Cluster no. 25

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Cluster is part of supercluster: 4

Cluster characteristics:

size 8538
size_real 8538
ecount 245995
supercluster 4
annotations_summary 26.60% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-RT
23.83% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-RH
16.67% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-aRH
0.52% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatIV_Ogre:Ty3-RT
0.37% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatIV_Ogre:Ty3-aRH
0.06% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatIV_Ogre:Ty3-INT
0.06% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatIV_Ogre:Ty3-RH
0.05% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatII:Ty3-aRH
0.05% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-INT
0.05% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatI:Ty3-RT
0.02% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RH
0.01% organelle/mitochondria
0.01% Class_I/LTR/Ty1_copia/Ale:Ty1-INT
0.01% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-RH
0.01% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila:Ty3-RT
0.01% Class_I/LTR/Ty1_copia/Ale:Ty1-RT
0.01% Class_I/LTR/Ty1_copia/Ivana:Ty1-RT
pair_completeness 0.748515257014131
pbs_score None
TR_score None
TR_monomer_length None
loop_index 0.00175685172171469
satellite_probability 6.84243327814155e-23
consensus None
TAREAN_annotation Other
orientation_score 1

comparative analysis:


Comparative analysis - species read counts:
Species Read count
S5 2820
S4 2880
S6 2830
comparative analysis - number of edges between species:
S5 S4 S6
S5 27400 27600 27000
S4 27600 27700 27400
S6 27000 27400 26700
comparative analysis - observed/expected number of edges between species
S5 S4 S6
S5 1.000 0.999 0.998
S4 0.999 0.996 1.000
S6 0.998 1.000 0.996

protein domains:

protein domains:


Reads annotation summary

  cl_string domain Freq proportion
mitochondria mitochondria 1 0.00012
Ale Ty1-INT Ale Ty1-INT 1 0.00012
Ale Ty1-RT Ale Ty1-RT 1 0.00012
Ivana Ty1-RT Ivana Ty1-RT 1 0.00012
TatIV_Ogre Ty3-INT TatIV_Ogre Ty3-INT 5 0.00059
TatV Ty3-INT TatV Ty3-INT 4 0.00047
Galadriel Ty3-RH Galadriel Ty3-RH 1 0.00012
TatIV_Ogre Ty3-RH TatIV_Ogre Ty3-RH 5 0.00059
TatV Ty3-RH TatV Ty3-RH 2035 0.23835
Tekay Ty3-RH Tekay Ty3-RH 2 0.00023
Athila Ty3-RT Athila Ty3-RT 1 0.00012
TatI Ty3-RT TatI Ty3-RT 4 0.00047
TatIV_Ogre Ty3-RT TatIV_Ogre Ty3-RT 44 0.00515
TatV Ty3-RT TatV Ty3-RT 2271 0.26599
TatII Ty3-aRH TatII Ty3-aRH 4 0.00047
TatIV_Ogre Ty3-aRH TatIV_Ogre Ty3-aRH 32 0.00375
TatV Ty3-aRH TatV Ty3-aRH 1423 0.16667

clusters with similarity:

Cluster Number of similarity hits
53 1330
60 161
44 37
164 15

clusters connected through mates:

Cluster Number of shared
read pairs		 k
53 400 0.342
60 148 0.168
164 84 0.11
44 54 0.0474
75 11 0.00978
1 10 0.00254
10 8 0.00281
49 7 0.00401
59 6 0.00392
61 6 0.00333
84 6 0.00456
74 5 0.00559
27 4 0.00264
30 4 0.00179
103 4 0.00299
107 4 0.00489
2 3 0.00081
6 3 0.000722
58 3 0.00166
5320 3 0.00487
4 2 0.00053
7 2 0.000724
9 2 0.00114
11 2 0.000729
19 2 0.000942
20 2 0.000886
45 2 0.00123
56 2 0.00114
62 2 0.00179
7820 2 0.00325
16400 2 0.00325
21000 2 0.00325
34800 2 0.00325
37800 2 0.00325
39600 2 0.00325
5 1 0.000354
13 1 0.000486
16 1 0.000596
17 1 0.000475
23 1 0.000338
24 1 0.000578
26 1 0.000377
32 1 0.000517
36 1 0.000598
38 1 0.00088
43 1 0.000686
67 1 0.000969
72 1 0.000623
80 1 0.00125
87 1 0.00083
94 1 0.000704
99 1 0.000782
109 1 0.000821
110 1 0.000766
111 1 0.00115
119 1 0.00094
128 1 0.0013
136 1 0.00132
138 1 0.00115
168 1 0.00133
291 1 0.00159
610 1 0.00162
1330 1 0.00162
1680 1 0.00162
1740 1 0.00162
2610 1 0.00162
3400 1 0.00162
8630 1 0.00163
8850 1 0.00162
11900 1 0.00163
13200 1 0.00162
20900 1 0.00163
21400 1 0.00163
31000 1 0.00163
35200 1 0.00163
40000 1 0.00163
42600 1 0.00163
44500 1 0.00163
45000 1 0.00163

CL25 ----> CL53

image

No. of shared pairs: :400

CL25 ----> CL60

image

No. of shared pairs: :148

CL25 ----> CL164

image

No. of shared pairs: :84

CL25 ----> CL44

image

No. of shared pairs: :54

CL25 ----> CL75

image

No. of shared pairs: :11

CL25 ----> CL1

image

No. of shared pairs: :10