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comparison repeathumfish.txt @ 54:d6b0feb22584 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 53aab6394c715dc2d7fdd9188d6c9834e0516b5c
author fubar
date Thu, 14 Mar 2024 00:59:36 +0000
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comparison
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53:bdfa6a7c4543 54:d6b0feb22584
1 Calypte Anna
2
3 ==================================================
4 file name: rm_input.fasta
5 sequences: 159
6 total length: 1059687259 bp (1043590636 bp excl N/X-runs)
7 GC level: 41.49 %
8 bases masked: 79638300 bp ( 7.63 %)
9 ==================================================
10 number of length percentage
11 elements* occupied of sequence
12 --------------------------------------------------
13 SINEs: 32491 3044030 bp 0.29 %
14 ALUs 0 0 bp 0.00 %
15 MIRs 23309 1792450 bp 0.17 %
16
17 LINEs: 168150 56100653 bp 5.38 %
18 LINE1 446 51456 bp 0.00 %
19 LINE2 3520 419909 bp 0.04 %
20 L3/CR1 161974 55206716 bp 5.29 %
21
22 LTR elements: 3415 1802798 bp 0.17 %
23 ERVL 649 266145 bp 0.03 %
24 ERVL-MaLRs 15 814 bp 0.00 %
25 ERV_classI 1341 795364 bp 0.08 %
26 ERV_classII 1159 705705 bp 0.07 %
27
28 DNA elements: 12073 1651025 bp 0.16 %
29 hAT-Charlie 338 55376 bp 0.01 %
30 TcMar-Tigger 787 83392 bp 0.01 %
31
32 Unclassified: 3325 445147 bp 0.04 %
33
34 Total interspersed repeats: 63043653 bp 6.04 %
35
36
37 Small RNA: 5543 745245 bp 0.07 %
38
39 Satellites: 109 8273 bp 0.00 %
40 Simple repeats: 284418 12956749 bp 1.24 %
41 Low complexity: 61652 3494878 bp 0.33 %
42 ==================================================
43
44 * most repeats fragmented by insertions or deletions
45 have been counted as one element
46 Runs of >=20 X/Ns in query were excluded in % calcs
47
48
49 The query species was assumed to be homo sapiens
50 RepeatMasker version 4.1.5 , default mode
51
52 run with rmblastn version 2.13.0+
53 FamDB: CONS-Dfam_3.7
54
55 Amphioxus
56 ==================================================
57 file name: rm_input.fasta
58 sequences: 96
59 total length: 458494623 bp (458485423 bp excl N/X-runs)
60 GC level: 41.61 %
61 bases masked: 9756877 bp ( 2.13 %)
62 ==================================================
63 number of length percentage
64 elements* occupied of sequence
65 --------------------------------------------------
66 SINEs: 10212 946135 bp 0.21 %
67 ALUs 0 0 bp 0.00 %
68 MIRs 5121 527992 bp 0.12 %
69
70 LINEs: 4019 622661 bp 0.14 %
71 LINE1 179 11937 bp 0.00 %
72 LINE2 662 63166 bp 0.01 %
73 L3/CR1 2144 286741 bp 0.06 %
74
75 LTR elements: 689 138371 bp 0.03 %
76 ERVL 20 1005 bp 0.00 %
77 ERVL-MaLRs 4 322 bp 0.00 %
78 ERV_classI 584 118702 bp 0.03 %
79 ERV_classII 28 1778 bp 0.00 %
80
81 DNA elements: 850 57478 bp 0.01 %
82 hAT-Charlie 46 2708 bp 0.00 %
83 TcMar-Tigger 73 5236 bp 0.00 %
84
85 Unclassified: 517 41430 bp 0.01 %
86
87 Total interspersed repeats: 1806075 bp 0.39 %
88
89
90 Small RNA: 5487 857233 bp 0.19 %
91
92 Satellites: 629 50630 bp 0.01 %
93 Simple repeats: 115914 6556304 bp 1.43 %
94 Low complexity: 9124 485904 bp 0.11 %
95 ==================================================
96
97 * most repeats fragmented by insertions or deletions
98 have been counted as one element
99 Runs of >=20 X/Ns in query were excluded in % calcs
100
101
102 The query species was assumed to be homo sapiens
103 RepeatMasker version 4.1.5 , default mode
104
105 run with rmblastn version 2.13.0+
106 FamDB: CONS-Dfam_3.7