Cluster no. 173

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Cluster is part of supercluster: 87

Cluster characteristics:

size 7605
size_real 7605
ecount 129195
supercluster 87
annotations_summary 13.10% Class_I/LTR/Ty3_gypsy/chromovirus/chromo-unclass:Ty3-INT
6.61% Class_I/LTR/Ty3_gypsy/chromovirus/chromo-unclass:Ty3-RT
5.88% Class_I/LTR/Ty3_gypsy/chromovirus/chromo-unclass:Ty3-RH
3.67% Class_I/LTR/Ty3_gypsy/chromovirus/chromo-unclass:Ty3-GAG
1.92% Class_I/LTR/Ty3_gypsy/chromovirus/chromo-unclass:Ty3-CHDII
1.89% Class_I/LTR/Ty3_gypsy/chromovirus/chromo-unclass:Ty3-PROT
1.89% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RT
1.08% organelle/mitochondria
0.42% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RH
0.34% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-INT
0.32% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-CHDII
0.30% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT
0.07% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-PROT
0.05% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-RH
0.04% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RH
0.04% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-RH
0.04% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-RT
0.03% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-INT
0.03% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-INT
pair_completeness 0.775624562222741
pbs_score 0.957082
TR_score 0.3411709320541229
TR_monomer_length 5016.0
loop_index 0.796449704142012
satellite_probability 0.0473063114528697
consensus
AGGTTCTCATGGAAGGGCCTCAAGGAGGACGTACTCCAGCACATCCGGGAGTGCGATGTTTGCCAGAGGAACAAGGGGGA
GATGAGCCATCCCGCAGGATTATTGCAGCCTCTTCCCATTCCGGAGGGGAAATGGGAGAGTATTTCGATGGACTTCATCA
CAGGGTTGCCCATGGTACAGGGCAAGGATTGTATCTTTGTCGTCGTTGATCGACTGACAAAGTACGCACATTTTTTTGCC
ATATCCGCACACTACACAGCAGCACAGGTGGCCGAGCTGTTCTTCAGAGAGATCTTCAGGCTACATGGTCTTCCTAAGAC
CATCGTCAGTGATAGGGACAGCCGTTTCATGGGCGGGTTTTGGCAGGAGCTTTTCCGGTTGGTGGGGACGGAGTTGACAC
CGAGTACCAGTTATCACCCACAGACGGATGGGCAGACAGAGATAGTTAACAAGTGGCTGGAGGGCTACTTGCGTAACTAT
GTCAGTGGGCAGCAGCGAGCATGGCTGAAGTGGCTGCATCTGGGGGAGTACTGCTACAACACTTCACATCACATGTCCAT
TGGTATGTCACCATTCTATGCTTTATATGGGTATCATCCTTTATCTTTTGCTGACGTGATGTTTGGTGATAGCAAGGCTC
