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
131	0.004483	0.1204	b2069	yegD	-6.32	0.360285	213 -- 222	48 -- 57	Hsp70 chaperone family protein	_____________212________223\n_____________\|__________\|\n5'-CAC...UUGGU__________GUACA...UGC-3'\n______________UUUGAUUACG\n______________\|::\|\|\|\|\|\|\|\n______________AGGCUAAUGC\n3'-AUU...GGUUU__________ACUUC...AUG-5'\n_____________\|__________\|\n_____________58_________47\n	216 -- 222	48 -- 54	-10.2333 kcal/mol	2.33693 kcal/mol	1.55976 kcal/mol	212 223@LB@ \| \|@LB@5'-CAC...UUGGU GUACA...UGC-3'@LB@ UUUGAUUACG@LB@ \|::\|\|\|\|\|\|\|@LB@ AGGCUAAUGC@LB@3'-AUU...GGUUU ACUUC...AUG-5'@LB@ \| \|@LB@ 58 47@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -10.2333 kcal/mol@LB@Unfolding Energy - mRNA 2.33693 kcal/mol@LB@Unfolding Energy - sRNA 1.55976 kcal/mol@LB@@LB@Position - mRNA 213 -- 222@LB@Position - sRNA 48 -- 57@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 48 -- 54@LB@
148	0.00596	0.1406	b3426	glpD	-7.81	0.172743	213 -- 222	50 -- 59	sn-glycerol-3-phosphate dehydrogenase aerobic FAD/NAD(P)-binding	_____________212________223\n_____________\|__________\|\n5'-AAC...CCAAA__________UGAUA...AGG-3'\n______________GAUCUGAUUG\n______________:\|\|\|:\|\|\|\|:\n______________UUAGGCUAAU\n3'-AUU...UCGGU__________GCACU...AUG-5'\n_____________\|__________\|\n_____________60_________49\n	216 -- 222	50 -- 56	-9.79708 kcal/mol	1.6903 kcal/mol	0.31771 kcal/mol	212 223@LB@ \| \|@LB@5'-AAC...CCAAA UGAUA...AGG-3'@LB@ GAUCUGAUUG@LB@ :\|\|\|:\|\|\|\|:@LB@ UUAGGCUAAU@LB@3'-AUU...UCGGU GCACU...AUG-5'@LB@ \| \|@LB@ 60 49@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -9.79708 kcal/mol@LB@Unfolding Energy - mRNA 1.6903 kcal/mol@LB@Unfolding Energy - sRNA 0.31771 kcal/mol@LB@@LB@Position - mRNA 213 -- 222@LB@Position - sRNA 50 -- 59@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 50 -- 56@LB@
127	0.004255	0.1179	b2838	lysA	-9.87	0.049362	214 -- 233	52 -- 69	diaminopimelate decarboxylase PLP-binding	_____________213__________________234\n_____________\|____________________\|\n5'-GGU...UUCAC________A_C___A_____CUCAC...CGC-3'\n______________UGUUCAGC_C_GAU_CCGAU\n______________\|:\|\|\|\|\|\|_\|_:\|\|_\|\|\|\|\|\n______________AUAAGUCG_G_UUA_GGCUA\n3'-AUU...AUUUU__________U_________AUGCA...AUG-5'\n_____________\|____________________\|\n_____________70___________________51\n	215 -- 221	62 -- 68	-18.1264 kcal/mol	2.0842 kcal/mol	6.19243 kcal/mol	213 234@LB@ \| \|@LB@5'-GGU...UUCAC A C A CUCAC...CGC-3'@LB@ UGUUCAGC C GAU CCGAU@LB@ \|:\|\|\|\|\|\| \| :\|\| \|\|\|\|\|@LB@ AUAAGUCG G UUA GGCUA@LB@3'-AUU...AUUUU U AUGCA...AUG-5'@LB@ \| \|@LB@ 70 51@LB@@LB@@LB@Energy -9.87 kcal/mol@LB@Hybridization Energy -18.1264 kcal/mol@LB@Unfolding Energy - mRNA 2.0842 kcal/mol@LB@Unfolding Energy - sRNA 6.19243 kcal/mol@LB@@LB@Position - mRNA 214 -- 233@LB@Position - sRNA 52 -- 69@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 62 -- 68@LB@
130	0.004431	0.1199	b3355	prkB	-7.29	0.227256	214 -- 220	52 -- 58	putative phosphoribulokinase	_____________213_____221\n_____________\|_______\|\n5'-GGC...CAAAC_______CAUUG...AUC-3'\n______________AUCCGGU\n______________\|\|\|\|\|:\|\n______________UAGGCUA\n3'-AUU...CGGUU_______AUGCA...AUG-5'\n_____________\|_______\|\n_____________59______51\n	214 -- 220	52 -- 58	-8.26146 kcal/mol	0.695321 kcal/mol	0.296688 kcal/mol	213 221@LB@ \| \|@LB@5'-GGC...CAAAC CAUUG...AUC-3'@LB@ AUCCGGU@LB@ \|\|\|\|\|:\|@LB@ UAGGCUA@LB@3'-AUU...CGGUU AUGCA...AUG-5'@LB@ \| \|@LB@ 59 51@LB@@LB@@LB@Energy -7.29 kcal/mol@LB@Hybridization Energy -8.26146 kcal/mol@LB@Unfolding Energy - mRNA 0.695321 kcal/mol@LB@Unfolding Energy - sRNA 0.296688 kcal/mol@LB@@LB@Position - mRNA 214 -- 220@LB@Position - sRNA 52 -- 58@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 52 -- 58@LB@
