Cluster no. 42

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Cluster is part of supercluster: 14

Cluster characteristics:

size 6599
size_real 6599
ecount 119975
supercluster 14
annotations_summary 11.34% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-INT
7.06% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT
6.89% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RH
3.18% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-CHDII
1.47% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-PROT
0.17% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RH
0.05% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-RT
0.05% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RT
0.03% Class_I/LTR/Ty3_gypsy/chromovirus/Tcn1:Ty3-RT
0.02% Class_I/LTR/Ty3_gypsy/chromovirus/Chlamyvir:Ty3-RT
0.02% Class_I/LTR/Ty1_copia/SIRE:Ty1-INT
0.02% Class_I/LTR/Ty1_copia/Tork:Ty1-RT
pair_completeness 0.700334965215151
pbs_score None
TR_score None
TR_monomer_length None
loop_index 0.000606152447340506
satellite_probability 1.64859681984477e-22
consensus None
TAREAN_annotation Other
orientation_score 1

comparative analysis:


Comparative analysis - species read counts:
Species Read count
S8 12
S5 17
S4 10
S7 16
S9 5
S6 18
S2 2020
S1 2200
S3 2300
comparative analysis - number of edges between species:
S8 S5 S4 S7 S9 S6 S2 S1 S3
S8 5.0 0.5 0.0 2.5 0.0 0 19.0 17.0 25.5
S5 0.5 1.0 0.5 0.0 0.0 0 89.0 99.5 106.0
S4 0.0 0.5 0.0 1.0 0.0 0 70.0 57.5 64.0
S7 2.5 0.0 1.0 9.0 1.0 0 32.0 34.5 39.0
S9 0.0 0.0 0.0 1.0 0.0 0 18.5 23.5 33.0
S6 0.0 0.0 0.0 0.0 0.0 6 85.0 103.0 102.0
S2 19.0 89.0 70.0 32.0 18.5 85 11700.0 12200.0 13200.0
S1 17.0 99.5 57.5 34.5 23.5 103 12200.0 13100.0 13800.0
S3 25.5 106.0 64.0 39.0 33.0 102 13200.0 13800.0 14700.0
comparative analysis - observed/expected number of edges between species
S8 S5 S4 S7 S9 S6 S2 S1 S3
S8 124.000 2.920 0.000 36.300 0.000 0.000 0.877 0.743 1.050
S5 2.920 1.370 1.050 0.000 0.000 0.000 0.965 1.020 1.020
S4 0.000 1.050 0.000 5.220 0.000 0.000 1.160 0.905 0.946
S7 36.300 0.000 5.220 76.200 13.300 0.000 0.863 0.880 0.935
S9 0.000 0.000 0.000 13.300 0.000 0.000 0.781 0.939 1.240
S6 0.000 0.000 0.000 0.000 0.000 8.220 0.922 1.060 0.984
S2 0.877 0.965 1.160 0.863 0.781 0.922 1.000 0.993 1.000
S1 0.743 1.020 0.905 0.880 0.939 1.060 0.993 1.010 0.997
S3 1.050 1.020 0.946 0.935 1.240 0.984 1.000 0.997 0.999

protein domains:

protein domains:


Reads annotation summary

  cl_string domain Freq proportion
SIRE Ty1-INT SIRE Ty1-INT 1 0.00015
Tork Ty1-RT Tork Ty1-RT 1 0.00015
Tekay Ty3-CHDII Tekay Ty3-CHDII 210 0.03182
Tekay Ty3-INT Tekay Ty3-INT 748 0.11335
Tekay Ty3-PROT Tekay Ty3-PROT 97 0.01470
Reina Ty3-RH Reina Ty3-RH 11 0.00167
Tekay Ty3-RH Tekay Ty3-RH 455 0.06895
Chlamyvir Ty3-RT Chlamyvir Ty3-RT 1 0.00015
Galadriel Ty3-RT Galadriel Ty3-RT 3 0.00045
Reina Ty3-RT Reina Ty3-RT 3 0.00045
Tcn1 Ty3-RT Tcn1 Ty3-RT 2 0.00030
Tekay Ty3-RT Tekay Ty3-RT 466 0.07062

clusters with similarity:

