Cluster no. 33

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Cluster is part of supercluster: 20

Cluster characteristics:

size 6787
size_real 6787
ecount 45674
supercluster 20
annotations_summary 8.74% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-INT
4.21% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT
4.20% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RH
3.30% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-GAG
1.80% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-CHDII
1.08% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-PROT
0.53% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-RT
0.32% Class_I/LTR/Ty3_gypsy/chromovirus/Tcn1:Ty3-RT
0.16% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-RH
0.13% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-RT
0.13% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RT
0.13% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-INT
0.12% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-INT
0.09% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-PROT
0.07% Class_I/LTR/Ty3_gypsy/chromovirus/Chlamyvir:Ty3-RT
0.06% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila:Ty3-RH
0.06% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-GAG
0.04% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RH
0.03% Class_I/LTR/Ty3_gypsy/chromovirus/chromo-unclass:Ty3-INT
0.03% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-GAG
0.01% Class_I/LTR/Ty3_gypsy/chromovirus/Tcn1:Ty3-INT
0.01% Class_I/LINE:LINE-ENDO
0.01% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-RH
0.01% Class_I/LTR/Ty1_copia/Bianca:Ty1-RT
0.01% Class_I/pararetrovirus:PARA-RT
0.01% Class_I/LTR/Ty1_copia/Ale:Ty1-RT
0.01% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatIV_Ogre:Ty3-RT
0.01% Class_I/LTR/Ty3_gypsy/chromovirus/chromo-outgroup:Ty3-RH
pair_completeness 0.609437989091771
pbs_score None
TR_score None
TR_monomer_length None
loop_index 0.578753499336968
satellite_probability 0.000704382170984147
consensus None
TAREAN_annotation Other
orientation_score 1

comparative analysis:


Comparative analysis - species read counts:
Species Read count
S5 2260
S4 2340
S6 2180
comparative analysis - number of edges between species:
S5 S4 S6
S5 5520 5330 4980
S4 5330 5240 4820
S6 4980 4820 4660
comparative analysis - observed/expected number of edges between species
S5 S4 S6
S5 1.010 1.000 0.994
S4 1.000 1.010 0.989
S6 0.994 0.989 1.020

protein domains:

protein domains:


Reads annotation summary

  cl_string domain Freq proportion
LINE LINE-ENDO LINE LINE-ENDO 1 0.00015
pararetrovirus PARA-RT pararetrovirus PARA-RT 1 0.00015
Ale Ty1-RT Ale Ty1-RT 1 0.00015
Bianca Ty1-RT Bianca Ty1-RT 1 0.00015
Tekay Ty3-CHDII Tekay Ty3-CHDII 122 0.01798
CRM Ty3-GAG CRM Ty3-GAG 2 0.00029
Reina Ty3-GAG Reina Ty3-GAG 4 0.00059
Tekay Ty3-GAG Tekay Ty3-GAG 224 0.03300
CRM Ty3-INT CRM Ty3-INT 8 0.00118
Reina Ty3-INT Reina Ty3-INT 9 0.00133
Tcn1 Ty3-INT Tcn1 Ty3-INT 1 0.00015
Tekay Ty3-INT Tekay Ty3-INT 593 0.08737
chromo-unclass Ty3-INT chromo-unclass Ty3-INT 2 0.00029
Reina Ty3-PROT Reina Ty3-PROT 6 0.00088
Tekay Ty3-PROT Tekay Ty3-PROT 73 0.01076
Athila Ty3-RH Athila Ty3-RH 4 0.00059
Galadriel Ty3-RH Galadriel Ty3-RH 1 0.00015
Reina Ty3-RH Reina Ty3-RH 3 0.00044
TatV Ty3-RH TatV Ty3-RH 11 0.00162
Tekay Ty3-RH Tekay Ty3-RH 285 0.04199
chromo-outgroup Ty3-RH chromo-outgroup Ty3-RH 1 0.00015
CRM Ty3-RT CRM Ty3-RT 36 0.00530
Chlamyvir Ty3-RT Chlamyvir Ty3-RT 5 0.00074
Galadriel Ty3-RT Galadriel Ty3-RT 9 0.00133
Reina Ty3-RT Reina Ty3-RT 9 0.00133
TatIV_Ogre Ty3-RT TatIV_Ogre Ty3-RT 1 0.00015
Tcn1 Ty3-RT Tcn1 Ty3-RT 22 0.00324
Tekay Ty3-RT Tekay Ty3-RT 286 0.04214

clusters with similarity:

Cluster Number of similarity hits
87 5
1 1
45 1
49 1
80 1

clusters connected through mates:

