Mercurial > repos > bgruening > repeat_masker
annotate test-data/small_dfam.fasta.stats @ 15:ba6d2c32f797 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker commit 7a5f368a5859e659aa36d0358bb96ca12574e2cc
| author | iuc |
|---|---|
| date | Mon, 24 Apr 2023 10:41:00 +0000 |
| parents | 7563ea7a922d |
| children |
| rev | line source |
|---|---|
|
10
bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
1 ================================================== |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
2 file name: rm_input.fasta |
|
bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
3 sequences: 1 |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
4 total length: 14220 bp (14220 bp excl N/X-runs) |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
5 GC level: 39.94 % |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
6 bases masked: 449 bp ( 3.16 %) |
|
bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
7 ================================================== |
|
bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
8 number of length percentage |
|
bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
9 elements* occupied of sequence |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
10 -------------------------------------------------- |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
11 SINEs: 0 0 bp 0.00 % |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
12 ALUs 0 0 bp 0.00 % |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
13 MIRs 0 0 bp 0.00 % |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
14 |
|
bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
15 LINEs: 1 71 bp 0.50 % |
|
bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
16 LINE1 0 0 bp 0.00 % |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
17 LINE2 1 71 bp 0.50 % |
|
bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
18 L3/CR1 0 0 bp 0.00 % |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
19 |
|
bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
20 LTR elements: 0 0 bp 0.00 % |
|
bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
21 ERVL 0 0 bp 0.00 % |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
22 ERVL-MaLRs 0 0 bp 0.00 % |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
23 ERV_classI 0 0 bp 0.00 % |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
24 ERV_classII 0 0 bp 0.00 % |
|
bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
25 |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
26 DNA elements: 0 0 bp 0.00 % |
|
bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
27 hAT-Charlie 0 0 bp 0.00 % |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
28 TcMar-Tigger 0 0 bp 0.00 % |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
29 |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
30 Unclassified: 0 0 bp 0.00 % |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
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31 |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
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32 Total interspersed repeats: 71 bp 0.50 % |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
33 |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
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34 |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
35 Small RNA: 0 0 bp 0.00 % |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
36 |
|
bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
37 Satellites: 0 0 bp 0.00 % |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
38 Simple repeats: 7 378 bp 2.66 % |
|
bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
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39 Low complexity: 0 0 bp 0.00 % |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
40 ================================================== |
|
bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
41 |
|
bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
42 * most repeats fragmented by insertions or deletions |
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bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
43 have been counted as one element |
|
bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
44 Runs of >=20 X/Ns in query were excluded in % calcs |
|
bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
45 |
|
bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
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46 |
|
bfc70c8cc5ca
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
iuc
parents:
diff
changeset
|
47 The query species was assumed to be human |
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14
7563ea7a922d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker commit 7a5f368a5859e659aa36d0358bb96ca12574e2cc
iuc
parents:
11
diff
changeset
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48 RepeatMasker version 4.1.5 , default mode |
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7563ea7a922d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker commit 7a5f368a5859e659aa36d0358bb96ca12574e2cc
iuc
parents:
11
diff
changeset
|
49 |
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7563ea7a922d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker commit 7a5f368a5859e659aa36d0358bb96ca12574e2cc
iuc
parents:
11
diff
changeset
|
50 run with rmblastn version 2.13.0+ |
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7563ea7a922d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker commit 7a5f368a5859e659aa36d0358bb96ca12574e2cc
iuc
parents:
11
diff
changeset
|
51 FamDB: CONS-Dfam_3.7 |