Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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
34	0.003032	0.2776	b3928	zapB	-12.77	0.066459	230 -- 240	51 -- 61	FtsZ stabilizer septal ring assembly factor cell division stimulator	_____________229_________241\n_____________\|___________\|\n5'-UUU...GAGAA___________AAGUA...AAG-3'\n______________ACUGGAAGCAA\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________UGACCUUCGUU\n3'-UUU...CAUUA___________ACACU...GCG-5'\n_____________\|___________\|\n_____________62__________50\n	234 -- 240	51 -- 57	-17.959 kcal/mol	2.30162 kcal/mol	2.8896 kcal/mol	229 241@LB@ \| \|@LB@5'-UUU...GAGAA AAGUA...AAG-3'@LB@ ACUGGAAGCAA@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ UGACCUUCGUU@LB@3'-UUU...CAUUA ACACU...GCG-5'@LB@ \| \|@LB@ 62 50@LB@@LB@@LB@Energy -12.77 kcal/mol@LB@Hybridization Energy -17.959 kcal/mol@LB@Unfolding Energy - mRNA 2.30162 kcal/mol@LB@Unfolding Energy - sRNA 2.8896 kcal/mol@LB@@LB@Position - mRNA 230 -- 240@LB@Position - sRNA 51 -- 61@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 51 -- 57@LB@
18	0.001289	0.2406	b3930	menA	-10.08	0.182848	73 -- 82	42 -- 51	1 4-dihydroxy-2-naphthoate octaprenyltransferase	_____________72_________83\n_____________\|__________\|\n5'-AGC...AGAUU__________ACAUC...CGC-3'\n______________AUGUGAGCAA\n______________\|\|\|\|\|\|\|\|\|\|\n______________UACACUCGUU\n3'-UUU...UUCGU__________ACAGC...GCG-5'\n_____________\|__________\|\n_____________52_________41\n	76 -- 82	42 -- 48	-14.1762 kcal/mol	2.92742 kcal/mol	1.16834 kcal/mol	72 83@LB@ \| \|@LB@5'-AGC...AGAUU ACAUC...CGC-3'@LB@ AUGUGAGCAA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UACACUCGUU@LB@3'-UUU...UUCGU ACAGC...GCG-5'@LB@ \| \|@LB@ 52 41@LB@@LB@@LB@Energy -10.08 kcal/mol@LB@Hybridization Energy -14.1762 kcal/mol@LB@Unfolding Energy - mRNA 2.92742 kcal/mol@LB@Unfolding Energy - sRNA 1.16834 kcal/mol@LB@@LB@Position - mRNA 73 -- 82@LB@Position - sRNA 42 -- 51@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 42 -- 48@LB@
12	0.0007887	0.2153	b3981	secE	-14.50	0.033700	225 -- 262	36 -- 90	preprotein translocase membrane subunit	_____________224_____________________________________________________263\n_____________\|_______________________________________________________\|\n5'-UAA...CUCAA______G___________________________________A____________UGUGG...ACU-3'\n______________GGAAGC_GGCGC__GGC_____________CUGGAAGCGAUG__AGUGG_GUCGU\n______________::\|\|\|\|_:\|\|:\|__\|\|\|_____________\|\|\|\|\|\|\|\|:\|\|\|__\|\|:::_\|\|\|\|\|\n______________UUUUCG_UCGUG__CCG_____________GACCUUCGUUAC__UCGUU_CAGCA\n___________3'-______G_____GG___ACCGAUUCAUUAU____________AC_____A_____CGAAA...GCG-5'\n______________\|______________________________________________________\|\n______________90_____________________________________________________35\n	