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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
author earlhaminst
date Fri, 11 Nov 2016 07:03:25 -0500
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3 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
4 miranda v3.3a microRNA Target Scanning Algorithm
5 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
6 (c) 2003 Memorial Sloan-Kettering Cancer Center, New York
7
8 Authors: Anton Enright, Bino John, Chris Sander and Debora Marks
9 (mirnatargets (at) cbio.mskcc.org - reaches all authors)
10
11 Software written by: Anton Enright
12 Distributed for anyone to use under the GNU Public License (GPL),
13 See the files 'COPYING' and 'LICENSE' for details
14
15 If you use this software please cite:
16 Enright AJ, John B, Gaul U, Tuschl T, Sander C and Marks DS;
17 (2003) Genome Biology; 5(1):R1.
18
19 miranda comes with ABSOLUTELY NO WARRANTY;
20 This is free software, and you are welcome to redistribute it
21 under certain conditions; type `miranda --license' for details.
22
23 Current Settings:
24 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
25 Query Filename: /tmp/tmpCIUFbf/files/000/dataset_109.dat
26 Reference Filename: /tmp/tmpCIUFbf/files/000/dataset_110.dat
27 Gap Open Penalty: -9.000000
28 Gap Extend Penalty: -4.000000
29 Score Threshold: 140.000000
30 Energy Threshold: 1.000000 kcal/mol
31 Scaling Parameter: 4.000000
32 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
33 Read Sequence:gi|29565487|emb|AJ550546.1| Drosophila melanogaster microRNA miR-bantam(21 nt)
34 Read Sequence:gi|945100|gb|U31226.1|DMU31226 Drosophila melanogaster head involution defective protein (hid) mRNA, complete cds (3'UTR only)(3902 nt)
35 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
36 Performing Scan: gi|29565487|emb|AJ550546.1| vs gi|945100|gb|U31226.1|DMU31226
37 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
38
39 Forward: Score: 167.000000 Q:2 to 20 R:3340 to 3360 Align Len (18) (83.33%) (94.44%)
40
41 Query: 3' gtCGAAAGTTTTACTAGAGTg 5'
42 |:||||| |||||||||:
43 Ref: 5' taGTTTTCACAATGATCTCGg 3'
44
45 Energy: -24.540001 kCal/Mol
46
47 Scores for this hit:
48 >gi|29565487|emb|AJ550546.1| gi|945100|gb|U31226.1|DMU31226 167.00 -24.54 2 20 3340 3360 18 83.33% 94.44%
49
50
51 Forward: Score: 156.000000 Q:2 to 17 R:2505 to 2525 Align Len (15) (86.67%) (93.33%)
52
53 Query: 3' gtcgaAAGTTTTACTAGAGTg 5'
54 |||||| ||:|||||
55 Ref: 5' tcataTTCAAATTGGTCTCAc 3'
56
57 Energy: -20.030001 kCal/Mol
58
59 Scores for this hit:
60 >gi|29565487|emb|AJ550546.1| gi|945100|gb|U31226.1|DMU31226 156.00 -20.03 2 17 2505 2525 15 86.67% 93.33%
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62
63 Forward: Score: 155.000000 Q:2 to 16 R:2852 to 2872 Align Len (14) (78.57%) (85.71%)
64
65 Query: 3' gtcgaaAGTTTTACTAGAGTg 5'
66 ||: | ||||||||
67 Ref: 5' caaaaaTCGCATTGATCTCAt 3'
68
69 Energy: -14.570000 kCal/Mol
70
71 Scores for this hit:
72 >gi|29565487|emb|AJ550546.1| gi|945100|gb|U31226.1|DMU31226 155.00 -14.57 2 16 2852 2872 14 78.57% 85.71%
73
74
75 Forward: Score: 152.000000 Q:2 to 18 R:3820 to 3841 Align Len (17) (76.47%) (76.47%)
76
77 Query: 3' gtcgAAAGT-TTTACTAGAGTg 5'
78 | ||| | ||||||||
79 Ref: 5' taaaTATCATTATTGATCTCAt 3'
80
81 Energy: -14.180000 kCal/Mol
82
83 Scores for this hit:
84 >gi|29565487|emb|AJ550546.1| gi|945100|gb|U31226.1|DMU31226 152.00 -14.18 2 18 3820 3841 17 76.47% 76.47%
85
86 Score for this Scan:
87 Seq1,Seq2,Tot Score,Tot Energy,Max Score,Max Energy,Strand,Len1,Len2,Positions
88 >>gi|29565487|emb|AJ550546.1| gi|945100|gb|U31226.1|DMU31226 630.00 -73.32 167.00 -24.54 1 21 3902 3340 2505 2852 3820
89 Complete
90
91 Scan Complete
92