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
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@
27	0.0002115	0.02687	b2607	trmD	-14.32	0.001383	229 -- 258	48 -- 75	tRNA m(1)G37 methyltransferase SAM-dependent	_____________228____________________________259\n_____________\|______________________________\|\n5'-UCG...GUUUC___________C__G___U_A_________GGGUA...UCC-3'\n______________CUGAAAUGUUC_GC_CAA_U_CCGAUUACG\n______________\|\|:\|\|\|\|:\|\|\|_\|\|_\|\|\|_\|_\|\|\|\|\|\|\|\|\|\n______________GAUUUUAUAAG_CG_GUU_A_GGCUAAUGC\n3'-AUU...CCGCC___________U______U___________ACUUC...AUG-5'\n_____________\|______________________________\|\n_____________76_____________________________47\n	252 -- 258	48 -- 54	-28.476 kcal/mol	6.50272 kcal/mol	7.67232 kcal/mol	228 259@LB@ \| \|@LB@5'-UCG...GUUUC C G U A GGGUA...UCC-3'@LB@ CUGAAAUGUUC GC CAA U CCGAUUACG@LB@ \|\|:\|\|\|\|:\|\|\| \|\| \|\|\| \| \|\|\|\|\|\|\|\|\|@LB@ GAUUUUAUAAG CG GUU A GGCUAAUGC@LB@3'-AUU...CCGCC U U ACUUC...AUG-5'@LB@ \| \|@LB@ 76 47@LB@@LB@@LB@Energy -14.32 kcal/mol@LB@Hybridization Energy -28.476 kcal/mol@LB@Unfolding Energy - mRNA 6.50272 kcal/mol@LB@Unfolding Energy - sRNA 7.67232 kcal/mol@LB@@LB@Position - mRNA 229 -- 258@LB@Position - sRNA 48 -- 75@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 48 -- 54@LB@
183	0.007903	0.1519	b2725	hycA	-8.51	0.115738	229 -- 236	49 -- 56	regulator of the transcriptional regulator FhlA	_____________228______237\n_____________\|________\|\n5'-UUA...GAAAG________AUCGC...AGG-3'\n______________CCGAUUAC\n______________\|\|\|\|\|\|\|\|\n______________GGCUAAUG\n3'-AUU...GUUUA________CACUU...AUG-5'\n_____________\|________\|\n_____________57_______48\n	230 -- 236	49 -- 55	-10.9203 kcal/mol	2.09518 kcal/mol	0.317884 kcal/mol	228 237@LB@ \| \|@LB@5'-UUA...GAAAG AUCGC...AGG-3'@LB@ CCGAUUAC@LB@ \|\|\|\|\|\|\|\|@LB@ GGCUAAUG@LB@3'-AUU...GUUUA CACUU...AUG-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -8.51 kcal/mol@LB@Hybridization Energy -10.9203 kcal/mol@LB@Unfolding Energy - mRNA 2.09518 kcal/mol@LB@Unfolding Energy - sRNA 0.317884 kcal/mol@LB@@LB@Position - mRNA 229 -- 236@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 49 -- 55@LB@
138	0.004994	0.127	b3633	waaA	-9.37	0.068643	230 -- 259	48 -- 75	3-deoxy-D-manno-octulosonic-acid transferase (KDO transferase)	_____________229____________________________260\n_____________\|______________________________\|\n5'-UCG...CUUCU___CCU__________CU_______A____GCUCU...AAC-3'\n______________CUA___UAUUCAGCCG__GAUCUGG_UACG\n______________\|\|\|___\|\|\|\|\|\|\|\|\|:__:\|\|\|:\|:_\|\|\|\|\n______________GAU___AUAAGUCGGU__UUAGGCU_AUGC\n3'-AUU...CCGCC___UUU___________________A____ACUUC...AUG-5'\n_____________\|______________________________\|\n_____________76_____________________________47\n	