Cluster no. 54

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Cluster is part of supercluster: 23

Cluster characteristics:

size	3883
size_real	3883
ecount	71807
supercluster	23
annotations_summary	22.30% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-INT 11.95% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT 10.97% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RH 6.18% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-GAG 5.74% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-CHDII 3.32% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-PROT 0.26% Class_I/LTR/Ty3_gypsy/chromovirus/Chlamyvir:Ty3-RT 0.23% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RH 0.23% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-PROT 0.05% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-CHDII 0.05% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-GAG 0.05% Class_I/LTR/Ty1_copia/SIRE:Ty1-GAG 0.03% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-RT 0.03% Class_I/LINE:LINE-ENDO 0.03% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RT 0.03% Class_I/LTR/Ty1_copia/Ale:Ty1-INT 0.03% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-RH
pair_completeness	0.793533487297922
pbs_score	None
TR_score	None
TR_monomer_length	None
loop_index	0.000257532835436518
satellite_probability	3.20953330666128e-23
consensus	None
TAREAN_annotation	Other
orientation_score	1

comparative analysis:

Comparative analysis - species read counts:

Species	Read count
S2	1270
S1	1300
S3	1320

comparative analysis - number of edges between species:

	S2	S1	S3
S2	8190	7890	8100
S1	7890	7700	7920
S3	8100	7920	8090

comparative analysis - observed/expected number of edges between species

	S2	S1	S3
S2	1.010	0.996	0.998
S1	0.996	1.000	1.000
S3	0.998	1.000	0.999

protein domains:

Reads annotation summary

cl_string domain Freq proportion

LINE LINE-ENDO LINE LINE-ENDO 1 0.00026

SIRE Ty1-GAG SIRE Ty1-GAG 2 0.00052

Ale Ty1-INT Ale Ty1-INT 1 0.00026

Reina Ty3-CHDII Reina Ty3-CHDII 2 0.00052

Tekay Ty3-CHDII Tekay Ty3-CHDII 223 0.05743

CRM Ty3-GAG CRM Ty3-GAG 2 0.00052

Tekay Ty3-GAG Tekay Ty3-GAG 240 0.06181

Tekay Ty3-INT Tekay Ty3-INT 866 0.22302

Reina Ty3-PROT Reina Ty3-PROT 9 0.00232

Tekay Ty3-PROT Tekay Ty3-PROT 129 0.03322

Reina Ty3-RH Reina Ty3-RH 9 0.00232

TatV Ty3-RH TatV Ty3-RH 1 0.00026

Tekay Ty3-RH Tekay Ty3-RH 426 0.10971

Chlamyvir Ty3-RT Chlamyvir Ty3-RT 10 0.00258

Galadriel Ty3-RT Galadriel Ty3-RT 1 0.00026

Reina Ty3-RT Reina Ty3-RT 1 0.00026

Tekay Ty3-RT Tekay Ty3-RT 464 0.11950

clusters with similarity:

Cluster	Number of similarity hits

42	135
9	125
71	7
55	4
43	1
78	1
180	1

clusters connected through mates:

Cluster	Number of shared read pairs	k

42	58	0.0468
9	52	0.0359
71	27	0.0556
69	14	0.0282
78	13	0.0325
180	13	0.053
866	6	0.0263
44	5	0.00479
125	5	0.0146
11	4	0.00274
2840	4	0.0176
6300	4	0.0177
43	3	0.00502
5080	3	0.0133
12	2	0.00104
22	2	0.00167
37	2	0.00149
48	2	0.00272
70	2	0.00374
80	2	0.00207
594	2	0.00887
1990	2	0.00885
2180	2	0.00887
4860	2	0.00885
7650	2	0.00887
9060	2	0.00889
38600	2	0.00891
47100	2	0.00891
3	1	0.000565
4	1	0.000403
6	1	0.000604
8	1	0.00126
13	1	0.00061
14	1	0.000514
25	1	0.000918
45	1	0.00152
51	1	0.00179
63	1	0.00223
72	1	0.00177
86	1	0.00239
92	1	0.00191
148	1	0.00325
291	1	0.00398
621	1	0.00426
897	1	0.00441
1940	1	0.00441
4100	1	0.00442
4330	1	0.00446
5330	1	0.00443
6950	1	0.00443
10800	1	0.00444
11400	1	0.00444
16400	1	0.00445
21300	1	0.00445
24700	1	0.00445
25400	1	0.00445
28800	1	0.00445
34600	1	0.00445
50100	1	0.00445

CL54 ----> CL42

No. of shared pairs: :58

CL54 ----> CL9

No. of shared pairs: :52

CL54 ----> CL71

No. of shared pairs: :27

CL54 ----> CL69

No. of shared pairs: :14

CL54 ----> CL78

No. of shared pairs: :13

CL54 ----> CL180

No. of shared pairs: :13