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
152	0.02492	0.526	b3665	adeD	-5.38	0.553104	121 -- 181	3 -- 52	cryptic adenine deaminase	b4328	_____________120____________________________________________________________182\n_____________\|______________________________________________________________\|\n5'-ACG...ACAUU___________UUU_______CUCGC____UUUCUUUA__________UAAUCAAAU_____AAAUC...UUA-3'\n______________AAUGGAUAUUC___AAU_AAU_____GACG________UGAUAAAUAA_________UGAUA\n______________\|\|::\|\|:\|\|\|\|___\|\|\|_\|\|\|_____\|\|\|\|________\|:\|\|\|\|\|\|\|\|_________\|\|\|\|\|\n______________UUGUCUGUAAG___UUA_UUA_____CUGC________AUUAUUUAUU_________ACUAU\n3'-UUU...CCCAU___________UCU___C____________C_________________UCAAUUACU_____CG-5'\n_____________\|______________________________________________________________\|\n_____________53_____________________________________________________________2\n	161 -- 167	17 -- 23	-19.4771 kcal/mol	7.76071 kcal/mol	6.33547 kcal/mol	120 182@LB@ \| \|@LB@5'-ACG...ACAUU UUU CUCGC UUUCUUUA UAAUCAAAU AAAUC...UUA-3'@LB@ AAUGGAUAUUC AAU AAU GACG UGAUAAAUAA UGAUA@LB@ \|\|::\|\|:\|\|\|\| \|\|\| \|\|\| \|\|\|\| \|:\|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ UUGUCUGUAAG UUA UUA CUGC AUUAUUUAUU ACUAU@LB@3'-UUU...CCCAU UCU C C UCAAUUACU CG-5'@LB@ \| \|@LB@ 53 2@LB@@LB@@LB@Energy -5.38 kcal/mol@LB@Hybridization Energy -19.4771 kcal/mol@LB@Unfolding Energy - mRNA 7.76071 kcal/mol@LB@Unfolding Energy - sRNA 6.33547 kcal/mol@LB@@LB@Position - mRNA 121 -- 181@LB@Position - sRNA 3 -- 52@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 17 -- 23@LB@
161	0.02632	0.526	b3670	ilvN	-9.27	0.134814	179 -- 196	49 -- 65	acetolactate synthase 1 small subunit		_____________178________________197\n_____________\|__________________\|\n5'-UCA...AAUAC________U___GG____AGCCA...CUU-3'\n______________UGAAAUGG_GGG__AAUA\n______________\|\|\|\|\|\|:\|_\|\|\|__\|\|:\|\n______________ACUUUAUC_CCC__UUGU\n3'-UUU...GGCCA____________AU____CUGUA...UCG-5'\n_____________\|__________________\|\n_____________66_________________48\n	180 -- 186	58 -- 64	-15.3061 kcal/mol	4.40463 kcal/mol	1.63404 kcal/mol	178 197@LB@ \| \|@LB@5'-UCA...AAUAC U GG AGCCA...CUU-3'@LB@ UGAAAUGG GGG AAUA@LB@ \|\|\|\|\|\|:\| \|\|\| \|\|:\|@LB@ ACUUUAUC CCC UUGU@LB@3'-UUU...GGCCA AU CUGUA...UCG-5'@LB@ \| \|@LB@ 66 48@LB@@LB@@LB@Energy -9.27 kcal/mol@LB@Hybridization Energy -15.3061 kcal/mol@LB@Unfolding Energy - mRNA 4.40463 kcal/mol@LB@Unfolding Energy - sRNA 1.63404 kcal/mol@LB@@LB@Position - mRNA 179 -- 196@LB@Position - sRNA 49 -- 65@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 58 -- 64@LB@
