Cluster no. 119

Go back to cluster table

Cluster is part of supercluster: 57

Cluster characteristics:

size 11787
size_real 11787
ecount 592673
supercluster 57
annotations_summary 10.04% Class_I/LTR/Ty1_copia/Gymco-II:Ty1-RT
6.89% Class_I/LTR/Ty1_copia/Gymco-II:Ty1-INT
6.29% Class_I/LTR/Ty1_copia/Gymco-II:Ty1-RH
1.75% Class_I/LTR/Ty1_copia/Gymco-II:Ty1-GAG
0.92% Class_I/LTR/Ty1_copia/Tork:Ty1-INT
0.75% Class_I/LTR/Ty1_copia/Gymco-II:Ty1-PROT
0.73% Class_I/LTR/Ty1_copia/SIRE:Ty1-RT
0.68% Class_I/LTR/Ty1_copia/Ivana:Ty1-RH
0.65% Class_I/LTR/Ty1_copia/Ivana:Ty1-PROT
0.52% Class_I/LTR/Ty1_copia/Ivana:Ty1-INT
0.48% Class_I/LTR/Ty1_copia/Ale:Ty1-GAG
0.39% organelle/mitochondria
0.32% Class_I/LTR/Ty1_copia/Ivana:Ty1-RT
0.27% Class_I/LTR/Ty1_copia/TAR:Ty1-PROT
0.15% Class_I/LTR/Ty1_copia/SIRE:Ty1-PROT
0.10% Class_I/LTR/Ty1_copia/Ale:Ty1-RT
0.06% Class_I/LTR/Ty1_copia/SIRE:Ty1-RH
0.03% Class_I/LTR/Ty1_copia/Ale:Ty1-INT
0.03% Class_I/LTR/Ty1_copia/Bryco:Ty1-RT
0.03% Class_I/LTR/Ty1_copia/Ale:Ty1-RH
0.02% Class_I/LTR/Ty1_copia/Tork:Ty1-PROT
0.02% Class_I/LTR/Ty1_copia/Angela:Ty1-INT
0.01% Class_I/LTR/Ty1_copia/Bryco:Ty1-RH
0.01% Class_I/LTR/Ty1_copia/Tork:Ty1-RT
0.01% Class_I/LTR/Ty1_copia/Ty1-outgroup:Ty1-INT
0.01% Class_I/LTR/Ty1_copia/Bryco:Ty1-PROT
0.01% Class_I/LTR/Ty1_copia/Gymco-I:Ty1-GAG
pair_completeness 0.835409529741514
pbs_score 52.3016566
TR_score 0.48042345679012344
TR_monomer_length 5465.0
loop_index 0.893441927547298
satellite_probability 0.100880927638755
consensus
CTGCCCGGAGCACCACCCCTCTGGCTCGGCGAGCCACTGCTCACTGACGGACCTGACATCCTCATAGATGTACCTCCGGA
TCCTCCTGATCCCTGCCCACTGGATCCCTGCGACTGACTCAACTGCTGCTGAGGGTCTGGCTGATCCAGATACTCTAACT
CCCGTGACCTCCTAAAGGCCCTGTCCTCCTCGAACTTCACATCCCGTCTGACAACAACTCTCCTCTGTGCAGGAATGTAA
ATCCGAAAGGCCTTTGAGGTCTCACTGTAGCCCACAAAGATACCCTTCTCTGCGGTGGGCTCTAGTTTGGTCCTCTTCTC
CTTGGGTATATAGGAGTATGTAATGCATCCAAAGATATGAAGATGACCAATATCAGGCTTCTTCCCAGAGAAAGCCTCCT
CCGGAGTCATGTGCCCCAAGGCACGATGCGGACTCCTGTTCTGCAAGTAAACAGCTGTGTTGCAGGCCTCTGCCCACAAG
AACAATGGCAACCCCTGATCATGTAACATGGCTTTGGCAGCCCCTATGATGGATCTGTTCTTCCTCTCCGCAACCCCGTT
CTGCTGGGGGTTGTAAGGAACAGTGAACTCCCTCCTAATGCCTGCCTCCGCACAATAGTCAACAAACTCTCCAAGGGTGT
ACTCTCCTCCATTGTCCGACCTCAAGGACTTGATCTTTCGACCTGTCTGAGTCTCCACAAGAGCTCTGAACTCCTGAAAC
CGCTTGAAGACCTCACTCTTGGTCTTCAAGAAATAAATCCAGGTCCTCCTGGAGTGATCATCAATGAATAAAACATAGTA
CTCATATCCACTCAAGGAAACATGAGACATCCGACCGCTCACATCGGAATGAATCAAATCAAGTATCCCCGTCGCTCTGC
