Cluster no. 79

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Cluster is part of supercluster: 13

Cluster characteristics:

size 4106
size_real 4106
ecount 22436
supercluster 13
annotations_summary 17.54% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RH
16.39% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT
7.48% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-GAG
6.02% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-PROT
1.32% Class_I/LTR/Ty3_gypsy/chromovirus/Chlamyvir:Ty3-RT
1.19% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-GAG
0.71% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RT
0.22% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-RT
0.10% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-GAG
0.10% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-PROT
0.07% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RH
0.07% Class_I/LTR/Ty3_gypsy/chromovirus/chromo-unclass:Ty3-RT
0.07% Class_I/LTR/Ty3_gypsy/chromovirus/Tcn1:Ty3-RT
0.07% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-RH
0.05% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-RH
0.05% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-RH
0.05% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-RT
0.02% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila:Ty3-RH
0.02% Class_I/LTR/Ty3_gypsy/chromovirus/Chlamyvir:Ty3-PROT
0.02% Class_II/Subclass_1/TIR/EnSpm_CACTA:CACTA-TPase
0.02% Class_II/Subclass_1/TIR/hAT:hAT-TPase
0.02% Class_I/LTR/Ty1_copia/Gymco-II:Ty1-INT
0.02% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-INT
0.02% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-INT
pair_completeness 0.682786885245902
pbs_score None
TR_score None
TR_monomer_length None
loop_index 0.000243546030199708
satellite_probability 2.29499556110385e-22
consensus None
TAREAN_annotation Other
orientation_score 1

comparative analysis:


Comparative analysis - species read counts:
Species Read count
S5 1380
S4 1380
S6 1350
comparative analysis - number of edges between species:
S5 S4 S6
S5 2610 2510 2530
S4 2510 2410 2440
S6 2530 2440 2460
comparative analysis - observed/expected number of edges between species
S5 S4 S6
S5 1.000 1.000 0.999
S4 1.000 0.999 1.000
S6 0.999 1.000 1.000

protein domains:

protein domains:


Reads annotation summary

  cl_string domain Freq proportion
EnSpm_CACTA CACTA-TPase EnSpm_CACTA CACTA-TPase 1 0.00024
Gymco-II Ty1-INT Gymco-II Ty1-INT 1 0.00024
CRM Ty3-GAG CRM Ty3-GAG 49 0.01193
Reina Ty3-GAG Reina Ty3-GAG 4 0.00097
Tekay Ty3-GAG Tekay Ty3-GAG 307 0.07477
Reina Ty3-INT Reina Ty3-INT 1 0.00024
Tekay Ty3-INT Tekay Ty3-INT 1 0.00024
Chlamyvir Ty3-PROT Chlamyvir Ty3-PROT 1 0.00024
Reina Ty3-PROT Reina Ty3-PROT 4 0.00097
Tekay Ty3-PROT Tekay Ty3-PROT 247 0.06016
Athila Ty3-RH Athila Ty3-RH 1 0.00024
CRM Ty3-RH CRM Ty3-RH 2 0.00049
Galadriel Ty3-RH Galadriel Ty3-RH 2 0.00049
Reina Ty3-RH Reina Ty3-RH 3 0.00073
TatV Ty3-RH TatV Ty3-RH 3 0.00073
Tekay Ty3-RH Tekay Ty3-RH 720 0.17535
CRM Ty3-RT CRM Ty3-RT 2 0.00049
Chlamyvir Ty3-RT Chlamyvir Ty3-RT 54 0.01315
Galadriel Ty3-RT Galadriel Ty3-RT 9 0.00219
Reina Ty3-RT Reina Ty3-RT 29 0.00706
Tcn1 Ty3-RT Tcn1 Ty3-RT 3 0.00073
Tekay Ty3-RT Tekay Ty3-RT 673 0.16391
chromo-unclass Ty3-RT chromo-unclass Ty3-RT 3 0.00073
hAT hAT-TPase hAT hAT-TPase 1 0.00024

clusters with similarity:

Cluster Number of similarity hits
27 74
1 18
100 9
2 1

clusters connected through mates:

Cluster Number of shared
read pairs		 k
27 179 0.139
1 109 0.0294
100 9 0.0134
804 9 0.0228
2060 7 0.0179
2 6 0.00172
56 4 0.00261
1680 4 0.0102
1890 4 0.0102
2830 4 0.0103
6150 4 0.0103
10 3 0.00115
212 3 0.00704
1470 3 0.00766
1530 3 0.00765
1820 3 0.00768
1910 3 0.00768
8260 3 0.00772
8990 3 0.00772
13000 3 0.00772
30 2 0.000999
49 2 0.00132
107 2 0.00338
168 2 0.00383
1040 2 0.0051
1740 2 0.00511
1860 2 0.00513
3060 2 0.00513
3980 2 0.00513
4160 2 0.00513
4380 2 0.00515
6040 2 0.00514
8950 2 0.00515
9110 2 0.00515
15300 2 0.00515
16200 2 0.00515
19600 2 0.00515
22900 2 0.00515
23100 2 0.00515
25700 2 0.00515
27000 2 0.00515
28000 2 0.00515
34700 2 0.00515
35200 2 0.00515
36600 2 0.00515
38400 2 0.00515
42100 2 0.00515
43000 2 0.00515
43300 2 0.00515
44200 2 0.00515
47500 2 0.00515
3 1 0.000388
6 1 0.000255
13 1 0.000547
16 1 0.000689
17 1 0.000533
19 1 0.000528
32 1 0.000586
52 1 0.000827
59 1 0.000767
62 1 0.00113
66 1 0.00102
83 1 0.000676
90 1 0.00114
94 1 0.000838
103 1 0.000899
113 1 0.00122
237 1 0.00248
1150 1 0.00254
2760 1 0.00257
3070 1 0.00258
5820 1 0.00258
6440 1 0.00258
7960 1 0.00257
10300 1 0.00257
10500 1 0.00258
12700 1 0.00257
17800 1 0.00258
20800 1 0.00258
21000 1 0.00258
22000 1 0.00258
22700 1 0.00258
23800 1 0.00258
24600 1 0.00258
26200 1 0.00258
32100 1 0.00258
35600 1 0.00258
40000 1 0.00258
40900 1 0.00258
41600 1 0.00258
45600 1 0.00258
46100 1 0.00258
46500 1 0.00258

CL79 ----> CL27

image

No. of shared pairs: :179

CL79 ----> CL1

image

No. of shared pairs: :109