167	0.02708	0.531	b3705	yidC	-10.20	0.088356	85 -- 115	24 -- 58	membrane protein insertase		_____________84____________________________________116\n_____________\|_____________________________________\|\n5'-CGC...GGUUU__A____UAAA_____GU_________U_________AACGC...CCC-3'\n______________GG_GUGA____AGGCA________UGG_UGACGGUGA\n______________\|\|_\|\|:\|____\|\|:\|\|________\|\|:_\|\|\|\|\|\|\|:\|\n______________CC_CAUU____UCUGU________ACU_ACUGCCAUU\n3'-UUU...UUUAU__C____UG_______AAGUCUUU___U_________AUUUA...UCG-5'\n_____________\|_____________________________________\|\n_____________59____________________________________23\n	109 -- 115	24 -- 30	-23.9536 kcal/mol	7.45063 kcal/mol	6.30019 kcal/mol	84 116@LB@ \| \|@LB@5'-CGC...GGUUU A UAAA GU U AACGC...CCC-3'@LB@ GG GUGA AGGCA UGG UGACGGUGA@LB@ \|\| \|\|:\| \|\|:\|\| \|\|: \|\|\|\|\|\|\|:\|@LB@ CC CAUU UCUGU ACU ACUGCCAUU@LB@3'-UUU...UUUAU C UG AAGUCUUU U AUUUA...UCG-5'@LB@ \| \|@LB@ 59 23@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -23.9536 kcal/mol@LB@Unfolding Energy - mRNA 7.45063 kcal/mol@LB@Unfolding Energy - sRNA 6.30019 kcal/mol@LB@@LB@Position - mRNA 85 -- 115@LB@Position - sRNA 24 -- 58@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 24 -- 30@LB@
158	0.0258	0.526	b3738	atpB	-11.34	0.051140	75 -- 89	1 -- 15	F0 sector of membrane-bound ATP synthase subunit a		_____________74______________90\n_____________\|_______________\|\n5'-CAU...UUGGU____C__________GUUGG...ACC-3'\n______________GUUA_UGGUGGUGGC\n______________\|\|\|\|_\|\|:\|\|:\|:\|\|\n______________CAAU_ACUACUAUCG\n3'-UUU...UAUUU____U__________-5'\n_____________\|______________\|\n_____________16_____________1\n	83 -- 89	1 -- 7	-16.9836 kcal/mol	5.59496 kcal/mol	0.0474282 kcal/mol	74 90@LB@ \| \|@LB@5'-CAU...UUGGU C GUUGG...ACC-3'@LB@ GUUA UGGUGGUGGC@LB@ \|\|\|\| \|\|:\|\|:\|:\|\|@LB@ CAAU ACUACUAUCG@LB@3'-UUU...UAUUU U -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -11.34 kcal/mol@LB@Hybridization Energy -16.9836 kcal/mol@LB@Unfolding Energy - mRNA 5.59496 kcal/mol@LB@Unfolding Energy - sRNA 0.0474282 kcal/mol@LB@@LB@Position - mRNA 75 -- 89@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 83 -- 89@LB@Position Seed - sRNA 1 -- 7@LB@
38	0.003831	0.3287	b3739	atpI	-13.67	0.015109	253 -- 271	1 -- 16	ATP synthase membrane-bound accessory factor		_____________252_________________272\n_____________\|___________________\|\n5'-GAA...CGUUC_____CUG___________AAGUG...ACC-3'\n______________AGUUA___GUGGUGAUAGC\n______________\|\|\|\|\|___:\|\|:\|\|\|\|\|\|\|\n______________UCAAU___UACUACUAUCG\n3'-UUU...UUAUU___________________-5'\n_____________\|__________________\|\n_____________17_________________1\n	265 -- 271	1 -- 7	-18.239 kcal/mol	4.52285 kcal/mol	0.0492804 kcal/mol	252 272@LB@ \| \|@LB@5'-GAA...CGUUC CUG AAGUG...ACC-3'@LB@ AGUUA GUGGUGAUAGC@LB@ \|\|\|\|\| :\|\|:\|\|\|\|\|\|\|@LB@ UCAAU UACUACUAUCG@LB@3'-UUU...UUAUU -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -13.67 kcal/mol@LB@Hybridization Energy -18.239 kcal/mol@LB@Unfolding Energy - mRNA 4.52285 kcal/mol@LB@Unfolding Energy - sRNA 0.0492804 kcal/mol@LB@@LB@Position - mRNA 253 -- 271@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 1 -- 7@LB@