TGTCACTGCTGGGAAAAGGGGATTTGGCAAACTTGCCCATCGCACAACCTCTGCAAGTATCAAAGTGATCAGTACTGAAA
TCTGGCACACCTGTAGTGATCTCCCGCAATGTCCTCAAGGCTCCATGATACATATGTCCCATCCTGCGGTGCCAAATCTC
ACACAGCTCAGAACTGCTAGCTCTGCTGTCGGTACTACTGCTCAATGCCAAAAGGGGCTGGAATGCAAACTTGTACACCT
TTGCATGGCGTACACCTATCACTCTAGCTGAATCAGCTGGAGTGCCCCTGGGATACATCAACACCTGTCCTCCCCTGAAC
AGTACCTCATATCCTCTGTCCTCCAAAGCTGAGACGGATATGAGGTTCTTCCTCATCCCTGGCACATAAAGAACCTCTGA
CACCTTCAAGGGAGGTTTGGACTCCCTCTGAAATGTCACTGTCCCCACCCCGACTGCTCTAACAACTCTGTCATCACCGA
GTACTACCTCAATATCAGTGCCACTCTCTGAAAGCTCTGAGAAGTACTCACGGACTCCTGTCATGTGACGTGAAGCCCCA
CTGTCCACATACCAGATACCTGAAGATGCTCCGCTAATCGAGGGAAAAGCATGCTCCCTCTGAACCTGTGTGGCAGGTGA
TCCTGCACTAGAGGACTCACACGTAGTGAACGCAAACTCCCGGTCAAAACGACCTGCAAAGTCCTCAATCTCTGCTGAAG
CTGCCACGTCCTGGTTCTTCCCCTTCTTCTTCTTCTTCTCCGGACACACAACTGCATAGTGTCCCATCTTTTGACAATTC
CAACACTTCACCTTGGAATAGTCCTTCTGTGTGTTCCCCTGTTTACCTTTACCTTTGCCTTTGCCCCCACCACTGCTTGT
GGAAGCCTGCTTCTTCCCTTTGCCTTTCTTGCCTCCTGCCACCAGTGCTACATCCTCATCCTGCTCAACTGGCTTGGCTG
CCCCAAGCTGACCTTTCCTGATCTCTGTCTGAATGCAATCATCCCAAAACCTCTCCCATGTGGGAAGGGTCTCACGTGCA
CAAACCCCATCAGCAAAGTTCAACCATGAACGGGGGAGGCCATTCACTGCAATCCGCACCAACTCAGTGGGTGGAATGGC
CTCTCCAATCGCTGCCAACTCATCTCTCACATTAGTAATCTTTGTGAGATATCCAGCTGCACTATCATTACCCATCTTAA
TGTTCTTCAGCTTCTCCTTCAGGACCATCTTCCGGTTCTCATTGGTACTCTGGTAGAGATTGGACAATGCTGTCCACATC
TCATGGGCATTGCTCTTTCCTCTCACATGAGGAATGCAATGGTCTTTGATTCCGTCTAGAATCAGCCTCTTACCCTTGTT
GTTCTTTTTATTATACTCAGCCAACTGAGTAACATCAGTGGGCACAACAACAGGGTTCTGTGTGGTATGCACCATGATAT
CCCAGACTTCTGCCTCCTCAAAGATACTCTGCATTCTCTCCTTCCAAACGCTGTAATTTGTATGCCCATCCAACCTATCC
TCCACCCTCAATCCCAATGACATCCTGCTGTCCTAAAACTGAAAAATAGCACTGCTGTAGTAAAGATAAAACTGTTGTTT
ATGAAAAAATCAGCTTGCTGGAATTTTCTGAGTGAAAAATCAGCAACTGTAATTTTTCCTTTTGCTGTCCCAAACTGCCC
TTCAGCACTCAAGCTCTGATACCATGTAAAAATTTCTCATTTCCCACCCCGGTTTTCAGTTTCACCTTATTTCTCCCATG
TAGTTAAATGCCCATTCCCATAACCATACATTTAACAGACTGAAAAAAATAAATATTGCTGAAAACACAAATTCTGGAAA
TTTTTCAGAATGCTGGAAATTGCAGAAATAAAAATCAGCAATTAAAAACAGCCATTAAAACACATTTAAACACTGAGATT
TTTGGTCAACTTGACCCTGGAAAAACCCCCTACAACTCTTGGGGAAAACCAGTTTGAGAGCTCTTCTTTATTTCTGAAAA
TTGCCTTTTTACAGTGAGAATTATTCAGCAAAAAATCAGCAAGCAAATTTACAACTTATCTCCTTTCCCGTGCCTCACAG
CAATCTGGAAATTACAGCAAACAGGACAGCAATAAATGTTGTACGACCTCCGTTTTGTGTGCAGAAAAATCAGCAAACTG
CTCCTCGATTTTTGTGCAAAAATCTGCCTTTCACTATGTGCTGAATCAGCTGTACAAATCTGCTCAACTGCTGCCTTGGA
ATGTGTGCCAAGCTGCTGTCTCCTTCTCCTCCCTGCTCAGAAATCTCTCTTGCTCTCTTGCTCTCCTTCTCCCAATCTGC