245 -- 251	49 -- 55	-44.4001 kcal/mol	14.9847 kcal/mol	14.9108 kcal/mol	224 263@LB@ \| \|@LB@5'-UAA...CUCAA G A UGUGG...ACU-3'@LB@ GGAAGC GGCGC GGC CUGGAAGCGAUG AGUGG GUCGU@LB@ ::\|\|\|\| :\|\|:\| \|\|\| \|\|\|\|\|\|\|\|:\|\|\| \|\|::: \|\|\|\|\|@LB@ UUUUCG UCGUG CCG GACCUUCGUUAC UCGUU CAGCA@LB@ 3'- G GG ACCGAUUCAUUAU AC A CGAAA...GCG-5'@LB@ \| \|@LB@ 90 35@LB@@LB@@LB@Energy -14.50 kcal/mol@LB@Hybridization Energy -44.4001 kcal/mol@LB@Unfolding Energy - mRNA 14.9847 kcal/mol@LB@Unfolding Energy - sRNA 14.9108 kcal/mol@LB@@LB@Position - mRNA 225 -- 262@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 49 -- 55@LB@
186	0.02299	0.4113	b3996	nudC	-11.58	0.104830	175 -- 203	40 -- 67	NADH pyrophosphatase	_____________174____________________________204\n_____________\|______________________________\|\n5'-GAU...AUGCC________AA_________CAA____U___GAUCG...CGG-3'\n______________AGUGAUGC___AGGUAGUG___GAGC_AUG\n______________\|\|\|:\|\|:\|___\|:\|:\|:\|\|___\|\|\|\|_\|\|\|\n______________UCAUUAUG___UUCGUUAC___CUCG_UAC\n3'-UUU...CCGAU________ACC________A______U___AGCAC...GCG-5'\n_____________\|______________________________\|\n_____________68_____________________________39\n	186 -- 192	49 -- 55	-21.6638 kcal/mol	6.77954 kcal/mol	3.30504 kcal/mol	174 204@LB@ \| \|@LB@5'-GAU...AUGCC AA CAA U GAUCG...CGG-3'@LB@ AGUGAUGC AGGUAGUG GAGC AUG@LB@ \|\|\|:\|\|:\| \|:\|:\|:\|\| \|\|\|\| \|\|\|@LB@ UCAUUAUG UUCGUUAC CUCG UAC@LB@3'-UUU...CCGAU ACC A U AGCAC...GCG-5'@LB@ \| \|@LB@ 68 39@LB@@LB@@LB@Energy -11.58 kcal/mol@LB@Hybridization Energy -21.6638 kcal/mol@LB@Unfolding Energy - mRNA 6.77954 kcal/mol@LB@Unfolding Energy - sRNA 3.30504 kcal/mol@LB@@LB@Position - mRNA 175 -- 203@LB@Position - sRNA 40 -- 67@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 49 -- 55@LB@
8	0.0004259	0.161	b4019	metH	-17.34	0.010954	191 -- 208	42 -- 58	homocysteine-N5-methyltetrahydrofolate transmethylase B12-dependent	_____________190________________209\n_____________\|__________________\|\n5'-UGA...GUGUC______A___________CAAAG...ACG-3'\n______________GGGAGC_AGUGUGAGCAG\n______________\|\|:\|\|\|_\|:\|\|\|\|\|\|\|\|:\n______________CCUUCG_UUACACUCGUU\n3'-UUU...UAUGA__________________ACAGC...GCG-5'\n_____________\|__________________\|\n_____________59_________________41\n	202 -- 208	42 -- 48	-25.1819 kcal/mol	4.63502 kcal/mol	3.2101 kcal/mol	190 209@LB@ \| \|@LB@5'-UGA...GUGUC A CAAAG...ACG-3'@LB@ GGGAGC AGUGUGAGCAG@LB@ \|\|:\|\|\| \|:\|\|\|\|\|\|\|\|:@LB@ CCUUCG UUACACUCGUU@LB@3'-UUU...UAUGA ACAGC...GCG-5'@LB@ \| \|@LB@ 59 41@LB@@LB@@LB@Energy -17.34 kcal/mol@LB@Hybridization Energy -25.1819 kcal/mol@LB@Unfolding Energy - mRNA 4.63502 kcal/mol@LB@Unfolding Energy - sRNA 3.2101 kcal/mol@LB@@LB@Position - mRNA 191 -- 208@LB@Position - sRNA 42 -- 58@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 42 -- 48@LB@
