.998	1.000	0.998
S7	1.010	0.998	0.994

protein domains:

Reads annotation summary

cl_string domain Freq proportion

pararetrovirus PARA-RT pararetrovirus PARA-RT 1 0.00024

Ivana Ty1-INT Ivana Ty1-INT 1 0.00024

Ale Ty1-PROT Ale Ty1-PROT 1 0.00024

CRM Ty3-GAG CRM Ty3-GAG 40 0.00956

Reina Ty3-GAG Reina Ty3-GAG 11 0.00263

Tekay Ty3-GAG Tekay Ty3-GAG 385 0.09206

CRM Ty3-INT CRM Ty3-INT 1 0.00024

Reina Ty3-PROT Reina Ty3-PROT 3 0.00072

Tekay Ty3-PROT Tekay Ty3-PROT 250 0.05978

CRM Ty3-RH CRM Ty3-RH 1 0.00024

Reina Ty3-RH Reina Ty3-RH 4 0.00096

Tekay Ty3-RH Tekay Ty3-RH 9 0.00215

CRM Ty3-RT CRM Ty3-RT 26 0.00622

Chlamyvir Ty3-RT Chlamyvir Ty3-RT 15 0.00359

Galadriel Ty3-RT Galadriel Ty3-RT 1 0.00024

Reina Ty3-RT Reina Ty3-RT 56 0.01339

Tcn1 Ty3-RT Tcn1 Ty3-RT 3 0.00072

Tekay Ty3-RT Tekay Ty3-RT 1079 0.25801

clusters with similarity:

Cluster	Number of similarity hits

10	1250
22	887
45	886
34	120
62	79
1	36
13	1

clusters connected through mates:

Cluster	Number of shared read pairs	k

45	202	0.339
22	157	0.0907
10	106	0.0903
1	49	0.0162
62	24	0.0399
34	8	0.0132
13	4	0.00155
12	3	0.00242
23	3	0.00237
8	2	0.00111
18	2	0.00154
24	2	0.00133
1920	2	0.00612
3750	2	0.00613
11200	2	0.00615
2	1	0.000437
5	1	0.000336
6	1	0.000351
16	1	0.000429
21	1	0.00102
33	1	0.00137
38	1	0.000846
40	1	0.00115
44	1	0.00155
50	1	0.00182
53	1	0.0016
61	1	0.00122
63	1	0.00113
90	1	0.00214
94	1	0.00284
294	1	0.00299
12200	1	0.00308
24300	1	0.00308

CL42 ----> CL45

No. of shared pairs: :202

CL42 ----> CL22

No. of shared pairs: :157

CL42 ----> CL10

No. of shared pairs: :106

CL42 ----> CL1

No. of shared pairs: :49

CL42 ----> CL62

No. of shared pairs: :24