82	0.0113	0.4523	b3747	kup	-9.05	0.148352	64 -- 70	53 -- 59	potassium transporter		_____________63______71\n_____________\|_______\|\n5'-AAA...AAAGG_______UUUUU...GUG-3'\n______________GGGGGUA\n______________:\|\|\|\|\|\|\n______________UCCCCAU\n3'-UUU...CUUUA_______UUGUC...UCG-5'\n_____________\|_______\|\n_____________60______52\n	64 -- 70	53 -- 59	-11.6233 kcal/mol	2.51972 kcal/mol	0.0564539 kcal/mol	63 71@LB@ \| \|@LB@5'-AAA...AAAGG UUUUU...GUG-3'@LB@ GGGGGUA@LB@ :\|\|\|\|\|\|@LB@ UCCCCAU@LB@3'-UUU...CUUUA UUGUC...UCG-5'@LB@ \| \|@LB@ 60 52@LB@@LB@@LB@Energy -9.05 kcal/mol@LB@Hybridization Energy -11.6233 kcal/mol@LB@Unfolding Energy - mRNA 2.51972 kcal/mol@LB@Unfolding Energy - sRNA 0.0564539 kcal/mol@LB@@LB@Position - mRNA 64 -- 70@LB@Position - sRNA 53 -- 59@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 53 -- 59@LB@
41	0.004182	0.3349	b3771	ilvD	-12.17	0.033695	175 -- 200	14 -- 53	dihydroxyacid dehydratase		_____________174______________________________________201\n_____________\|________________________________________\|\n5'-GCG...UUACG_________C_________________GA___________AUGCC...GUA-3'\n______________AGACAGACA_______________UGG__GUAAAUAAAGU\n______________\|:\|\|\|\|\|\|\|_______________:\|\|__:\|\|\|\|\|\|\|\|\|\|\n______________UUUGUCUGU_______________GCC__UAUUUAUUUCA\n3'-UUU...CCCCA_________AAGUCUUUACUUACU___AU___________AUUAC...UCG-5'\n_____________\|________________________________________\|\n_____________54_______________________________________13\n	194 -- 200	14 -- 20	-22.054 kcal/mol	3.56189 kcal/mol	6.32552 kcal/mol	174 201@LB@ \| \|@LB@5'-GCG...UUACG C GA AUGCC...GUA-3'@LB@ AGACAGACA UGG GUAAAUAAAGU@LB@ \|:\|\|\|\|\|\|\| :\|\| :\|\|\|\|\|\|\|\|\|\|@LB@ UUUGUCUGU GCC UAUUUAUUUCA@LB@3'-UUU...CCCCA AAGUCUUUACUUACU AU AUUAC...UCG-5'@LB@ \| \|@LB@ 54 13@LB@@LB@@LB@Energy -12.17 kcal/mol@LB@Hybridization Energy -22.054 kcal/mol@LB@Unfolding Energy - mRNA 3.56189 kcal/mol@LB@Unfolding Energy - sRNA 6.32552 kcal/mol@LB@@LB@Position - mRNA 175 -- 200@LB@Position - sRNA 14 -- 53@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 14 -- 20@LB@
