Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
47	0.001402	0.105	b2297	pta	-18.38	0.002042	9 -- 40	45 -- 75	phosphate acetyltransferase		_____________8__________________________________41\n_____________\|__________________________________\|\n___5'-CGCAACCU_________UUU______A__UG___________ACAAA...GUC-3'\n______________GGCUGCACG___CGGCAA_UC___GUUUCA_UCA\n______________\|:\|\|:\|\|\|:___\|:\|\|\|\|_\|\|___\|\|\|\|\|\|_\|\|\|\n______________CUGAUGUGU___GUCGUU_AG___CAAAGU_AGU\n3'-UUU...CGUUU__________________A__CAA______G___CCCCU...GCA-5'\n_____________\|__________________________________\|\n_____________76_________________________________44\n	11 -- 17	67 -- 73	-26.9548 kcal/mol	4.83173 kcal/mol	3.74078 kcal/mol	8 41@LB@ \| \|@LB@ 5'-CGCAACCU UUU A UG ACAAA...GUC-3'@LB@ GGCUGCACG CGGCAA UC GUUUCA UCA@LB@ \|:\|\|:\|\|\|: \|:\|\|\|\| \|\| \|\|\|\|\|\| \|\|\|@LB@ CUGAUGUGU GUCGUU AG CAAAGU AGU@LB@3'-UUU...CGUUU A CAA G CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -18.38 kcal/mol@LB@Hybridization Energy -26.9548 kcal/mol@LB@Unfolding Energy - mRNA 4.83173 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 9 -- 40@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 67 -- 73@LB@
56	0.001982	0.1223	b2304	yfcH	-16.49	0.008143	193 -- 225	40 -- 77	putative NAD-dependent nucleotide-sugar epimerase		_____________192_________________________________________226\n_____________\|___________________________________________\|\n5'-AAA...AUCGG________AUGA__________________________A____CAGGA...ACC-3'\n______________GAGGCUGC____ACAUAGUGA_________UCAC_CGG_GGGA\n______________:\|\|:\|\|:\|____\|\|\|:\|\|::\|_________\|\|\|\|_\|:\|_\|\|\|\|\n______________UUCUGAUG____UGUGUCGUU_________AGUG_GUC_CCCU\n3'-UUU...CCCGU_____________________AAGCAACAA____A________AAAGG...GCA-5'\n_____________\|___________________________________________\|\n_____________78__________________________________________39\n	206 -- 212	62 -- 68	-29.217 kcal/mol	7.9505 kcal/mol	4.77871 kcal/mol	192 226@LB@ \| \|@LB@5'-AAA...AUCGG AUGA A CAGGA...ACC-3'@LB@ GAGGCUGC ACAUAGUGA UCAC CGG GGGA@LB@ :\|\|:\|\|:\| \|\|\|:\|\|::\| \|\|\|\| \|:\| \|\|\|\|@LB@ UUCUGAUG UGUGUCGUU AGUG GUC CCCU@LB@3'-UUU...CCCGU AAGCAACAA A AAAGG...GCA-5'@LB@ \| \|@LB@ 78 39@LB@@LB@@LB@Energy -16.49 kcal/mol@LB@Hybridization Energy -29.217 kcal/mol@LB@Unfolding Energy - mRNA 7.9505 kcal/mol@LB@Unfolding Energy - sRNA 4.77871 kcal/mol@LB@@LB@Position - mRNA 193 -- 225@LB@Position - sRNA 40 -- 77@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 62 -- 68@LB@
12	9.939e-05	0.0245	b2308	hisQ	-13.21	0.056865	186 -- 218	34 -- 75	histidine ABC transporter permease		_____________185__________________________________________219\n_____________\|____________________________________________\|\n5'-GAU...CACAC___AGG___G_______________AU_________________GGUGU...UUG-3'\n______________GAC___ACA_GCAGCA___UGUUGU__________GGGUUUUCA\n______________\|\|\|___\|\|\|_:\|\|\|\|\|___:\|\|\|\|\|__________\|\|:\|\|\|:\|\|\n______________CUG___UGU_UGUCGU___GCAACA__________CCUAAAGGU\n3'-UUU...CGUUU___A_____G______UAA______AAGUGAGUCC_________ACGAA...GCA-5'\n_____________\|____________________________________________\|\n_____________76___________________________________________33\n	