Cluster no. 74

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Cluster is part of supercluster: 34

Cluster characteristics:

size 4103
size_real 4103
ecount 23572
supercluster 34
annotations_summary 31.25% Class_I/LTR/Ty1_copia/SIRE:Ty1-RT
18.86% Class_I/LTR/Ty1_copia/SIRE:Ty1-INT
11.70% Class_I/LTR/Ty1_copia/SIRE:Ty1-RH
3.66% Class_I/LTR/Ty1_copia/SIRE:Ty1-PROT
2.29% Class_I/LTR/Ty1_copia/Ivana:Ty1-RH
0.46% Class_I/LTR/Ty1_copia/Ivana:Ty1-PROT
0.37% Class_I/LTR/Ty1_copia/Ivana:Ty1-INT
0.32% Class_I/LTR/Ty1_copia/Ale:Ty1-PROT
0.07% Class_I/LTR/Ty1_copia/Ale:Ty1-RT
0.05% Class_I/LTR/Ty1_copia/Tork:Ty1-PROT
0.02% Class_I/LTR/Ty1_copia/TAR:Ty1-INT
0.02% Class_I/LTR/Ty1_copia/Alesia:Ty1-PROT
0.02% Class_I/LTR/Ty1_copia/Tork:Ty1-INT
0.02% Class_I/LTR/Ty1_copia/Ivana:Ty1-RT
0.02% Class_I/LTR/Ty1_copia/Alesia:Ty1-RT
0.02% Class_I/LTR/Ty1_copia/Angela:Ty1-INT
pair_completeness 0.725399495374264
pbs_score None
TR_score None
TR_monomer_length None
loop_index 0.000243724104313917
satellite_probability 9.81425038973844e-23
consensus None
TAREAN_annotation Other
orientation_score 1

comparative analysis:


Comparative analysis - species read counts:
Species Read count
S8 72
S5 963
S4 951
S7 78
S9 77
S6 954
S2 295
S1 371
S3 342
comparative analysis - number of edges between species:
S8 S5 S4 S7 S9 S6 S2 S1 S3
S8 48.0 16.5 18.5 37.0 35.5 11.0 31.5 50.5 45.0
S5 16.5 2120.0 2060.0 3.5 8.0 1990.0 3.0 4.0 15.0
S4 18.5 2060.0 2170.0 0.0 11.0 2010.0 1.0 5.0 7.5
S7 37.0 3.5 0.0 62.0 57.0 0.5 39.0 59.5 64.5
S9 35.5 8.0 11.0 57.0 56.0 3.5 43.5 65.5 70.0
S6 11.0 1990.0 2010.0 0.5 3.5 1940.0 2.0 2.5 14.5
S2 31.5 3.0 1.0 39.0 43.5 2.0 297.0 374.0 322.0
S1 50.5 4.0 5.0 59.5 65.5 2.5 374.0 469.0 480.0
S3 45.0 15.0 7.5 64.5 70.0 14.5 322.0 480.0 490.0
comparative analysis - observed/expected number of edges between species
S8 S5 S4 S7 S9 S6 S2 S1 S3
S8 13.100 0.2130 0.23700 9.20000 8.1500 0.14800 2.27000 2.69000 2.4000
S5 0.213 1.2900 1.24000 0.04100 0.0866 1.26000 0.01020 0.01000 0.0377
S4 0.237 1.2400 1.30000 0.00000 0.1180 1.26000 0.00337 0.01240 0.0187
S7 9.200 0.0410 0.00000 14.00000 11.9000 0.00611 2.56000 2.87000 3.1200
S9 8.150 0.0866 0.11800 11.90000 10.8000 0.03950 2.63000 2.92000 3.1300
S6 0.148 1.2600 1.26000 0.00611 0.0395 1.28000 0.00709 0.00653 0.0379
S2 2.270 0.0102 0.00337 2.56000 2.6300 0.00709 5.65000 5.25000 4.5200
S1 2.690 0.0100 0.01240 2.87000 2.9200 0.00653 5.25000 4.85000 4.9700
S3 2.400 0.0377 0.01870 3.12000 3.1300 0.03790 4.52000 4.97000 5.0800

protein domains:

protein domains:


Reads annotation summary

  cl_string domain Freq proportion
Angela Ty1-INT Angela Ty1-INT 1 0.00024
Ivana Ty1-INT Ivana Ty1-INT 15 0.00366
SIRE Ty1-INT SIRE Ty1-INT 774 0.18864
TAR Ty1-INT TAR Ty1-INT 1 0.00024
Tork Ty1-INT Tork Ty1-INT 1 0.00024
Ale Ty1-PROT Ale Ty1-PROT 13 0.00317
Alesia Ty1-PROT Alesia Ty1-PROT 1 0.00024
Ivana Ty1-PROT Ivana Ty1-PROT 19 0.00463
SIRE Ty1-PROT SIRE Ty1-PROT 150 0.03656
Tork Ty1-PROT Tork Ty1-PROT 2 0.00049
Ivana Ty1-RH Ivana Ty1-RH 94 0.02291
SIRE Ty1-RH SIRE Ty1-RH 480 0.11699
Ale Ty1-RT Ale Ty1-RT 3 0.00073
Alesia Ty1-RT Alesia Ty1-RT 1 0.00024
Ivana Ty1-RT Ivana Ty1-RT 1 0.00024
SIRE Ty1-RT SIRE Ty1-RT 1282 0.31245

clusters with similarity:

Cluster Number of similarity hits
135 13
177 7
117 3
131 3
282 1

clusters connected through mates:

Cluster Number of shared
read pairs		 k
135 46 0.0839
131 30 0.045
117 22 0.0317
672 10 0.0294
1130 10 0.0298
282 8 0.0229
1580 8 0.0241
1960 7 0.0211
2140 7 0.0211
3320 6 0.0182
14 5 0.00259
2080 5 0.0151
5690 5 0.0152
1960 4 0.0121
2300 4 0.0121
6410 4 0.0122
7500 4 0.0122
3 3 0.000953
6 3 0.00101
43 3 0.00189
48 3 0.00231
1560 3 0.00908
4580 3 0.0091
4910 3 0.00913
6320 3 0.00912
7800 3 0.00913
10300 3 0.00913
15200 3 0.00915
18400 3 0.00915
19900 3 0.00915
2 2 0.00107
7 2 0.00113
23 2 0.00137
61 2 0.00172
87 2 0.00211
186 2 0.00463
2230 2 0.00604
4040 2 0.00608
4400 2 0.00609
4550 2 0.00607
5210 2 0.00607
5690 2 0.0061
7080 2 0.0061
8320 2 0.00609
8550 2 0.00611
10300 2 0.00609
10900 2 0.00609
16500 2 0.0061
17600 2 0.0061
19200 2 0.0061
25900 2 0.00611
26700 2 0.00611
26900 2 0.00611
29500 2 0.00611
29700 2 0.00611
30200 2 0.00611
44400 2 0.00611
46700 2 0.00611
50600 2 0.00611
54100 2 0.00611
54100 2 0.00611
59900 2 0.00611
64800 2 0.00611
65400 2 0.00611
1 1 0.000489
8 1 0.000467
13 1 0.000541
28 1 0.000734
35 1 0.000767
47 1 0.000783
54 1 0.000861
58 1 0.00111
67 1 0.000846
80 1 0.000938
85 1 0.0012
89 1 0.00125
106 1 0.00137
108 1 0.00136
120 1 0.00137
130 1 0.00137
143 1 0.00134
171 1 0.0016
177 1 0.00226
182 1 0.002
192 1 0.00199
225 1 0.00234
295 1 0.00273
339 1 0.00291
342 1 0.00274
1090 1 0.00301
1240 1 0.00301
2610 1 0.00303
2720 1 0.00303
2950 1 0.00305
4850 1 0.00304
5280 1 0.00304
7440 1 0.00305
7460 1 0.00305
7600 1 0.00304
8840 1 0.00304
9150 1 0.00305
9440 1 0.00304
9480 1 0.00304
9520 1 0.00304
9540 1 0.00304
9570 1 0.00304
10800 1 0.00304
11000 1 0.00304
11600 1 0.00305
12300 1 0.00305
12300 1 0.00305
12500 1 0.00305
12500 1 0.00305
12600 1 0.00306
13000 1 0.00305
13100 1 0.00305
14500 1 0.00305
14900 1 0.00305
15300 1 0.00306
16100 1 0.00305
19600 1 0.00305
20200 1 0.00305
23600 1 0.00305
24200 1 0.00305
25200 1 0.00305
28000 1 0.00305
29300 1 0.00305
33100 1 0.00305
33100 1 0.00305
33700 1 0.00305
36500 1 0.00305
38300 1 0.00305
38300 1 0.00305
38300 1 0.00305
39600 1 0.00305
40400 1 0.00305
42200 1 0.00305
47100 1 0.00305
48300 1 0.00305
50200 1 0.00305
51300 1 0.00305
53500 1 0.00305
62300 1 0.00305
62800 1 0.00305
66700 1 0.00305
69100 1 0.00305
69400 1 0.00305

CL74 ----> CL135

image

No. of shared pairs: :46

CL74 ----> CL131

image

No. of shared pairs: :30

CL74 ----> CL117

image

No. of shared pairs: :22

CL74 ----> CL672

image

No. of shared pairs: :10

CL74 ----> CL1129

image

No. of shared pairs: :10