Cluster no. 33

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Cluster is part of supercluster: 29

Cluster characteristics:

size 25241
size_real 25241
ecount 339437
supercluster 29
annotations_summary 0.61% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatII:Ty3-GAG
0.19% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-GAG
0.00% Class_I/LTR/Ty1_copia/Bianca:Ty1-INT
0.00% Class_I/LTR/Ty1_copia/Gymco-I:Ty1-RT
0.00% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila:Ty3-GAG
0.00% Class_I/LTR/Ty1_copia/Tork:Ty1-RH
pair_completeness 0.81733746130031
pbs_score 27.22793764
TR_score 0.07857808219178083
TR_monomer_length 3076.0
loop_index 0.791433891992551
satellite_probability 0.0490841221366278
consensus
GCCTTATCCATTTATGACAAACAGAAATTTGCTTGACAAGCATGACTGTAGGAGAAAGAAAACTATTTCTACTGAAAAAT
GCTCAGTTGACCTTGAGCTTATTTGCACTTTCCTACCTACCTACCCTATCAGCTGCAACTCCACTTGTAGCTCAAGCAAC
ATGATATTTCCAATGTAGCCAATCATTTATCTTATCTGATATTGGAGGCTCTTGACTGCATTCAACCTCAAAATAACCAT
GATAGTGAGATGACCAAATCAACTTATAATGTACCTGATCTTCATAATGCAAATGAAAATGAAAGACTGGTGTGCAAAGC
TTTTCCATGTATTCATTTATAGGGTCAAAGAAGACATGGTTATTTTGATGATCATCATAACATTCTATATCTTTAGACAA
CTGATTCTCAGCCACACAAAATTCCTTTGATGTGCTATCCAACTGCCTTTCTGCATGATTCCCACAAACAATGTAATTTT
CCTCACTATTATGATCATTATTTGATGTAAGCTGCTGCAAGGAATTACAAAAATGAACAACCTTTTCCTCTGCCTGAGGG
TTATAAAAGCTATCTTCCAGTATTTCTTCTTGGTGTTTGTAATCATTTTCATATTCATTATGATCCGAAGACTGACAAGT
CTGCTGCATCTCTACATCAATCTCAGAGGATGTAACATGGTTTTCATAAGTAAACCCCTGCTGATCTTCATGCTGCATTT
CATGAGATGTTATACTTTCTTCTTGGTGTTGAAATGCATTGTTATGAAGAGCCTCTAAAATTTCTTCATCCATAAATTCA
TCATCATCATAACAATCCTCCAAATATTGAATAAAACTCAAAGAATGTTTACAACAATCTTTGACCAGCAATAAGGAAGG
ATGACATTCTTTATACATGTCATAGAATACATCATGAAAATCAGCAAGAGAATATAATGAACCATTTTCCAAACTTTTAT
ACCAAGACCATGCTTTTCCTTCTAAAGTGGCCATAAACATCCTCATGAGACAATCCTCAGGAAAGTGAACCTTAAGACTG
CGTACATGCATATGGAACCTAACCAAATGAAGAGCAGCATTGTCTTTCTTTTCATCTTTGAATATTGGAAGATCATCTAA
CCAATCAACCTTTGGCATAGGATTTGGAAAACCAGGGATATGAGACCGATTCATAGGAGCATACCTGGCATTCATTCTTG