212 -- 218	34 -- 40	-26.3199 kcal/mol	8.29445 kcal/mol	4.816 kcal/mol	185 219@LB@ \| \|@LB@5'-GAU...CACAC AGG G AU GGUGU...UUG-3'@LB@ GAC ACA GCAGCA UGUUGU GGGUUUUCA@LB@ \|\|\| \|\|\| :\|\|\|\|\| :\|\|\|\|\| \|\|:\|\|\|:\|\|@LB@ CUG UGU UGUCGU GCAACA CCUAAAGGU@LB@3'-UUU...CGUUU A G UAA AAGUGAGUCC ACGAA...GCA-5'@LB@ \| \|@LB@ 76 33@LB@@LB@@LB@Energy -13.21 kcal/mol@LB@Hybridization Energy -26.3199 kcal/mol@LB@Unfolding Energy - mRNA 8.29445 kcal/mol@LB@Unfolding Energy - sRNA 4.816 kcal/mol@LB@@LB@Position - mRNA 186 -- 218@LB@Position - sRNA 34 -- 75@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 34 -- 40@LB@
199	0.01026	0.1776	b2324	mnmC	-11.15	0.152427	29 -- 45	45 -- 74	fused 5-methylaminomethyl-2-thiouridine-forming enzyme methyltransferase and FAD-dependent demodification enzyme		_____________28_____________________________46\n_____________\|______________________________\|\n5'-GCU...UAAUC______________________________AUACC...ACG-3'\n______________ACUGCAC_____________GUUUCAUUCA\n______________\|\|\|:\|\|\|_____________\|\|\|\|\|\|:\|\|\|\n______________UGAUGUG_____________CAAAGUGAGU\n3'-UUU...GUUUC_______UGUCGUUAAGCAA__________CCCCU...GCA-5'\n_____________\|______________________________\|\n_____________75_____________________________44\n	39 -- 45	45 -- 51	-17.885 kcal/mol	2.99426 kcal/mol	3.74056 kcal/mol	28 46@LB@ \| \|@LB@5'-GCU...UAAUC AUACC...ACG-3'@LB@ ACUGCAC GUUUCAUUCA@LB@ \|\|\|:\|\|\| \|\|\|\|\|\|:\|\|\|@LB@ UGAUGUG CAAAGUGAGU@LB@3'-UUU...GUUUC UGUCGUUAAGCAA CCCCU...GCA-5'@LB@ \| \|@LB@ 75 44@LB@@LB@@LB@Energy -11.15 kcal/mol@LB@Hybridization Energy -17.885 kcal/mol@LB@Unfolding Energy - mRNA 2.99426 kcal/mol@LB@Unfolding Energy - sRNA 3.74056 kcal/mol@LB@@LB@Position - mRNA 29 -- 45@LB@Position - sRNA 45 -- 74@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 45 -- 51@LB@
31	0.0004964	0.05552	b2325	yfcL	-14.31	0.031288	272 -- 297	32 -- 57	uncharacterized protein		_____________271__________________________298\n_____________\|____________________________\|\n5'-AAC...GAUGA______________U___U____G____GCC-3'\n______________GUUGUUU_GC_CAG_GGG_AUUU_CGUG\n______________\|\|\|\|\|\|\|_:\|_\|\|\|_\|\|\|_\|\|\|\|_\|:\|\|\n______________CAACAAA_UG_GUC_CCC_UAAA_GUAC\n3'-UUU...UUAAG_______G__A____________G____GAAUA...GCA-5'\n_____________\|____________________________\|\n_____________58___________________________31\n	272 -- 278	51 -- 57	-23.7407 kcal/mol	4.96676 kcal/mol	4.4642 kcal/mol	271 298@LB@ \| \|@LB@5'-AAC...GAUGA U U G GCC-3'@LB@ GUUGUUU GC CAG GGG AUUU CGUG@LB@ \|\|\|\|\|\|\| :\| \|\|\| \|\|\| \|\|\|\| \|:\|\|@LB@ CAACAAA UG GUC CCC UAAA GUAC@LB@3'-UUU...UUAAG G A G GAAUA...GCA-5'@LB@ \| \|@LB@ 58 31@LB@@LB@@LB@Energy -14.31 kcal/mol@LB@Hybridization Energy -23.7407 kcal/mol@LB@Unfolding Energy - mRNA 4.96676 kcal/mol@LB@Unfolding Energy - sRNA 4.4642 kcal/mol@LB@@LB@Position - mRNA 272 -- 297@LB@Position - sRNA 32 -- 57@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 51 -- 57@LB@
