Cluster no. 39

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Cluster is part of supercluster: 18

Cluster characteristics:

size 6496
size_real 6496
ecount 70503
supercluster 18
annotations_summary 20.78% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT
15.38% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RH
9.07% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-GAG
4.22% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-PROT
0.65% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-RH
0.40% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RH
0.26% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-PROT
0.22% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila:Ty3-RH
0.15% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-GAG
0.14% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-RT
0.14% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-GAG
0.09% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RT
0.06% Class_I/LTR/Ty3_gypsy/chromovirus/Tcn1:Ty3-RT
0.06% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-RH
0.05% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatIV_Ogre:Ty3-RH
0.03% Class_I/LINE:LINE-ENDO
0.03% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-PROT
0.03% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-RT
0.02% Class_I/LTR/Ty1_copia/Ale:Ty1-INT
0.02% Class_II/Subclass_1/TIR/MuDR_Mutator:MuDR-TPase
0.02% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-RH
0.02% Class_I/LTR/Ty1_copia/Ale:Ty1-RT
0.02% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-INT
pair_completeness 0.627254509018036
pbs_score None
TR_score None
TR_monomer_length None
loop_index 0.000461822660098522
satellite_probability 4.97759293480724e-22
consensus None
TAREAN_annotation Other
orientation_score 1

comparative analysis:


Comparative analysis - species read counts:
Species Read count
S5 2160
S4 2130
S6 2200
comparative analysis - number of edges between species:
S5 S4 S6
S5 7870 7770 7630
S4 7770 7940 7950
S6 7630 7950 7990
comparative analysis - observed/expected number of edges between species
S5 S4 S6
S5 1.020 0.995 0.981
S4 0.995 1.000 1.000
S6 0.981 1.000 1.010

protein domains:

protein domains:


Reads annotation summary

  cl_string domain Freq proportion
LINE LINE-ENDO LINE LINE-ENDO 2 0.00031
MuDR_Mutator MuDR-TPase MuDR_Mutator MuDR-TPase 1 0.00015
Ale Ty1-INT Ale Ty1-INT 1 0.00015
Ale Ty1-RT Ale Ty1-RT 1 0.00015
CRM Ty3-GAG CRM Ty3-GAG 9 0.00139
Reina Ty3-GAG Reina Ty3-GAG 10 0.00154
Tekay Ty3-GAG Tekay Ty3-GAG 589 0.09067
Tekay Ty3-INT Tekay Ty3-INT 1 0.00015
Galadriel Ty3-PROT Galadriel Ty3-PROT 2 0.00031
Reina Ty3-PROT Reina Ty3-PROT 17 0.00262
Tekay Ty3-PROT Tekay Ty3-PROT 274 0.04218
Athila Ty3-RH Athila Ty3-RH 14 0.00216
CRM Ty3-RH CRM Ty3-RH 1 0.00015
Galadriel Ty3-RH Galadriel Ty3-RH 42 0.00647
Reina Ty3-RH Reina Ty3-RH 26 0.00400
TatIV_Ogre Ty3-RH TatIV_Ogre Ty3-RH 3 0.00046
TatV Ty3-RH TatV Ty3-RH 4 0.00062
Tekay Ty3-RH Tekay Ty3-RH 999 0.15379
CRM Ty3-RT CRM Ty3-RT 2 0.00031
Galadriel Ty3-RT Galadriel Ty3-RT 9 0.00139
Reina Ty3-RT Reina Ty3-RT 6 0.00092
Tcn1 Ty3-RT Tcn1 Ty3-RT 4 0.00062
Tekay Ty3-RT Tekay Ty3-RT 1350 0.20782

clusters with similarity:

Cluster Number of similarity hits
87 56
73 4
22 3
35 1

clusters connected through mates:

Cluster Number of shared
read pairs		 k
87 158 0.118
73 103 0.0633
1 11 0.00271
10 10 0.00336
695 9 0.0119
30 8 0.00339
19 6 0.00266
35 5 0.00281
57 5 0.00269
59 5 0.00301
62 5 0.00401
13 4 0.00183
94 4 0.00258
103 4 0.00272
2480 4 0.00535
4500 4 0.00536
2 3 0.000782
42 3 0.00181
49 3 0.0016
58 3 0.00155
90 3 0.00244
178 3 0.00365
2630 3 0.00401
3320 3 0.00402
3670 3 0.00402
4480 3 0.00402
5120 3 0.00402
8580 3 0.00402
7 2 0.000692
9 2 0.00107
27 2 0.00122
41 2 0.00109
45 2 0.00114
83 2 0.00109
84 2 0.00138
142 2 0.0018
149 2 0.00223
255 2 0.00258
1800 2 0.00268
1990 2 0.00268
2720 2 0.00268
4810 2 0.00268
6110 2 0.00268
7290 2 0.00268
10800 2 0.00268
12900 2 0.00268
13200 2 0.00268
15600 2 0.00268
18100 2 0.00268
20600 2 0.00268
21100 2 0.00268
22600 2 0.00268
22700 2 0.00268
26600 2 0.00268
28500 2 0.00268
30200 2 0.00268
30300 2 0.00268
30900 2 0.00268
31700 2 0.00268
31900 2 0.00268
32800 2 0.00268
32900 2 0.00268
38500 2 0.00268
40000 2 0.00268
42500 2 0.00268
44800 2 0.00268
46400 2 0.00268
46800 2 0.00268
5 1 0.000338
8 1 0.000362
15 1 0.000584
17 1 0.000448
21 1 0.000335
22 1 0.000645
23 1 0.000324
29 1 0.00034
33 1 0.000638
40 1 0.000626
55 1 0.000567
56 1 0.000529
61 1 0.000517
63 1 0.000531
68 1 0.000533
74 1 0.000976
82 1 0.000697
88 1 0.000962
98 1 0.000668
106 1 0.00104
107 1 0.00105
113 1 0.000848
120 1 0.000903
147 1 0.00101
205 1 0.00129
214 1 0.00122
218 1 0.00124
391 1 0.00131
1220 1 0.00134
1740 1 0.00134
3390 1 0.00134
3800 1 0.00134
5130 1 0.00134
5920 1 0.00134
6270 1 0.00134
6270 1 0.00134
6370 1 0.00134
6430 1 0.00134
7080 1 0.00134
8390 1 0.00134
8860 1 0.00134
9370 1 0.00134
10500 1 0.00134
10700 1 0.00134
11200 1 0.00134
11400 1 0.00134
11700 1 0.00134
12200 1 0.00134
12300 1 0.00134
13600 1 0.00134
14300 1 0.00134
14400 1 0.00134
14800 1 0.00134
14900 1 0.00134
17200 1 0.00134
17600 1 0.00134
19800 1 0.00134
20800 1 0.00134
22900 1 0.00134
23000 1 0.00134
24000 1 0.00134
25400 1 0.00134
27200 1 0.00134
27400 1 0.00134
28300 1 0.00134
29700 1 0.00134
29800 1 0.00134
30300 1 0.00134
30900 1 0.00134
33800 1 0.00134
33900 1 0.00134
34600 1 0.00134
36000 1 0.00134
37800 1 0.00134
38300 1 0.00134
40700 1 0.00134
40700 1 0.00134
41000 1 0.00134
45200 1 0.00134
45500 1 0.00134
45700 1 0.00134
46800 1 0.00134
47300 1 0.00134

CL39 ----> CL87

image

No. of shared pairs: :158

CL39 ----> CL73

image

No. of shared pairs: :103

CL39 ----> CL1

image

No. of shared pairs: :11

CL39 ----> CL10

image

No. of shared pairs: :10