Cluster Number of shared
read pairs		 k
10 15 0.00491
795 11 0.0132
1 9 0.00217
49 8 0.00409
59 8 0.0046
2 7 0.00179
7 7 0.00236
30 7 0.00287
846 7 0.00842
56 6 0.00305
2940 6 0.00726
35 5 0.00269
40 5 0.00298
94 5 0.00307
4450 5 0.00605
4770 5 0.00605
19 4 0.00172
22 4 0.00245
54 4 0.00219
58 4 0.00199
61 4 0.00199
83 4 0.00209
103 4 0.00258
113 4 0.00318
3750 4 0.00484
15 3 0.00167
26 3 0.00105
28 3 0.00121
41 3 0.00157
45 3 0.00164
72 3 0.00165
80 3 0.00298
84 3 0.00197
85 3 0.00272
87 3 0.00212
90 3 0.00229
95 3 0.00298
132 3 0.00307
466 3 0.00359
1300 3 0.00362
2030 3 0.00363
4580 3 0.00364
7160 3 0.00363
9560 3 0.00364
10500 3 0.00364
13300 3 0.00364
13 2 0.000883
37 2 0.00111
57 2 0.00103
62 2 0.00151
63 2 0.00102
73 2 0.00117
127 2 0.00202
168 2 0.00209
178 2 0.00222
214 2 0.00223
2070 2 0.00242
2710 2 0.00242
2770 2 0.00242
3290 2 0.00242
4580 2 0.00242
4630 2 0.00242
5010 2 0.00242
6480 2 0.00242
8590 2 0.00242
9820 2 0.00242
14400 2 0.00243
14600 2 0.00243
15500 2 0.00243
15900 2 0.00243
16400 2 0.00243
17200 2 0.00243
17400 2 0.00243
20600 2 0.00243
20700 2 0.00243
21700 2 0.00243
23800 2 0.00243
25300 2 0.00243
27200 2 0.00243
33700 2 0.00243
34400 2 0.00243
36700 2 0.00243
37200 2 0.00243
37300 2 0.00243
38000 2 0.00243
39300 2 0.00243
39800 2 0.00243
40900 2 0.00243
42100 2 0.00243
42900 2 0.00243
43700 2 0.00243
44300 2 0.00243
46700 2 0.00243
4 1 0.000251
5 1 0.000329
6 1 0.000229
8 1 0.000351
9 1 0.000511
16 1 0.00053
21 1 0.000326
27 1 0.000581
32 1 0.000467
38 1 0.000743
39 1 0.000638
42 1 0.000575
48 1 0.00063
52 1 0.000608
69 1 0.000672
75 1 0.00075
78 1 0.000722
96 1 0.000716
98 1 0.000634
100 1 0.000903
107 1 0.000973
130 1 0.000876
137 1 0.00084
142 1 0.000838
190 1 0.00118
210 1 0.00116
234 1 0.00116
268 1 0.00118
312 1 0.00118
326 1 0.00118
368 1 0.00119
482 1 0.0012
530 1 0.0012
888 1 0.0012
1430 1 0.00121
2250 1 0.00121
3120 1 0.00121
3170 1 0.00121
3410 1 0.00121
4320 1 0.00121
4910 1 0.00121
4980 1 0.00121
5970 1 0.00121
6310 1 0.00121
6540 1 0.00121
6890 1 0.00121
6900 1 0.00121
7700 1 0.00121
7940 1 0.00121
8080 1 0.00121
8490 1 0.00121
8770 1 0.00121
9130 1 0.00121
9660 1 0.00121
10900 1 0.00121
10900 1 0.00121
11400 1 0.00121
11500 1 0.00121
11500 1 0.00121
11700 1 0.00121
12100 1 0.00121
12400 1 0.00121
12500 1 0.00121
12700 1 0.00121
13100 1 0.00121
13900 1 0.00121
14200 1 0.00121
15100 1 0.00121
15200 1 0.00121
15200 1 0.00121
15700 1 0.00121
15800 1 0.00121
16800 1 0.00121
18100 1 0.00121
19100 1 0.00121
19100 1 0.00121
19200 1 0.00121
19700 1 0.00121
19800 1 0.00121
21100 1 0.00121
21600 1 0.00121
22200 1 0.00121
23300 1 0.00121
23500 1 0.00121
23600 1 0.00121
24200 1 0.00121
24300 1 0.00121
25400 1 0.00121
26400 1 0.00121
27000 1 0.00121
27000 1 0.00121
27200 1 0.00121
27700 1 0.00121
29000 1 0.00121
30700 1 0.00121
31900 1 0.00121
32000 1 0.00121
32600 1 0.00121
33400 1 0.00121
33600 1 0.00121
34500 1 0.00121
36100 1 0.00121
37000 1 0.00121
37200 1 0.00121
37700 1 0.00121
37800 1 0.00121
38200 1 0.00121
40200 1 0.00121
42200 1 0.00121
42900 1 0.00121
43100 1 0.00121
43300 1 0.00121
44500 1 0.00121
44600 1 0.00121
45700 1 0.00121
47800 1 0.00121

CL33 ----> CL10

image

No. of shared pairs: :15

CL33 ----> CL795

image

No. of shared pairs: :11