Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
38	0.002093	0.1727	b1174	minE	-11.55	0.070176	37 -- 55	69 -- 87	cell division topological specificity factor	_____________36___________________56\n_____________\|____________________\|\n5'-AAC...AGUAU_________UCUA_______UGAAC...AUG-3'\n______________UGC_GCGCC____ACCAGGG\n______________\|:\|_\|\|\|\|\|____\|\|\|\|\|\|\|\n______________AUG_CGCGG____UGGUCCC\n3'-UUU...CGCUU___A_____UUG________UUUAG...GUG-5'\n_____________\|____________________\|\n_____________88___________________68\n	49 -- 55	69 -- 75	-25.7186 kcal/mol	6.79304 kcal/mol	7.3743 kcal/mol	36 56@LB@ \| \|@LB@5'-AAC...AGUAU UCUA UGAAC...AUG-3'@LB@ UGC GCGCC ACCAGGG@LB@ \|:\| \|\|\|\|\| \|\|\|\|\|\|\|@LB@ AUG CGCGG UGGUCCC@LB@3'-UUU...CGCUU A UUG UUUAG...GUG-5'@LB@ \| \|@LB@ 88 68@LB@@LB@@LB@Energy -11.55 kcal/mol@LB@Hybridization Energy -25.7186 kcal/mol@LB@Unfolding Energy - mRNA 6.79304 kcal/mol@LB@Unfolding Energy - sRNA 7.3743 kcal/mol@LB@@LB@Position - mRNA 37 -- 55@LB@Position - sRNA 69 -- 87@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 69 -- 75@LB@
76	0.003978	0.182	b0336	codB	-6.71	0.504284	39 -- 48	1 -- 11	cytosine transporter	_____________38__________49\n_____________\|___________\|\n5'-CCA...UCUUA___________CCACU...UUU-3'\n______________UCAGGCC_UAC\n______________\|\|\|\|\|\|\|_:\|\|\n______________AGUCCGG_GUG\n3'-UUU...CAAAA_______C___-5'\n_____________\|__________\|\n_____________12_________1\n	39 -- 45	5 -- 11	-14.8291 kcal/mol	2.46298 kcal/mol	5.60325 kcal/mol	38 49@LB@ \| \|@LB@5'-CCA...UCUUA CCACU...UUU-3'@LB@ UCAGGCC UAC@LB@ \|\|\|\|\|\|\| :\|\|@LB@ AGUCCGG GUG@LB@3'-UUU...CAAAA C -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -6.71 kcal/mol@LB@Hybridization Energy -14.8291 kcal/mol@LB@Unfolding Energy - mRNA 2.46298 kcal/mol@LB@Unfolding Energy - sRNA 5.60325 kcal/mol@LB@@LB@Position - mRNA 39 -- 48@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 5 -- 11@LB@
106	0.005731	0.1855	b0867	amiD	-15.82	0.010089	39 -- 60	64 -- 86	1 6-anhydro-N-acetylmuramyl-L-alanine amidase Zn-dependent; OM lipoprotein	_____________38_______________________61\n_____________\|________________________\|\n5'-GAU...AAAGA_______AA_______________GCCUU...CCC-3'\n______________ACUGCGU__AGCAC__GGGAGAUC\n______________\|\|\|\|\|\|:__\|:\|\|\|__\|\|\|\|:\|\|\|\n______________UGACGCG__UUGUG__CCCUUUAG\n3'-UUU...GCUUA_______G______GU________AACCG...GUG-5'\n_____________\|________________________\|\n_____________87_______________________63\n	54 -- 60	64 -- 70	-27.7093 kcal/mol	4.50209 kcal/mol	7.38435 kcal/mol	38 61@LB@ \| \|@LB@5'-GAU...AAAGA AA