Cluster no. 22

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Cluster is part of supercluster: 7

Cluster characteristics:

size 9052
size_real 9052
ecount 126795
supercluster 7
annotations_summary 20.56% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT
14.63% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RH
8.33% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-GAG
2.74% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-PROT
1.39% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-RH
0.76% Class_I/pararetrovirus:PARA-PROT
0.41% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-GAG
0.41% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-PROT
0.31% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-PROT
0.18% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RH
0.14% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila:Ty3-RH
0.13% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-RT
0.13% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-RH
0.08% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-RT
0.08% Class_I/LTR/Ty3_gypsy/chromovirus/Chlamyvir:Ty3-RT
0.03% Class_I/LTR/Ty3_gypsy/chromovirus/Tcn1:Ty3-RT
0.02% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RT
0.02% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-GAG
0.01% Class_I/LTR/Ty1_copia/Ikeros:Ty1-PROT
0.01% Class_I/LTR/Ty3_gypsy/non-chromovirus/nonchromo-outgroup:Ty3-RT
0.01% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatIV_Ogre:Ty3-RH
0.01% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-PROT
0.01% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-aRH
0.01% Class_I/LTR/Ty3_gypsy/chromovirus/chromo-unclass:Ty3-RH
0.01% Class_I/LTR/Ty3_gypsy/chromovirus/chromo-unclass:Ty3-RT
0.01% Class_I/LTR/Ty1_copia/Ivana:Ty1-RT
0.01% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-INT
0.01% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-INT
pair_completeness 0.697674418604651
pbs_score None
TR_score None
TR_monomer_length None
loop_index 0.000110472823685373
satellite_probability 1.64859681984477e-22
consensus None
TAREAN_annotation Other
orientation_score 1

comparative analysis:


Comparative analysis - species read counts:
Species Read count
S5 3050
S4 3040
S6 2960
comparative analysis - number of edges between species:
S5 S4 S6
S5 14900 14400 14000
S4 14400 14500 13700
S6 14000 13700 13300
comparative analysis - observed/expected number of edges between species
S5 S4 S6
S5 1.01 0.990 1.000
S4 0.99 1.010 0.996
S6 1.00 0.996 1.000

protein domains:

protein domains:


Reads annotation summary

  cl_string domain Freq proportion
pararetrovirus PARA-PROT pararetrovirus PARA-PROT 69 0.00762
Ikeros Ty1-PROT Ikeros Ty1-PROT 1 0.00011
Ivana Ty1-RT Ivana Ty1-RT 1 0.00011
CRM Ty3-GAG CRM Ty3-GAG 37 0.00409
Galadriel Ty3-GAG Galadriel Ty3-GAG 2 0.00022
Tekay Ty3-GAG Tekay Ty3-GAG 754 0.08330
CRM Ty3-INT CRM Ty3-INT 1 0.00011
Galadriel Ty3-INT Galadriel Ty3-INT 1 0.00011
Galadriel Ty3-PROT Galadriel Ty3-PROT 28 0.00309
Reina Ty3-PROT Reina Ty3-PROT 37 0.00409
TatV Ty3-PROT TatV Ty3-PROT 1 0.00011
Tekay Ty3-PROT Tekay Ty3-PROT 248 0.02740
Athila Ty3-RH Athila Ty3-RH 13 0.00144
Galadriel Ty3-RH Galadriel Ty3-RH 126 0.01392
Reina Ty3-RH Reina Ty3-RH 16 0.00177
TatIV_Ogre Ty3-RH TatIV_Ogre Ty3-RH 1 0.00011
TatV Ty3-RH TatV Ty3-RH 12 0.00133
Tekay Ty3-RH Tekay Ty3-RH 1324 0.14627
chromo-unclass Ty3-RH chromo-unclass Ty3-RH 1 0.00011
CRM Ty3-RT CRM Ty3-RT 7 0.00077
Chlamyvir Ty3-RT Chlamyvir Ty3-RT 7 0.00077
Galadriel Ty3-RT Galadriel Ty3-RT 12 0.00133
Reina Ty3-RT Reina Ty3-RT 2 0.00022
Tcn1 Ty3-RT Tcn1 Ty3-RT 3 0.00033
Tekay Ty3-RT Tekay Ty3-RT 1861 0.20559
chromo-unclass Ty3-RT chromo-unclass Ty3-RT 1 0.00011
nonchromo-outgroup Ty3-RT nonchromo-outgroup Ty3-RT 1 0.00011
TatV Ty3-aRH TatV Ty3-aRH 1 0.00011

clusters with similarity:

Cluster Number of similarity hits
40 377
45 35
39 3
1 1

clusters connected through mates:

Cluster Number of shared
read pairs		 k
40 264 0.159
45 217 0.119
1 13 0.00315
10 10 0.0033
83 8 0.00421
58 7 0.00351
61 7 0.00351
32 6 0.00282
56 6 0.00307
19 5 0.00216
30 5 0.00207
35 5 0.00271
57 5 0.0026
103 5 0.00327
27 4 0.00235
33 4 0.00245
84 4 0.00265
132 4 0.00417
142 4 0.0034
2070 4 0.00494
4660 4 0.00495
7 3 0.00102
11 3 0.00102
74 3 0.00276
80 3 0.00303
107 3 0.00297
3250 3 0.00371
11800 3 0.00372
2 2 0.000513
13 2 0.000889
18 2 0.000987
31 2 0.00102
38 2 0.00151
41 2 0.00106
59 2 0.00116
62 2 0.00153
63 2 0.00103
111 2 0.00188
149 2 0.00209
3440 2 0.00248
5000 2 0.00248
11000 2 0.00248
12100 2 0.00248
14600 2 0.00248
17800 2 0.00248
19100 2 0.00248
22700 2 0.00248
27600 2 0.00248
31100 2 0.00248
32100 2 0.00248
39600 2 0.00248
41200 2 0.00248
47200 2 0.00248
3 1 0.000334
9 1 0.000516
15 1 0.000564
16 1 0.000535
26 1 0.000351
36 1 0.000536
39 1 0.000645
42 1 0.000581
46 1 0.000494
48 1 0.000637
49 1 0.000516
54 1 0.000552
60 1 0.000932
65 1 0.000714
71 1 0.000652
72 1 0.000556
75 1 0.00076
81 1 0.00057
85 1 0.000922
89 1 0.000905
94 1 0.00062
95 1 0.00101
98 1 0.000641
113 1 0.000806
114 1 0.000918
136 1 0.00105
137 1 0.000852
147 1 0.000947
150 1 0.000938
168 1 0.00106
178 1 0.00113
190 1 0.0012
237 1 0.00122
243 1 0.00122
273 1 0.00121
888 1 0.00123
915 1 0.00123
938 1 0.00123
1130 1 0.00123
1240 1 0.00123
2460 1 0.00124
3240 1 0.00124
4620 1 0.00124
4800 1 0.00124
4830 1 0.00124
5060 1 0.00124
5880 1 0.00124
6240 1 0.00124
8060 1 0.00124
8180 1 0.00124
8430 1 0.00124
8470 1 0.00124
8990 1 0.00124
9280 1 0.00124
9890 1 0.00124
9890 1 0.00124
12700 1 0.00124
12800 1 0.00124
14100 1 0.00124
18700 1 0.00124
20400 1 0.00124
20500 1 0.00124
22400 1 0.00124
22800 1 0.00124
26500 1 0.00124
26900 1 0.00124
29600 1 0.00124
30700 1 0.00124
33500 1 0.00124
33700 1 0.00124
35200 1 0.00124
36300 1 0.00124
38700 1 0.00124
41900 1 0.00124
44500 1 0.00124
48100 1 0.00124

CL22 ----> CL40

image

No. of shared pairs: :264

CL22 ----> CL45

image

No. of shared pairs: :217

CL22 ----> CL1

image

No. of shared pairs: :13

CL22 ----> CL10

image

No. of shared pairs: :10