Cluster no. 25

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Cluster is part of supercluster: 6

Cluster characteristics:

size 6356
size_real 6356
ecount 119044
supercluster 6
annotations_summary 27.45% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-INT
14.58% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT
12.82% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RH
5.54% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-CHDII
3.40% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-PROT
1.31% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RT
0.71% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-GAG
0.52% Class_I/pararetrovirus:PARA-RT
0.46% Class_I/LTR/Ty3_gypsy/chromovirus/Chlamyvir:Ty3-RT
0.30% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-RH
0.20% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-RH
0.19% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-RH
0.14% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-PROT
0.09% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-RT
0.06% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RH
0.06% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-PROT
0.05% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-INT
0.03% organelle/plastid
0.02% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-RT
0.02% Class_I/LTR/Ty1_copia/Ale:Ty1-INT
0.02% Class_I/LTR/Ty3_gypsy/non-chromovirus/Selgy:Ty3-RH
0.02% Class_II/Subclass_2/Helitron:Helitron-HEL1
0.02% Class_I/LTR/Ty3_gypsy/chromovirus/chromo-outgroup:Ty3-RT
0.02% Class_I/LTR/Ty3_gypsy/chromovirus/Tcn1:Ty3-RT
pair_completeness 0.771460423634337
pbs_score None
TR_score None
TR_monomer_length None
loop_index 0.000471994965387036
satellite_probability 4.71413703996316e-23
consensus None
TAREAN_annotation Other
orientation_score 1

comparative analysis:


Comparative analysis - species read counts:
Species Read count
S8 2070
S9 2260
S7 2030
comparative analysis - number of edges between species:
S8 S9 S7
S8 12600 13600 12300
S9 13600 14700 13600
S7 12300 13600 12900
comparative analysis - observed/expected number of edges between species
S8 S9 S7
S8 1.010 1.000 0.982
S9 1.000 0.999 0.997
S7 0.982 0.997 1.020

protein domains:

protein domains:


Reads annotation summary

  cl_string domain Freq proportion
plastid plastid 2 0.00031
Helitron Helitron-HEL1 Helitron Helitron-HEL1 1 0.00016
pararetrovirus PARA-RT pararetrovirus PARA-RT 33 0.00519
Ale Ty1-INT Ale Ty1-INT 1 0.00016
Tekay Ty3-CHDII Tekay Ty3-CHDII 352 0.05538
Tekay Ty3-GAG Tekay Ty3-GAG 45 0.00708
Reina Ty3-INT Reina Ty3-INT 3 0.00047
Tekay Ty3-INT Tekay Ty3-INT 1745 0.27454
Galadriel Ty3-PROT Galadriel Ty3-PROT 9 0.00142
Reina Ty3-PROT Reina Ty3-PROT 4 0.00063
Tekay Ty3-PROT Tekay Ty3-PROT 216 0.03398
CRM Ty3-RH CRM Ty3-RH 13 0.00205
Galadriel Ty3-RH Galadriel Ty3-RH 12 0.00189
Reina Ty3-RH Reina Ty3-RH 4 0.00063
Selgy Ty3-RH Selgy Ty3-RH 1 0.00016
TatV Ty3-RH TatV Ty3-RH 19 0.00299
Tekay Ty3-RH Tekay Ty3-RH 815 0.12823
CRM Ty3-RT CRM Ty3-RT 6 0.00094
Chlamyvir Ty3-RT Chlamyvir Ty3-RT 29 0.00456
Galadriel Ty3-RT Galadriel Ty3-RT 1 0.00016
Reina Ty3-RT Reina Ty3-RT 83 0.01306
Tcn1 Ty3-RT Tcn1 Ty3-RT 1 0.00016
Tekay Ty3-RT Tekay Ty3-RT 927 0.14585
chromo-outgroup Ty3-RT chromo-outgroup Ty3-RT 1 0.00016

clusters with similarity:

Cluster Number of similarity hits
63 333
13 331
68 159
24 33
4 4
44 1
60 1

clusters connected through mates:

Cluster Number of shared
read pairs		 k
63 91 0.0934
24 82 0.0516
68 80 0.125
13 46 0.0172
4 18 0.00627
1 12 0.00386
403 11 0.0263
644 9 0.0216
22 7 0.00385
16 4 0.00165
23 4 0.00296
1920 4 0.00969
9 3 0.0012
1310 3 0.00725
1370 3 0.00725
1650 3 0.00726
1920 3 0.00726
4790 3 0.00729
12 2 0.00151
44 2 0.00274
53 2 0.00281
59 2 0.00172
65 2 0.003
70 2 0.00282
130 2 0.00449
597 2 0.00482
1210 2 0.00485
2440 2 0.00485
2740 2 0.00485
3220 2 0.00487
4040 2 0.00487
4150 2 0.00485
4830 2 0.00486
4840 2 0.00486
5350 2 0.00486
6250 2 0.00486
10400 2 0.00487
11400 2 0.00487
13500 2 0.00487
14000 2 0.00487
15000 2 0.00487
15200 2 0.00487
16000 2 0.00487
16700 2 0.00487
17800 2 0.00487
20700 2 0.00487
25200 2 0.00487
25500 2 0.00487
3 1 0.000292
5 1 0.000326
6 1 0.000341
8 1 0.000531
10 1 0.000793
17 1 0.000781
18 1 0.000721
27 1 0.000537
29 1 0.000602
31 1 0.00091
32 1 0.000521
33 1 0.00123
36 1 0.00095
38 1 0.000789
50 1 0.00157
52 1 0.000685
60 1 0.00137
69 1 0.00165
79 1 0.00167
126 1 0.00221
203 1 0.00232
240 1 0.00241
284 1 0.0024
406 1 0.00242
609 1 0.00241
985 1 0.00241
1500 1 0.00242
2210 1 0.00243
2390 1 0.00242
2540 1 0.00242
2680 1 0.00242
2930 1 0.00243
3220 1 0.00243
5080 1 0.00243
5170 1 0.00243
5380 1 0.00244
5590 1 0.00244
6140 1 0.00244
7630 1 0.00243
8060 1 0.00243
8790 1 0.00243
9700 1 0.00243
11100 1 0.00243
12300 1 0.00243
12500 1 0.00243
12500 1 0.00243
12800 1 0.00243
12900 1 0.00243
13400 1 0.00243
13600 1 0.00243
14600 1 0.00243
15300 1 0.00243
15900 1 0.00243
16800 1 0.00243
17100 1 0.00243
18100 1 0.00243
18500 1 0.00243
21300 1 0.00243
21500 1 0.00243
23300 1 0.00243
23700 1 0.00243

CL25 ----> CL63

image

No. of shared pairs: :91

CL25 ----> CL24

image

No. of shared pairs: :82

CL25 ----> CL68

image

No. of shared pairs: :80

CL25 ----> CL13

image

No. of shared pairs: :46

CL25 ----> CL4

image

No. of shared pairs: :18

CL25 ----> CL1

image

No. of shared pairs: :12

CL25 ----> CL403

image

No. of shared pairs: :11