Input and runtime details for job 5882223 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation
188	0.008316	0.1556	b3406	greB	-8.11	0.146040	42 -- 55	52 -- 65	transcript cleavage factor	_____________41_____________56\n_____________\|______________\|\n5'-AUU...GUCAC______________AUGAA...UGA-3'\n______________CAGCUAAAUCUGGU\n______________\|\|\|\|:\|\|\|\|\|:\|:\|\n______________GUCGGUUUAGGCUA\n3'-AUU...UAUAA______________AUGCA...AUG-5'\n_____________\|______________\|\n_____________66_____________51\n	49 -- 55	52 -- 58	-18.5321 kcal/mol	4.27254 kcal/mol	6.17277 kcal/mol	41 56@LB@ \| \|@LB@5'-AUU...GUCAC AUGAA...UGA-3'@LB@ CAGCUAAAUCUGGU@LB@ \|\|\|\|:\|\|\|\|\|:\|:\|@LB@ GUCGGUUUAGGCUA@LB@3'-AUU...UAUAA AUGCA...AUG-5'@LB@ \| \|@LB@ 66 51@LB@@LB@@LB@Energy -8.11 kcal/mol@LB@Hybridization Energy -18.5321 kcal/mol@LB@Unfolding Energy - mRNA 4.27254 kcal/mol@LB@Unfolding Energy - sRNA 6.17277 kcal/mol@LB@@LB@Position - mRNA 42 -- 55@LB@Position - sRNA 52 -- 65@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 52 -- 58@LB@
104	0.003257	0.1101	b0858	ybjO	-8.07	0.149394	228 -- 257	2 -- 30	DUF2593 family inner membrane protein	_____________227______________________________258\n_____________\|________________________________\|\n5'-AUG...UUUUU____A__________C_____A__CU_G____AAUGU...UUA-3'\n______________AAGA___AACAUCUU_AUCUC_UG__C_CCUG\n______________\|\|\|\|___\|\|\|\|\|\|\|\|_\|:\|\|\|_\|\|__\|_\|\|\|:\n______________UUCU___UUGUAGAA_UGGAG_AC__G_GGAU\n3'-AUU...AGACU____AUC_________________AU______G-5'\n_____________\|________________________________\|\n_____________31_______________________________1\n	234 -- 240	16 -- 22	-20.5501 kcal/mol	4.45089 kcal/mol	8.05308 kcal/mol	227 258@LB@ \| \|@LB@5'-AUG...UUUUU A C A CU G AAUGU...UUA-3'@LB@ AAGA AACAUCUU AUCUC UG C CCUG@LB@ \|\|\|\| \|\|\|\|\|\|\|\| \|:\|\|\| \|\| \| \|\|\|:@LB@ UUCU UUGUAGAA UGGAG AC G GGAU@LB@3'-AUU...AGACU AUC AU G-5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -8.07 kcal/mol@LB@Hybridization Energy -20.5501 kcal/mol@LB@Unfolding Energy - mRNA 4.45089 kcal/mol@LB@Unfolding Energy - sRNA 8.05308 kcal/mol@LB@@LB@Position - mRNA 228 -- 257@LB@Position - sRNA 2 -- 30@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 16 -- 22@LB@
119	0.003968	0.1172	b2765	queD	-8.07	0.149030	164 -- 172	1 -- 9	6-pyruvoyl tetrahydrobiopterin synthase (PTPS)	_____________163_______173\n_____________\|_________\|\n5'-AAC...UUCCG_________GGCGG...AUU-3'\n______________GUACUCUAC\n______________\|\|\|\|:\|\|\|\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	166 -- 172	1 -- 7	-12.1088 kcal/mol	1.92954 kcal/mol	2.12872 kcal/mol	163 173@LB@ \| \|@LB@5'-AAC...UUCCG GGCGG...AUU-3'@LB@ GUACUCUAC@LB@ \|\|\|\|:\|\|\|\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.07 kcal/mol@LB@Hybridization Energy -12.1088 kcal/mol@LB@Unfolding Energy - mRNA 1.92954 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 164 -- 172@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 1 -- 7@LB@