248 -- 254	53 -- 59	-25.3567 kcal/mol	8.33931 kcal/mol	7.67232 kcal/mol	229 260@LB@ \| \|@LB@5'-UCG...CUUCU CCU CU A GCUCU...AAC-3'@LB@ CUA UAUUCAGCCG GAUCUGG UACG@LB@ \|\|\| \|\|\|\|\|\|\|\|\|: :\|\|\|:\|: \|\|\|\|@LB@ GAU AUAAGUCGGU UUAGGCU AUGC@LB@3'-AUU...CCGCC UUU A ACUUC...AUG-5'@LB@ \| \|@LB@ 76 47@LB@@LB@@LB@Energy -9.37 kcal/mol@LB@Hybridization Energy -25.3567 kcal/mol@LB@Unfolding Energy - mRNA 8.33931 kcal/mol@LB@Unfolding Energy - sRNA 7.67232 kcal/mol@LB@@LB@Position - mRNA 230 -- 259@LB@Position - sRNA 48 -- 75@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 53 -- 59@LB@
78	0.001629	0.07345	b2624	alpA	-3.42	0.861549	231 -- 237	49 -- 55	CP4-57 prophage; DNA-binding transcriptional activator	_____________230_____238\n_____________\|_______\|\n5'-CGC...UACUA_______CAGCG...AAU-3'\n______________CGGUUAC\n______________\|\|:\|\|\|\|\n______________GCUAAUG\n3'-AUU...UUUAG_______CACUU...AUG-5'\n_____________\|_______\|\n_____________56______48\n	231 -- 237	49 -- 55	-7.04991 kcal/mol	3.33366 kcal/mol	0.311712 kcal/mol	230 238@LB@ \| \|@LB@5'-CGC...UACUA CAGCG...AAU-3'@LB@ CGGUUAC@LB@ \|\|:\|\|\|\|@LB@ GCUAAUG@LB@3'-AUU...UUUAG CACUU...AUG-5'@LB@ \| \|@LB@ 56 48@LB@@LB@@LB@Energy -3.42 kcal/mol@LB@Hybridization Energy -7.04991 kcal/mol@LB@Unfolding Energy - mRNA 3.33366 kcal/mol@LB@Unfolding Energy - sRNA 0.311712 kcal/mol@LB@@LB@Position - mRNA 231 -- 237@LB@Position - sRNA 49 -- 55@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 49 -- 55@LB@
134	0.004727	0.1241	b1655	mepH	-9.70	0.055155	231 -- 243	1 -- 13	murein DD-endopeptidase space-maker hydrolase	_____________230___________244\n_____________\|_____________\|\n5'-CGU...UCACG_____________UUUUU...AGA-3'\n______________CUCUGUGCUUUAC\n______________\|\|\|\|\|\|:\|::\|\|\|\n______________GAGACAUGGGAUG\n3'-AUU...GAAUG_____________-5'\n_____________\|____________\|\n_____________14___________1\n	237 -- 243	1 -- 7	-18.9465 kcal/mol	4.13106 kcal/mol	5.13393 kcal/mol	230 244@LB@ \| \|@LB@5'-CGU...UCACG UUUUU...AGA-3'@LB@ CUCUGUGCUUUAC@LB@ \|\|\|\|\|\|:\|::\|\|\|@LB@ GAGACAUGGGAUG@LB@3'-AUU...GAAUG -5'@LB@ \| \|@LB@ 14 1@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -18.9465 kcal/mol@LB@Unfolding Energy - mRNA 4.13106 kcal/mol@LB@Unfolding Energy - sRNA 5.13393 kcal/mol@LB@@LB@Position - mRNA 231 -- 243@LB@Position - sRNA 1 -- 13@LB@Position Seed - mRNA 237 -- 243@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@