CAGTGGAATTCATCTTGAAACTTCATCAAGCTACTGATCTTCTAGCAGTGGAGTCACCTTCCAATTTCTTATTCGATGTG
TGGAGTCGCCAAGGTAGTTTTGCAGCCTCAAAAAGATGTCTGAGCTCCTGCTACCTTCAGAAGTTCAGCTTCATAATTTC
GGGAATGAGTAATCTTCAGACTCCCGGCAGACGCACCAAAATGTTATCACAAAATCACCCTGGAAGGCTGCAGCCCAGGA
AGACTTCAAGTAACTATTTCAAACCAACTTTAGACTAAGGCTTAGCCTCCTCAACCTGAGAGGGCTCTCTCAAAAGGCTT
AATAATATTCATTAAAGACAAAGATGGCTAACTCTTTTATAACTAATGAAAAAAATATGAAGGTTGGAAACACATCAAAC
TAAATCCCATTGGGCTATGGAGTCTAAAATACCTCAGTATAACAATGAACTCAACCTTACATGGAAGTCAGGGCATTCAG
CATTTAAATATTCAGAACATAAACACATATGGGACCACACAGTTTATAAATGCATACAGGAAGTCAGAGCACAATCAGTG
AATTCTGAGTGATTATACATCCATACCACTGTAAGAATTAAGAAAAGGACAACATCACATATTCTGAACATAAAAAATCC
TTCGTGAATCCTGAGAAGAAAAGAACTCTAACTTGTATTACTGAAAATGAGTCTTACATAGGCCAAAACAAGCTTGTTTT
TCATAAAAATTTCCAACCCTTTGTACATCAGATCTTCTTCTATATATAGAGCTCTTTACATAACTGAGATTCCTCCTCCA
GCATGAGGGGAATTCGAATTCTACCTGATCTGACACCTATTGACACTCAAAACTAACTATTAAATGCAAATGACACCTAA
CTAGCAGTCCTAGAGACCTAATACAACTAGGAGTGTAACTCCTTATTATGATTACAACAACCTTATCTAAACATTTAAAG
CATTCTTTGACACCTAACACTCCATGAAGTCGAATTTGATGAAGCCCATAACCTTCCAGCTGGCCCTTGATGACTCATCC
TTTTGTTGTTCCTAGAAACTAGGAGACTGTCCCTTGCTCTGTTCTGGCTGAAAAATAGGTCTTGGGACAGAGCTCATAAC
TTCTCGTAAAAAATGTATTTGGAAAAACTGAAGGAGGATTTTGTGAACCAATCCGTGCTGAACAAAAACCTCTCTTGGTT
TTTTGAAACACCACTCCAACCGCCCAGAATGTGTCTTTGAAAAACAGGTGTAAAACAGAAAATGAAAAACTGCACCTACA
GCAGTTTCGTAGCGCAACTTTGGTCATTAATTTCTCTCAGATCGTAATGGATTTGAGGAAACTGAAGGAGGTTTTTGTAG
TTCAGTCTGTTAGGAAGAAAAACCTCTTTCAGTTTGAAAAATTGAGTTTTCAGTTGCTTTAGAGACCTCCTGGAAGTTGA
CTAGTAAACACAGAAAGCAAAGTTTTTTATGCTGAAACAGGCTGCTACAGGGGTTTCGCAGCGCGCTGCGAAAACACTGA
TTTCGTAGCGCAAAACAGGATTTTTACACTGTCTGCGCTACGAAAACGTGGATTCATAGCTAGTTTCAAAATTTCTCCAA
AATAATGTGAGATATGACTTCTAAACTCATGGTGAGGCTTCTAGGACATGGAATGAGGCTATCAAACTTTATTTGAAGAT
GGACATGAGACTCTAACCCTATGACTTAGACTCTAAAACATAAAAATGACTTGAGCATGACTTGACCATGACTGATACAA
GAATTGAGAAACCATGTAAGTTGTCCAAACTTTTTAAGGAAGTTTTACAGTGATAACAGTGGCTCCACTAGGGATAGTGT
GCCCTTGTGGTATACTAAGAACTCGCAGGTCCAGT
TAREAN_annotation Putative LTR element
orientation_score 0.99999705470011

