Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
142	0.005204	0.1284	b3931	hslU	-6.88	0.277791	3 -- 17	52 -- 65	molecular chaperone and ATPase component of HslUV protease		_____________2_______________18\n_____________\|_______________\|\n_________5'-UG________AAA____CUUAU...ACC-3'\n______________CAGCCAGA___CGAU\n______________\|\|\|\|\|\|:\|___\|\|\|\|\n______________GUCGGUUU___GCUA\n3'-AUU...UAUAA________AG_____AUGCA...AUG-5'\n_____________\|_______________\|\n_____________66______________51\n	4 -- 10	58 -- 64	-14.8174 kcal/mol	1.78514 kcal/mol	6.17277 kcal/mol	2 18@LB@ \| \|@LB@ 5'-UG AAA CUUAU...ACC-3'@LB@ CAGCCAGA CGAU@LB@ \|\|\|\|\|\|:\| \|\|\|\|@LB@ GUCGGUUU GCUA@LB@3'-AUU...UAUAA AG AUGCA...AUG-5'@LB@ \| \|@LB@ 66 51@LB@@LB@@LB@Energy -6.88 kcal/mol@LB@Hybridization Energy -14.8174 kcal/mol@LB@Unfolding Energy - mRNA 1.78514 kcal/mol@LB@Unfolding Energy - sRNA 6.17277 kcal/mol@LB@@LB@Position - mRNA 3 -- 17@LB@Position - sRNA 52 -- 65@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 58 -- 64@LB@
97	0.002764	0.1002	b3935	priA	-7.71	0.181779	237 -- 247	3 -- 14	Primosome factor n' (replication factor Y)		_____________236__________248\n_____________\|____________\|\n5'-GAA...CGCUU____________UGACU...GCG-3'\n______________CCUC_GUACCUU\n______________\|\|\|\|_\|\|\|\|\|:\|\n______________GGAG_CAUGGGA\n3'-AUU...AGAAU____A_______UG-5'\n_____________\|____________\|\n_____________15___________2\n	241 -- 247	3 -- 9	-14.2439 kcal/mol	1.19768 kcal/mol	5.35591 kcal/mol	236 248@LB@ \| \|@LB@5'-GAA...CGCUU UGACU...GCG-3'@LB@ CCUC GUACCUU@LB@ \|\|\|\| \|\|\|\|\|:\|@LB@ GGAG CAUGGGA@LB@3'-AUU...AGAAU A UG-5'@LB@ \| \|@LB@ 15 2@LB@@LB@@LB@Energy -7.71 kcal/mol@LB@Hybridization Energy -14.2439 kcal/mol@LB@Unfolding Energy - mRNA 1.19768 kcal/mol@LB@Unfolding Energy - sRNA 5.35591 kcal/mol@LB@@LB@Position - mRNA 237 -- 247@LB@Position - sRNA 3 -- 14@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 3 -- 9@LB@
122	0.004081	0.1177	b3940	metL	-10.48	0.032541	261 -- 280	41 -- 59	Bifunctional aspartokinase/homoserine dehydrogenase 2		_____________260__________________281\n_____________\|____________________\|\n5'-ACG...GCAGU_______CUG__________UUAUU...GCA-3'\n______________AGUCUGG___AUGUGAAGUG\n______________\|:\|\|:\|:___\|:\|\|\|\|\|\|\|:\n______________UUAGGCU___UGCACUUCAU\n3'-AUU...UCGGU_______AA___________UUUCC...AUG-5'\n_____________\|____________________\|\n_____________60___________________40\n	274 -- 280	41 -- 47	-17.3741 kcal/mol	3.59224 kcal/mol	3.31634 kcal/mol	260 281@LB@ \| \|@LB@5'-ACG...GCAGU CUG UUAUU...GCA-3'@LB@ AGUCUGG AUGUGAAGUG@LB@ \|:\|\|:\|: \|:\|\|\|\|\|\|\|:@LB@ UUAGGCU UGCACUUCAU@LB@3'-AUU...UCGGU AA UUUCC...AUG-5'@LB@ \| \|@LB@ 60 40@LB@@LB@@LB@Energy -10.48 kcal/mol@LB@Hybridization Energy -17.3741 kcal/mol@LB@Unfolding Energy - mRNA 3.59224 kcal/mol@LB@Unfolding Energy - sRNA 3.31634 kcal/mol@LB@@LB@Position - mRNA 261 -- 280@LB@Position - sRNA 41 -- 59@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 41 -- 47@LB@
