Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
65	0.001098	0.05953	b1479	maeA	-10.62	0.077885	180 -- 205	37 -- 65	malate dehydrogenase decarboxylating NAD-requiring; malic enzyme	_____________179___________________________206\n_____________\|_____________________________\|\n5'-UAG...UGGAU_______________________C_____ACCAA...GCA-3'\n______________AUUCAAAAAAG__AGUGAG_UGA_AUGGA\n______________\|\|\|\|\|\|\|\|\|\|\|__\|\|\|:\|\|_::\|_\|\|\|\|\|\n______________UAAGUUUUUUC__UCAUUC_GUU_UACCU\n3'-UUU...GUCAU___________CU______U___A_____CGCGU...ACG-5'\n_____________\|_____________________________\|\n_____________66____________________________36\n	184 -- 190	55 -- 61	-21.4117 kcal/mol	4.89609 kcal/mol	5.88101 kcal/mol	179 206@LB@ \| \|@LB@5'-UAG...UGGAU C ACCAA...GCA-3'@LB@ AUUCAAAAAAG AGUGAG UGA AUGGA@LB@ \|\|\|\|\|\|\|\|\|\|\| \|\|\|:\|\| ::\| \|\|\|\|\|@LB@ UAAGUUUUUUC UCAUUC GUU UACCU@LB@3'-UUU...GUCAU CU U A CGCGU...ACG-5'@LB@ \| \|@LB@ 66 36@LB@@LB@@LB@Energy -10.62 kcal/mol@LB@Hybridization Energy -21.4117 kcal/mol@LB@Unfolding Energy - mRNA 4.89609 kcal/mol@LB@Unfolding Energy - sRNA 5.88101 kcal/mol@LB@@LB@Position - mRNA 180 -- 205@LB@Position - sRNA 37 -- 65@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 55 -- 61@LB@
163	0.006379	0.1377	b2210	mqo	-11.85	0.037664	161 -- 168	1 -- 8	malate dehydrogenase FAD/NAD(P)-binding domain	_____________160______169\n_____________\|________\|\n5'-GGC...AAAUC________AAUAA...AUG-3'\n______________UCACCUGC\n______________\|\|\|\|\|\|\|\|\n______________AGUGGACG\n3'-UUU...ACGUA________-5'\n_____________\|_______\|\n_____________9_______1\n	162 -- 168	1 -- 7	-15.6271 kcal/mol	1.41654 kcal/mol	2.36381 kcal/mol	160 169@LB@ \| \|@LB@5'-GGC...AAAUC AAUAA...AUG-3'@LB@ UCACCUGC@LB@ \|\|\|\|\|\|\|\|@LB@ AGUGGACG@LB@3'-UUU...ACGUA -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -11.85 kcal/mol@LB@Hybridization Energy -15.6271 kcal/mol@LB@Unfolding Energy - mRNA 1.41654 kcal/mol@LB@Unfolding Energy - sRNA 2.36381 kcal/mol@LB@@LB@Position - mRNA 161 -- 168@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 1 -- 7@LB@
68	0.001184	0.06134	b3188	sfsB	-9.82	0.121108	186 -- 205	37 -- 57	malPQ operon transcriptional activator	_____________185___________________206\n_____________\|_____________________\|\n5'-CGG...AACUU____________AAAA_____AAGUA...UGA-3'\n______________AAGG_AGUGAGG____AUGGA\n______________\|\|\|\|_\|\|\|:\|\|:____\|\|\|\|\|\n______________UUCC_UCAUUCU____UACCU\n3'-UUU...GUUUU____U_______GUUA_____CGCGU...ACG-5'\n_____________\|_____________________\|\n_____________58____________________36\n	190 -- 196	46 -- 52	-17.294 kcal/mol	3.7439 kcal/mol	3.68958 kcal/mol	185 206@LB@ \| \|@LB@5'-CGG...AACUU AAAA AAGUA...UGA-3'@LB@ AAGG AGUGAGG AUGGA@LB@ \|\|\|\| \|\|\|:\|\|: \|\|\|\|\|@LB@ UUCC UCAUUCU UACCU@LB@3'-UUU...GUUUU U GUUA CGCGU...ACG-5'@LB@ \| \|@LB@ 58 36@LB@@LB@@LB@Energy -9.82 kcal/mol@LB@Hybridization Energy -17.294 kcal/mol@LB@Unfolding Energy - mRNA 3.7439 kcal/mol@LB@Unfolding Energy - sRNA 3.68958 kcal/mol@LB@@LB@Position - mRNA 186 -- 205@LB@Position - sRNA 37 -- 57@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 46 -- 52@LB@