CGAGAGCCAAGATTTGGATCCAAGAGAGTCAGGATATCCTCCGAGCTCTCAAGGATAACATGGCTACAACGCAGAACCAG
CAGAAGCTGTATGCCGACAGGGGTCGGGTGGAGAGACAGTTTGAGGTAGGGGACATGGTCTACCTACGATTACAGCCATA
CCGACAGTCGTCACTGAAGCAGAAGGGGGCTGAGAAGCTCAAGCCCCGCTTTTATGGGCCATACAGGGTGATACGCAGGA
TTGGACAGGTTGCATATGAGTTGGAGCTGCCCCAAGGCAGCAAGATTCATAACGTTTTTCATGTATCATGCCTGAAGAAG
GCATTGGGGCAGCAGGTGACAGTGACAGATGAGCTACCACCCATGGATGATGAGGGGCATTTGGTATTGCAGCCAGAGGC
TATCATTGATACCAGGGAGAGGCAGCTGCGGAGCAGGACGGTCCGGGAATTCTTGGTGAGGTGGAAGAATTTACCGGATG
AGGATGCCACTTGGGAGAGTGAGAAGATCTTGCAGCATCCATCACTTCAGTTGCTTGAGGACAAGCAACATTTTGCCGGG
GGAGACTGTAATATTCCTAATTAGCCATGGCTAATTGGAATATTCGATTTTGCTCAATTTTGCCTTCTATAGTTATTTAT
AAATAAAAAGTGAGGAAGGGGGACATAACTCACTTTTAGAATAAAAGTCACTTCCTAGTAGCACAACGTTGTGACTTAAA
GGGGAGCCAAGGGGGCCAAAGGGGGACGCAGAAATGGGGCCCACGCAGACACATGGAGGGACTGCGCAGATGGAGAAGAA
CACATGGCAAGAGGGGAATCACGCAGGAGGAGGTGAGCCTTGGGATTGAGAGAGGCAAAGGCTATAAAGGAGAGAGGAGC
CTCCTCATTTTGGCATTCGATTATGTGCATTTGAGCTAGTCACTTCGACTTAGAGCACGCTGGCTGTTTAGCTAGTCTGC
AGCACTGTTTAGTGCATTGAGTGTCTCCGTTCGGAGATCTCACCCTTAGCCCCGGGGGACTTCGAGTGCCTGCTCGGGCA
AGGTATTTCCATTGGCATTTCAGCAGTAGTTTCATCAGCATTTCAGCAGCAGTTTCATCAGCGTCTTTGAGGAACTGCGC
AGAACCCCAAGGGGGTGATTTTCGGGGGTCGGCCATTTCAGAAAAGCTTTCTGGGTTTTTCTGGGTTTCTTGAGTAGAGT
CTGATTCCAGAGTTTCAGCATTTTCTGAGGAGGGGAACAGCCCCAAATCCTCATTTGATTCCAGCAGTAGCAGCAGCACA
ACAGTTCTCCAGCAGCTTGGACGCAGTTCAGAGAGAGGCCATTCCTTTGCTATTCTGAGTGTATTTCTTCACTTGCCTTG
TGCAAGTCGAGGTGCCATCTTTCTGATCACCTCCTGTACTCATTCCATTACTCAGTATAATAAAATGGCTTAGCATTTCT
CTCTGCATTTCTTGAGTATCTGCTTATATTTCAGGTTTACATTATTATATGTTGTTCCACTGTTATTTTATCACTTCTGG
GTTATTATATCATTTGCACATATTTGGTTGGAGTTTTTGCTGGGGTTTGAGGAATATTCTGGGTTAGGAATATTACAGTG
GTATCAGAGCATAGATCTGGCTCAGCCTGTGGAGCTAGCAATCTATGACACCGGGGGAAAAACCCTACATCTGTTACAGA
GGTAGGAGATACAGAGACACTGGGCGTAGGTTGGAGAACACCTACGGAGAGGGAGACTGTGTTCCGGTGGTGGACGCAGA
ACAGGAGGAGCCTGTGGTGGACGCAGAGCAGGAGGATCCGATGGCAGATGAGGACGGGAAGAGATTTGCGGATATGCTCC
TCAAATCAGTGCAGGATCTGTCGAGGCAGATTGAGGTGATGGGGCAGAGATTCACGGCAGTAGAGGCCAGACAGCGTGAG
AGCCCACGGGTTTTCCAGGTTGGTGAGGGATCGGGTGCATCCCACCATTTGCCAGAGCAGCGTGATACTGCGCAGCAGGT
GGCCTCACATGCCCCTACACGCTCTACCATGCCCACTTTCTTAGGAGCAGACACGGGGGCCGGAGCCCAGCAGGAGGCAG
AGCCCGGACATATGGGCGATTATTTTGCAGAGTACCAGGCCTATGGGCAGGAGTTCAGGGATGCTCTCTCATTCAGAGAC
TTTGTTCAGCTCCAGCGGGATAGTAGACCCCGCGACCATCACAGAGGATACCGGCATTACCATGATGGTGACACCCACCG
