Cluster no. 41

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Cluster is part of supercluster: 9

Cluster characteristics:

size	4895
size_real	4895
ecount	124809
supercluster	9
annotations_summary	11.58% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-RT 10.99% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-RH 9.05% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-aRH 7.03% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-GAG 5.01% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-PROT 0.39% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatIV_Ogre:Ty3-aRH 0.08% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila:Ty3-GAG 0.08% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-INT 0.06% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatIV_Ogre:Ty3-RH 0.06% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatIV_Ogre:Ty3-RT 0.04% Class_I/LTR/Ty1_copia/Ale:Ty1-INT 0.02% organelle/plastid 0.02% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila:Ty3-RT 0.02% 45S_rDNA/25S_rDNA 0.02% Class_I/LINE:LINE-RT 0.02% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatIV_Ogre:Ty3-INT
pair_completeness	0.870462361482614
pbs_score	None
TR_score	None
TR_monomer_length	None
loop_index	0.000612870275791624
satellite_probability	6.1246173690846e-24
consensus	None
TAREAN_annotation	Other
orientation_score	1

comparative analysis:

Comparative analysis - species read counts:

Species	Read count
S2	1590
S1	1650
S3	1660

comparative analysis - number of edges between species:

	S2	S1	S3
S2	13100	13300	13600
S1	13300	14200	14400
S3	13600	14400	14700

comparative analysis - observed/expected number of edges between species

	S2	S1	S3
S2	1.020	0.989	0.993
S1	0.989	1.010	1.000
S3	0.993	1.000	1.000

protein domains:

Reads annotation summary

cl_string domain Freq proportion

25S_rDNA 25S_rDNA 1 0.00020

plastid plastid 1 0.00020

LINE LINE-RT LINE LINE-RT 1 0.00020

Ale Ty1-INT Ale Ty1-INT 2 0.00041

Athila Ty3-GAG Athila Ty3-GAG 4 0.00082

TatV Ty3-GAG TatV Ty3-GAG 344 0.07028

TatIV_Ogre Ty3-INT TatIV_Ogre Ty3-INT 1 0.00020

TatV Ty3-INT TatV Ty3-INT 4 0.00082

TatV Ty3-PROT TatV Ty3-PROT 245 0.05005

TatIV_Ogre Ty3-RH TatIV_Ogre Ty3-RH 3 0.00061

TatV Ty3-RH TatV Ty3-RH 538 0.10991

Athila Ty3-RT Athila Ty3-RT 1 0.00020

TatIV_Ogre Ty3-RT TatIV_Ogre Ty3-RT 3 0.00061

TatV Ty3-RT TatV Ty3-RT 567 0.11583

TatIV_Ogre Ty3-aRH TatIV_Ogre Ty3-aRH 19 0.00388

TatV Ty3-aRH TatV Ty3-aRH 443 0.09050

clusters with similarity:

Cluster	Number of similarity hits

77	423
75	172

clusters connected through mates:

Cluster	Number of shared read pairs	k

77	159	0.48
75	107	0.18
96	2	0.0043
2	1	0.000424
3	1	0.000583
4	1	0.000412
7	1	0.000432
20	1	0.00225
30	1	0.000798
34	1	0.00225
37	1	0.000776
38	1	0.000905
46	1	0.00133
50	1	0.00131
56	1	0.000891
60	1	0.00171
64	1	0.0021
72	1	0.00196
81	1	0.00347
86	1	0.00275
92	1	0.00213
95	1	0.00263
158	1	0.00456
2640	1	0.00581
45000	1	0.00587
50200	1	0.00587

CL41 ----> CL77

No. of shared pairs: :159

CL41 ----> CL75

No. of shared pairs: :107