198	0.008802	0.1558	b1905	ftnA	-8.07	0.149574	234 -- 260	3 -- 24	ferritin iron storage protein (cytoplasmic)	_____________233_________________________261\n_____________\|___________________________\|\n5'-CAU...UUAAU_____GA_GA____GGAA_________UCACU...AUC-3'\n______________GAGCA__U__ACCU____CUGUACUCU\n______________\|\|:\|\|__\|__\|\|\|\|____\|\|\|\|\|\|:\|\|\n______________CUUGU__A__UGGA____GACAUGGGA\n3'-AUU...UCUAU_____AG_A__________________UG-5'\n_____________\|___________________________\|\n_____________25__________________________2\n	254 -- 260	3 -- 9	-20.546 kcal/mol	4.48094 kcal/mol	8.02061 kcal/mol	233 261@LB@ \| \|@LB@5'-CAU...UUAAU GA GA GGAA UCACU...AUC-3'@LB@ GAGCA U ACCU CUGUACUCU@LB@ \|\|:\|\| \| \|\|\|\| \|\|\|\|\|\|:\|\|@LB@ CUUGU A UGGA GACAUGGGA@LB@3'-AUU...UCUAU AG A UG-5'@LB@ \| \|@LB@ 25 2@LB@@LB@@LB@Energy -8.07 kcal/mol@LB@Hybridization Energy -20.546 kcal/mol@LB@Unfolding Energy - mRNA 4.48094 kcal/mol@LB@Unfolding Energy - sRNA 8.02061 kcal/mol@LB@@LB@Position - mRNA 234 -- 260@LB@Position - sRNA 3 -- 24@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 3 -- 9@LB@
92	0.002567	0.09816	b4120	melB	-8.04	0.151444	195 -- 202	1 -- 8	melibiose:sodium symporter	_____________194______203\n_____________\|________\|\n5'-AUA...CCCGA________GAGCA...ACA-3'\n______________UACCCUAU\n______________\|\|\|\|\|\|\|:\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	196 -- 202	1 -- 7	-10.9179 kcal/mol	0.779946 kcal/mol	2.11603 kcal/mol	194 203@LB@ \| \|@LB@5'-AUA...CCCGA GAGCA...ACA-3'@LB@ UACCCUAU@LB@ \|\|\|\|\|\|\|:@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -8.04 kcal/mol@LB@Hybridization Energy -10.9179 kcal/mol@LB@Unfolding Energy - mRNA 0.779946 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 195 -- 202@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 1 -- 7@LB@
157	0.006279	0.1407	b0312	betB	-8.02	0.153308	1 -- 12	52 -- 63	betaine aldehyde dehydrogenase NAD-dependent	______________1___________13\n______________\|___________\|\n___________5'-____________GAGCG...ACG-3'\n______________GUCGAAUCUGGU\n______________\|:\|:\|\|\|\|:\|:\|\n______________CGGUUUAGGCUA\n3'-AUU...UAAGU____________AUGCA...AUG-5'\n_____________\|____________\|\n_____________64___________51\n	6 -- 12	52 -- 58	-15.0997 kcal/mol	0.969406 kcal/mol	6.13017 kcal/mol	1 13@LB@ \| \|@LB@ 5'- GAGCG...ACG-3'@LB@ GUCGAAUCUGGU@LB@ \|:\|:\|\|\|\|:\|:\|@LB@ CGGUUUAGGCUA@LB@3'-AUU...UAAGU AUGCA...AUG-5'@LB@ \| \|@LB@ 64 51@LB@@LB@@LB@Energy -8.02 kcal/mol@LB@Hybridization Energy -15.0997 kcal/mol@LB@Unfolding Energy - mRNA 0.969406 kcal/mol@LB@Unfolding Energy - sRNA 6.13017 kcal/mol@LB@@LB@Position - mRNA 1 -- 12@LB@Position - sRNA 52 -- 63@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 52 -- 58@LB@
174	0.007262	0.1466	b0473	htpG	-8.02	0.153160	10 -- 17	50 -- 57	protein refolding molecular co-chaperone Hsp90 Hsp70-dependent; heat-shock protein; ATPase	_____________9________18\n_____________\|________\|\n5'-UCA...GGCGU________GCGGC...GUG-3'\n______________UCCGGUUG\n______________\|\|\|\|:\|\|:\n______________AGGCUAAU\n3'-AUU...GGUUU________GCACU...AUG-5'\n_____________\|________\|\n_____________58_______49\n	11 -- 17	50 -- 56	-9.07782 kcal/mol	0.753256 kcal/mol	0.317388 kcal/mol	9 18@LB@ \| \|@LB@5'-UCA...GGCGU GCGGC...GUG-3'@LB@ UCCGGUUG@LB@ \|\|\|\|:\|\|:@LB@ AGGCUAAU@LB@3'-AUU...GGUUU GCACU...AUG-5'@LB@ \| \|@LB@ 58 49@LB@@LB@@LB@Energy -8.02 kcal/mol@LB@Hybridization Energy -9.07782 kcal/mol@LB@Unfolding Energy - mRNA 0.753256 kcal/mol@LB@Unfolding Energy - sRNA 0.317388 kcal/mol@LB@@LB@Position - mRNA 10 -- 17@LB@Position - sRNA 50 -- 57@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 50 -- 56@LB@