TGCAGCTAGTAGATTCCACTTGCCTACGTTTGATGGCTCATCAAACAGTTCGGCAAAGTCTTGGGTGGAGAAGCTGGACA
TTTATTTCCAGCTTAACCAGATGTCGGAGACAGAGGCCATCAAGGTGGCAACATTGCATTTGGATGGTGAGGCCCAGGAT
TGGTGGTTTCATGGGATGGTTACACTCGGGCACTCCACAGTGACGACATATGCCGAGTTTACCAGGAGATTGATGGAGCG
ATTTGATCGGAGGGATCCAGAGCAGCATTTTGTTGAGCTGACGAGGCTCAAACAGACAGGGAGCCCAGAGACCTACATTG
CAGATTTCTTGAGGGTCTCAGTGATGGTGCCAGATCTATCCACGGCACGGAGGATCTACATGTATGTTGAGGGGTTAGCA
GAGCCACTTCGGGGTCTAGTCAGATCCACTAGACCAGCCACACTCCAGGACGCTATTAGCAGGACCCGGGACTTACAGGA
TGTCTTACCCAGGACCCGGACACCTTACCCCCAGAGACAGACTTTCCAGCCTAAGGGGAAGGATGTGAGGATTCCGCCTC
CAAAGGGGAATCCAGGACGAGTACAGATTGATGATGATGCCAGGAGGGAGCTGAAGAAGAAGCGGTTGTGCTTCACCTGT
CAGGAGCCGTGGGCACCAGGACATAGATGTGCTGCTGGCAAAGCACATTTTATTGAGGTCTTCTCCGAGAGCAGTGGAGA
AGAGGATGACGAGGATGATGTGGAGGCAGGAGATAGCCATGCCATACAGGGACCTTTGCCACCTCCACCACCAGCAGCAG
GTGGTGCATCTTTTGCACCTACCGGAGGGGCCCTTGCAGCATTGCGAGGAGTTCCCAAGTATCTGACGCTACGCGTACGA
GGGACAGTACGTGGCCAGCGAGTATCAGTTTTGGTTGACAGTGGGGCAACCCACAACTTCATCGATGCACAGATGGTTGA
GCGGAGAGGTATACAGACAGAGAGCTTCGATGGGTTTTCAGTCTTGGTCCCAGGAGATCAGACCATGATGTGTGCTCGTT
ATGTTCCAGAGCTATCAGTGACGATGGGCACCTACACACTGACTGACCACTTTTTCGTGGTCGATATTCCGGACACCAAC
ATGATACTGGGTGTTCAGTGGCTTATCACTCTAGGGAAGGTCACGACAGATTGGAAGACCCTAGAGATGGAGTGGGATGA
TGAGAAGACAGGGAGGCATGAGAAGATACGGGGACAACACACATATCCGCCTCAGACTGTTTCGGCTCATCGGATGGAGG
CAGTCTTCCGGAAGGGAGACATAGAGTGGGCAGTGGAGCTGCGTGCATCAGAGGCAGGGACTACAGGGCAGACAGTGCAC
CCAGAGATACAGTCCATCCTTGATCGGTATGCCATAGTGTTTGGGGAGATTCCACCAGGACAGCCACCAGACCGGGGGTT
TGAGCACACCATTGAGCTTGAGCAGGGCATACAGGCAGTGATTACTACCCCCTATAGGCATCCCAAGGCCTATCGGGATG
AGATTGAGCGGGCCATTCAGGAGTTGCTGGCTCTTGGGCACATTCGGCCGAGCACGAGTCCTTTTGCTTCTTCCGTGGTG
TTGGTGAAGAAGAAGGACGGCACATTGAGGATGTGCATTGACTACAGGGCCCTGAACAAGAAGACCCTGAAGAACAGGTA
CCCCATACCCAGGATCGATGAGTTGATGGATGAGTTGAGAGGAGCACGGTTCTTCTCAAAGATTGATTTGAGATCTGGGT
ACCATCAGATTCGCGTGAGGGAGCAGGACATTCCCAAGACCGCCTTCAGGTGTCACTATGGGCACTTTGAGTTTTTGGTG
ATGCCCTTTGGGCTAACCAACGCCCCAGCTACATTCCAGTCCTGCATGAATCACATCTTCCGCAGTCACTTGAGGAAGTT
TGTGTTGGTGTTCTTTGATGATATTCTCATTTACAGCAGGACTTGGGAGGAGCATCTCCAGCACATTGAGACAGTATTGC
GCATCTTGGAGGAGCAGCAGTTCTATGCCAAGCTCTCCAAGTGTGAGTTTGGGTTGACGGAGATGTTGTACTTGGGACAC
ATCATAGGGGTGGACGGAGTGAGAGTCCACGAGGAGAAGATCAGGGCCATTAGAGAG
TAREAN_annotation Putative LTR element
orientation_score 1