TCATGAAAGAATGAATGACCTTTTCCTCCTTTTCCTCCTTTAATATAACCCCAAGTGACTTTTGGGTGATCCCTAAATCC
AATGGCTGAAATAGATTTAGATCAATGGCTGAGATTAAATGCTCATTTAAATCTCACTTTCTATTTTTTAATTCACCCCA
CTTTAATAAAGACCCACTTAGTCATTTATTTCCAAAGTCACTTTTCCTTTCTAATTTTTCATTGACTTTATAAAAGTCAC
TTTAAAATTAGACTTAGTAACTTTATCACTTAAAGTCACTTTTAAATTAGATTTAACTTTATAAAATTATAAAGTCACTT
TAGGAGAAAAATTAAATTCTTTTGGACACTTTTCCCTAGGCCAAAGATCAAAGCCTAAGGGAACCACCTGTCCTCCGGTA
CCAAATTTCAACACTCCCTCTTACCGAGGAAGGTGTTCCTCACCACACCCATCTTGTCTCTGAAGTAGACATGCTTGCCC
CGTGGTAAGGCTTTGGTAAGAATATCTGCAACCTGCTCATCAGTGGAAATATACTCAAGCTTCACAGCTCCCTTCTGAAC
ATAGTCTCTGATGAAATGATATCTGATCCCGATATGCTTTGACCTGTCATGAAATACTGGATTCTCCGTGAGTTTAATGC
AACTCTGATTATCACAGTAAATCACTGAAGGTCTCAACGGCTGACCAAATAAGCCAAACAACATCTTGCGAAGCCAGATG
GCCTCACAACTAGCTAGACTGGCTGCCATATACTCTGCTTCCGCTGAACTCAGTGCTACTGACTGCTGCTTCCGGCTGAA
CCATGACACTACTGCTGAACCCAACCCAAAACAACACCCTGAAGTGCTCTTCCTATCAGAAGCACAACCTGCCCAATCAG
AATCAGTGTATCCTGCCAATCTCACTCCATCTCCCTGCCTGTAGTCCAGACCATAATCCACTGTCCCCTGCAAGTACCGC
AAAATGTGTTTTGCAGCCACCCAGTGAACCTTCCTAGGCTCACACATAAACTGACTCATCGTGTTGACTGCAAAACAGAT
ATCTGGTCTAGTGTTGACCAAATACATCAAGGAACCAATCAGCTGCCTGTACAATGTGGGATCCACCAACTCGGAATCCG
AAGCATGAAGCTTCTTCCAGTTGGTGATCATCGGTGTCGACATGGGTCTACAATCCTCCATGTGGAATCTGCTAAGGATG
TCCACAATATACTTCCCCTGCCCCAGGAAGAAATGCCCCTCCTCCTGCCACACCTCCAAACCCAAAAAGTAATGCATCAA
GCCGATGTCCTTCATCTCAAACTCCGCCGCAAGATCTCTCTTGCAGTGCTCTATGAGTCTCTCTGCACCTGTAATGATCA
AGTCATCCACATACAGCACCAGAATGAGAGGCTCCTCACCAATCACAATAAAGTAAAGGTTCGGATCTGCCTCACTCTTT
GTGAAACCCATCCCCTGCAAGTATGTATCTATCCTGGAGTACCAAGCTCTGGGAGCTTGCTTCAGGCCATAAAGGGCCTT
CTTCAATCTGCACACATGGGACTCCTTCCCATGCACCTCAAAGCCCTGTGGCTGCTCAATGTACACCTCCTCCTGTATGA
AGCCATTGAGAAATGCGGTCTTCACATCCATCTGGTGGATCTTCCAACCCATCTCTGCTGCTATCGATATAATGGAGCGG
ATCGAAGTATATCGAGCCACGGGAGCGAAGGTCTCCTCATAATCAACTCCCTCTACCTGGGAGAACCCTCTAGCCACAAA
CCTCGCTTTGAATTTCTCAATGCTGCCATCTGCAGCATGCTTTACCTTGTAAAGCCATCTGGAAGTAACCACGGATTTGC
CCTCAGGCCTCGGCACCACCTCCCAAACATCATTCTTCATGATAGAAGAATACTCCTCCTGCATGGCCTCTCTCCAGACC
TGCTGGCTAGCTGCCTCCTCATAGCTAGAAGGCTCAGAGTCAAGGATGCTGGTAACCATCGCCATATAGCTACAAAACCT
CTCAGGTGGTCTACTCTCTCTGACCGGCCTCTTCGGCTCAGCAACAGATGTGGCATCTCTCAAGGTGTCCTGAAGCCACT
TGGGCTTCCTCTTCCCTGAGCATGCTTCTCCCATAGGAGAATGAAACTCCTCCTCCTCATCACCATCAGTAGCCTGAACT
CCTGACTGTCTGTCTGCTGTCCTCCTGCCTGCACCTGAACCTGTAGAAGCTGAGGTACCGTGTGAACTGTCCATCAGTGG
ACTCCCTAGTGAACTGCTCTGCATG
TAREAN_annotation Putative LTR element
orientation_score 1