165	0.006672	0.1423	b1651	gloA	-7.94	0.160716	101 -- 108	49 -- 56	glyoxalase I Ni-dependent	_____________100______109\n_____________\|________\|\n5'-UGG...CUAUA________CCGAC...AAA-3'\n______________CCGAUUAC\n______________\|\|\|\|\|\|\|\|\n______________GGCUAAUG\n3'-AUU...GUUUA________CACUU...AUG-5'\n_____________\|________\|\n_____________57_______48\n	102 -- 108	49 -- 55	-10.6899 kcal/mol	2.44421 kcal/mol	0.317884 kcal/mol	100 109@LB@ \| \|@LB@5'-UGG...CUAUA CCGAC...AAA-3'@LB@ CCGAUUAC@LB@ \|\|\|\|\|\|\|\|@LB@ GGCUAAUG@LB@3'-AUU...GUUUA CACUU...AUG-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -7.94 kcal/mol@LB@Hybridization Energy -10.6899 kcal/mol@LB@Unfolding Energy - mRNA 2.44421 kcal/mol@LB@Unfolding Energy - sRNA 0.317884 kcal/mol@LB@@LB@Position - mRNA 101 -- 108@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 102 -- 108@LB@Position Seed - sRNA 49 -- 55@LB@
172	0.007198	0.1466	b2395	yfeA	-7.88	0.166321	272 -- 292	49 -- 69	putative diguanylate cyclase	_____________271____________________293\n_____________\|______________________\|\n5'-ACC...GUACU__________UC____UU____UUCGCCAC-3'\n______________UAUUCAGCUA___CCG__UUAU\n______________\|\|\|\|\|\|\|\|:\|___\|\|\|__\|\|\|:\n______________AUAAGUCGGU___GGC__AAUG\n3'-AUU...AUUUU__________UUA___U_____CACUU...AUG-5'\n_____________\|______________________\|\n_____________70_____________________48\n	275 -- 281	60 -- 66	-16.2546 kcal/mol	2.18624 kcal/mol	6.21499 kcal/mol	271 293@LB@ \| \|@LB@5'-ACC...GUACU UC UU UUCGCCAC-3'@LB@ UAUUCAGCUA CCG UUAU@LB@ \|\|\|\|\|\|\|\|:\| \|\|\| \|\|\|:@LB@ AUAAGUCGGU GGC AAUG@LB@3'-AUU...AUUUU UUA U CACUU...AUG-5'@LB@ \| \|@LB@ 70 48@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -16.2546 kcal/mol@LB@Unfolding Energy - mRNA 2.18624 kcal/mol@LB@Unfolding Energy - sRNA 6.21499 kcal/mol@LB@@LB@Position - mRNA 272 -- 292@LB@Position - sRNA 49 -- 69@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 60 -- 66@LB@
101	0.00315	0.1097	b1822	rlmA	-7.85	0.169074	182 -- 190	1 -- 9	23S rRNA m(1)G745 methyltransferase SAM-dependent	_____________181_______191\n_____________\|_________\|\n5'-AAG...CUUUA_________CGGAG...GGU-3'\n______________GUAUCCUGC\n______________\|\|\|:\|\|\|:\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	184 -- 190	1 -- 7	-13.1594 kcal/mol	3.20778 kcal/mol	2.12872 kcal/mol	181 191@LB@ \| \|@LB@5'-AAG...CUUUA CGGAG...GGU-3'@LB@ GUAUCCUGC@LB@ \|\|\|:\|\|\|:\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.85 kcal/mol@LB@Hybridization Energy -13.1594 kcal/mol@LB@Unfolding Energy - mRNA 3.20778 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 182 -- 190@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 1 -- 7@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

Job resubmission

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When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

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