131	0.005914	0.1577	b2360	yfdQ	-15.68	0.013816	114 -- 143	46 -- 74	CPS-53 (KpLE1) prophage; uncharacterized protein		_____________113____________________________144\n_____________\|______________________________\|\n5'-UCC...GGAAA___C__________G__AUUAAUA______UUAAU...CUG-3'\n______________ACU_CGCGCAGCAG_UC_______UCAUUC\n______________\|\|\|_\|:\|:\|\|\|\|\|:_\|\|_______\|\|\|:\|\|\n______________UGA_GUGUGUCGUU_AG_______AGUGAG\n3'-UUU...GUUUC___U__________A__CAACAA_______UCCCC...GCA-5'\n_____________\|______________________________\|\n_____________75_____________________________45\n	121 -- 127	61 -- 67	-23.4619 kcal/mol	4.06011 kcal/mol	3.72594 kcal/mol	113 144@LB@ \| \|@LB@5'-UCC...GGAAA C G AUUAAUA UUAAU...CUG-3'@LB@ ACU CGCGCAGCAG UC UCAUUC@LB@ \|\|\| \|:\|:\|\|\|\|\|: \|\| \|\|\|:\|\|@LB@ UGA GUGUGUCGUU AG AGUGAG@LB@3'-UUU...GUUUC U A CAACAA UCCCC...GCA-5'@LB@ \| \|@LB@ 75 45@LB@@LB@@LB@Energy -15.68 kcal/mol@LB@Hybridization Energy -23.4619 kcal/mol@LB@Unfolding Energy - mRNA 4.06011 kcal/mol@LB@Unfolding Energy - sRNA 3.72594 kcal/mol@LB@@LB@Position - mRNA 114 -- 143@LB@Position - sRNA 46 -- 74@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 61 -- 67@LB@
36	0.0006028	0.05893	b2398	yfeC	-12.67	0.075056	159 -- 178	42 -- 76	DUF1323 family putative DNA-binding protein	b2399	_____________158_________________________________179\n_____________\|___________________________________\|\n5'-AUA...CUAAU____C______________________________AAUUG...GCG-3'\n______________AGAC__CACAUA______________CAUUCAGGG\n______________\|\|\|\|__\|\|\|\|:\|______________\|\|:\|\|\|\|\|\|\n______________UCUG__GUGUGU______________GUGAGUCCC\n3'-UUU...CCGUU____AU______CGUUAAGCAACAAA_________CUAAA...GCA-5'\n_____________\|___________________________________\|\n_____________77__________________________________41\n	172 -- 178	42 -- 48	-21.7854 kcal/mol	4.35612 kcal/mol	4.76453 kcal/mol	158 179@LB@ \| \|@LB@5'-AUA...CUAAU C AAUUG...GCG-3'@LB@ AGAC CACAUA CAUUCAGGG@LB@ \|\|\|\| \|\|\|\|:\| \|\|:\|\|\|\|\|\|@LB@ UCUG GUGUGU GUGAGUCCC@LB@3'-UUU...CCGUU AU CGUUAAGCAACAAA CUAAA...GCA-5'@LB@ \| \|@LB@ 77 41@LB@@LB@@LB@Energy -12.67 kcal/mol@LB@Hybridization Energy -21.7854 kcal/mol@LB@Unfolding Energy - mRNA 4.35612 kcal/mol@LB@Unfolding Energy - sRNA 4.76453 kcal/mol@LB@@LB@Position - mRNA 159 -- 178@LB@Position - sRNA 42 -- 76@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 42 -- 48@LB@
107	0.004745	0.1538	b2413	cysZ	-9.47	0.298503	222 -- 238	58 -- 74	sulfate transporter sulfite inhibited		_____________221_______________239\n_____________\|_________________\|\n5'-ACC...CAUCU__CC_____________UUACU...UUU-3'\n______________GC__CACGCAGCGGUUU\n______________:\|__\|\|\|:\|\|\|\|::\|\|:\n______________UG__GUGUGUCGUUAAG\n3'-UUU...GUUUC__AU_____________CAACA...GCA-5'\n_____________\|_________________\|\n_____________75________________57\n	232 -- 238	58 -- 64	-18.5455 kcal/mol	5.77464 kcal/mol	3.3008 kcal/mol	221 239@LB@ \| \|@LB@5'-ACC...CAUCU CC UUACU...UUU-3'@LB@ GC CACGCAGCGGUUU@LB@ :\| \|\|\|:\|\|\|\|::\|\|:@LB@ UG GUGUGUCGUUAAG@LB@3'-UUU...GUUUC AU CAACA...GCA-5'@LB@ \| \|@LB@ 75 57@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -18.5455 kcal/mol@LB@Unfolding Energy - mRNA 5.77464 kcal/mol@LB@Unfolding Energy - sRNA 3.3008 kcal/mol@LB@@LB@Position - mRNA 222 -- 238@LB@Position - sRNA 58 -- 74@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 58 -- 64@LB@