protein domains:

protein domains:


Reads annotation summary

  cl_string domain Freq proportion
mitochondria mitochondria 46 3.9e-03
Ale Ty1-GAG Ale Ty1-GAG 56 4.8e-03
Gymco-I Ty1-GAG Gymco-I Ty1-GAG 1 8.5e-05
Gymco-II Ty1-GAG Gymco-II Ty1-GAG 206 1.7e-02
Ale Ty1-INT Ale Ty1-INT 3 2.5e-04
Angela Ty1-INT Angela Ty1-INT 2 1.7e-04
Gymco-II Ty1-INT Gymco-II Ty1-INT 812 6.9e-02
Ivana Ty1-INT Ivana Ty1-INT 61 5.2e-03
Tork Ty1-INT Tork Ty1-INT 109 9.2e-03
Ty1-outgroup Ty1-INT Ty1-outgroup Ty1-INT 1 8.5e-05
Bryco Ty1-PROT Bryco Ty1-PROT 1 8.5e-05
Gymco-II Ty1-PROT Gymco-II Ty1-PROT 88 7.5e-03
Ivana Ty1-PROT Ivana Ty1-PROT 77 6.5e-03
SIRE Ty1-PROT SIRE Ty1-PROT 18 1.5e-03
TAR Ty1-PROT TAR Ty1-PROT 32 2.7e-03
Tork Ty1-PROT Tork Ty1-PROT 2 1.7e-04
Ale Ty1-RH Ale Ty1-RH 3 2.5e-04
Bryco Ty1-RH Bryco Ty1-RH 1 8.5e-05
Gymco-II Ty1-RH Gymco-II Ty1-RH 741 6.3e-02
Ivana Ty1-RH Ivana Ty1-RH 80 6.8e-03
SIRE Ty1-RH SIRE Ty1-RH 7 5.9e-04
Ale Ty1-RT Ale Ty1-RT 12 1.0e-03
Bryco Ty1-RT Bryco Ty1-RT 3 2.5e-04
Gymco-II Ty1-RT Gymco-II Ty1-RT 1183 1.0e-01
Ivana Ty1-RT Ivana Ty1-RT 38 3.2e-03
SIRE Ty1-RT SIRE Ty1-RT 86 7.3e-03
Tork Ty1-RT Tork Ty1-RT 1 8.5e-05