GCCUU...CCC-3'@LB@ ACUGCGU AGCAC GGGAGAUC@LB@ \|\|\|\|\|\|: \|:\|\|\| \|\|\|\|:\|\|\|@LB@ UGACGCG UUGUG CCCUUUAG@LB@3'-UUU...GCUUA G GU AACCG...GUG-5'@LB@ \| \|@LB@ 87 63@LB@@LB@@LB@Energy -15.82 kcal/mol@LB@Hybridization Energy -27.7093 kcal/mol@LB@Unfolding Energy - mRNA 4.50209 kcal/mol@LB@Unfolding Energy - sRNA 7.38435 kcal/mol@LB@@LB@Position - mRNA 39 -- 60@LB@Position - sRNA 64 -- 86@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 64 -- 70@LB@
2	1.572e-09	2.767e-06	b3749	rbsA	-20.95	0.000983	43 -- 64	65 -- 86	D-ribose ABC transporter ATPase	_____________42_____________________65\n_____________\|______________________\|\n5'-UAA...GAGCA_____AAA______________ACCAU...UGG-3'\n______________GCUGC___AACACCAGGGAAAU\n______________:\|\|\|\|___\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________UGACG___UUGUGGUCCCUUUA\n3'-UUU...GCUUA_____CGG______________GAACC...GUG-5'\n_____________\|______________________\|\n_____________87_____________________64\n	58 -- 64	65 -- 71	-31.8331 kcal/mol	3.49898 kcal/mol	7.38332 kcal/mol	42 65@LB@ \| \|@LB@5'-UAA...GAGCA AAA ACCAU...UGG-3'@LB@ GCUGC AACACCAGGGAAAU@LB@ :\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UGACG UUGUGGUCCCUUUA@LB@3'-UUU...GCUUA CGG GAACC...GUG-5'@LB@ \| \|@LB@ 87 64@LB@@LB@@LB@Energy -20.95 kcal/mol@LB@Hybridization Energy -31.8331 kcal/mol@LB@Unfolding Energy - mRNA 3.49898 kcal/mol@LB@Unfolding Energy - sRNA 7.38332 kcal/mol@LB@@LB@Position - mRNA 43 -- 64@LB@Position - sRNA 65 -- 86@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 65 -- 71@LB@
183	0.011	0.2089	b0906	ycaP	-11.77	0.063722	48 -- 74	48 -- 75	UPF0702 family putative inner membrane protein	_____________47___________________________75\n_____________\|____________________________\|\n5'-AGU...UCUUU________UAAA___U_______A____AAUCA...UCU-3'\n______________GCCGGGGA_____UG_UUGCGUC_UGAA\n______________:\|\|:\|\|\|\|_____\|\|_:\|\|\|\|:\|_\|:\|\|\n______________UGGUCCCU_____AC_GACGCGG_AUUU\n3'-UUU...GGUUG________UUAGA__C_______C____AAUAA...GUG-5'\n_____________\|____________________________\|\n_____________76___________________________47\n	63 -- 69	53 -- 59	-25.8143 kcal/mol	5.22968 kcal/mol	8.81811 kcal/mol	47 75@LB@ \| \|@LB@5'-AGU...UCUUU UAAA U A AAUCA...UCU-3'@LB@ GCCGGGGA UG UUGCGUC UGAA@LB@ :\|\|:\|\|\|\| \|\| :\|\|\|\|:\| \|:\|\|@LB@ UGGUCCCU AC GACGCGG AUUU@LB@3'-UUU...GGUUG UUAGA C C AAUAA...GUG-5'@LB@ \| \|@LB@ 76 47@LB@@LB@@LB@Energy -11.77 kcal/mol@LB@Hybridization Energy -25.8143 kcal/mol@LB@Unfolding Energy - mRNA 5.22968 kcal/mol@LB@Unfolding Energy - sRNA 8.81811 kcal/mol@LB@@LB@Position - mRNA 48 -- 74@LB@Position - sRNA 48 -- 75@LB@Position Seed - mRNA 63 -- 69@LB@Position Seed - sRNA 53 -- 59@LB@
