Cluster no. 227

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Cluster is part of supercluster: 128

Cluster characteristics:

size 565
size_real 565
ecount 2568
supercluster 128
annotations_summary 20.71% Class_I/LTR/Ty1_copia/TAR:Ty1-RT
13.45% Class_I/LTR/Ty1_copia/TAR:Ty1-INT
9.20% Class_I/LTR/Ty1_copia/TAR:Ty1-RH
4.25% Class_I/LTR/Ty1_copia/TAR:Ty1-GAG
3.89% Class_I/LTR/Ty1_copia/TAR:Ty1-PROT
0.88% Class_I/LTR/Ty1_copia/Ikeros:Ty1-INT
0.35% organelle/mitochondria
0.35% Class_I/LTR/Ty1_copia/Ale:Ty1-INT
0.35% Class_I/LTR/Ty1_copia/Angela:Ty1-INT
0.18% Class_I/LTR/Ty1_copia/Ivana:Ty1-RH
0.18% Class_I/LTR/Ty1_copia/Ivana:Ty1-INT
pair_completeness 0.712121212121212
pbs_score None
TR_score None
TR_monomer_length None
loop_index 0.00176991150442478
satellite_probability 1.39099901770407e-22
consensus None
TAREAN_annotation Other
orientation_score 1

comparative analysis:


Comparative analysis - species read counts:
Species Read count
S8 113
S5 4
S4 1
S7 94
S9 110
S6 0
S2 85
S1 79
S3 79
comparative analysis - number of edges between species:
S8 S5 S4 S7 S9 S6 S2 S1 S3
S8 119.0 7.5 0.0 86.5 116.0 0 52.0 45.0 66.5
S5 7.5 0.0 0.0 3.5 7.0 0 1.0 6.0 4.5
S4 0.0 0.0 0.0 0.0 0.0 0 1.0 0.5 0.0
S7 86.5 3.5 0.0 98.0 98.0 0 49.5 48.0 44.5
S9 116.0 7.0 0.0 98.0 103.0 0 46.5 56.0 55.0
S6 0.0 0.0 0.0 0.0 0.0 0 0.0 0.0 0.0
S2 52.0 1.0 1.0 49.5 46.5 0 92.0 72.0 80.0
S1 45.0 6.0 0.5 48.0 56.0 0 72.0 79.0 49.5
S3 66.5 4.5 0.0 44.5 55.0 0 80.0 49.5 86.0
comparative analysis - observed/expected number of edges between species
S8 S5 S4 S7 S9 S6 S2 S1 S3
S8 1.260 1.330 0.00 1.050 1.250 NA 0.689 0.660 0.899
S5 1.330 0.000 0.00 0.712 1.270 NA 0.221 1.470 1.010
S4 0.000 0.000 0.00 0.000 0.000 NA 4.350 2.400 0.000
S7 1.050 0.712 0.00 1.370 1.220 NA 0.754 0.809 0.692
S9 1.250 1.270 0.00 1.220 1.140 NA 0.630 0.840 0.761
S6 NA NA NA NA NA NA NA NA NA
S2 0.689 0.221 4.35 0.754 0.630 NA 1.520 1.320 1.350
S1 0.660 1.470 2.40 0.809 0.840 NA 1.320 1.600 0.925
S3 0.899 1.010 0.00 0.692 0.761 NA 1.350 0.925 1.480

protein domains:

protein domains:


Reads annotation summary

  cl_string domain Freq proportion
mitochondria mitochondria 2 0.0035
TAR Ty1-GAG TAR Ty1-GAG 24 0.0425
Ale Ty1-INT Ale Ty1-INT 2 0.0035
Angela Ty1-INT Angela Ty1-INT 2 0.0035
Ikeros Ty1-INT Ikeros Ty1-INT 5 0.0088
Ivana Ty1-INT Ivana Ty1-INT 1 0.0018
TAR Ty1-INT TAR Ty1-INT 76 0.1345
TAR Ty1-PROT TAR Ty1-PROT 22 0.0389
Ivana Ty1-RH Ivana Ty1-RH 1 0.0018
TAR Ty1-RH TAR Ty1-RH 52 0.0920
TAR Ty1-RT TAR Ty1-RT 117 0.2071

clusters connected through mates:

Cluster Number of shared
read pairs		 k
1380 7 0.128
17 3 0.0018
5120 3 0.0594
22 2 0.00119
6950 2 0.04
10400 2 0.0404
60300 2 0.0412
9 1 0.00134
23 1 0.000849
42 1 0.00159
53 1 0.00166
83 1 0.00237
91 1 0.00142
110 1 0.00147
148 1 0.00238
1270 1 0.0182
14800 1 0.0208
15400 1 0.0204
24700 1 0.0206
29700 1 0.0206
49300 1 0.0206
64700 1 0.0206
66200 1 0.0206