clusters with similarity:

Cluster Number of similarity hits
7 1620
97 1210
21 1160
32 111
51 12
25 5
64 3
81 2
6 1
18 1
29 1
189 1
214 1
238 1
352 1

clusters connected through mates:

Cluster Number of shared
read pairs
k
21 23 0.00827
25 16 0.00696
51 14 0.00422
122 12 0.007
2 10 0.00167
30 10 0.00247
798 10 0.0185
4350 9 0.0169
68 8 0.00414
6 7 0.00166
634 7 0.0129
10500 7 0.0132
13 6 0.00309
143 6 0.00355
173 6 0.00595
5940 6 0.0113
1 5 0.00126
3 5 0.00123
63 5 0.00145
74 5 0.00258
77 5 0.00286
78 5 0.00168
81 5 0.00185
99 5 0.00421
161 5 0.00276
7 4 0.000809
14 4 0.00106
17 4 0.000648
20 4 0.00103
29 4 0.00176
47 4 0.00136
49 4 0.00185
53 4 0.0012
54 4 0.00268
62 4 0.00128
97 4 0.00195
116 4 0.00158
130 4 0.00158
214 4 0.00477
9540 4 0.00753
11 3 0.000754
16 3 0.001
18 3 0.00131
22 3 0.000948
31 3 0.000553
34 3 0.00106
48 3 0.000816
57 3 0.00197
91 3 0.00254
93 3 0.00235
126 3 0.00183
128 3 0.00247
172 3 0.00179
177 3 0.00312
181 3 0.00238
48500 3 0.00566
5 2 0.000976
9 2 0.000648
32 2 0.00102
41 2 0.000586
42 2 0.00088
56 2 0.00267
66 2 0.000613
79 2 0.000697
82 2 0.00135
85 2 0.0011
95 2 0.00137
96 2 0.00134
98 2 0.00144
105 2 0.00103
113 2 0.00112
114 2 0.00175
120 2 0.00112
137 2 0.00138
139 2 0.00125
145 2 0.00105
155 2 0.0016
159 2 0.00152
160 2 0.00147
165 2 0.00119
167 2 0.00109
200 2 0.00148
201 2 0.00318
213 2 0.00125
223 2 0.00234
238 2 0.00247
254 2 0.00302
352 2 0.00292
1180 2 0.00369
1780 2 0.00367
2740 2 0.00373
18300 2 0.00377
42800 2 0.00378
50300 2 0.00377
73800 2 0.00377
193000 2 0.00378
207000 2 0.00378
243000 2 0.00378
311000 2 0.00378
318000 2 0.00378
8 1 0.000484
10 1 0.000539
15 1 0.000354
23 1 0.000357
24 1 0.000285
27 1 0.000554
28 1 0.000525
33 1 0.000556
35 1 0.000273
36 1 0.000494
40 1 0.00025
43 1 0.000328
44 1 0.00029
45 1 0.000321
46 1 0.000489
50 1 0.000474
52 1 0.000433
58 1 0.00075
59 1 0.000631
64 1 0.000724
67 1 0.000382
69 1 0.000646
70 1 0.000735
73 1 0.000743
76 1 0.000546
80 1 0.000544
83 1 0.000595
84 1 0.000491
87 1 0.000555
88 1 0.00036
89 1 0.000553
92 1 0.00089
94 1 0.00122
101 1 0.000498
104 1 0.00075
106 1 0.000528
107 1 0.000825
123 1 0.000653
124 1 0.000715
125 1 0.000794
129 1 0.000904
133 1 0.00031
142 1 0.00075
144 1 0.000979
148 1 0.000645
151 1 0.000716
154 1 0.000941
162 1 0.000596
168 1 0.000604
