Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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	Additional homologs
107	0.01649	0.5059	b0830	gsiB	-12.67	0.025954	282 -- 298	1 -- 18	glutathione ABC transporter periplasmic binding protein		_____________281________________299\n_____________\|__________________\|\n5'-GGC...CUGCC____AU____________GG-3'\n______________AAAG___GUGGUGGUGGC\n______________\|\|\|\|___:\|\|:\|\|:\|:\|\|\n______________UUUC___UACUACUAUCG\n3'-UUU...AUUUA____AAU___________-5'\n_____________\|_________________\|\n_____________19________________1\n	292 -- 298	1 -- 7	-15.5562 kcal/mol	2.82856 kcal/mol	0.0611543 kcal/mol	281 299@LB@ \| \|@LB@5'-GGC...CUGCC AU GG-3'@LB@ AAAG GUGGUGGUGGC@LB@ \|\|\|\| :\|\|:\|\|:\|:\|\|@LB@ UUUC UACUACUAUCG@LB@3'-UUU...AUUUA AAU -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -12.67 kcal/mol@LB@Hybridization Energy -15.5562 kcal/mol@LB@Unfolding Energy - mRNA 2.82856 kcal/mol@LB@Unfolding Energy - sRNA 0.0611543 kcal/mol@LB@@LB@Position - mRNA 282 -- 298@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 1 -- 7@LB@
108	0.01698	0.5123	b0078	ilvH	-10.97	0.061484	141 -- 180	1 -- 51	acetolactate synthase 3 small subunit valine-sensitive		_____________140_________________________________________________181\n_____________\|___________________________________________________\|\n5'-GCC...CCGAU______UCG___________________________AU_______UA____AAAAC...UGA-3'\n______________GCAGAU___CGGG_______GGCGG_AAUGGAUGAA____GUGGU___AGC\n______________:\|\|\|\|:___\|:\|:_______\|:\|\|\|_\|\|\|::\|\|:\|\|____:\|\|:\|___\|\|\|\n______________UGUCUG___GUCU_______CUGCC_UUAUUUAUUU____UACUA___UCG\n3'-UUU...CCAUU______UAA____UUACUUA_____A__________CAAU_____CUA___-5'\n_____________\|__________________________________________________\|\n_____________52_________________________________________________1\n	162 -- 168	16 -- 22	-27.7823 kcal/mol	10.4814 kcal/mol	6.33528 kcal/mol	140 181@LB@ \| \|@LB@5'-GCC...CCGAU UCG AU UA AAAAC...UGA-3'@LB@ GCAGAU CGGG GGCGG AAUGGAUGAA GUGGU AGC@LB@ :\|\|\|\|: \|:\|: \|:\|\|\| \|\|\|::\|\|:\|\| :\|\|:\| \|\|\|@LB@ UGUCUG GUCU CUGCC UUAUUUAUUU UACUA UCG@LB@3'-UUU...CCAUU UAA UUACUUA A CAAU CUA -5'@LB@ \| \|@LB@ 52 1@LB@@LB@@LB@Energy -10.97 kcal/mol@LB@Hybridization Energy -27.7823 kcal/mol@LB@Unfolding Energy - mRNA 10.4814 kcal/mol@LB@Unfolding Energy - sRNA 6.33528 kcal/mol@LB@@LB@Position - mRNA 141 -- 180@LB@Position - sRNA 1 -- 51@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 16 -- 22@LB@