65	0.003263	0.1727	b2584	pka	-7.67	0.359085	49 -- 62	69 -- 82	protein lysine acetyltransferase	_____________48_____________63\n_____________\|______________\|\n5'-AGG...AUGGC__G___________CGGCG...GUA-3'\n______________CG_CGAUACCGGGG\n______________\|\|_\|:\|:\|\|\|:\|\|\|\n______________GC_GUUGUGGUCCC\n3'-UUU...AUGAC__G___________UUUAG...GUG-5'\n_____________\|______________\|\n_____________83_____________68\n	56 -- 62	69 -- 75	-21.7159 kcal/mol	7.18281 kcal/mol	6.85849 kcal/mol	48 63@LB@ \| \|@LB@5'-AGG...AUGGC G CGGCG...GUA-3'@LB@ CG CGAUACCGGGG@LB@ \|\| \|:\|:\|\|\|:\|\|\|@LB@ GC GUUGUGGUCCC@LB@3'-UUU...AUGAC G UUUAG...GUG-5'@LB@ \| \|@LB@ 83 68@LB@@LB@@LB@Energy -7.67 kcal/mol@LB@Hybridization Energy -21.7159 kcal/mol@LB@Unfolding Energy - mRNA 7.18281 kcal/mol@LB@Unfolding Energy - sRNA 6.85849 kcal/mol@LB@@LB@Position - mRNA 49 -- 62@LB@Position - sRNA 69 -- 82@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 69 -- 75@LB@
123	0.00672	0.1913	b0882	clpA	-10.14	0.130927	50 -- 58	66 -- 74	ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity	_____________49________59\n_____________\|_________\|\n5'-UUU...CACUA_________GGCCA...CGC-3'\n______________CCAGGGGAA\n______________\|\|\|\|\|\|:\|\|\n______________GGUCCCUUU\n3'-UUU...GUUGU_________AGAAC...GUG-5'\n_____________\|_________\|\n_____________75________65\n	52 -- 58	66 -- 72	-13.8898 kcal/mol	0.70189 kcal/mol	3.04768 kcal/mol	49 59@LB@ \| \|@LB@5'-UUU...CACUA GGCCA...CGC-3'@LB@ CCAGGGGAA@LB@ \|\|\|\|\|\|:\|\|@LB@ GGUCCCUUU@LB@3'-UUU...GUUGU AGAAC...GUG-5'@LB@ \| \|@LB@ 75 65@LB@@LB@@LB@Energy -10.14 kcal/mol@LB@Hybridization Energy -13.8898 kcal/mol@LB@Unfolding Energy - mRNA 0.70189 kcal/mol@LB@Unfolding Energy - sRNA 3.04768 kcal/mol@LB@@LB@Position - mRNA 50 -- 58@LB@Position - sRNA 66 -- 74@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 66 -- 72@LB@
85	0.004761	0.1855	b2077	iceT	-11.46	0.073016	53 -- 74	64 -- 86	putative citrate/iron-citrate/zinc-citrate efflux transporter	_____________52______________________75\n_____________\|_______________________\|\n5'-CGG...UCGGA______G_______CU_______ACCAU...UUC-3'\n______________GCUGCG_CAAC_CC__GGGGAUC\n______________:\|\|\|\|\|_\|\|\|\|_\|\|__\|\|::\|\|\|\n______________UGACGC_GUUG_GG__CCUUUAG\n3'-UUU...GCUUA______G____U__UC_______AACCG...GUG-5'\n_____________\|_______________________\|\n_____________87______________________63\n	68 -- 74	64 -- 70	-29.0378 kcal/mol	10.1908 kcal/mol	7.38435 kcal/mol	52 75@LB@ \| \|@LB@5'-CGG...UCGGA G CU ACCAU...UUC-3'@LB@ GCUGCG CAAC CC GGGGAUC@LB@ :\|\|\|\|\| \|\|\|\| \|\| \|\|::\|\|\|@LB@ UGACGC GUUG GG CCUUUAG@LB@3'-UUU...GCUUA G U UC AACCG...GUG-5'@LB@ \| \|@LB@ 87 63@LB@@LB@@LB@Energy -11.46 kcal/mol@LB@Hybridization Energy -29.0378 kcal/mol@LB@Unfolding Energy - mRNA 10.1908 kcal/mol@LB@Unfolding Energy - sRNA 7.38435 kcal/mol@LB@@LB@Position - mRNA 53 -- 74@LB@Position - sRNA 64 -- 86@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 64 -- 70@LB@
142	0.00825	0.2033	b3457	livH	-8.25	0.287512	56 -- 64	3 -- 11	branched-chain amino acid ABC transporter permease	_____________55________65\n_____________\|_________\|\n5'-GAU...CGUGA_________UGAAC...ACG-3'\n______________UUGGGCCGC\n______________\|::\|\|\|\|\|\|\n______________AGUCCGGCG\n3'-UUU...CAAAA_________UG-5'\n_____________\|_________\|\n_____________12________2\n	58 -- 64	3 -- 9	-16.0849 kcal/mol	2.23282 kcal/mol	5.54194 kcal/mol	55 65@LB@ \| \|@LB@5'-GAU...CGUGA UGAAC...ACG-3'@LB@ UUGGGCCGC@LB@ \|::\|\|\|\|\|\|@LB@ AGUCCGGCG@LB@3'-UUU...CAAAA UG-5'@LB@ \| \|@LB@ 12 2@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -16.0849 kcal/mol@LB@Unfolding Energy - mRNA 2.23282 kcal/mol@LB@Unfolding Energy - sRNA 5.54194 kcal/mol@LB@@LB@Position - mRNA 56 -- 64@LB@Position - sRNA 3 -- 11@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 3 -- 9@LB@
56	0.002848	0.1727	b0797	rhlE	-14.47	0.018687	57 -- 89	53 -- 82	ATP-dependent RNA helicase	_____________56_________________________________90\n_____________\|__________________________________\|\n5'-GAU...AGCAA______U_________U_____A__C________ACAAA...CUG-3'\n______________CGCCAG_CA_CAGGGA_AAUUU_UG_GCUGCGUC\n______________\|\|\|\|\|:_\|\|_\|\|\|\|\|\|_\|\|\|:\|_\|\|_\|\|\|\|\|\|:\|\n______________GCGGUU_GU_GUCCCU_UUAGA_AC_CGACGCGG\n3'-UUU...AUGAC_________G________________________CAUUU...GUG-5'\n_____________\|__________________________________\|\n_____________83_________________________________52\n	83 -- 89	53 -- 59	-38.8186 kcal/mol	7.89252 kcal/mol	16.4547 kcal/mol	56 90@LB@ \| \|@LB@5'-GAU...AGCAA U U A C ACAAA...CUG-3'@LB@ CGCCAG CA CAGGGA AAUUU UG GCUGCGUC@LB@ \|\|\|\|\|: \|\| \|\|\|\|\|\| \|\|\|:\| \|\| \|\|\|\|\|\|:\|@LB@ GCGGUU GU GUCCCU UUAGA AC CGACGCGG@LB@3'-UUU...AUGAC G CAUUU...GUG-5'@LB@ \| \|@LB@ 83 52@LB@@LB@@LB@Energy -14.47 kcal/mol@LB@Hybridization Energy -38.8186 kcal/mol@LB@Unfolding Energy - mRNA 7.89252 kcal/mol@LB@Unfolding Energy - sRNA 16.4547 kcal/mol@LB@@LB@Position - mRNA 57 -- 89@LB@Position - sRNA 53 -- 82@LB@Position Seed - mRNA 83 -- 89@LB@Position Seed - sRNA 53 -- 59@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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