Mercurial > repos > iuc > hmmer3
comparison test-data/MADE1.out @ 0:62479bdcc059 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
author | iuc |
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date | Tue, 12 May 2015 15:04:26 -0400 |
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1 # hmmscan :: search sequence(s) against a profile database | |
2 # HMMER 3.1b1 (May 2013); http://hmmer.org/ | |
3 # Copyright (C) 2013 Howard Hughes Medical Institute. | |
4 # Freely distributed under the GNU General Public License (GPLv3). | |
5 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | |
6 # query sequence file: test-data/dna_target.fa | |
7 # target HMM database: test-data/MADE1.hmm | |
8 # per-seq hits tabular output: t.tbl | |
9 # per-dom hits tabular output: t.domtbl | |
10 # pfam-style tabular hit output: t.pfamtbl | |
11 # max ASCII text line length: unlimited | |
12 # Vit filter P threshold: <= 0.001 | |
13 # Fwd filter P threshold: <= 1e-05 | |
14 # random number seed set to: 4 | |
15 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | |
16 | |
17 Query: humanchr1/239220001-239550000 [L=330000] | |
18 Scores for complete sequence (score includes all domains): | |
19 --- full sequence --- --- best 1 domain --- -#dom- | |
20 E-value score bias E-value score bias exp N Model Description | |
21 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- | |
22 7.1e-18 51.5 28.5 2e-12 34.0 0.7 9.6 5 MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon | |
23 | |
24 | |
25 Domain annotation for each model (and alignments): | |
26 >> MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon | |
27 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc | |
28 --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- | |
29 1 ? -4.3 0.1 1 1 30 54 .. 80044 80068 .. 80030 80073 .. 0.80 | |
30 2 ? -6.7 3.3 1 1 13 71 .. 154012 154072 .. 154011 154076 .. 0.75 | |
31 3 ! 27.6 0.7 2e-10 2e-10 1 44 [. 174456 174514 .. 174456 174577 .. 0.62 | |
32 4 ! 34.0 0.7 2e-12 2e-12 2 80 .] 302388 302466 .. 302387 302466 .. 0.86 | |
33 5 ? 2.8 0.7 0.011 0.011 27 75 .. 304060 304107 .. 304021 304109 .. 0.61 | |
34 | |
35 Alignments for each domain: | |
36 == domain 1 score: -4.3 bits; conditional E-value: 1 | |
37 xxxxxxxxxxxxxxxxxxxxxxxxx RF | |
38 MADE1 30 ttgccattacttttaatggcaaaaa 54 | |
39 t g catt ttt aatggcaaa a | |
40 humanchr1/239220001-239550000 80044 TAGTCATTCATTTCAATGGCAAATA 80068 | |
41 45789****************9966 PP | |
42 | |
43 == domain 2 score: -6.7 bits; conditional E-value: 1 | |
44 xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF | |
45 MADE1 13 aaaagtaattgcggtttttgccatt......acttttaatggcaaaaaccgcaattacttttgca 71 | |
46 aaaagta tt + ttttgc att a tttaa gcaaa a + tta tttgca | |
47 humanchr1/239220001-239550000 154012 AAAAGTAGTTTTCAATTTTGCAATTtgaccaATATTTAAATGCAAATATT----TTATATTTGCA 154072 | |
48 78999999999999999999999984444444457777777899998876....77777888876 PP | |
49 | |
50 == domain 3 score: 27.6 bits; conditional E-value: 2e-10 | |
51 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............x RF | |
52 MADE1 1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt...............a 44 | |
53 ttaggtt gtgcaaaagtaattg+ggtttttg cattactttt a | |
54 humanchr1/239220001-239550000 174456 TTAGGTTAGTGCAAAAGTAATTGTGGTTTTTGTCATTACTTTTctgcatgctagaagtA 174514 | |
55 79***************************************964443333333333330 PP | |
56 | |
57 == domain 4 score: 34.0 bits; conditional E-value: 2e-12 | |
58 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF | |
59 MADE1 2 taggttggtgcaaaagtaattgcggtttttgccattacttttaatggcaaaaaccgcaattacttttgcaccaacctaa 80 | |
60 t ggt ggtgcaaaa aattg+ggtttttgccatt cttttaat gc a + a t ctttt caccaa ctaa | |
61 humanchr1/239220001-239550000 302388 TTGGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCTTTTAAAAGTAATGCTTTTACACCAATCTAA 302466 | |
62 56899******************************************963333233345578**************997 PP | |
63 | |
64 == domain 5 score: 2.8 bits; conditional E-value: 0.011 | |
65 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF | |
66 MADE1 27 tttttgccattacttttaatggcaaaaaccgcaattacttttgcaccaa 75 | |
67 tttt g c ta tt a tgg aaaaa ++ca tta ttttgca aa | |
68 humanchr1/239220001-239550000 304060 TTTTAGACTATA-GTTAAGTGGGAAAAAATACACTTATTTTTGCATTAA 304107 | |
69 222222222222.3455779************************98765 PP | |
70 | |
71 | |
72 | |
73 Internal pipeline statistics summary: | |
74 ------------------------------------- | |
75 Query sequence(s): 1 (330000 residues searched) | |
76 Target model(s): 1 (80 nodes) | |
77 Passed MSV filter: 1 (1); expected 0.0 (0.02) | |
78 Passed bias filter: 1 (1); expected 0.0 (0.02) | |
79 Passed Vit filter: 1 (1); expected 0.0 (0.001) | |
80 Passed Fwd filter: 1 (1); expected 0.0 (1e-05) | |
81 Initial search space (Z): 1 [actual number of targets] | |
82 Domain search space (domZ): 1 [number of targets reported over threshold] | |
83 # CPU time: 0.52u 0.03s 00:00:00.55 Elapsed: 00:00:00.54 | |
84 # Mc/sec: 48.89 | |
85 // | |
86 [ok] |