Mercurial > repos > bgruening > repeat_masker

annotate test-data/small.fasta.stats @ 4:04f5c3d7448e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit cbba6947f1380751e1db3fa5b043af630523fd86
author iuc
date Fri, 04 May 2018 07:59:50 -0400
parents bdfc22c1c3e3
children 438f65cb1d14
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
1 ==================================================
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
2 file name: dataset_12.dat
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
3 sequences: 1
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
4 total length: 14220 bp (14220 bp excl N/X-runs)
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
5 GC level: 39.94 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
6 bases masked: 378 bp ( 2.66 %)
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
7 ==================================================
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
8 number of length percentage
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
9 elements* occupied of sequence
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
10 --------------------------------------------------
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
11 SINEs: 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
12 ALUs 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
13 MIRs 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
14
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
15 LINEs: 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
16 LINE1 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
17 LINE2 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
18 L3/CR1 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
19
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
20 LTR elements: 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
21 ERVL 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
22 ERVL-MaLRs 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
23 ERV_classI 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
24 ERV_classII 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
25
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
26 DNA elements: 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
27 hAT-Charlie 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
28 TcMar-Tigger 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
29
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
30 Unclassified: 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
31
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
32 Total interspersed repeats: 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
33
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
34
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
35 Small RNA: 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
36
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
37 Satellites: 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
38 Simple repeats: 8 378 bp 2.66 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
39 Low complexity: 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
40 ==================================================
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
41
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
42 * most repeats fragmented by insertions or deletions
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
43 have been counted as one element
4
04f5c3d7448e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit cbba6947f1380751e1db3fa5b043af630523fd86
iuc
parents: 3
diff changeset
44 Runs of >=20 X/Ns in query were excluded in % calcs
04f5c3d7448e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit cbba6947f1380751e1db3fa5b043af630523fd86
iuc
parents: 3
diff changeset
45
3
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
46
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
47 The query species was assumed to be homo
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
48 RepeatMasker Combined Database: Dfam_Consensus-20170127
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
49
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
50 run with rmblastn version 2.2.27+
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
51 The query was compared to unclassified sequences in ".../dataset_2.dat"
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
52