91	0.01489	0.5059	b3805	hemC	-12.98	0.021909	168 -- 195	24 -- 52	hydroxymethylbilane synthase		_____________167___________________________196\n_____________\|_____________________________\|\n5'-AAA...GUUAG_______CA_____UGAU___________CAAGC...GCC-3'\n______________GAUGGAC___CGGA____AAUGACGGUAA\n______________:\|::\|\|\|___\|:\|\|____\|\|\|\|\|\|\|\|\|\|\|\n______________UUGUCUG___GUCU____UUACUGCCAUU\n3'-UUU...CCCAU_______UAA____UUAC___________AUUUA...UCG-5'\n_____________\|_____________________________\|\n_____________53____________________________23\n	189 -- 195	24 -- 30	-23.6136 kcal/mol	4.33145 kcal/mol	6.2974 kcal/mol	167 196@LB@ \| \|@LB@5'-AAA...GUUAG CA UGAU CAAGC...GCC-3'@LB@ GAUGGAC CGGA AAUGACGGUAA@LB@ :\|::\|\|\| \|:\|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ UUGUCUG GUCU UUACUGCCAUU@LB@3'-UUU...CCCAU UAA UUAC AUUUA...UCG-5'@LB@ \| \|@LB@ 53 23@LB@@LB@@LB@Energy -12.98 kcal/mol@LB@Hybridization Energy -23.6136 kcal/mol@LB@Unfolding Energy - mRNA 4.33145 kcal/mol@LB@Unfolding Energy - sRNA 6.2974 kcal/mol@LB@@LB@Position - mRNA 168 -- 195@LB@Position - sRNA 24 -- 52@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 24 -- 30@LB@
88	0.01388	0.5059	b3809	dapF	-7.53	0.274407	192 -- 207	1 -- 17	diaminopimelate epimerase		_____________191_______________208\n_____________\|_________________\|\n5'-UCU...GAUUG____A_______C____UCUCG...UGG-3'\n______________GAGU_AAUGAUG__AGU\n______________:\|\|\|_\|\|\|\|\|\|\|__\|\|:\n______________UUCA_UUACUAC__UCG\n3'-UUU...UUUAU____A_______UA___-5'\n_____________\|________________\|\n_____________18_______________1\n	197 -- 203	6 -- 12	-9.99588 kcal/mol	2.41483 kcal/mol	0.0529402 kcal/mol	191 208@LB@ \| \|@LB@5'-UCU...GAUUG A C UCUCG...UGG-3'@LB@ GAGU AAUGAUG AGU@LB@ :\|\|\| \|\|\|\|\|\|\| \|\|:@LB@ UUCA UUACUAC UCG@LB@3'-UUU...UUUAU A UA -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -7.53 kcal/mol@LB@Hybridization Energy -9.99588 kcal/mol@LB@Unfolding Energy - mRNA 2.41483 kcal/mol@LB@Unfolding Energy - sRNA 0.0529402 kcal/mol@LB@@LB@Position - mRNA 192 -- 207@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 6 -- 12@LB@
51	0.006039	0.3887	b3822	recQ	-9.34	0.130811	192 -- 200	50 -- 58	ATP-dependent DNA helicase		_____________191_______201\n_____________\|_________\|\n5'-CGC...CAAUC_________GUGGC...UUA-3'\n______________GGGGUGAAU\n______________\|\|\|\|\|:\|\|:\n______________CCCCAUUUG\n3'-UUU...UUUAU_________UCUGU...UCG-5'\n_____________\|_________\|\n_____________59________49\n	194 -- 200	50 -- 56	-13.8974 kcal/mol	3.8337 kcal/mol	0.72763 kcal/mol	191 201@LB@ \| \|@LB@5'-CGC...CAAUC GUGGC...UUA-3'@LB@ GGGGUGAAU@LB@ \|\|\|\|\|:\|\|:@LB@ CCCCAUUUG@LB@3'-UUU...UUUAU UCUGU...UCG-5'@LB@ \| \|@LB@ 59 49@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -13.8974 kcal/mol@LB@Unfolding Energy - mRNA 3.8337 kcal/mol@LB@Unfolding Energy - sRNA 0.72763 kcal/mol@LB@@LB@Position - mRNA 192 -- 200@LB@Position - sRNA 50 -- 58@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 50 -- 56@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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