protein domains:

protein domains:


Reads annotation summary

  cl_string domain Freq proportion
Bianca Ty1-INT Bianca Ty1-INT 1 0.00004
Tork Ty1-RH Tork Ty1-RH 1 0.00004
Gymco-I Ty1-RT Gymco-I Ty1-RT 1 0.00004
Athila Ty3-GAG Athila Ty3-GAG 1 0.00004
TatII Ty3-GAG TatII Ty3-GAG 155 0.00614
TatV Ty3-GAG TatV Ty3-GAG 48 0.00190

clusters with similarity:

Cluster Number of similarity hits
225 31
2 2
13 1
20 1
29 1
48 1
50 1
63 1
85 1
142 1
146 1
152 1
169 1
180 1
206 1
263 1

clusters connected through mates:

Cluster Number of shared
read pairs
k
225 91 0.062
2 27 0.00402
974 15 0.0117
6 13 0.00262
12 12 0.0023
1810 12 0.00941
3 11 0.00229
9 11 0.00287
15 11 0.00309
18 11 0.00363
4 10 0.00217
11 10 0.00212
102 10 0.00282
1 9 0.00192
8 9 0.00321
27 9 0.00354
30 9 0.00188
32 9 0.00334
67 9 0.00268
1400 9 0.00703
2170 9 0.00706
4790 9 0.00706
10 8 0.00308
16 8 0.00214
19 8 0.00259
22 8 0.00205
23 8 0.00226
26 8 0.00244
36 8 0.00289
42 8 0.00266
47 8 0.00217
134 8 0.00321
206 8 0.00466
7840 8 0.00628
14 7 0.00155
44 7 0.00167
63 7 0.00168
64 7 0.0033
85 7 0.00274
169 7 0.00353
4800 7 0.00549
13 6 0.00224
17 6 0.000868
20 6 0.0013
25 6 0.00197
34 6 0.00168
39 6 0.00225
43 6 0.00158
45 6 0.00156
46 6 0.00215
48 6 0.00136
74 6 0.00224
88 6 0.0017
106 6 0.00228
127 6 0.00247
137 6 0.00274
141 6 0.00241
154 6 0.00333
6780 6 0.00472
7070 6 0.00472
7 5 0.00088
21 5 0.00142
24 5 0.00118
31 5 0.000811
35 5 0.00113
37 5 0.00117
49 5 0.00172
51 5 0.00123
54 5 0.00224
55 5 0.00102
59 5 0.00215
75 5 0.0012
76 5 0.00194
90 5 0.00138
91 5 0.0026
103 5 0.00155
105 5 0.00186
117 5 0.00207
121 5 0.00283
126 5 0.0021
145 5 0.00189
182 5 0.00245
220 5 0.00302
1190 5 0.00391
2150 5 0.00391
2200 5 0.00391
3070 5 0.00393
9230 5 0.00393
11100 5 0.00393
12300 5 0.00393
13700 5 0.00393
13800 5 0.00393
18100 5 0.00393
21300 5 0.00393
21400 5 0.00393
24700 5 0.00393
27000 5 0.00393
5 4 0.00143
40 4 0.000845
53 4 0.000984
60 4 0.00174
66 4 0.001
69 4 0.00175
71 4 0.00116
72 4 0.0016
78 4 0.00108
80 4 0.00155
83 4 0.00165
89 4 0.00157
97 4 0.00143
100 4 0.00183
110 4 0.00189
124 4 0.00187
143 4 0.00164
148 4 0.00175
149 4 0.00207
152 4 0.00134
158 4 0.00182
163 4 0.00158
174 4 0.00173
213 4 0.00171
238 4 0.00258
259 4 0.00271
4550 4 0.00313
4810 4 0.00314
6410 4 0.00314
9280 4 0.00314
11300 4 0.00315
18600 4 0.00315
23900 4 0.00315
24800 4 0.00315
25100 4 0.00315
27900 4 0.00315
29800 4 0.00315
30600 4 0.00315
32100 4 0.00315
34900 4 0.00315
50 3 0.00105
52 3 0.000984
58 3 0.00145
62 3 0.000775
70 3 0.00143
77 3 0.0012
79 3 0.000831
84 3 0.00108
86 3 0.000819
98 3 0.00141
99 3 0.00156
101 3 0.00109
108 3 0.00146
111 3 0.000798
115 3 0.00101
120 3 0.00119
125 3 0.0015
128 3 0.00153
129 3 0.00162
133 3 0.000757
139 3 0.00128
140 3 0.000948
147 3 0.000781
150 3 0.00135
155 3 0.00151
