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
72	0.001216	0.05856	b3699	gyrB	-10.53	0.031588	1 -- 17	9 -- 25	DNA gyrase subunit B	______________1________________18\n______________\|________________\|\n___________5'-___UG____________AGCUU...GCA-3'\n______________AGA__AUUUUGCCUCUG\n______________\|\|\|__\|\|:\|\|:\|\|\|\|\|\|\n______________UCU__UAGAAUGGAGAC\n3'-AUU...UUCUA___UG____________AUGGGAUG-5'\n_____________\|_________________\|\n_____________26________________8\n	11 -- 17	9 -- 15	-19.3204 kcal/mol	1.07855 kcal/mol	7.71376 kcal/mol	1 18@LB@ \| \|@LB@ 5'- UG AGCUU...GCA-3'@LB@ AGA AUUUUGCCUCUG@LB@ \|\|\| \|\|:\|\|:\|\|\|\|\|\|@LB@ UCU UAGAAUGGAGAC@LB@3'-AUU...UUCUA UG AUGGGAUG-5'@LB@ \| \|@LB@ 26 8@LB@@LB@@LB@Energy -10.53 kcal/mol@LB@Hybridization Energy -19.3204 kcal/mol@LB@Unfolding Energy - mRNA 1.07855 kcal/mol@LB@Unfolding Energy - sRNA 7.71376 kcal/mol@LB@@LB@Position - mRNA 1 -- 17@LB@Position - sRNA 9 -- 25@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 9 -- 15@LB@
166	0.006804	0.1439	b0475	hemH	-7.56	0.197603	220 -- 228	1 -- 9	ferrochelatase	_____________219_______229\n_____________\|_________\|\n5'-CGG...AACCG_________UGGCA...GCG-3'\n______________GUAUCCUGC\n______________\|\|\|:\|\|\|:\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	222 -- 228	1 -- 7	-12.5413 kcal/mol	2.87943 kcal/mol	2.12872 kcal/mol	219 229@LB@ \| \|@LB@5'-CGG...AACCG UGGCA...GCG-3'@LB@ GUAUCCUGC@LB@ \|\|\|:\|\|\|:\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.56 kcal/mol@LB@Hybridization Energy -12.5413 kcal/mol@LB@Unfolding Energy - mRNA 2.87943 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 220 -- 228@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 1 -- 7@LB@
28	0.0002139	0.02687	b4174	hflK	-10.82	0.025576	125 -- 140	42 -- 58	modulator for HflB protease specific for phage lambda cII repressor	_____________124_______________141\n_____________\|_________________\|\n5'-AGA...GUAGC______A__________CAUAU...GUC-3'\n______________GUCUGA__GCGUGGAGU\n______________:\|\|:\|\|__:\|\|\|\|:\|\|\|\n______________UAGGCU__UGCACUUCA\n3'-AUU...CGGUU______AA_________UUUUC...AUG-5'\n_____________\|_________________\|\n_____________59________________41\n	134 -- 140	42 -- 48	-18.0833 kcal/mol	3.99428 kcal/mol	3.27972 kcal/mol	124 141@LB@ \| \|@LB@5'-AGA...GUAGC A CAUAU...GUC-3'@LB@ GUCUGA GCGUGGAGU@LB@ :\|\|:\|\| :\|\|\|\|:\|\|\|@LB@ UAGGCU UGCACUUCA@LB@3'-AUU...CGGUU AA UUUUC...AUG-5'@LB@ \| \|@LB@ 59 41@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -18.0833 kcal/mol@LB@Unfolding Energy - mRNA 3.99428 kcal/mol@LB@Unfolding Energy - sRNA 3.27972 kcal/mol@LB@@LB@Position - mRNA 125 -- 140@LB@Position - sRNA 42 -- 58@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 42 -- 48@LB@