169 1 0.000804
171 1 0.000737
174 1 0.000635
180 1 0.00108
183 1 0.000778
189 1 0.000678
196 1 0.000639
199 1 0.00126
203 1 0.000935
205 1 0.000869
206 1 0.00102
212 1 0.00117
216 1 0.00125
218 1 0.00137
219 1 0.00121
220 1 0.00109
222 1 0.00112
232 1 0.00109
236 1 0.00172
241 1 0.00124
242 1 0.00101
248 1 0.00136
250 1 0.00147
251 1 0.00143
253 1 0.00111
269 1 0.00152
271 1 0.00159
278 1 0.00152
289 1 0.00159
302 1 0.00158
313 1 0.00153
326 1 0.00156
335 1 0.0017
341 1 0.00161
349 1 0.00162
425 1 0.00169
435 1 0.00162
451 1 0.00174
461 1 0.00171
473 1 0.00186
480 1 0.00182
516 1 0.00182
540 1 0.00184
546 1 0.00177
728 1 0.00184
816 1 0.00185
1250 1 0.00186
1390 1 0.00186
1460 1 0.00185
1500 1 0.00186
1720 1 0.00185
1720 1 0.00185
1810 1 0.00187
2340 1 0.00186
2420 1 0.00188
2790 1 0.00187
2800 1 0.00187
5500 1 0.00188
5930 1 0.00188
7720 1 0.00188
7840 1 0.00188
8600 1 0.00188
9470 1 0.00188
10000 1 0.00188
10400 1 0.00188
10500 1 0.00188
12900 1 0.00188
13000 1 0.00188
13500 1 0.00188
16500 1 0.00189
17300 1 0.00189
18000 1 0.00188
23000 1 0.00188
24000 1 0.00189
24500 1 0.00188
25100 1 0.00189
27800 1 0.00189
28200 1 0.00188
29200 1 0.00188
32400 1 0.00189
37900 1 0.00189
39100 1 0.00189
40000 1 0.00189
41800 1 0.00189
42100 1 0.00189
42100 1 0.00189
44600 1 0.00189
46500 1 0.00189
47100 1 0.00189
47600 1 0.00189
54500 1 0.00189
58600 1 0.00189
64100 1 0.00189
65100 1 0.00189
73900 1 0.00189
74100 1 0.00189
75400 1 0.00189
77100 1 0.00189
77400 1 0.00189
78200 1 0.00189
79100 1 0.00189
79500 1 0.00189
80600 1 0.00189
84600 1 0.00189
92300 1 0.00189
97700 1 0.00189
101000 1 0.00189
115000 1 0.00189
131000 1 0.00189
141000 1 0.00189
177000 1 0.00189
186000 1 0.00189
195000 1 0.00189
211000 1 0.00189
232000 1 0.00189
250000 1 0.00189
285000 1 0.00189
302000 1 0.00189
305000 1 0.00189
309000 1 0.00189
309000 1 0.00189
314000 1 0.00189
328000 1 0.00189
329000 1 0.00189
338000 1 0.00189
338000 1 0.00189
350000 1 0.00189

CL119 ----> CL21

image

No. of shared pairs: :23

CL119 ----> CL25

image

No. of shared pairs: :16

CL119 ----> CL51

image

No. of shared pairs: :14

CL119 ----> CL122

image

No. of shared pairs: :12

CL119 ----> CL2

image

No. of shared pairs: :10

CL119 ----> CL30

image

No. of shared pairs: :10

CL119 ----> CL798

image

No. of shared pairs: :10