6	1.448e-05	0.00754	b3863	polA	-11.40	0.016745	236 -- 262	1 -- 29	5' to 3' DNA polymerase and 3' to 5'/5' to 3' exonuclease	_____________235___________________________263\n_____________\|_____________________________\|\n5'-AGA...CUUGU______UU_________________GC__AUAUC...GCG-3'\n______________AGAUGG__CAUCUUAUCUU__UAUC__GC\n______________\|\|\|\|:\|__\|\|\|\|\|\|\|:\|\|:__\|\|:\|__:\|\n______________UCUAUC__GUAGAAUGGAG__AUGG__UG\n3'-AUU...GACUU______UU___________AC____GA__-5'\n_____________\|____________________________\|\n_____________30___________________________1\n	244 -- 250	15 -- 21	-25.0693 kcal/mol	5.64295 kcal/mol	8.05079 kcal/mol	235 263@LB@ \| \|@LB@5'-AGA...CUUGU UU GC AUAUC...GCG-3'@LB@ AGAUGG CAUCUUAUCUU UAUC GC@LB@ \|\|\|\|:\| \|\|\|\|\|\|\|:\|\|: \|\|:\| :\|@LB@ UCUAUC GUAGAAUGGAG AUGG UG@LB@3'-AUU...GACUU UU AC GA -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -11.40 kcal/mol@LB@Hybridization Energy -25.0693 kcal/mol@LB@Unfolding Energy - mRNA 5.64295 kcal/mol@LB@Unfolding Energy - sRNA 8.05079 kcal/mol@LB@@LB@Position - mRNA 236 -- 262@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 15 -- 21@LB@
97	0.002764	0.1002	b3935	priA	-7.71	0.181779	237 -- 247	3 -- 14	Primosome factor n' (replication factor Y)	_____________236__________248\n_____________\|____________\|\n5'-GAA...CGCUU____________UGACU...GCG-3'\n______________CCUC_GUACCUU\n______________\|\|\|\|_\|\|\|\|\|:\|\n______________GGAG_CAUGGGA\n3'-AUU...AGAAU____A_______UG-5'\n_____________\|____________\|\n_____________15___________2\n	241 -- 247	3 -- 9	-14.2439 kcal/mol	1.19768 kcal/mol	5.35591 kcal/mol	236 248@LB@ \| \|@LB@5'-GAA...CGCUU UGACU...GCG-3'@LB@ CCUC GUACCUU@LB@ \|\|\|\| \|\|\|\|\|:\|@LB@ GGAG CAUGGGA@LB@3'-AUU...AGAAU A UG-5'@LB@ \| \|@LB@ 15 2@LB@@LB@@LB@Energy -7.71 kcal/mol@LB@Hybridization Energy -14.2439 kcal/mol@LB@Unfolding Energy - mRNA 1.19768 kcal/mol@LB@Unfolding Energy - sRNA 5.35591 kcal/mol@LB@@LB@Position - mRNA 237 -- 247@LB@Position - sRNA 3 -- 14@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 3 -- 9@LB@
140	0.005114	0.1284	b3993	thiE	-7.64	0.188958	243 -- 250	4 -- 11	thiamine phosphate synthase (thiamine phosphate pyrophosphorylase)	_____________242______251\n_____________\|________\|\n5'-CAC...CAGGA________GGUGG...UAC-3'\n______________CUGUACCC\n______________\|\|\|\|\|\|\|\|\n______________GACAUGGG\n3'-AUU...AUGGA________AUG-5'\n_____________\|________\|\n_____________12_______3\n	244 -- 250	4 -- 10	-13.9053 kcal/mol	2.83489 kcal/mol	3.45361 kcal/mol	242 251@LB@ \| \|@LB@5'-CAC...CAGGA GGUGG...UAC-3'@LB@ CUGUACCC@LB@ \|\|\|\|\|\|\|\|@LB@ GACAUGGG@LB@3'-AUU...AUGGA AUG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -7.64 kcal/mol@LB@Hybridization Energy -13.9053 kcal/mol@LB@Unfolding Energy - mRNA 2.83489 kcal/mol@LB@Unfolding Energy - sRNA 3.45361 kcal/mol@LB@@LB@Position - mRNA 243 -- 250@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 4 -- 10@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)

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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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