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
28	0.0004009	0.04965	b3511	hdeD	-17.16	0.005105	126 -- 176	35 -- 75	acid-resistance membrane protein	_____________125__________________________________________________177\n_____________\|____________________________________________________\|\n5'-GAG...AAAUC________U_UUA__CG________G__AUAGAUUGAUAG____________UUCUU...UCG-3'\n______________GACUGCAU_C___GA__CGUU_UUU_GC____________CAGGGGAUUUUC\n______________\|\|\|\|:\|\|:_\|___:\|__\|\|\|\|_\|\|\|_:\|____________\|\|\|\|\|\|\|\|\|\|:\|\n______________CUGAUGUG_G___UU__GCAA_AAA_UG____________GUCCCCUAAAGG\n3'-UUU...CGUUU________U_UCG__AA____C___G__A_______________________UACGA...GCA-5'\n_____________\|____________________________________________________\|\n_____________76___________________________________________________34\n	170 -- 176	35 -- 41	-34.0299 kcal/mol	12.0619 kcal/mol	4.80541 kcal/mol	125 177@LB@ \| \|@LB@5'-GAG...AAAUC U UUA CG G AUAGAUUGAUAG UUCUU...UCG-3'@LB@ GACUGCAU C GA CGUU UUU GC CAGGGGAUUUUC@LB@ \|\|\|\|:\|\|: \| :\| \|\|\|\| \|\|\| :\| \|\|\|\|\|\|\|\|\|\|:\|@LB@ CUGAUGUG G UU GCAA AAA UG GUCCCCUAAAGG@LB@3'-UUU...CGUUU U UCG AA C G A UACGA...GCA-5'@LB@ \| \|@LB@ 76 34@LB@@LB@@LB@Energy -17.16 kcal/mol@LB@Hybridization Energy -34.0299 kcal/mol@LB@Unfolding Energy - mRNA 12.0619 kcal/mol@LB@Unfolding Energy - sRNA 4.80541 kcal/mol@LB@@LB@Position - mRNA 126 -- 176@LB@Position - sRNA 35 -- 75@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 35 -- 41@LB@
51	0.001671	0.1153	b3527	yhjJ	-13.34	0.053290	153 -- 204	31 -- 75	putative periplasmic M16 family chaperone	_____________152_____________________________________________________205\n_____________\|_______________________________________________________\|\n5'-CUC...UGACC___A___G_____UU___UAUUACCAGGAUA___GA____________CA_____AGGGC...GGC-3'\n______________GAC_ACG_GCAGU__UUU_____________GUU____UCAGGGG_UU__CAUGC\n______________\|\|\|_\|\|:_:\|\|\|:__\|\|:_____________\|\|\|____\|\|\|\|\|\|\|_\|\|__\|\|\|\|\|\n______________CUG_UGU_UGUCG__AAG_____________CAA____AGUCCCC_AA__GUACG\n3'-UUU...CGUUU___A___G_____UU___CAA_____________AGUG_______U__AG_____AAUAU...GCA-5'\n_____________\|_______________________________________________________\|\n_____________76______________________________________________________30\n	189 -- 195	41 -- 47	-32.6504 kcal/mol	12.0549 kcal/mol	7.26183 kcal/mol	152 205@LB@ \| \|@LB@5'-CUC...UGACC A G UU UAUUACCAGGAUA GA CA AGGGC...GGC-3'@LB@ GAC ACG GCAGU UUU GUU UCAGGGG UU CAUGC@LB@ \|\|\| \|\|: :\|\|\|: \|\|: \|\|\| \|\|\|\|\|\|\| \|\| \|\|\|\|\|@LB@ CUG UGU UGUCG AAG CAA AGUCCCC AA GUACG@LB@3'-UUU...CGUUU A G UU CAA AGUG U AG AAUAU...GCA-5'@LB@ \| \|@LB@ 76 30@LB@@LB@@LB@Energy -13.34 kcal/mol@LB@Hybridization Energy -32.6504 kcal/mol@LB@Unfolding Energy - mRNA 12.0549 kcal/mol@LB@Unfolding Energy - sRNA 7.26183 kcal/mol@LB@@LB@Position - mRNA 153 -- 204@LB@Position - sRNA 31 -- 75@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 41 -- 47@LB@