45	0.0004696	0.03623	b4035	malK	-9.83	0.120497	188 -- 201	44 -- 57	maltose ABC transportor ATPase	_____________187____________202\n_____________\|______________\|\n5'-CGC...UUACA_______A______UGGCG...UGU-3'\n______________AAGGGAG_AGGGCA\n______________\|\|\|\|:\|\|_\|:\|:\|\|\n______________UUCCUUC_UUCUGU\n3'-UUU...GUUUU_______A______UAUAC...ACG-5'\n_____________\|______________\|\n_____________58_____________43\n	188 -- 194	51 -- 57	-14.5332 kcal/mol	2.95068 kcal/mol	1.74831 kcal/mol	187 202@LB@ \| \|@LB@5'-CGC...UUACA A UGGCG...UGU-3'@LB@ AAGGGAG AGGGCA@LB@ \|\|\|\|:\|\| \|:\|:\|\|@LB@ UUCCUUC UUCUGU@LB@3'-UUU...GUUUU A UAUAC...ACG-5'@LB@ \| \|@LB@ 58 43@LB@@LB@@LB@Energy -9.83 kcal/mol@LB@Hybridization Energy -14.5332 kcal/mol@LB@Unfolding Energy - mRNA 2.95068 kcal/mol@LB@Unfolding Energy - sRNA 1.74831 kcal/mol@LB@@LB@Position - mRNA 188 -- 201@LB@Position - sRNA 44 -- 57@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 51 -- 57@LB@
146	0.005657	0.1365	b4322	uxuA	-7.47	0.371307	180 -- 195	52 -- 75	mannonate hydrolase	_____________179______________________196\n_____________\|________________________\|\n5'-CAU...ACCCA________________________AAAUC...AUA-3'\n______________CUAUGU________GAAAGAGGAA\n______________\|\|\|\|\|:________:\|\|\|:\|\|\|\|\|\n______________GAUACG________UUUUUUCCUU\n3'-UUU...AACAC______UCAUUAAG__________CAUUC...ACG-5'\n_____________\|________________________\|\n_____________76_______________________51\n	189 -- 195	52 -- 58	-13.8583 kcal/mol	2.68591 kcal/mol	3.70263 kcal/mol	179 196@LB@ \| \|@LB@5'-CAU...ACCCA AAAUC...AUA-3'@LB@ CUAUGU GAAAGAGGAA@LB@ \|\|\|\|\|: :\|\|\|:\|\|\|\|\|@LB@ GAUACG UUUUUUCCUU@LB@3'-UUU...AACAC UCAUUAAG CAUUC...ACG-5'@LB@ \| \|@LB@ 76 51@LB@@LB@@LB@Energy -7.47 kcal/mol@LB@Hybridization Energy -13.8583 kcal/mol@LB@Unfolding Energy - mRNA 2.68591 kcal/mol@LB@Unfolding Energy - sRNA 3.70263 kcal/mol@LB@@LB@Position - mRNA 180 -- 195@LB@Position - sRNA 52 -- 75@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 52 -- 58@LB@
162	0.006351	0.1377	b1869	yecN	-10.06	0.106335	266 -- 273	1 -- 8	MAPEG family inner membrane protein	_____________265______274\n_____________\|________\|\n5'-UCA...GUCGU________GAAUG...GCG-3'\n______________UCGCCUGC\n______________\|\|:\|\|\|\|\|\n______________AGUGGACG\n3'-UUU...ACGUA________-5'\n_____________\|_______\|\n_____________9_______1\n	267 -- 273	1 -- 7	-14.5941 kcal/mol	2.17055 kcal/mol	2.36381 kcal/mol	265 274@LB@ \| \|@LB@5'-UCA...GUCGU GAAUG...GCG-3'@LB@ UCGCCUGC@LB@ \|\|:\|\|\|\|\|@LB@ AGUGGACG@LB@3'-UUU...ACGUA -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -10.06 kcal/mol@LB@Hybridization Energy -14.5941 kcal/mol@LB@Unfolding Energy - mRNA 2.17055 kcal/mol@LB@Unfolding Energy - sRNA 2.36381 kcal/mol@LB@@LB@Position - mRNA 266 -- 273@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 1 -- 7@LB@