156 3 0.00144
171 3 0.00143
172 3 0.00124
193 3 0.00175
198 3 0.0018
227 3 0.00191
245 3 0.00161
3130 3 0.00236
4520 3 0.00236
4550 3 0.00236
4960 3 0.00235
5510 3 0.00236
6960 3 0.00236
8190 3 0.00236
9740 3 0.00236
13800 3 0.00236
16800 3 0.00236
21300 3 0.00236
21400 3 0.00236
22200 3 0.00236
22500 3 0.00236
24800 3 0.00236
25400 3 0.00236
27700 3 0.00236
27900 3 0.00236
40400 3 0.00236
41900 3 0.00236
43300 3 0.00236
50100 3 0.00236
59400 3 0.00236
62800 3 0.00236
65600 3 0.00236
68100 3 0.00236
76400 3 0.00236
76600 3 0.00236
28 2 0.000756
29 2 0.000663
57 2 0.000883
61 2 0.000702
65 2 0.000795
68 2 0.000749
82 2 9e-04
87 2 0.000787
93 2 0.000991
104 2 0.000965
109 2 0.00103
113 2 0.000793
116 2 0.000611
132 2 0.001
136 2 0.00109
138 2 0.00101
146 2 0.00101
153 2 0.000788
159 2 0.000974
161 2 0.000783
164 2 0.00135
165 2 0.000824
167 2 0.000775
168 2 0.000835
177 2 0.00118
178 2 0.00116
179 2 0.00108
180 2 0.0012
183 2 0.000987
185 2 0.000979
202 2 0.00127
204 2 0.00127
268 2 0.00132
274 2 0.00148
283 2 0.00145
286 2 0.00123
382 2 0.00153
1220 2 0.00157
2090 2 0.00157
3270 2 0.00157
9430 2 0.00157
9650 2 0.00157
10200 2 0.00157
11200 2 0.00157
11300 2 0.00157
12300 2 0.00157
12400 2 0.00157
13500 2 0.00157
14900 2 0.00157
19000 2 0.00157
19200 2 0.00158
19500 2 0.00158
23000 2 0.00157
23600 2 0.00157
24300 2 0.00157
28900 2 0.00157
29300 2 0.00157
29900 2 0.00158
32100 2 0.00157
38500 2 0.00157
39100 2 0.00157
39300 2 0.00157
41300 2 0.00158
42700 2 0.00158
44700 2 0.00158
48300 2 0.00157
54000 2 0.00157
57400 2 0.00157
61500 2 0.00157
66200 2 0.00157
67300 2 0.00157
71100 2 0.00157
72900 2 0.00157
74000 2 0.00157
77100 2 0.00157
82500 2 0.00157
86300 2 0.00158
88000 2 0.00158
88800 2 0.00158
89900 2 0.00158
105000 2 0.00158
113000 2 0.00158
122000 2 0.00158
126000 2 0.00158
129000 2 0.00158
145000 2 0.00158
152000 2 0.00158
154000 2 0.00158
187000 2 0.00158
195000 2 0.00158
210000 2 0.00158
220000 2 0.00158
222000 2 0.00158
229000 2 0.00158
234000 2 0.00158
240000 2 0.00158
247000 2 0.00158
251000 2 0.00158
253000 2 0.00158
276000 2 0.00158
286000 2 0.00158
295000 2 0.00158
296000 2 0.00158
298000 2 0.00158
305000 2 0.00158
313000 2 0.00158
317000 2 0.00158
321000 2 0.00158
337000 2 0.00158
344000 2 0.00158
345000 2 0.00158
346000 2 0.00158
41 1 0.000241
56 1 0.000671
92 1 0.000536
94 1 0.00064
95 1 0.000456
96 1 0.000447
107 1 0.000512
112 1 0.000523
118 1 0.000488
119 1 0.000556
123 1 0.00044
130 1 0.000306
135 1 0.000452
142 1 0.000482
144 1 0.000568
157 1 0.000494
160 1 0.000477
162 1 0.000413
170 1 0.000431
176 1 0.000572
184 1 6e-04
187 1 0.00053
189 1 0.000452
190 1 0.000497
191 1 0.000457
195 1 0.000613
196 1 0.000434
197 1 0.000462
200 1 0.000477
203 1 0.000553
205 1 0.000529
208 1 0.000602
209 1 0.000681
210 1 0.000705
211 1 0.000565