151	0.006118	0.1406	b1103	hinT	-6.52	0.328434	216 -- 241	45 -- 70	purine nucleoside phosphoramidase dadA activator protein	_____________215________________________242\n_____________\|__________________________\|\n5'-CAA...AAACU_________A_____AUUCGU_____GAUCC...CGC-3'\n______________AUAUUCAGC_AAAUU______CGUGA\n______________\|\|\|\|\|\|\|\|\|_\|\|\|\|:______\|\|\|\|\|\n______________UAUAAGUCG_UUUAG______GCACU\n3'-AUU...GAUUU_________G_____GCUAAU_____UCAUU...AUG-5'\n_____________\|__________________________\|\n_____________71_________________________44\n	218 -- 224	62 -- 68	-20.3535 kcal/mol	5.67357 kcal/mol	8.1779 kcal/mol	215 242@LB@ \| \|@LB@5'-CAA...AAACU A AUUCGU GAUCC...CGC-3'@LB@ AUAUUCAGC AAAUU CGUGA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|: \|\|\|\|\|@LB@ UAUAAGUCG UUUAG GCACU@LB@3'-AUU...GAUUU G GCUAAU UCAUU...AUG-5'@LB@ \| \|@LB@ 71 44@LB@@LB@@LB@Energy -6.52 kcal/mol@LB@Hybridization Energy -20.3535 kcal/mol@LB@Unfolding Energy - mRNA 5.67357 kcal/mol@LB@Unfolding Energy - sRNA 8.1779 kcal/mol@LB@@LB@Position - mRNA 216 -- 241@LB@Position - sRNA 45 -- 70@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 62 -- 68@LB@
186	0.008252	0.1556	b2026	hisI	-8.65	0.106637	17 -- 26	42 -- 51	phosphoribosyl-AMP cyclohydrolase and phosphoribosyl-ATP pyrophosphatase	_____________16_________27\n_____________\|__________\|\n5'-GAA...AAAAG__________UUGCC...UGC-3'\n______________UGCGUGAAGU\n______________\|:\|\|\|\|\|\|\|\|\n______________AUGCACUUCA\n3'-AUU...GGCUA__________UUUUC...AUG-5'\n_____________\|__________\|\n_____________52_________41\n	20 -- 26	42 -- 48	-13.8545 kcal/mol	1.95631 kcal/mol	3.26026 kcal/mol	16 27@LB@ \| \|@LB@5'-GAA...AAAAG UUGCC...UGC-3'@LB@ UGCGUGAAGU@LB@ \|:\|\|\|\|\|\|\|\|@LB@ AUGCACUUCA@LB@3'-AUU...GGCUA UUUUC...AUG-5'@LB@ \| \|@LB@ 52 41@LB@@LB@@LB@Energy -8.65 kcal/mol@LB@Hybridization Energy -13.8545 kcal/mol@LB@Unfolding Energy - mRNA 1.95631 kcal/mol@LB@Unfolding Energy - sRNA 3.26026 kcal/mol@LB@@LB@Position - mRNA 17 -- 26@LB@Position - sRNA 42 -- 51@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 42 -- 48@LB@
177	0.007672	0.1511	b2307	hisM	-10.48	0.032509	175 -- 237	1 -- 57	histidine ABC transporter permease	_____________174__________________________________________________________________238\n_____________\|____________________________________________________________________\|\n5'-CUC...GCUAC____UGGG___________________CCUGU___C___________AUGAAUA___GAA___G____UGUGG...CGG-3'\n______________UCCG____UGUGAAG___AGGG_CUGA_____GAU_GAA_AUCUUAC_______CUG___ACC_CUGC\n______________\|\|\|\|____:\|\|\|\|\|\|___\|:\|\|_\|\|\|\|_____\|\|\|_\|\|\|_\|\|\|\|\|\|\|_______\|\|\|___\|\|\|_\|\|:\|\n______________AGGC____GCACUUC___UUCC_GACU_____CUA_CUU_UAGAAUG_______GAC___UGG_GAUG\n3'-AUU...GGUUU____UAAU_______AUU____A____UU______U___G_______GA________A__________-5'\n_____________\|___________________________________________________________________\|\n_____________58__________________________________________________________________1\n	210 -- 216	14 -- 20	-38.5224 kcal/mol	15.358 kcal/mol	12.7026 kcal/mol	174 238@LB@ \| \|@LB@5'-CUC...GCUAC UGGG CCUGU C AUGAAUA GAA G UGUGG...CGG-3'@LB@ UCCG UGUGAAG AGGG CUGA GAU GAA AUCUUAC CUG ACC CUGC@LB@ \|\|\|\| :\|\|\|\|\|\| \|:\|\| \|\|\|\| \|\|\| \|\|\| \|\|\|\|\|\|\| \|\|\| \|\|\| \|\|:\|@LB@ AGGC GCACUUC UUCC GACU CUA CUU UAGAAUG GAC UGG GAUG@LB@3'-AUU...GGUUU UAAU AUU A UU U G GA A -5'@LB@ \| \|@LB@ 58 1@LB@@LB@@LB@Energy -10.48 kcal/mol@LB@Hybridization Energy -38.5224 kcal/mol@LB@Unfolding Energy - mRNA 15.358 kcal/mol@LB@Unfolding Energy - sRNA 12.7026 kcal/mol@LB@@LB@Position - mRNA 175 -- 237@LB@Position - sRNA 1 -- 57@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 14 -- 20@LB@
