Cluster no. 104

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Cluster is part of supercluster: 3

Cluster characteristics:

size	3287
size_real	3287
ecount	36249
supercluster	3
annotations_summary	18.41% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-INT 13.93% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT 8.79% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RH 2.98% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-PROT 1.73% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-GAG 0.94% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RT 0.76% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RH 0.46% Class_I/LTR/Ty3_gypsy/chromovirus/Chlamyvir:Ty3-RT 0.30% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-GAG 0.30% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-RT 0.24% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-PROT 0.15% Class_I/LTR/Ty3_gypsy/chromovirus/Tcn1:Ty3-RT 0.12% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-INT 0.03% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-CHDII 0.03% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila:Ty3-RH 0.03% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-RT 0.03% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-GAG 0.03% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-INT 0.03% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-RH
pair_completeness	0.795193883123976
pbs_score	None
TR_score	None
TR_monomer_length	None
loop_index	0.000304228780042592
satellite_probability	2.63652108321905e-23
consensus	None
TAREAN_annotation	Other
orientation_score	1

comparative analysis:

Comparative analysis - species read counts:

Species	Read count
S8	1120
S5	3
S4	4
S7	1060
S9	1090
S6	4
S2	8
S1	2
S3	2

comparative analysis - number of edges between species:

	S8	S5	S4	S7	S9	S6	S2	S1	S3
S8	4320.0	9.0	23.0	3900.0	4110.0	27.5	52.5	6.5	12.5
S5	9.0	0.0	0.0	8.0	7.0	0.0	0.0	0.0	0.5
S4	23.0	0.0	0.0	19.5	18.0	1.5	0.0	0.0	0.0
S7	3900.0	8.0	19.5	3680.0	3840.0	29.0	39.5	2.5	12.0
S9	4110.0	7.0	18.0	3840.0	3860.0	24.5	41.0	4.0	6.5
S6	27.5	0.0	1.5	29.0	24.5	2.0	0.0	0.0	0.0
S2	52.5	0.0	0.0	39.5	41.0	0.0	1.0	0.0	0.0
S1	6.5	0.0	0.0	2.5	4.0	0.0	0.0	0.0	0.0
S3	12.5	0.5	0.0	12.0	6.5	0.0	0.0	0.0	0.0

comparative analysis - observed/expected number of edges between species

	S8	S5	S4	S7	S9	S6	S2	S1	S3
S8	1.010	1.070	1.080	0.983	1.000	0.947	1.140	1.450	1.150
S5	1.070	0.000	0.000	1.030	0.869	0.000	0.000	0.000	23.500
S4	1.080	0.000	0.000	0.989	0.883	10.400	0.000	0.000	0.000
S7	0.983	1.030	0.989	1.000	1.010	1.080	0.927	0.605	1.200
S9	1.000	0.869	0.883	1.010	0.985	0.882	0.931	0.936	0.628
S6	0.947	0.000	10.400	1.080	0.882	10.200	0.000	0.000	0.000
S2	1.140	0.000	0.000	0.927	0.931	0.000	2.020	0.000	0.000
S1	1.450	0.000	0.000	0.605	0.936	0.000	0.000	0.000	0.000
S3	1.150	23.500	0.000	1.200	0.628	0.000	0.000	0.000	0.000

protein domains:

Reads annotation summary

cl_string domain Freq proportion

Tekay Ty3-CHDII Tekay Ty3-CHDII 1 0.0003

CRM Ty3-GAG CRM Ty3-GAG 10 0.0030

Reina Ty3-GAG Reina Ty3-GAG 1 0.0003

Tekay Ty3-GAG Tekay Ty3-GAG 57 0.0173

CRM Ty3-INT CRM Ty3-INT 1 0.0003

Reina Ty3-INT Reina Ty3-INT 4 0.0012

Tekay Ty3-INT Tekay Ty3-INT 605 0.1841

Reina Ty3-PROT Reina Ty3-PROT 8 0.0024

Tekay Ty3-PROT Tekay Ty3-PROT 98 0.0298

Athila Ty3-RH Athila Ty3-RH 1 0.0003

CRM Ty3-RH CRM Ty3-RH 1 0.0003

Reina Ty3-RH Reina Ty3-RH 25 0.0076

Tekay Ty3-RH Tekay Ty3-RH 289 0.0879

CRM Ty3-RT CRM Ty3-RT 10 0.0030

Chlamyvir Ty3-RT Chlamyvir Ty3-RT 15 0.0046

Galadriel Ty3-RT Galadriel Ty3-RT 1 0.0003

Reina Ty3-RT Reina Ty3-RT 31 0.0094

Tcn1 Ty3-RT Tcn1 Ty3-RT 5 0.0015

Tekay Ty3-RT Tekay Ty3-RT 458 0.1393

clusters with similarity:

Cluster	Number of similarity hits

4	141
32	101
53	72
79	54
221	10
75	3
102	1

clusters connected through mates:

Cluster	Number of shared read pairs	k

53	118	0.159
4	116	0.065
79	18	0.045
32	8	0.0103
75	7	0.00882
102	7	0.0126
9	5	0.00565
221	5	0.0169
12	3	0.00218
5	2	0.000977
22	2	0.0011
54	2	0.00196
1350	2	0.0103
3330	2	0.0104
11800	2	0.0106
18300	2	0.0106
38600	2	0.0106
58600	2	0.0106
8	1	0.000499
11	1	7e-04
40	1	0.00132
83	1	0.00178
100	1	0.00162
107	1	0.00132
114	1	0.00187
131	1	0.0019
2950	1	0.00524
5550	1	0.00526
5650	1	0.00529
6770	1	0.00529
16600	1	0.00529
36800	1	0.00531
65600	1	0.00531
69200	1	0.00531

CL104 ----> CL53

No. of shared pairs: :118

CL104 ----> CL4

No. of shared pairs: :116

CL104 ----> CL79

No. of shared pairs: :18