212 1 0.000627
214 1 0.000633
216 1 0.000651
218 1 0.000679
224 1 0.000739
226 1 0.000679
229 1 0.000533
233 1 0.000703
235 1 0.000527
243 1 0.000538
252 1 0.00065
258 1 0.000559
272 1 0.000613
276 1 0.000605
279 1 0.000665
287 1 0.000741
293 1 0.000717
301 1 0.000728
326 1 0.000724
329 1 0.000769
333 1 0.000729
353 1 0.000755
363 1 0.000771
368 1 0.000756
385 1 0.000781
421 1 0.000778
438 1 0.000763
448 1 0.000759
450 1 0.000754
452 1 0.000767
455 1 0.000762
464 1 0.000764
481 1 0.00075
501 1 0.000765
545 1 0.000763
546 1 0.000766
574 1 0.000781
601 1 0.000767
721 1 0.000771
802 1 0.000779
839 1 0.000782
943 1 0.000777
1010 1 0.000778
1030 1 0.00078
1210 1 0.000779
1280 1 0.000779
1460 1 0.00078
1530 1 0.000782
1660 1 0.000781
1770 1 0.000782
2210 1 0.000782
2420 1 0.000782
2440 1 0.000787
2620 1 0.000783
2800 1 0.000786
3080 1 0.000785
3150 1 0.000784
3490 1 0.000784
4670 1 0.000784
4740 1 0.000785
4780 1 0.000786
5140 1 0.000786
5250 1 0.000787
5470 1 0.000785
6000 1 0.000786
6870 1 0.000785
6970 1 0.000786
7200 1 0.000786
7510 1 0.000786
7640 1 0.000786
7700 1 0.000786
7890 1 0.000787
8440 1 0.000787
8500 1 0.000786
8510 1 0.000787
8810 1 0.000787
9260 1 0.000787
9390 1 0.000787
9470 1 0.000787
9560 1 0.000787
10100 1 0.000788
10400 1 0.000787
10900 1 0.000786
10900 1 0.000787
11000 1 0.000786
11600 1 0.000786
11800 1 0.000788
12400 1 0.000786
13000 1 0.000788
13700 1 0.000787
13800 1 0.000787
13900 1 0.000787
14600 1 0.000787
14800 1 0.000786
14900 1 0.000787
14900 1 0.000787
15400 1 0.000786
16000 1 0.000787
16600 1 0.000788
16700 1 0.000787
17100 1 0.000786
17400 1 0.000788
17600 1 0.000788
17900 1 0.000787
18700 1 0.000787
19000 1 0.000786
19500 1 0.000786
19700 1 0.000787
20000 1 0.000788
20600 1 0.000787
20700 1 0.000787
20900 1 0.000787
21700 1 0.000787
21900 1 0.000787
21900 1 0.000787
22300 1 0.000787
22300 1 0.000787
22600 1 0.000787
22700 1 0.000787
23300 1 0.000787
24300 1 0.000788
24600 1 0.000787
26000 1 0.000787
26900 1 0.000787
27200 1 0.000787
27700 1 0.000788
27800 1 0.000788
28100 1 0.000787
29400 1 0.000787
29900 1 0.000788
30300 1 0.000787
30400 1 0.000787
30500 1 0.000787
32300 1 0.000787
33300 1 0.000788
34000 1 0.000788
34000 1 0.000787
34300 1 0.000787
34800 1 0.000788
35300 1 0.000788
36100 1 0.000788
36100 1 0.000788
36300 1 0.000788
37000 1 0.000787
37400 1 0.000788
37700 1 0.000788
39000 1 0.000787
40000 1 0.000788
40800 1 0.000788
40900 1 0.000788
41000 1 0.000787
41200 1 0.000787
42100 1 0.000788
43200 1 0.000787
43400 1 0.000788
43600 1 0.000787
43700 1 0.000788
44000 1 0.000788
44600 1 0.000787
44800 1 0.000787
46100 1 0.000788
47700 1 0.000788
48100 1 0.000788
48500 1 0.000788
48900 1 0.000787
49100 1 0.000788
51400 1 0.000787
52600 1 0.000788
53900 1 0.000788
55800 1 0.000787
56000 1 0.000787
56100 1 0.000788