110	0.01732	0.5155	b1800	dmlA	-11.31	0.051964	127 -- 183	1 -- 58	D-malate oxidase NAD-dependent; putative tartrate dehydrogenase		_____________126___________________________________________________________184\n_____________\|_____________________________________________________________\|\n5'-GGU...GUUAC____AUU___UCCUU_____UCAAUUAUAG__________UU______C___UU_______CAGGA...GCU-3'\n______________GGGG___AAU_____UUCAG__________GAUGGUGAUG______GU_AAU__UGAUGGU\n______________\|\|\|\|___\|\|:_____\|\|\|\|\|__________\|\|:\|\|\|:\|\|:______\|\|_\|\|\|__\|\|\|\|:\|:\n______________CCCC___UUG_____AAGUC__________CUGCCAUUAU______CA_UUA__ACUAUCG\n3'-UUU...UUUAU____AU____UCUGU_____UUUACUUA____________UUAUUU__A___CU_______-5'\n_____________\|____________________________________________________________\|\n_____________59___________________________________________________________1\n	177 -- 183	1 -- 7	-30.6237 kcal/mol	12.9772 kcal/mol	6.33758 kcal/mol	126 184@LB@ \| \|@LB@5'-GGU...GUUAC AUU UCCUU UCAAUUAUAG UU C UU CAGGA...GCU-3'@LB@ GGGG AAU UUCAG GAUGGUGAUG GU AAU UGAUGGU@LB@ \|\|\|\| \|\|: \|\|\|\|\| \|\|:\|\|\|:\|\|: \|\| \|\|\| \|\|\|\|:\|:@LB@ CCCC UUG AAGUC CUGCCAUUAU CA UUA ACUAUCG@LB@3'-UUU...UUUAU AU UCUGU UUUACUUA UUAUUU A CU -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -11.31 kcal/mol@LB@Hybridization Energy -30.6237 kcal/mol@LB@Unfolding Energy - mRNA 12.9772 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 127 -- 183@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 1 -- 7@LB@
111	0.01748	0.5155	b4012	yjaB	-9.42	0.126217	155 -- 212	1 -- 59	GNAT-family putative N-acetyltransferase; acetyl coenzyme A-binding protein		_____________154_____________________________________________________________213\n_____________\|_______________________________________________________________\|\n5'-AAG...UUUCA___AAA____U___________UAUAA____________A________AA______UAU____AUUCG...CAG-3'\n______________AGG___AGAC__ACG_UUAGAA_____GAAUGAC__UAA_AGG_AGAG__AAUGGU___UAGU\n______________\|\|\|___\|:\|\|__\|\|:_\|:\|\|\|\|_____\|\|\|\|\|\|\|__\|\|\|_\|::_\|:\|\|__\|\|\|\|:\|___\|\|\|:\n______________UCC___UUUG__UGU_AGUCUU_____CUUACUG__AUU_UUU_UUUC__UUACUA___AUCG\n3'-UUU...CUUUA___CCA____UC___A______UA__________CC___A___A____AA______CU_____-5'\n_____________\|______________________________________________________________\|\n_____________60_____________________________________________________________1\n	180 -- 186	29 -- 35	-23.4815 kcal/mol	7.7268 kcal/mol	6.33764 kcal/mol	154 213@LB@ \| \|@LB@5'-AAG...UUUCA AAA U UAUAA A AA UAU AUUCG...CAG-3'@LB@ AGG AGAC ACG UUAGAA GAAUGAC UAA AGG AGAG AAUGGU UAGU@LB@ \|\|\| \|:\|\| \|\|: \|:\|\|\|\| \|\|\|\|\|\|\| \|\|\| \|:: \|:\|\| \|\|\|\|:\| \|\|\|:@LB@ UCC UUUG UGU AGUCUU CUUACUG AUU UUU UUUC UUACUA AUCG@LB@3'-UUU...CUUUA CCA UC A UA CC A A AA CU -5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -9.42 kcal/mol@LB@Hybridization Energy -23.4815 kcal/mol@LB@Unfolding Energy - mRNA 7.7268 kcal/mol@LB@Unfolding Energy - sRNA 6.33764 kcal/mol@LB@@LB@Position - mRNA 155 -- 212@LB@Position - sRNA 1 -- 59@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 29 -- 35@LB@