140	0.01604	0.3851	b4022	rluF	-13.68	0.046602	82 -- 103	39 -- 60	23S rRNA pseudouridine(2604) synthase	_____________81______________________104\n_____________\|_______________________\|\n5'-UUA...UGCUU____A_______U__________AACGA...UGU-3'\n______________CUGG_AAGUGAU_UGAGCAG_GU\n______________\|\|\|\|_\|\|\|::\|\|_\|\|\|\|\|\|:_\|\|\n______________GACC_UUCGUUA_ACUCGUU_CA\n3'-UUU...AUUAU____________C_______A__GCACG...GCG-5'\n_____________\|_______________________\|\n_____________61______________________38\n	95 -- 101	42 -- 48	-22.0004 kcal/mol	5.021 kcal/mol	3.3001 kcal/mol	81 104@LB@ \| \|@LB@5'-UUA...UGCUU A U AACGA...UGU-3'@LB@ CUGG AAGUGAU UGAGCAG GU@LB@ \|\|\|\| \|\|\|::\|\| \|\|\|\|\|\|: \|\|@LB@ GACC UUCGUUA ACUCGUU CA@LB@3'-UUU...AUUAU C A GCACG...GCG-5'@LB@ \| \|@LB@ 61 38@LB@@LB@@LB@Energy -13.68 kcal/mol@LB@Hybridization Energy -22.0004 kcal/mol@LB@Unfolding Energy - mRNA 5.021 kcal/mol@LB@Unfolding Energy - sRNA 3.3001 kcal/mol@LB@@LB@Position - mRNA 82 -- 103@LB@Position - sRNA 39 -- 60@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 42 -- 48@LB@
151	0.01843	0.4072	b4028	yjbG	-13.08	0.058794	282 -- 297	40 -- 55	extracellular polysaccharide export OMA protein	_____________281______________298\n_____________\|________________\|\n5'-AAA...UGUUC_______GC_______AGG-3'\n______________AGCAAUG__AGCAGUG\n______________\|\|\|\|\|\|\|__\|\|\|\|:\|\|\n______________UCGUUAC__UCGUUAC\n3'-UUU...GACCU_______AC_______AGCAC...GCG-5'\n_____________\|________________\|\n_____________56_______________39\n	291 -- 297	40 -- 46	-18.8155 kcal/mol	2.52344 kcal/mol	3.20849 kcal/mol	281 298@LB@ \| \|@LB@5'-AAA...UGUUC GC AGG-3'@LB@ AGCAAUG AGCAGUG@LB@ \|\|\|\|\|\|\| \|\|\|\|:\|\|@LB@ UCGUUAC UCGUUAC@LB@3'-UUU...GACCU AC AGCAC...GCG-5'@LB@ \| \|@LB@ 56 39@LB@@LB@@LB@Energy -13.08 kcal/mol@LB@Hybridization Energy -18.8155 kcal/mol@LB@Unfolding Energy - mRNA 2.52344 kcal/mol@LB@Unfolding Energy - sRNA 3.20849 kcal/mol@LB@@LB@Position - mRNA 282 -- 297@LB@Position - sRNA 40 -- 55@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 40 -- 46@LB@
48	0.004482	0.2905	b4045	yjbJ	-14.69	0.031336	242 -- 268	42 -- 68	stress-induced protein UPF0337 family	_____________241___________________________269\n_____________\|_____________________________\|\n5'-CGU...UUUAA________G__AAA_______________ACUGA...AAG-3'\n______________AGGUAA_A_UG___GAGCAAUG_GGGCAA\n______________\|:\|\|\|\|_\|_\|\|___:\|\|\|\|\|\|\|_\|:\|\|\|\|\n______________UUCAUU_U_AC___UUCGUUAC_CUCGUU\n3'-UUU...ACCGA______A_G__C__________A______ACAGC...GCG-5'\n_____________\|_____________________________\|\n_____________69____________________________41\n	256 -- 262	49 -- 55	-22.1594 kcal/mol	4.16538 kcal/mol	3.30492 kcal/mol	241 269@LB@ \| \|@LB@5'-CGU...UUUAA G AAA ACUGA...AAG-3'@LB@ AGGUAA A UG GAGCAAUG GGGCAA@LB@ \|:\|\|\|\| \| \|\| :\|\|\|\|\|\|\| \|:\|\|\|\|@LB@ UUCAUU U AC UUCGUUAC CUCGUU@LB@3'-UUU...ACCGA A G C A ACAGC...GCG-5'@LB@ \| \|@LB@ 69 41@LB@@LB@@LB@Energy -14.69 kcal/mol@LB@Hybridization Energy -22.1594 kcal/mol@LB@Unfolding Energy - mRNA 4.16538 kcal/mol@LB@Unfolding Energy - sRNA 3.30492 kcal/mol@LB@@LB@Position - mRNA 242 -- 268@LB@Position - sRNA 42 -- 68@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 49 -- 55@LB@
23	0.001852	0.2682	b4059	ssb	-13.81	0.044308	47 -- 78	34 -- 64	single-stranded DNA-binding protein	_____________46_______________________________79\n_____________\|________________________________\|\n5'-AUC...UAUAC__________U___UUACCC_G__________AACAA...UUA-3'\n______________AGUAUUGGAA_GCA______G_AGUGUUGUGU\n______________\|:\|\|:\|\|\|\|\|_\|\|\|______\|_\|:\|\|\|:\|\|\|:\n______________UUAUGACCUU_CGU______C_UUACAGCACG\n3'-UUU...AUUCA______________UACACU_G__________AAAGU...GCG-5'\n_____________\|________________________________\|\n_____________65_______________________________33\n	72 -- 78	34 -- 40	-28.8532 kcal/mol	8.27543 kcal/mol	6.76952 kcal/mol	46 79@LB@ \| \|@LB@5'-AUC...UAUAC U UUACCC G AACAA...UUA-3'@LB@ AGUAUUGGAA GCA G AGUGUUGUGU@LB@ \|:\|\|:\|\|\|\|\| \|\|\| \| \|:\|\|\|:\|\|\|:@LB@ UUAUGACCUU CGU C UUACAGCACG@LB@3'-UUU...AUUCA UACACU G AAAGU...GCG-5'@LB@ \| \|@LB@ 65 33@LB@@LB@@LB@Energy -13.81 kcal/mol@LB@Hybridization Energy -28.8532 kcal/mol@LB@Unfolding Energy - mRNA 8.27543 kcal/mol@LB@Unfolding Energy - sRNA 6.76952 kcal/mol@LB@@LB@Position - mRNA 47 -- 78@LB@Position - sRNA 34 -- 64@LB@Position Seed - mRNA 72 -- 78@LB@Position Seed - sRNA 34 -- 40@LB@
183	0.02251	0.4113	b4067	actP	-16.98	0.012652	22 -- 44	66 -- 86	acetate transporter	_____________21______________________45\n_____________\|_______________________\|\n5'-AUC...UGAUC___UUC_________________CACGC...GGC-3'\n______________GCC___GCGCCCGGCUGGCUGGG\n______________\|\|\|___\|\|:\|\|\|\|\|\|\|\|\|\|\|::\|\n______________CGG___CGUGGGCCGACCGAUUC\n_______3'-UUUU___U___________________AUUAU...GCG-5'\n_____________\|_______________________\|\n_____________87______________________65\n	38 -- 44	66 -- 72	-41.8503 kcal/mol	13.121 kcal/mol	11.7541 kcal/mol	21 45@LB@ \| \|@LB@5'-AUC...UGAUC UUC CACGC...GGC-3'@LB@ GCC GCGCCCGGCUGGCUGGG@LB@ \|\|\| \|\|:\|\|\|\|\|\|\|\|\|\|\|::\|@LB@ CGG CGUGGGCCGACCGAUUC@LB@ 3'-UUUU U AUUAU...GCG-5'@LB@ \| \|@LB@ 87 65@LB@@LB@@LB@Energy -16.98 kcal/mol@LB@Hybridization Energy -41.8503 kcal/mol@LB@Unfolding Energy - mRNA 13.121 kcal/mol@LB@Unfolding Energy - sRNA 11.7541 kcal/mol@LB@@LB@Position - mRNA 22 -- 44@LB@Position - sRNA 66 -- 86@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 66 -- 72@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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