140	0.005308	0.1336	b0055	djlA	-7.67	0.341620	49 -- 94	41 -- 89	membrane-anchored DnaK co-chaperone DNA-binding protein	_____________48_________________________________________________95\n_____________\|__________________________________________________\|\n5'-GAC...GAAUA__________G______G___C_GC___G__U__C_______U_______CAAAU...UUG-3'\n______________GCG__UCAGU_GUGUUA_GCA_G__AUU_AA_GA___AGGUA_GAUAAUG\n______________:\|\|__\|\|\|:\|_\|\|\|:\|\|_\|\|\|_\|__\|\|\|_\|\|_:\|___\|:\|\|\|_\|\|:\|\|\|:\n______________UGC__AGUUA_CACGAU_CGU_C__UAA_UU_UU___UUCAU_CUGUUAU\n3'-UUU...CAGCA___UU_____A______A_____AU___G__U__UCC_____U_______ACCUC...ACG-5'\n_____________\|__________________________________________________\|\n_____________90_________________________________________________40\n	88 -- 94	41 -- 47	-26.3807 kcal/mol	12.8315 kcal/mol	5.88014 kcal/mol	48 95@LB@ \| \|@LB@5'-GAC...GAAUA G G C GC G U C U CAAAU...UUG-3'@LB@ GCG UCAGU GUGUUA GCA G AUU AA GA AGGUA GAUAAUG@LB@ :\|\| \|\|\|:\| \|\|\|:\|\| \|\|\| \| \|\|\| \|\| :\| \|:\|\|\| \|\|:\|\|\|:@LB@ UGC AGUUA CACGAU CGU C UAA UU UU UUCAU CUGUUAU@LB@3'-UUU...CAGCA UU A A AU G U UCC U ACCUC...ACG-5'@LB@ \| \|@LB@ 90 40@LB@@LB@@LB@Energy -7.67 kcal/mol@LB@Hybridization Energy -26.3807 kcal/mol@LB@Unfolding Energy - mRNA 12.8315 kcal/mol@LB@Unfolding Energy - sRNA 5.88014 kcal/mol@LB@@LB@Position - mRNA 49 -- 94@LB@Position - sRNA 41 -- 89@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 41 -- 47@LB@
152	0.005935	0.1368	b2701	mltB	-9.57	0.138424	83 -- 107	69 -- 92	membrane-bound lytic murein transglycosylase B	_____________82________________________108\n_____________\|_________________________\|\n5'-AGA...GAUAG__AG_G____G_____A________AAGUC...GAA-3'\n______________CG__G_GAAU_AGUUG_GUUAUGUA\n______________\|\|__:_\|\|\|\|_\|:\|\|\|_\|:\|\|\|\|:\|\n______________GC__U_CUUA_UUAAC_CGAUACGU\n3'-UUU...CCGCA__A__G____G_____A________CAUUA...ACG-5'\n_____________\|_________________________\|\n_____________93________________________68\n	101 -- 107	69 -- 75	-19.8359 kcal/mol	5.60429 kcal/mol	4.66371 kcal/mol	82 108@LB@ \| \|@LB@5'-AGA...GAUAG AG G G A AAGUC...GAA-3'@LB@ CG G GAAU AGUUG GUUAUGUA@LB@ \|\| : \|\|\|\| \|:\|\|\| \|:\|\|\|\|:\|@LB@ GC U CUUA UUAAC CGAUACGU@LB@3'-UUU...CCGCA A G G A CAUUA...ACG-5'@LB@ \| \|@LB@ 93 68@LB@@LB@@LB@Energy -9.57 kcal/mol@LB@Hybridization Energy -19.8359 kcal/mol@LB@Unfolding Energy - mRNA 5.60429 kcal/mol@LB@Unfolding Energy - sRNA 4.66371 kcal/mol@LB@@LB@Position - mRNA 83 -- 107@LB@Position - sRNA 69 -- 92@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 69 -- 75@LB@