115	0.01846	0.5155	b4483	tatD	-10.31	0.084235	251 -- 265	1 -- 13	quality control of Tat-exported FeS proteins; Mg-dependent cytoplasmic DNase		_____________250_____________266\n_____________\|_______________\|\n5'-CUG...GACCG________UU_____GUGCG...UCA-3'\n______________UGAUGAUG__GUAGC\n______________\|:\|\|\|\|\|\|__:\|\|\|\|\n______________AUUACUAC__UAUCG\n3'-UUU...UUUCA_______________-5'\n_____________\|______________\|\n_____________14_____________1\n	252 -- 258	6 -- 12	-13.1693 kcal/mol	2.8194 kcal/mol	0.0446954 kcal/mol	250 266@LB@ \| \|@LB@5'-CUG...GACCG UU GUGCG...UCA-3'@LB@ UGAUGAUG GUAGC@LB@ \|:\|\|\|\|\|\| :\|\|\|\|@LB@ AUUACUAC UAUCG@LB@3'-UUU...UUUCA -5'@LB@ \| \|@LB@ 14 1@LB@@LB@@LB@Energy -10.31 kcal/mol@LB@Hybridization Energy -13.1693 kcal/mol@LB@Unfolding Energy - mRNA 2.8194 kcal/mol@LB@Unfolding Energy - sRNA 0.0446954 kcal/mol@LB@@LB@Position - mRNA 251 -- 265@LB@Position - sRNA 1 -- 13@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 6 -- 12@LB@
119	0.019	0.5155	b0904	focA	-10.20	0.088413	192 -- 208	1 -- 18	formate channel		_____________191________________209\n_____________\|__________________\|\n5'-GAG...AAGAG______________A___UGACA...AGA-3'\n______________AGAGUUAGUG_UGA_AGC\n______________\|:\|\|\|\|\|:\|\|_\|\|\|_\|\|\|\n______________UUUCAAUUAC_ACU_UCG\n3'-UUU...AUUUA__________U___A___-5'\n_____________\|_________________\|\n_____________19________________1\n	195 -- 201	9 -- 15	-16.1977 kcal/mol	5.93514 kcal/mol	0.0611543 kcal/mol	191 209@LB@ \| \|@LB@5'-GAG...AAGAG A UGACA...AGA-3'@LB@ AGAGUUAGUG UGA AGC@LB@ \|:\|\|\|\|\|:\|\| \|\|\| \|\|\|@LB@ UUUCAAUUAC ACU UCG@LB@3'-UUU...AUUUA U A -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -16.1977 kcal/mol@LB@Unfolding Energy - mRNA 5.93514 kcal/mol@LB@Unfolding Energy - sRNA 0.0611543 kcal/mol@LB@@LB@Position - mRNA 192 -- 208@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 9 -- 15@LB@
120	0.01923	0.5155	b4004	zraR	-8.11	0.219313	234 -- 248	1 -- 12	fused DNA-binding response regulator in two-component regulatory system with ZraS: response regulator/sigma54 interaction protein	b2220	_____________233_____________249\n_____________\|_______________\|\n5'-GGA...UGGUG________CAU____CACUG...CGC-3'\n______________GAUGAUGA___UAGC\n______________:\|\|\|\|\|\|\|___\|\|\|\|\n______________UUACUACU___AUCG\n3'-UUU...UUCAA_______________-5'\n_____________\|______________\|\n_____________13_____________1\n	235 -- 241	5 -- 11	-11.3572 kcal/mol	3.21186 kcal/mol	0.0394463 kcal/mol	233 249@LB@ \| \|@LB@5'-GGA...UGGUG CAU CACUG...CGC-3'@LB@ GAUGAUGA UAGC@LB@ :\|\|\|\|\|\|\| \|\|\|\|@LB@ UUACUACU AUCG@LB@3'-UUU...UUCAA -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -8.11 kcal/mol@LB@Hybridization Energy -11.3572 kcal/mol@LB@Unfolding Energy - mRNA 3.21186 kcal/mol@LB@Unfolding Energy - sRNA 0.0394463 kcal/mol@LB@@LB@Position - mRNA 234 -- 248@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 5 -- 11@LB@