103	0.004595	0.1538	b3554	yiaF	-10.61	0.191588	8 -- 38	46 -- 75	barrier effect co-colonization resistance factor; DUF3053 family lipoprotein	_____________7_________________________________39\n_____________\|_________________________________\|\n____5'-AAUCUCU_______AAAAA_________GCACUA______UUUAA...AGC-3'\n______________GGCUACA_____GGCAA__CG______UCAUUU\n______________\|:\|\|\|\|\|_____:\|\|\|\|__\|\|______\|\|\|:\|:\n______________CUGAUGU_____UCGUU__GC______AGUGAG\n3'-UUU...CGUUU_______GUG_______AA__AACAA_______UCCCC...GCA-5'\n_____________\|_________________________________\|\n_____________76________________________________45\n	8 -- 14	69 -- 75	-17.9003 kcal/mol	3.5618 kcal/mol	3.72616 kcal/mol	7 39@LB@ \| \|@LB@ 5'-AAUCUCU AAAAA GCACUA UUUAA...AGC-3'@LB@ GGCUACA GGCAA CG UCAUUU@LB@ \|:\|\|\|\|\| :\|\|\|\| \|\| \|\|\|:\|:@LB@ CUGAUGU UCGUU GC AGUGAG@LB@3'-UUU...CGUUU GUG AA AACAA UCCCC...GCA-5'@LB@ \| \|@LB@ 76 45@LB@@LB@@LB@Energy -10.61 kcal/mol@LB@Hybridization Energy -17.9003 kcal/mol@LB@Unfolding Energy - mRNA 3.5618 kcal/mol@LB@Unfolding Energy - sRNA 3.72616 kcal/mol@LB@@LB@Position - mRNA 8 -- 38@LB@Position - sRNA 46 -- 75@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 69 -- 75@LB@
62	0.002558	0.1417	b3579	yiaO	-11.31	0.142375	245 -- 258	62 -- 75	2 3-diketo-L-gulonate-binding periplasmic protein	_____________244____________259\n_____________\|______________\|\n5'-ACU...GGCCU________U_____CAUCU...AAA-3'\n______________GGCUGCAU_CAGCA\n______________\|:\|\|:\|\|:_\|\|\|\|\|\n______________CUGAUGUG_GUCGU\n3'-UUU...CGUUU________U_____UAAGC...GCA-5'\n_____________\|______________\|\n_____________76_____________61\n	246 -- 252	68 -- 74	-19.3904 kcal/mol	4.83304 kcal/mol	3.25167 kcal/mol	244 259@LB@ \| \|@LB@5'-ACU...GGCCU U CAUCU...AAA-3'@LB@ GGCUGCAU CAGCA@LB@ \|:\|\|:\|\|: \|\|\|\|\|@LB@ CUGAUGUG GUCGU@LB@3'-UUU...CGUUU U UAAGC...GCA-5'@LB@ \| \|@LB@ 76 61@LB@@LB@@LB@Energy -11.31 kcal/mol@LB@Hybridization Energy -19.3904 kcal/mol@LB@Unfolding Energy - mRNA 4.83304 kcal/mol@LB@Unfolding Energy - sRNA 3.25167 kcal/mol@LB@@LB@Position - mRNA 245 -- 258@LB@Position - sRNA 62 -- 75@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 68 -- 74@LB@
150	0.006982	0.1638	b3581	sgbH	-9.48	0.297019	138 -- 176	34 -- 74	3-keto-L-gulonate 6-phosphate decarboxylase	_____________137________________________________________177\n_____________\|__________________________________________\|\n5'-UUU...UAUCA__GU_________UC__A___CCG__C_______C_______CGCCC...AAG-3'\n______________AC__UAU_CAGCA__UC_UUG___CA_UUCAGGG___UUUCA\n______________\|\|__:\|:_\|\|\|\|\|__\|\|_\|\|\|___\|\|_:\|\|\|\|\|\|___\|\|:\|\|\n______________UG__GUG_GUCGU__AG_AAC___GU_GAGUCCC___AAGGU\n3'-UUU...GUUUC__AU___U_____UA__C___AAA__________CUA_____ACGAA...GCA-5'\n_____________\|__________________________________________\|\n_____________75_________________________________________33\n	164 -- 170	42 -- 48	-24.4875 kcal/mol	10.188 kcal/mol	4.81599 kcal/mol	137 177@LB@ \| \|@LB@5'-UUU...UAUCA GU UC A CCG C C CGCCC...AAG-3'@LB@ AC UAU CAGCA UC UUG CA UUCAGGG UUUCA@LB@ \|\| :\|: \|\|\|\|\| \|\| \|\|\| \|\| :\|\|\|\|\|\| \|\|:\|\|@LB@ UG GUG GUCGU AG AAC GU GAGUCCC AAGGU@LB@3'-UUU...GUUUC AU U UA C AAA CUA ACGAA...GCA-5'@LB@ \| \|@LB@ 75 33@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -24.4875 kcal/mol@LB@Unfolding Energy - mRNA 10.188 kcal/mol@LB@Unfolding Energy - sRNA 4.81599 kcal/mol@LB@@LB@Position - mRNA 138 -- 176@LB@Position - sRNA 34 -- 74@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 42 -- 48@LB@