37	0.0003769	0.03584	b1212	prmC	-14.52	0.001141	215 -- 228	43 -- 56	RF-1 and RF-2 N5-glutamine methyltransferase	_____________214____________229\n_____________\|______________\|\n5'-CGU...CAACA______________CAAUA...GCA-3'\n______________CUGGUUACGUGAAG\n______________\|:\|:\|\|\|\|\|\|\|\|\|\|\n______________GGCUAAUGCACUUC\n3'-AUU...GUUUA______________AUUUU...AUG-5'\n_____________\|______________\|\n_____________57_____________42\n	222 -- 228	43 -- 49	-20.863 kcal/mol	3.08488 kcal/mol	3.27327 kcal/mol	214 229@LB@ \| \|@LB@5'-CGU...CAACA CAAUA...GCA-3'@LB@ CUGGUUACGUGAAG@LB@ \|:\|:\|\|\|\|\|\|\|\|\|\|@LB@ GGCUAAUGCACUUC@LB@3'-AUU...GUUUA AUUUU...AUG-5'@LB@ \| \|@LB@ 57 42@LB@@LB@@LB@Energy -14.52 kcal/mol@LB@Hybridization Energy -20.863 kcal/mol@LB@Unfolding Energy - mRNA 3.08488 kcal/mol@LB@Unfolding Energy - sRNA 3.27327 kcal/mol@LB@@LB@Position - mRNA 215 -- 228@LB@Position - sRNA 43 -- 56@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 43 -- 49@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@
81	0.001761	0.07647	b3311	rpsQ	-9.62	0.058411	217 -- 225	1 -- 9	30S ribosomal subunit protein S17	_____________216_______226\n_____________\|_________\|\n5'-GGU...AAUCC_________AAGGU...UCU-3'\n______________GUACUCUGC\n______________\|\|\|\|:\|\|:\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	219 -- 225	1 -- 7	-13.7932 kcal/mol	2.07071 kcal/mol	2.12872 kcal/mol	216 226@LB@ \| \|@LB@5'-GGU...AAUCC AAGGU...UCU-3'@LB@ GUACUCUGC@LB@ \|\|\|\|:\|\|:\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -9.62 kcal/mol@LB@Hybridization Energy -13.7932 kcal/mol@LB@Unfolding Energy - mRNA 2.07071 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 217 -- 225@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 1 -- 7@LB@
155	0.00623	0.1406	b4178	nsrR	-8.53	0.114937	220 -- 228	48 -- 56	nitric oxide-sensitive repressor for NO regulon	_____________219_______229\n_____________\|_________\|\n5'-GGU...UUUCA_________GAUUA...ACG-3'\n______________CUGAUUACG\n______________\|:\|\|\|\|\|\|\|\n______________GGCUAAUGC\n3'-AUU...GUUUA_________ACUUC...AUG-5'\n_____________\|_________\|\n_____________57________47\n	222 -- 228	48 -- 54	-11.8869 kcal/mol	1.78283 kcal/mol	1.55919 kcal/mol	219 229@LB@ \| \|@LB@5'-GGU...UUUCA GAUUA...ACG-3'@LB@ CUGAUUACG@LB@ \|:\|\|\|\|\|\|\|@LB@ GGCUAAUGC@LB@3'-AUU...GUUUA ACUUC...AUG-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -8.53 kcal/mol@LB@Hybridization Energy -11.8869 kcal/mol@LB@Unfolding Energy - mRNA 1.78283 kcal/mol@LB@Unfolding Energy - sRNA 1.55919 kcal/mol@LB@@LB@Position - mRNA 220 -- 228@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 48 -- 54@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@
80	0.001713	0.07533	b1343	dbpA	-13.62	0.002663	221 -- 243	1 -- 24	ATP-dependent RNA helicase specific for 23S rRNA	_____________220______________________244\n_____________\|________________________\|\n5'-ACG...ACCCU______________CC_____A__UCACG...CGC-3'\n______________GAAUGUUUUGCCUC___GCCC_AC\n______________\|\|\|::\|:\|\|:\|\|\|\|___:\|\|\|_\|\|\n______________CUUGUAGAAUGGAG___UGGG_UG\n3'-AUU...UCUAU______________ACA____A__-5'\n_____________\|_______________________\|\n_____________25______________________1\n	228 -- 234	11 -- 17	-24.5457 kcal/mol	2.92371 kcal/mol	8.02158 kcal/mol	220 244@LB@ \| \|@LB@5'-ACG...ACCCU CC A UCACG...CGC-3'@LB@ GAAUGUUUUGCCUC GCCC AC@LB@ \|\|\|::\|:\|\|:\|\|\|\| :\|\|\| \|\|@LB@ CUUGUAGAAUGGAG UGGG UG@LB@3'-AUU...UCUAU ACA A -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -13.62 kcal/mol@LB@Hybridization Energy -24.5457 kcal/mol@LB@Unfolding Energy - mRNA 2.92371 kcal/mol@LB@Unfolding Energy - sRNA 8.02158 kcal/mol@LB@@LB@Position - mRNA 221 -- 243@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 11 -- 17@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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service.

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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