annotate test-data/raw_output.txt @ 2:9c8ff1bdd041 draft default tip

"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda commit a9aa47b387ab4d4ee8628956aaea80d7aabca936"

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miranda v3.3a    microRNA Target Scanning Algorithm
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(c) 2003 Memorial Sloan-Kettering Cancer Center, New York

Authors: Anton Enright, Bino John, Chris Sander and Debora Marks
(mirnatargets (at) cbio.mskcc.org - reaches all authors)

Software written by: Anton Enright
Distributed for anyone to use under the GNU Public License (GPL),
See the files 'COPYING' and 'LICENSE' for details

If you use this software please cite:
Enright AJ, John B, Gaul U, Tuschl T, Sander C and Marks DS;
(2003) Genome Biology; 5(1):R1.

   miranda comes with ABSOLUTELY NO WARRANTY;
   This is free software, and you are welcome to redistribute it
   under certain conditions; type `miranda --license' for details.

Current Settings:
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Query Filename: 	/tmp/tmpCIUFbf/files/000/dataset_109.dat
Reference Filename:	/tmp/tmpCIUFbf/files/000/dataset_110.dat
Gap Open Penalty:	-9.000000
Gap Extend Penalty:	-4.000000
Score Threshold:	140.000000
Energy Threshold:	1.000000 kcal/mol
Scaling Parameter:	4.000000
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Read Sequence:gi|29565487|emb|AJ550546.1| Drosophila melanogaster microRNA miR-bantam(21 nt)
Read Sequence:gi|945100|gb|U31226.1|DMU31226 Drosophila melanogaster head involution defective protein (hid) mRNA, complete cds (3'UTR only)(3902 nt)
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Performing Scan: gi|29565487|emb|AJ550546.1| vs gi|945100|gb|U31226.1|DMU31226
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   Forward:	Score: 167.000000  Q:2 to 20  R:3340 to 3360 Align Len (18) (83.33%) (94.44%)

   Query:    3' gtCGAAAGTTTTACTAGAGTg 5'
                  |:||||| |||||||||: 
   Ref:      5' taGTTTTCACAATGATCTCGg 3'

   Energy:  -24.540001 kCal/Mol

Scores for this hit:
>gi|29565487|emb|AJ550546.1|	gi|945100|gb|U31226.1|DMU31226	167.00	-24.54	2 20	3340 3360	18	83.33%	94.44%


   Forward:	Score: 156.000000  Q:2 to 17  R:2505 to 2525 Align Len (15) (86.67%) (93.33%)

   Query:    3' gtcgaAAGTTTTACTAGAGTg 5'
                     |||||| ||:||||| 
   Ref:      5' tcataTTCAAATTGGTCTCAc 3'

   Energy:  -20.030001 kCal/Mol

Scores for this hit:
>gi|29565487|emb|AJ550546.1|	gi|945100|gb|U31226.1|DMU31226	156.00	-20.03	2 17	2505 2525	15	86.67%	93.33%


   Forward:	Score: 155.000000  Q:2 to 16  R:2852 to 2872 Align Len (14) (78.57%) (85.71%)

   Query:    3' gtcgaaAGTTTTACTAGAGTg 5'
                      ||: | |||||||| 
   Ref:      5' caaaaaTCGCATTGATCTCAt 3'

   Energy:  -14.570000 kCal/Mol

Scores for this hit:
>gi|29565487|emb|AJ550546.1|	gi|945100|gb|U31226.1|DMU31226	155.00	-14.57	2 16	2852 2872	14	78.57%	85.71%


   Forward:	Score: 152.000000  Q:2 to 18  R:3820 to 3841 Align Len (17) (76.47%) (76.47%)

   Query:    3' gtcgAAAGT-TTTACTAGAGTg 5'
                    | |||  | |||||||| 
   Ref:      5' taaaTATCATTATTGATCTCAt 3'

   Energy:  -14.180000 kCal/Mol

Scores for this hit:
>gi|29565487|emb|AJ550546.1|	gi|945100|gb|U31226.1|DMU31226	152.00	-14.18	2 18	3820 3841	17	76.47%	76.47%

Score for this Scan:
Seq1,Seq2,Tot Score,Tot Energy,Max Score,Max Energy,Strand,Len1,Len2,Positions
>>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
Complete

Scan Complete