54	0.00187	0.1218	b3607	cysE	-14.87	0.022582	98 -- 129	42 -- 78	serine acetyltransferase	_____________97_________________________________________130\n_____________\|__________________________________________\|\n5'-CGG...CACGC______GA__________C_____________AACCC_____AACCU...CGA-3'\n______________AAGGAC___GCGCAGCAG__________CACU_____CAGGG\n______________\|\|:\|\|\|___:\|:\|\|\|\|\|:__________\|\|\|\|_____\|\|\|\|\|\n______________UUUCUG___UGUGUCGUU__________GUGA_____GUCCC\n3'-UUU...ACCCG______AUG_________AAGCAACAAA______________CUAAA...GCA-5'\n_____________\|__________________________________________\|\n_____________79_________________________________________41\n	108 -- 114	61 -- 67	-27.0645 kcal/mol	7.42824 kcal/mol	4.76487 kcal/mol	97 130@LB@ \| \|@LB@5'-CGG...CACGC GA C AACCC AACCU...CGA-3'@LB@ AAGGAC GCGCAGCAG CACU CAGGG@LB@ \|\|:\|\|\| :\|:\|\|\|\|\|: \|\|\|\| \|\|\|\|\|@LB@ UUUCUG UGUGUCGUU GUGA GUCCC@LB@3'-UUU...ACCCG AUG AAGCAACAAA CUAAA...GCA-5'@LB@ \| \|@LB@ 79 41@LB@@LB@@LB@Energy -14.87 kcal/mol@LB@Hybridization Energy -27.0645 kcal/mol@LB@Unfolding Energy - mRNA 7.42824 kcal/mol@LB@Unfolding Energy - sRNA 4.76487 kcal/mol@LB@@LB@Position - mRNA 98 -- 129@LB@Position - sRNA 42 -- 78@LB@Position Seed - mRNA 108 -- 114@LB@Position Seed - sRNA 61 -- 67@LB@
72	0.002899	0.1417	b3688	yidQ	-12.98	0.064171	231 -- 261	39 -- 71	DUF1375 family outer membrane protein	_____________230_______________________________262\n_____________\|_________________________________\|\n5'-AUG...UCAUG___________AAUGACA__________A____GCUCC...GAA-3'\n______________AUAUGCAGCGG_________UUACUCGG_GGAU\n______________\|:\|::\|\|\|\|::_________\|:\|\|\|\|:\|_\|\|\|\|\n______________UGUGUGUCGUU_________AGUGAGUC_CCUA\n3'-UUU...UCUGA___________AAGCAACAA________C____AAGGU...GCA-5'\n_____________\|_________________________________\|\n_____________72________________________________38\n	250 -- 256	44 -- 50	-25.1937 kcal/mol	7.46905 kcal/mol	4.74947 kcal/mol	230 262@LB@ \| \|@LB@5'-AUG...UCAUG AAUGACA A GCUCC...GAA-3'@LB@ AUAUGCAGCGG UUACUCGG GGAU@LB@ \|:\|::\|\|\|\|:: \|:\|\|\|\|:\| \|\|\|\|@LB@ UGUGUGUCGUU AGUGAGUC CCUA@LB@3'-UUU...UCUGA AAGCAACAA C AAGGU...GCA-5'@LB@ \| \|@LB@ 72 38@LB@@LB@@LB@Energy -12.98 kcal/mol@LB@Hybridization Energy -25.1937 kcal/mol@LB@Unfolding Energy - mRNA 7.46905 kcal/mol@LB@Unfolding Energy - sRNA 4.74947 kcal/mol@LB@@LB@Position - mRNA 231 -- 261@LB@Position - sRNA 39 -- 71@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 44 -- 50@LB@