Cluster Number of similarity hits
98 118
85 63
183 23
202 11
142 2
188 2
23 1
177 1

clusters connected through mates:

Cluster Number of shared
read pairs		 k
98 145 0.146
85 118 0.108
183 36 0.0541
188 32 0.0454
202 20 0.0304
23 11 0.00642
7 9 0.00446
30 7 0.0044
38 7 0.00435
57 6 0.00435
1160 6 0.0102
108 5 0.00504
143 5 0.005
1920 5 0.00853
2140 5 0.00853
27 4 0.00275
46 4 0.00268
96 4 0.00354
116 4 0.00434
125 4 0.00375
2740 4 0.00683
5970 4 0.00685
7170 4 0.00685
58 3 0.00259
129 3 0.00368
177 3 0.0043
189 3 0.00422
5490 3 0.00514
8760 3 0.00514
18400 3 0.00515
64 2 0.00142
113 2 0.00208
137 2 0.00279
153 2 0.00204
170 2 0.00272
171 2 0.00227
249 2 0.00325
260 2 0.00301
275 2 0.0031
724 2 0.00338
1140 2 0.00341
2350 2 0.00343
4560 2 0.00343
4730 2 0.00342
5320 2 0.00342
6240 2 0.00343
6840 2 0.00342
12300 2 0.00343
12800 2 0.00343
15700 2 0.00343
18000 2 0.00343
18000 2 0.00343
24400 2 0.00343
31900 2 0.00343
32200 2 0.00343
47000 2 0.00343
50400 2 0.00343
51600 2 0.00343
56100 2 0.00343
60700 2 0.00343
64400 2 0.00343
66300 2 0.00343
66400 2 0.00343
50 1 0.00126
77 1 0.00122
110 1 0.000822
124 1 0.00124
127 1 0.00138
148 1 0.00105
152 1 0.00106
154 1 0.0014
168 1 0.00113
175 1 0.00129
225 1 0.00147
227 1 0.00159
239 1 0.00142
290 1 0.00163
301 1 0.00153
340 1 0.00164
413 1 0.00167
425 1 0.00165
450 1 0.00168
562 1 0.00168
649 1 0.00168
992 1 0.0017
1000 1 0.0017
1390 1 0.0017
1690 1 0.0017
1690 1 0.0017
2110 1 0.00171
3240 1 0.00171
3330 1 0.00171
3380 1 0.00171
3790 1 0.00171
3940 1 0.00171
4420 1 0.00172
4440 1 0.00171
4920 1 0.00171
7070 1 0.00171
7160 1 0.00171
8040 1 0.00171
8120 1 0.00171
8500 1 0.00171
9850 1 0.00171
9910 1 0.00171
10900 1 0.00172
11000 1 0.00172
11800 1 0.00172
13100 1 0.00172
13600 1 0.00172
14300 1 0.00172
15600 1 0.00172
16100 1 0.00172
17300 1 0.00172
17800 1 0.00172
19900 1 0.00172
21300 1 0.00172
21500 1 0.00172
25000 1 0.00172
26300 1 0.00172
27200 1 0.00172
28900 1 0.00172
31400 1 0.00172
34300 1 0.00172
36500 1 0.00172
39700 1 0.00172
42200 1 0.00172
43000 1 0.00172
43800 1 0.00172
46300 1 0.00172
48000 1 0.00172
50300 1 0.00172
51000 1 0.00172
51500 1 0.00172
52300 1 0.00172
52400 1 0.00172
54500 1 0.00172
56500 1 0.00172
58200 1 0.00172
60100 1 0.00172
61100 1 0.00172
62300 1 0.00172
62300 1 0.00172
63000 1 0.00172
65100 1 0.00172
65300 1 0.00172
66300 1 0.00172
66500 1 0.00172
68300 1 0.00172
70900 1 0.00172

CL42 ----> CL98

image

No. of shared pairs: :145

CL42 ----> CL85

image

No. of shared pairs: :118

CL42 ----> CL183

image

No. of shared pairs: :36

CL42 ----> CL188

image

No. of shared pairs: :32

CL42 ----> CL202

image

No. of shared pairs: :20

CL42 ----> CL23

image

No. of shared pairs: :11