Cluster no. 106

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Cluster is part of supercluster: 34

Cluster characteristics:

size 2876
size_real 2876
ecount 39588
supercluster 34
annotations_summary 16.55% Class_I/LTR/Ty1_copia/TAR:Ty1-RT
11.72% Class_I/LTR/Ty1_copia/TAR:Ty1-INT
7.23% Class_I/LTR/Ty1_copia/TAR:Ty1-RH
4.49% Class_I/LTR/Ty1_copia/TAR:Ty1-PROT
3.44% Class_I/LTR/Ty1_copia/TAR:Ty1-GAG
0.21% Class_I/LTR/Ty1_copia/SIRE:Ty1-RT
0.03% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RH
0.03% Class_I/LTR/Ty1_copia/Ale:Ty1-INT
0.03% Class_I/LTR/Ty1_copia/Ikeros:Ty1-INT
0.03% Class_I/LTR/Ty1_copia/Ivana:Ty1-RH
0.03% Class_I/LTR/Ty1_copia/Angela:Ty1-INT
pair_completeness 0.7409200968523
pbs_score None
TR_score None
TR_monomer_length None
loop_index 0.00139082058414465
satellite_probability 8.20691448488047e-23
consensus None
TAREAN_annotation Other
orientation_score 1

comparative analysis:


Comparative analysis - species read counts:
Species Read count
S5 982
S4 928
S6 966
comparative analysis - number of edges between species:
S5 S4 S6
S5 4460 4460 4350
S4 4460 4460 4350
S6 4350 4350 4350
comparative analysis - observed/expected number of edges between species
S5 S4 S6
S5 1.000 1.000 0.994
S4 1.000 1.000 0.995
S6 0.994 0.995 1.010

protein domains:

protein domains:


Reads annotation summary

  cl_string domain Freq proportion
TAR Ty1-GAG TAR Ty1-GAG 99 0.03442
Ale Ty1-INT Ale Ty1-INT 1 0.00035
Angela Ty1-INT Angela Ty1-INT 1 0.00035
Ikeros Ty1-INT Ikeros Ty1-INT 1 0.00035
TAR Ty1-INT TAR Ty1-INT 337 0.11718
TAR Ty1-PROT TAR Ty1-PROT 129 0.04485
Ivana Ty1-RH Ivana Ty1-RH 1 0.00035
TAR Ty1-RH TAR Ty1-RH 208 0.07232
SIRE Ty1-RT SIRE Ty1-RT 6 0.00209
TAR Ty1-RT TAR Ty1-RT 476 0.16551
Reina Ty3-RH Reina Ty3-RH 1 0.00035

clusters with similarity:

Cluster Number of similarity hits
27 1

clusters connected through mates:

Cluster Number of shared
read pairs		 k
166 17 0.0627
57 4 0.003
27 3 0.0027
49 3 0.00223
84 3 0.00327
132 3 0.00817
1680 3 0.0138
10 2 0.000819
13 2 0.00121
35 2 0.0016
38 2 0.00272
58 2 0.00142
61 2 0.00142
7400 2 0.00928
1 1 0.000283
4 1 0.000296
6 1 0.000266
7 1 0.000424
8 1 0.000447
9 1 0.000742
12 1 0.000338
15 1 0.000846
16 1 0.000783
19 1 0.000581
23 1 0.000391
28 1 0.000536
32 1 0.000652
39 1 0.00104
41 1 0.000768
45 1 0.000817
54 1 0.00082
55 1 0.00081
62 1 0.0014
63 1 0.000739
65 1 0.00124
89 1 0.00195
90 1 0.00143
103 1 0.00106
111 1 0.00213
137 1 0.00172
149 1 0.00274
159 1 0.00229
170 1 0.00331
218 1 0.0036
247 1 0.00423
451 1 0.00439
745 1 0.00449
1510 1 0.0046
4180 1 0.00462
5280 1 0.00465
9820 1 0.00464
10300 1 0.00464
10700 1 0.00464
12500 1 0.00466
12600 1 0.00464
12900 1 0.00466
18300 1 0.00465
18600 1 0.00465
19400 1 0.00465
22800 1 0.00465
25000 1 0.00465
31100 1 0.00465
35500 1 0.00465
36500 1 0.00465
41800 1 0.00465
43600 1 0.00465

CL106 ----> CL166

image

No. of shared pairs: :17