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@
174	0.007262	0.1466	b0473	htpG	-8.02	0.153160	10 -- 17	50 -- 57	protein refolding molecular co-chaperone Hsp90 Hsp70-dependent; heat-shock protein; ATPase	_____________9________18\n_____________\|________\|\n5'-UCA...GGCGU________GCGGC...GUG-3'\n______________UCCGGUUG\n______________\|\|\|\|:\|\|:\n______________AGGCUAAU\n3'-AUU...GGUUU________GCACU...AUG-5'\n_____________\|________\|\n_____________58_______49\n	11 -- 17	50 -- 56	-9.07782 kcal/mol	0.753256 kcal/mol	0.317388 kcal/mol	9 18@LB@ \| \|@LB@5'-UCA...GGCGU GCGGC...GUG-3'@LB@ UCCGGUUG@LB@ \|\|\|\|:\|\|:@LB@ AGGCUAAU@LB@3'-AUU...GGUUU GCACU...AUG-5'@LB@ \| \|@LB@ 58 49@LB@@LB@@LB@Energy -8.02 kcal/mol@LB@Hybridization Energy -9.07782 kcal/mol@LB@Unfolding Energy - mRNA 0.753256 kcal/mol@LB@Unfolding Energy - sRNA 0.317388 kcal/mol@LB@@LB@Position - mRNA 10 -- 17@LB@Position - sRNA 50 -- 57@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 50 -- 56@LB@
108	0.003398	0.1101	b0973	hyaB	-11.40	0.016694	267 -- 275	48 -- 56	hydrogenase 1 large subunit	_____________266_______276\n_____________\|_________\|\n5'-GGU...UCGAC_________CGCAU...GCG-3'\n______________CCGAUUACG\n______________\|\|\|\|\|\|\|\|\|\n______________GGCUAAUGC\n3'-AUU...GUUUA_________ACUUC...AUG-5'\n_____________\|_________\|\n_____________57________47\n	269 -- 275	48 -- 54	-14.3171 kcal/mol	1.33562 kcal/mol	1.55919 kcal/mol	266 276@LB@ \| \|@LB@5'-GGU...UCGAC CGCAU...GCG-3'@LB@ CCGAUUACG@LB@ \|\|\|\|\|\|\|\|\|@LB@ GGCUAAUGC@LB@3'-AUU...GUUUA ACUUC...AUG-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -11.40 kcal/mol@LB@Hybridization Energy -14.3171 kcal/mol@LB@Unfolding Energy - mRNA 1.33562 kcal/mol@LB@Unfolding Energy - sRNA 1.55919 kcal/mol@LB@@LB@Position - mRNA 267 -- 275@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 48 -- 54@LB@
183	0.007903	0.1519	b2725	hycA	-8.51	0.115738	229 -- 236	49 -- 56	regulator of the transcriptional regulator FhlA	_____________228______237\n_____________\|________\|\n5'-UUA...GAAAG________AUCGC...AGG-3'\n______________CCGAUUAC\n______________\|\|\|\|\|\|\|\|\n______________GGCUAAUG\n3'-AUU...GUUUA________CACUU...AUG-5'\n_____________\|________\|\n_____________57_______48\n	230 -- 236	49 -- 55	-10.9203 kcal/mol	2.09518 kcal/mol	0.317884 kcal/mol	228 237@LB@ \| \|@LB@5'-UUA...GAAAG AUCGC...AGG-3'@LB@ CCGAUUAC@LB@ \|\|\|\|\|\|\|\|@LB@ GGCUAAUG@LB@3'-AUU...GUUUA CACUU...AUG-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -8.51 kcal/mol@LB@Hybridization Energy -10.9203 kcal/mol@LB@Unfolding Energy - mRNA 2.09518 kcal/mol@LB@Unfolding Energy - sRNA 0.317884 kcal/mol@LB@@LB@Position - mRNA 229 -- 236@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 49 -- 55@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)

Job resubmission

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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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