protein domains:

protein domains:


Reads annotation summary

  cl_string domain Freq proportion
mitochondria mitochondria 82 0.01078
Reina Ty3-CHDII Reina Ty3-CHDII 24 0.00316
chromo-unclass Ty3-CHDII chromo-unclass Ty3-CHDII 146 0.01920
chromo-unclass Ty3-GAG chromo-unclass Ty3-GAG 279 0.03669
CRM Ty3-INT CRM Ty3-INT 2 0.00026
Reina Ty3-INT Reina Ty3-INT 26 0.00342
Tekay Ty3-INT Tekay Ty3-INT 2 0.00026
chromo-unclass Ty3-INT chromo-unclass Ty3-INT 996 0.13097
Reina Ty3-PROT Reina Ty3-PROT 5 0.00066
chromo-unclass Ty3-PROT chromo-unclass Ty3-PROT 144 0.01893
CRM Ty3-RH CRM Ty3-RH 4 0.00053
Galadriel Ty3-RH Galadriel Ty3-RH 3 0.00039
Reina Ty3-RH Reina Ty3-RH 32 0.00421
Tekay Ty3-RH Tekay Ty3-RH 3 0.00039
chromo-unclass Ty3-RH chromo-unclass Ty3-RH 447 0.05878
CRM Ty3-RT CRM Ty3-RT 3 0.00039
Reina Ty3-RT Reina Ty3-RT 144 0.01893
Tekay Ty3-RT Tekay Ty3-RT 23 0.00302
chromo-unclass Ty3-RT chromo-unclass Ty3-RT 503 0.06614

clusters with similarity:

Cluster Number of similarity hits
13 4
87 3
107 1
187 1

clusters connected through mates:

Cluster Number of shared
read pairs
k
1510 16 0.0325
78 11 0.00376
30 9 0.00225
51 9 0.00275
3420 8 0.0164
68 7 0.00372
120 7 0.00402
531 7 0.0136
15100 7 0.0145
17 6 0.00098
119 6 0.00595
334 6 0.0118
4090 6 0.0123
2 5 0.000843
200 5 0.00382
1020 5 0.01
4620 5 0.0103
5200 5 0.0103
14200 5 0.0103
11 4 0.00102
15 4 0.00144
19 4 0.00174
29 4 0.0018
40 4 0.00101
8040 4 0.00826
8650 4 0.00826
11900 4 0.00826
18400 4 0.00829
7 3 0.000613
14 3 0.000802
20 3 0.000784
25 3 0.00133
26 3 0.00121
27 3 0.00171
31 3 0.000558
37 3 0.000856
42 3 0.00135
48 3 0.000827
59 3 0.00195
77 3 0.00176
97 3 0.0015
212 3 0.00371
214 3 0.00379
243 3 0.00281
288 3 0.00414
332 3 0.00524
3780 3 0.00618
59000 3 0.00622
3 2 0.000498
4 2 0.000525
10 2 0.00111
12 2 0.000451
22 2 0.000642
23 2 0.000727
24 2 0.000579
34 2 0.000721
36 2 0.00101
47 2 0.000691
50 2 0.00097
53 2 0.000611
74 2 0.00106
76 2 0.00112
81 2 0.000751
85 2 0.00113
89 2 0.00114
96 2 0.00138
102 2 0.000724
115 2 0.000913
122 2 0.0012
126 2 0.00126
127 2 0.00122
129 2 0.00189
130 2 0.000808
132 2 0.00165
158 2 0.00141
159 2 0.00158
160 2 0.00153
163 2 0.00115
165 2 0.00122
249 2 0.00276
253 2 0.00234
3500 2 0.00409
9260 2 0.00415
13200 2 0.00414
13300 2 0.00414
14300 2 0.00414
19700 2 0.00414
21600 2 0.00415
38700 2 0.00415
43800 2 0.00415
46700 2 0.00415
56500 2 0.00415
69100 2 0.00415
99100 2 0.00415
131000 2 0.00415
169000 2 0.00415
183000 2 0.00415
280000 2 0.00415
282000 2 0.00415
335000 2 0.00415
337000 2 0.00415
1 1 0.000256
6 1 0.000239
8 1 0.000495
9 1 0.000329
13 1 0.000528
16 1 0.00034
21 1 0.000366
32 1 0.000524
35 1 0.000276
38 1 0.00061
41 1 0.000297
44 1 0.000294
45 1 0.000326
56 1 0.00142
60 1 0.000661
61 1 0.000485
63 1 0.000295
64 1 0.00075
69 1 0.000666
75 1 0.000295
79 1 0.000354
92 1 0.000929
98 1 0.000745
107 1 0.000859
114 1 0.000911
116 1 0.000402
123 1 0.000674
124 1 0.00074
128 1 0.000856
131 1 0.00136
134 1 0.000587
136 1 0.00095
137 1 0.000715
142 1 0.000778
145 1 0.000537
146 1 0.000834
153 1 0.000571
155 1 0.000834
157 1 0.000808
162 1 0.000613
172 1 0.000616
175 1 0.000949
176 1 0.00104
177 1 0.0011
178 1 0.00106
179 1 0.000935
181 1 0.000824
182 1 8e-04
183 1 0.000808
185 1 0.000796
186 1 0.000578
187 1 0.00091
197 1 0.000726
202 1 0.00127
204 1 0.00127
215 1 0.00115
217 1 0.00101
223 1 0.00124
224 1 0.00177
225 1 0.00147
226 1 0.00146
232 1 0.00115
247 1 0.00103
250 1 0.00158
268 1 0.00137
293 1 0.00165
294 1 0.00156
299 1 0.00189
308 1 0.00178
313 1 0.00166
314 1 0.00164
335 1 0.00185
342 1 0.00179
347 1 0.0016
352 1 0.00157
501 1 0.00192
740 1 0.00203
1070 1 0.00203
1250 1 0.00203
1410 1 0.00205
1620 1 0.00203
1780 1 0.00201
1860 1 0.00203
1930 1 0.00204
2480 1 0.00203
2970 1 0.00204
3580 1 0.00204
3640 1 0.00205
4060 1 0.00205
5150 1 0.00205
5290 1 0.00206
5400 1 0.00206
5640 1 0.00206
7110 1 0.00207
7560 1 0.00207
7720 1 0.00206
7740 1 0.00207
7920 1 0.00207
8370 1 0.00206
9200 1 0.00207
9880 1 0.00207
10900 1 0.00207
12000 1 0.00207
13000 1 0.00207
17800 1 0.00207
18500 1 0.00207
19000 1 0.00207
19400 1 0.00208
20000 1 0.00207
21000 1 0.00207
22000 1 0.00207
22200 1 0.00207
23100 1 0.00207
23200 1 0.00207
25500 1 0.00207
27800 1 0.00207
28100 1 0.00207
28200 1 0.00207
37000 1 0.00208
38200 1 0.00207
39300 1 0.00207
40600 1 0.00207
41300 1 0.00208
42500 1 0.00208
49700 1 0.00207
50400 1 0.00207
51500 1 0.00207
57400 1 0.00207
57800 1 0.00208
58300 1 0.00207
59100 1 0.00207
59500 1 0.00208
60100 1 0.00208
61700 1 0.00207
63700 1 0.00208
66300 1 0.00207
66600 1 0.00207
67800 1 0.00207
71700 1 0.00207
78500 1 0.00208
83800 1 0.00207
84500 1 0.00208
84600 1 0.00208
92300 1 0.00208
101000 1 0.00208
110000 1 0.00208
117000 1 0.00208
121000 1 0.00208
128000 1 0.00208
167000 1 0.00208
168000 1 0.00208
183000 1 0.00208
196000 1 0.00208
206000 1 0.00208
206000 1 0.00208
209000 1 0.00208
214000 1 0.00208
219000 1 0.00208
229000 1 0.00208
244000 1 0.00208
256000 1 0.00208
261000 1 0.00208
263000 1 0.00208
279000 1 0.00208
283000 1 0.00208
286000 1 0.00208
312000 1 0.00208
316000 1 0.00208
320000 1 0.00208
320000 1 0.00208
321000 1 0.00208
327000 1 0.00208
327000 1 0.00208
345000 1 0.00208
346000 1 0.00208

CL173 ----> CL1510

image

No. of shared pairs: :16

CL173 ----> CL78

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No. of shared pairs: :11