52	0.0006736	0.04557	b3964	yijD	-9.23	0.074829	177 -- 192	43 -- 57	DUF1422 family inner membrane protein		_____________176______________193\n_____________\|________________\|\n5'-ACU...AUUAU_____GAA________GACGA...UGC-3'\n______________UCCGG___AUGUGAAG\n______________\|\|\|\|:___\|:\|\|\|\|\|\|\n______________AGGCU___UGCACUUC\n3'-AUU...GGUUU_____AA_________AUUUU...AUG-5'\n_____________\|________________\|\n_____________58_______________42\n	186 -- 192	43 -- 49	-16.7307 kcal/mol	4.24116 kcal/mol	3.27382 kcal/mol	176 193@LB@ \| \|@LB@5'-ACU...AUUAU GAA GACGA...UGC-3'@LB@ UCCGG AUGUGAAG@LB@ \|\|\|\|: \|:\|\|\|\|\|\|@LB@ AGGCU UGCACUUC@LB@3'-AUU...GGUUU AA AUUUU...AUG-5'@LB@ \| \|@LB@ 58 42@LB@@LB@@LB@Energy -9.23 kcal/mol@LB@Hybridization Energy -16.7307 kcal/mol@LB@Unfolding Energy - mRNA 4.24116 kcal/mol@LB@Unfolding Energy - sRNA 3.27382 kcal/mol@LB@@LB@Position - mRNA 177 -- 192@LB@Position - sRNA 43 -- 57@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 43 -- 49@LB@
140	0.005114	0.1284	b3993	thiE	-7.64	0.188958	243 -- 250	4 -- 11	thiamine phosphate synthase (thiamine phosphate pyrophosphorylase)		_____________242______251\n_____________\|________\|\n5'-CAC...CAGGA________GGUGG...UAC-3'\n______________CUGUACCC\n______________\|\|\|\|\|\|\|\|\n______________GACAUGGG\n3'-AUU...AUGGA________AUG-5'\n_____________\|________\|\n_____________12_______3\n	244 -- 250	4 -- 10	-13.9053 kcal/mol	2.83489 kcal/mol	3.45361 kcal/mol	242 251@LB@ \| \|@LB@5'-CAC...CAGGA GGUGG...UAC-3'@LB@ CUGUACCC@LB@ \|\|\|\|\|\|\|\|@LB@ GACAUGGG@LB@3'-AUU...AUGGA AUG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -7.64 kcal/mol@LB@Hybridization Energy -13.9053 kcal/mol@LB@Unfolding Energy - mRNA 2.83489 kcal/mol@LB@Unfolding Energy - sRNA 3.45361 kcal/mol@LB@@LB@Position - mRNA 243 -- 250@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 4 -- 10@LB@
29	0.0002348	0.02849	b4015	aceA	-10.12	0.041760	186 -- 214	1 -- 27	isocitrate lyase		_____________185____________________________215\n_____________\|______________________________\|\n5'-UUG...UAACU______________ACA__AAA____G___ACAAC...UGA-3'\n______________AUGGAGCAUCU_GC___UG___ACCC_UAC\n______________\|\|:\|\|:\|\|\|\|\|_:\|___\|\|___\|\|\|\|_\|\|\|\n______________UAUCUUGUAGA_UG___AC___UGGG_AUG\n3'-AUU...CUUUC___________A__GAG__A__________-5'\n_____________\|_____________________________\|\n_____________28____________________________1\n	190 -- 196	17 -- 23	-23.282 kcal/mol	5.13768 kcal/mol	8.046 kcal/mol	185 215@LB@ \| \|@LB@5'-UUG...UAACU ACA AAA G ACAAC...UGA-3'@LB@ AUGGAGCAUCU GC UG ACCC UAC@LB@ \|\|:\|\|:\|\|\|\|\| :\| \|\| \|\|\|\| \|\|\|@LB@ UAUCUUGUAGA UG AC UGGG AUG@LB@3'-AUU...CUUUC A GAG A -5'@LB@ \| \|@LB@ 28 1@LB@@LB@@LB@Energy -10.12 kcal/mol@LB@Hybridization Energy -23.282 kcal/mol@LB@Unfolding Energy - mRNA 5.13768 kcal/mol@LB@Unfolding Energy - sRNA 8.046 kcal/mol@LB@@LB@Position - mRNA 186 -- 214@LB@Position - sRNA 1 -- 27@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 17 -- 23@LB@
179	0.007709	0.1511	b4111	proP	-8.76	0.100034	225 -- 232	49 -- 56	proline/glycine betaine transporter		_____________224______233\n_____________\|________\|\n5'-CAC...UAAAA________CCUUC...GUA-3'\n______________CCGAUUAC\n______________\|\|\|\|\|\|\|\|\n______________GGCUAAUG\n3'-AUU...GUUUA________CACUU...AUG-5'\n_____________\|________\|\n_____________57_______48\n	226 -- 232	49 -- 55	-10.6643 kcal/mol	1.60159 kcal/mol	0.317884 kcal/mol	224 233@LB@ \| \|@LB@5'-CAC...UAAAA CCUUC...GUA-3'@LB@ CCGAUUAC@LB@ \|\|\|\|\|\|\|\|@LB@ GGCUAAUG@LB@3'-AUU...GUUUA CACUU...AUG-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -10.6643 kcal/mol@LB@Unfolding Energy - mRNA 1.60159 kcal/mol@LB@Unfolding Energy - sRNA 0.317884 kcal/mol@LB@@LB@Position - mRNA 225 -- 232@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 49 -- 55@LB@