115	0.003699	0.1133	b3343	tusB	-8.43	0.243717	216 -- 222	20 -- 26	mnm(5)-s(2)U34-tRNA synthesis 2-thiolation protein	_____________215_____223\n_____________\|_______\|\n5'-GCU...CAUUA_______CACCC...GCG-3'\n______________CAUCGCU\n______________\|\|\|\|\|\|\|\n______________GUAGCGA\n3'-UUU...UGCGG_______ACUGC...ACG-5'\n_____________\|_______\|\n_____________27______19\n	216 -- 222	20 -- 26	-9.55221 kcal/mol	1.0434 kcal/mol	0.0768517 kcal/mol	215 223@LB@ \| \|@LB@5'-GCU...CAUUA CACCC...GCG-3'@LB@ CAUCGCU@LB@ \|\|\|\|\|\|\|@LB@ GUAGCGA@LB@3'-UUU...UGCGG ACUGC...ACG-5'@LB@ \| \|@LB@ 27 19@LB@@LB@@LB@Energy -8.43 kcal/mol@LB@Hybridization Energy -9.55221 kcal/mol@LB@Unfolding Energy - mRNA 1.0434 kcal/mol@LB@Unfolding Energy - sRNA 0.0768517 kcal/mol@LB@@LB@Position - mRNA 216 -- 222@LB@Position - sRNA 20 -- 26@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 20 -- 26@LB@
13	2.167e-05	0.005627	b0123	cueO	-18.83	0.000188	100 -- 180	1 -- 93	multicopper oxidase (laccase)	_____________99__________________________________________________________________________________________________181\n_____________\|___________________________________________________________________________________________________\|\n5'-CUG...CAUUA________UUA________C______CU___CC___CCGU_______________U___________________A________U______________UUAAG...CGU-3'\n______________UUGU_CGA___AAUUGUGU__UGCGG__UGA__UUC____AAGGGGAAG___GAC_____________AUGCUCA_CGUUUGAU_UUGU_UUCGCCUGC\n______________\|:\|\|_\|\|\|___\|\|\|\|\|\|\|:__\|\|\|:\|__\|:\|__\|\|\|____\|\|::\|\|\|\|\|___\|\|\|_____________\|:\|\|:\|\|_\|\|:\|\|\|\|:_\|\|\|:_\|\|\|:\|\|\|\|\|\n______________AGCA_GCU___UUAACACG__ACGUC__AUU__AAG____UUUUCCUUC___CUG_____________UGCGGGU_GCGAACUG_AACG_AAGUGGACG\n3'-UUU...GCCGC____U___UAG________AU_______________UU___________AUU___UUAUACCUCGCGU_______A________C____U_________-5'\n_____________\|__________________________________________________________________________________________________\|\n_____________94_________________________________________________________________________________________________1\n	174 -- 180	1 -- 7	-64.9216 kcal/mol	25.1682 kcal/mol	20.925 kcal/mol	99 181@LB@ \| \|@LB@5'-CUG...CAUUA UUA C CU CC CCGU U A U UUAAG...CGU-3'@LB@ UUGU CGA AAUUGUGU UGCGG UGA UUC AAGGGGAAG GAC AUGCUCA CGUUUGAU UUGU UUCGCCUGC@LB@ \|:\|\| \|\|\| \|\|\|\|\|\|\|: \|\|\|:\| \|:\| \|\|\| \|\|::\|\|\|\|\| \|\|\| \|:\|\|:\|\| \|\|:\|\|\|\|: \|\|\|: \|\|\|:\|\|\|\|\|@LB@ AGCA GCU UUAACACG ACGUC AUU AAG UUUUCCUUC CUG UGCGGGU GCGAACUG AACG AAGUGGACG@LB@3'-UUU...GCCGC U UAG AU UU AUU UUAUACCUCGCGU A C U -5'@LB@ \| \|@LB@ 94 1@LB@@LB@@LB@Energy -18.83 kcal/mol@LB@Hybridization Energy -64.9216 kcal/mol@LB@Unfolding Energy - mRNA 25.1682 kcal/mol@LB@Unfolding Energy - sRNA 20.925 kcal/mol@LB@@LB@Position - mRNA 100 -- 180@LB@Position - sRNA 1 -- 93@LB@Position Seed - mRNA 174 -- 180@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)

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service.

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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