127	0.01998	0.5155	b2922	yggE	-8.69	0.172995	232 -- 253	1 -- 26	oxidative stress defense protein		_____________231________________________254\n_____________\|__________________________\|\n5'-GCA...GGCAU________________C_________AGCGC...CCG-3'\n______________UAAUGGGUA___UUAG_GG_GAUGGC\n______________\|\|\|\|:::\|\|___\|\|\|:_\|:_\|\|\|:\|\|\n______________AUUAUUUAU___AAUU_CU_CUAUCG\n3'-UUU...CUGCC_________UUC____A__A______-5'\n_____________\|_________________________\|\n_____________27________________________1\n	234 -- 240	18 -- 24	-12.7828 kcal/mol	3.51669 kcal/mol	0.580494 kcal/mol	231 254@LB@ \| \|@LB@5'-GCA...GGCAU C AGCGC...CCG-3'@LB@ UAAUGGGUA UUAG GG GAUGGC@LB@ \|\|\|\|:::\|\| \|\|\|: \|: \|\|\|:\|\|@LB@ AUUAUUUAU AAUU CU CUAUCG@LB@3'-UUU...CUGCC UUC A A -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -8.69 kcal/mol@LB@Hybridization Energy -12.7828 kcal/mol@LB@Unfolding Energy - mRNA 3.51669 kcal/mol@LB@Unfolding Energy - sRNA 0.580494 kcal/mol@LB@@LB@Position - mRNA 232 -- 253@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 18 -- 24@LB@
128	0.0201	0.5155	b2782	mazF	-10.78	0.067406	32 -- 50	1 -- 23	mRNA interferase toxin antitoxin is MazE	b4225	_____________31______________________51\n_____________\|_______________________\|\n5'-AUC...CAAUC_______________________GAAGA...UCC-3'\n______________UGAAUA___UUGAUGAUGA_AGU\n______________\|:\|\|\|\|___\|\|:\|\|\|\|\|\|\|_\|\|:\n______________AUUUAU___AAUUACUACU_UCG\n3'-UUU...CCAUU______UUC__________A___-5'\n_____________\|______________________\|\n_____________24_____________________1\n	41 -- 47	5 -- 11	-13.6359 kcal/mol	2.75565 kcal/mol	0.105066 kcal/mol	31 51@LB@ \| \|@LB@5'-AUC...CAAUC GAAGA...UCC-3'@LB@ UGAAUA UUGAUGAUGA AGU@LB@ \|:\|\|\|\| \|\|:\|\|\|\|\|\|\| \|\|:@LB@ AUUUAU AAUUACUACU UCG@LB@3'-UUU...CCAUU UUC A -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -10.78 kcal/mol@LB@Hybridization Energy -13.6359 kcal/mol@LB@Unfolding Energy - mRNA 2.75565 kcal/mol@LB@Unfolding Energy - sRNA 0.105066 kcal/mol@LB@@LB@Position - mRNA 32 -- 50@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 5 -- 11@LB@
129	0.02061	0.5217	b0633	rlpA	-9.57	0.117965	261 -- 273	1 -- 12	septal ring protein suppressor of prc minor lipoprotein		_____________260___________274\n_____________\|_____________\|\n5'-CGG...CAAGC_________C___AACAG...CUG-3'\n______________GAUGAUGGU_AGC\n______________:\|\|\|\|\|\|:\|_\|\|\|\n______________UUACUACUA_UCG\n3'-UUU...UUCAA_____________-5'\n_____________\|____________\|\n_____________13___________1\n	263 -- 269	4 -- 10	-13.3317 kcal/mol	3.7231 kcal/mol	0.0394463 kcal/mol	260 274@LB@ \| \|@LB@5'-CGG...CAAGC C AACAG...CUG-3'@LB@ GAUGAUGGU AGC@LB@ :\|\|\|\|\|\|:\| \|\|\|@LB@ UUACUACUA UCG@LB@3'-UUU...UUCAA -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -9.57 kcal/mol@LB@Hybridization Energy -13.3317 kcal/mol@LB@Unfolding Energy - mRNA 3.7231 kcal/mol@LB@Unfolding Energy - sRNA 0.0394463 kcal/mol@LB@@LB@Position - mRNA 261 -- 273@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 263 -- 269@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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