56800 1 0.000788
56900 1 0.000788
57200 1 0.000787
58400 1 0.000788
58800 1 0.000788
60000 1 0.000788
61000 1 0.000787
61500 1 0.000787
61900 1 0.000787
63000 1 0.000787
64300 1 0.000788
64800 1 0.000787
65000 1 0.000787
65200 1 0.000788
68300 1 0.000787
69300 1 0.000787
69500 1 0.000788
73200 1 0.000788
74500 1 0.000788
74700 1 0.000787
75000 1 0.000787
75700 1 0.000787
77600 1 0.000788
78100 1 0.000788
78400 1 0.000788
78600 1 0.000788
78600 1 0.000788
79500 1 0.000787
79600 1 0.000787
79700 1 0.000787
81200 1 0.000787
81200 1 0.000788
82400 1 0.000788
82700 1 0.000788
83200 1 0.000787
84000 1 0.000788
84500 1 0.000788
84600 1 0.000788
84900 1 0.000787
90900 1 0.000788
93400 1 0.000788
96600 1 0.000788
98800 1 0.000788
101000 1 0.000788
114000 1 0.000788
116000 1 0.000788
117000 1 0.000788
117000 1 0.000788
118000 1 0.000788
120000 1 0.000788
123000 1 0.000788
126000 1 0.000788
126000 1 0.000788
127000 1 0.000788
131000 1 0.000788
134000 1 0.000788
137000 1 0.000788
139000 1 0.000788
139000 1 0.000788
140000 1 0.000788
147000 1 0.000788
161000 1 0.000788
168000 1 0.000788
172000 1 0.000788
175000 1 0.000788
180000 1 0.000788
184000 1 0.000788
185000 1 0.000788
190000 1 0.000788
190000 1 0.000788
194000 1 0.000788
195000 1 0.000788
198000 1 0.000788
198000 1 0.000788
202000 1 0.000788
202000 1 0.000788
204000 1 0.000788
207000 1 0.000788
212000 1 0.000788
215000 1 0.000788
217000 1 0.000788
218000 1 0.000788
223000 1 0.000788
223000 1 0.000788
226000 1 0.000788
235000 1 0.000788
240000 1 0.000788
250000 1 0.000788
250000 1 0.000788
251000 1 0.000788
251000 1 0.000788
256000 1 0.000788
267000 1 0.000788
273000 1 0.000788
277000 1 0.000788
277000 1 0.000788
277000 1 0.000788
279000 1 0.000788
280000 1 0.000788
286000 1 0.000788
287000 1 0.000788
289000 1 0.000788
289000 1 0.000788
290000 1 0.000788
290000 1 0.000788
302000 1 0.000788
303000 1 0.000788
305000 1 0.000788
306000 1 0.000788
310000 1 0.000788
320000 1 0.000788
323000 1 0.000788
324000 1 0.000788
325000 1 0.000788
329000 1 0.000788
330000 1 0.000788
342000 1 0.000788
344000 1 0.000788
345000 1 0.000788
345000 1 0.000788
347000 1 0.000788
349000 1 0.000788

CL33 ----> CL225

image

No. of shared pairs: :91

CL33 ----> CL2

image

No. of shared pairs: :27

CL33 ----> CL974

image

No. of shared pairs: :15

CL33 ----> CL6

image

No. of shared pairs: :13

CL33 ----> CL12

image

No. of shared pairs: :12

CL33 ----> CL1808

image

No. of shared pairs: :12

CL33 ----> CL3

image

No. of shared pairs: :11

CL33 ----> CL9

image

No. of shared pairs: :11

CL33 ----> CL15

image

No. of shared pairs: :11

CL33 ----> CL18

image

No. of shared pairs: :11

CL33 ----> CL4

image

No. of shared pairs: :10

CL33 ----> CL11

image

No. of shared pairs: :10

CL33 ----> CL102

image

No. of shared pairs: :10