92	0.002567	0.09816	b4120	melB	-8.04	0.151444	195 -- 202	1 -- 8	melibiose:sodium symporter		_____________194______203\n_____________\|________\|\n5'-AUA...CCCGA________GAGCA...ACA-3'\n______________UACCCUAU\n______________\|\|\|\|\|\|\|:\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	196 -- 202	1 -- 7	-10.9179 kcal/mol	0.779946 kcal/mol	2.11603 kcal/mol	194 203@LB@ \| \|@LB@5'-AUA...CCCGA GAGCA...ACA-3'@LB@ UACCCUAU@LB@ \|\|\|\|\|\|\|:@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -8.04 kcal/mol@LB@Hybridization Energy -10.9179 kcal/mol@LB@Unfolding Energy - mRNA 0.779946 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 195 -- 202@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 1 -- 7@LB@
26	0.0002109	0.02687	b4122	fumB	-13.50	0.002989	276 -- 286	47 -- 57	anaerobic class I fumarate hydratase (fumarase B)	b1612	_____________275_________287\n_____________\|___________\|\n5'-UCC...UCACU___________UAGCG...ACU-3'\n______________UCCGAUUACGU\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________AGGCUAAUGCA\n3'-AUU...GGUUU___________CUUCA...AUG-5'\n_____________\|___________\|\n_____________58__________46\n	280 -- 286	47 -- 53	-16.5827 kcal/mol	1.51899 kcal/mol	1.56839 kcal/mol	275 287@LB@ \| \|@LB@5'-UCC...UCACU UAGCG...ACU-3'@LB@ UCCGAUUACGU@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ AGGCUAAUGCA@LB@3'-AUU...GGUUU CUUCA...AUG-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -13.50 kcal/mol@LB@Hybridization Energy -16.5827 kcal/mol@LB@Unfolding Energy - mRNA 1.51899 kcal/mol@LB@Unfolding Energy - sRNA 1.56839 kcal/mol@LB@@LB@Position - mRNA 276 -- 286@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 47 -- 53@LB@
45	0.0004826	0.03773	b4133	cadC	-9.27	0.072737	38 -- 110	5 -- 66	cadBA operon transcriptional activator		_____________37______________________________________________________________________________111\n_____________\|_______________________________________________________________________________\|\n5'-GAU...GGUUC_____A______U_______AAUACUAUGUAAUCAA_____UUAU_______UAAAAAU__________A_________AAUAA...UAA-3'\n______________UCAGU_AAAUCC__UU_CGU________________GAAGU____GG_CUGG_______AACGUCUUGC_UUC___ACC\n______________\|\|\|\|:_\|\|\|\|\|\|__\|\|_\|\|\|________________\|\|\|\|\|____\|\|_\|\|\|:_______\|\|\|:\|\|\|\|:\|_:\|\|___\|\|\|\n______________AGUCG_UUUAGG__AA_GCA________________CUUCA____CC_GACU_______UUGUAGAAUG_GAG___UGG\n3'-AUU...UUAUA_____G______CU__U________________________UUUU__A____UUCUAUC______________ACA___GAUG-5'\n_____________\|_______________________________________________________________________________\|\n_____________67______________________________________________________________________________4\n	97 -- 103	14 -- 20	-38.0459 kcal/mol	10.2122 kcal/mol	18.5819 kcal/mol	37 111@LB@ \| \|@LB@5'-GAU...GGUUC A U AAUACUAUGUAAUCAA UUAU UAAAAAU A AAUAA...UAA-3'@LB@ UCAGU AAAUCC UU CGU GAAGU GG CUGG AACGUCUUGC UUC ACC@LB@ \|\|\|\|: \|\|\|\|\|\| \|\| \|\|\| \|\|\|\|\| \|\| \|\|\|: \|\|\|:\|\|\|\|:\| :\|\| \|\|\|@LB@ AGUCG UUUAGG AA GCA CUUCA CC GACU UUGUAGAAUG GAG UGG@LB@3'-AUU...UUAUA G CU U UUUU A UUCUAUC ACA GAUG-5'@LB@ \| \|@LB@ 67 4@LB@@LB@@LB@Energy -9.27 kcal/mol@LB@Hybridization Energy -38.0459 kcal/mol@LB@Unfolding Energy - mRNA 10.2122 kcal/mol@LB@Unfolding Energy - sRNA 18.5819 kcal/mol@LB@@LB@Position - mRNA 38 -- 110@LB@Position - sRNA 5 -- 66@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 14 -- 20@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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