71	0.002886	0.1417	b2431	yfeX	-11.26	0.145044	235 -- 277	40 -- 74	porphyrinogen oxidase cytoplasmic		_____________234_________________________________________278\n_____________\|___________________________________________\|\n5'-AUU...AGAAC____C______________GAUCGAA__CAACGUGAA______AGUUG...CCA-3'\n______________AUUG_CGCGCGGCGAUUUG_______GC_________AGGGGA\n______________\|:\|:_\|:\|:\|:\|\|:\|\|\|:\|_______:\|_________\|\|\|\|\|\|\n______________UGAU_GUGUGUCGUUAAGC_______UG_________UCCCCU\n3'-UUU...GUUUC___________________AACAAAG__AG_____________AAAGG...GCA-5'\n_____________\|___________________________________________\|\n_____________75__________________________________________39\n	246 -- 252	58 -- 64	-30.0675 kcal/mol	14.0273 kcal/mol	4.77707 kcal/mol	234 278@LB@ \| \|@LB@5'-AUU...AGAAC C GAUCGAA CAACGUGAA AGUUG...CCA-3'@LB@ AUUG CGCGCGGCGAUUUG GC AGGGGA@LB@ \|:\|: \|:\|:\|:\|\|:\|\|\|:\| :\| \|\|\|\|\|\|@LB@ UGAU GUGUGUCGUUAAGC UG UCCCCU@LB@3'-UUU...GUUUC AACAAAG AG AAAGG...GCA-5'@LB@ \| \|@LB@ 75 39@LB@@LB@@LB@Energy -11.26 kcal/mol@LB@Hybridization Energy -30.0675 kcal/mol@LB@Unfolding Energy - mRNA 14.0273 kcal/mol@LB@Unfolding Energy - sRNA 4.77707 kcal/mol@LB@@LB@Position - mRNA 235 -- 277@LB@Position - sRNA 40 -- 74@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 58 -- 64@LB@
45	0.001296	0.1014	b2465	tktB	-16.90	0.006168	210 -- 248	39 -- 78	transketolase 2 thiamine triphosphate-binding		_____________209__________________________________________249\n_____________\|____________________________________________\|\n5'-AGU...CCCGA______CU______AU________CG___________UAU____GCGGU...CUG-3'\n______________AAAGAC__UGC_CA__GCGAUUCG______CACUCAG___GGAU\n______________\|\|\|\|\|\|__\|:\|_\|\|__\|\|:\|\|\|\|\|______\|\|\|\|\|\|\|___\|\|\|\|\n______________UUUCUG__AUG_GU__CGUUAAGC______GUGAGUC___CCUA\n3'-UUU...ACCCG___________U__GU________AACAAA_______C______AAGGU...GCA-5'\n_____________\|____________________________________________\|\n_____________79___________________________________________38\n	235 -- 241	44 -- 50	-32.1578 kcal/mol	10.4844 kcal/mol	4.77966 kcal/mol	209 249@LB@ \| \|@LB@5'-AGU...CCCGA CU AU CG UAU GCGGU...CUG-3'@LB@ AAAGAC UGC CA GCGAUUCG CACUCAG GGAU@LB@ \|\|\|\|\|\| \|:\| \|\| \|\|:\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|@LB@ UUUCUG AUG GU CGUUAAGC GUGAGUC CCUA@LB@3'-UUU...ACCCG U GU AACAAA C AAGGU...GCA-5'@LB@ \| \|@LB@ 79 38@LB@@LB@@LB@Energy -16.90 kcal/mol@LB@Hybridization Energy -32.1578 kcal/mol@LB@Unfolding Energy - mRNA 10.4844 kcal/mol@LB@Unfolding Energy - sRNA 4.77966 kcal/mol@LB@@LB@Position - mRNA 210 -- 248@LB@Position - sRNA 39 -- 78@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 44 -- 50@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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