Cluster no. 67

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Cluster is part of supercluster: 14

Cluster characteristics:

size 4884
size_real 4884
ecount 106291
supercluster 14
annotations_summary 49.16% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-INT
18.59% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RH
9.83% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-CHDII
1.90% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT
0.23% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-INT
0.12% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-RT
0.12% Class_I/LTR/Ty1_copia/Gymco-II:Ty1-INT
0.12% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-RH
0.10% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RH
0.04% Class_I/LTR/Ty1_copia/Ale:Ty1-INT
0.04% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-CHDII
0.04% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-INT
0.02% Class_I/LTR/Ty3_gypsy/chromovirus/Tcn1:Ty3-RT
0.02% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-RH
0.02% Class_I/LTR/Ty3_gypsy/chromovirus/Chlamyvir:Ty3-RT
0.02% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-RH
0.02% Class_I/LTR/Ty1_copia/Ale:Ty1-RH
pair_completeness 0.707692307692308
pbs_score None
TR_score None
TR_monomer_length None
loop_index 0.000614250614250614
satellite_probability 1.39099901770407e-22
consensus None
TAREAN_annotation Other
orientation_score 1

comparative analysis:


Comparative analysis - species read counts:
Species Read count
S5 1650
S4 1550
S6 1690
comparative analysis - number of edges between species:
S5 S4 S6
S5 11700 11600 11900
S4 11600 11700 11900
S6 11900 11900 12300
comparative analysis - observed/expected number of edges between species
S5 S4 S6
S5 1.010 0.995 0.997
S4 0.995 1.010 0.998
S6 0.997 0.998 1.000

protein domains:

protein domains:


Reads annotation summary

  cl_string domain Freq proportion
Ale Ty1-INT Ale Ty1-INT 2 0.00041
Gymco-II Ty1-INT Gymco-II Ty1-INT 6 0.00123
Ale Ty1-RH Ale Ty1-RH 1 0.00020
CRM Ty3-CHDII CRM Ty3-CHDII 2 0.00041
Tekay Ty3-CHDII Tekay Ty3-CHDII 480 0.09828
CRM Ty3-INT CRM Ty3-INT 2 0.00041
Reina Ty3-INT Reina Ty3-INT 11 0.00225
Tekay Ty3-INT Tekay Ty3-INT 2401 0.49161
CRM Ty3-RH CRM Ty3-RH 6 0.00123
Galadriel Ty3-RH Galadriel Ty3-RH 1 0.00020
Reina Ty3-RH Reina Ty3-RH 5 0.00102
TatV Ty3-RH TatV Ty3-RH 1 0.00020
Tekay Ty3-RH Tekay Ty3-RH 908 0.18591
Chlamyvir Ty3-RT Chlamyvir Ty3-RT 1 0.00020
Galadriel Ty3-RT Galadriel Ty3-RT 6 0.00123
Tcn1 Ty3-RT Tcn1 Ty3-RT 1 0.00020
Tekay Ty3-RT Tekay Ty3-RT 93 0.01904

clusters with similarity:

Cluster Number of similarity hits
84 368
100 194
101 73
27 48
97 32
165 12
102 9
13 6

clusters connected through mates:

Cluster Number of shared
read pairs		 k
84 135 0.12
100 117 0.167
13 56 0.0301
165 46 0.0858
98 14 0.012
1 6 0.0016
19 6 0.00311
27 5 0.0038
2 4 0.00114
97 4 0.00462
1930 4 0.00947
3010 4 0.0095
62 3 0.00326
3720 3 0.00713
4290 3 0.00713
8700 3 0.00715
5 2 0.00076
32 2 0.00115
58 2 0.00124
59 2 0.0015
101 2 0.00235
103 2 0.00175
142 2 0.00254
5600 2 0.00476
13900 2 0.00477
20900 2 0.00477
37200 2 0.00477
7 1 0.00039
8 1 0.00041
9 1 0.000645
16 1 0.000675
25 1 0.000969
30 1 0.000492
40 1 0.000787
45 1 7e-04
49 1 0.000645
52 1 0.000807
54 1 0.000702
55 1 0.000695
61 1 0.000622
63 1 0.000642
73 1 0.000768
80 1 0.00166
83 1 0.000662
87 1 0.000992
102 1 0.00103
113 1 0.00117
120 1 0.00128
130 1 0.00136
134 1 0.00147
137 1 0.00127
785 1 0.00237
1290 1 0.00237
2500 1 0.00237
2750 1 0.00238
8520 1 0.00238
9960 1 0.00239
10500 1 0.00239
11700 1 0.00238
16600 1 0.00239
20400 1 0.00239
22300 1 0.00239
25100 1 0.00239
29000 1 0.00239
29200 1 0.00239
31100 1 0.00239
33400 1 0.00239
36200 1 0.00239
36500 1 0.00239
37200 1 0.00239
37800 1 0.00239
38900 1 0.00239
40000 1 0.00239
41300 1 0.00239
42400 1 0.00239
43400 1 0.00239
46500 1 0.00239

CL67 ----> CL84

image

No. of shared pairs: :135

CL67 ----> CL100

image

No. of shared pairs: :117

CL67 ----> CL13

image

No. of shared pairs: :56

CL67 ----> CL165

image

No. of shared pairs: :46

CL67 ----> CL98

image

No. of shared pairs: :14