3	3.356e-06	0.003937	b3724	phoU	-15.84	0.012477	157 -- 192	43 -- 78	negative regulator of PhoR/PhoB two-component regulator	_____________156____________________________________193\n_____________\|______________________________________\|\n5'-ACC...AAACA______________C_________ACGG__G_______AGUGC...AGC-3'\n______________GAAGACUACAU_CA_CGG_UCGUU____UU_AUUCAGG\n______________:\|\|\|\|\|\|\|\|\|:_\|\|_\|::_\|\|\|\|\|____\|\|_\|:\|\|\|\|\|\n______________UUUCUGAUGUG_GU_GUU_AGCAA____AA_UGAGUCC\n3'-UUU...ACCCG___________U__C___A_____CA____G_______CCUAA...GCA-5'\n_____________\|______________________________________\|\n_____________79_____________________________________42\n	186 -- 192	43 -- 49	-29.823 kcal/mol	9.63349 kcal/mol	4.35315 kcal/mol	156 193@LB@ \| \|@LB@5'-ACC...AAACA C ACGG G AGUGC...AGC-3'@LB@ GAAGACUACAU CA CGG UCGUU UU AUUCAGG@LB@ :\|\|\|\|\|\|\|\|\|: \|\| \|:: \|\|\|\|\| \|\| \|:\|\|\|\|\|@LB@ UUUCUGAUGUG GU GUU AGCAA AA UGAGUCC@LB@3'-UUU...ACCCG U C A CA G CCUAA...GCA-5'@LB@ \| \|@LB@ 79 42@LB@@LB@@LB@Energy -15.84 kcal/mol@LB@Hybridization Energy -29.823 kcal/mol@LB@Unfolding Energy - mRNA 9.63349 kcal/mol@LB@Unfolding Energy - sRNA 4.35315 kcal/mol@LB@@LB@Position - mRNA 157 -- 192@LB@Position - sRNA 43 -- 78@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 43 -- 49@LB@
123	0.005464	0.1553	b3746	ravA	-13.51	0.048673	243 -- 263	41 -- 65	hexameric AAA+ MoxR family ATPase putative molecular chaperone	_____________242_______________________264\n_____________\|_________________________\|\n5'-UGA...GCCUG____________GAAA_________CUUUA...UAU-3'\n______________AGCAGUUCGUUG________AGGGG\n______________\|\|\|\|:\|\|\|\|\|\|\|________\|\|\|\|\|\n______________UCGUUAAGCAAC________UCCCC\n3'-UUU...GUGUG____________AAAGUGAG_____UAAAG...GCA-5'\n_____________\|_________________________\|\n_____________66________________________40\n	248 -- 254	54 -- 60	-25.3509 kcal/mol	7.14336 kcal/mol	4.70281 kcal/mol	242 264@LB@ \| \|@LB@5'-UGA...GCCUG GAAA CUUUA...UAU-3'@LB@ AGCAGUUCGUUG AGGGG@LB@ \|\|\|\|:\|\|\|\|\|\|\| \|\|\|\|\|@LB@ UCGUUAAGCAAC UCCCC@LB@3'-UUU...GUGUG AAAGUGAG UAAAG...GCA-5'@LB@ \| \|@LB@ 66 40@LB@@LB@@LB@Energy -13.51 kcal/mol@LB@Hybridization Energy -25.3509 kcal/mol@LB@Unfolding Energy - mRNA 7.14336 kcal/mol@LB@Unfolding Energy - sRNA 4.70281 kcal/mol@LB@@LB@Position - mRNA 243 -- 263@LB@Position - sRNA 41 -- 65@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 54 -- 60@LB@
42	0.0009586	0.08031	b3747	kup	-11.44	0.134185	159 -- 185	49 -- 77	potassium transporter	_____________158___________________________186\n_____________\|_____________________________\|\n5'-AAA...GCCAA_______A________U___AUA______ACGAA...GUG-3'\n______________GGGACUA_GCACA_CA_UUC____UUUCA\n______________::\|\|\|\|\|_:\|\|\|\|_\|\|_\|\|\|____\|\|\|\|\|\n______________UUCUGAU_UGUGU_GU_AAG____AAAGU\n3'-UUU...CCCGU_______G_____C__U___CAAC_____GAGUC...GCA-5'\n_____________\|_____________________________\|\n_____________78____________________________48\n	159 -- 165	71 -- 77	-19.3471 kcal/mol	4.22429 kcal/mol	3.68465 kcal/mol	158 186@LB@ \| \|@LB@5'-AAA...GCCAA A U AUA ACGAA...GUG-3'@LB@ GGGACUA GCACA CA UUC UUUCA@LB@ ::\|\|\|\|\| :\|\|\|\| \|\| \|\|\| \|\|\|\|\|@LB@ UUCUGAU UGUGU GU AAG AAAGU@LB@3'-UUU...CCCGU G C U CAAC GAGUC...GCA-5'@LB@ \| \|@LB@ 78 48@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -19.3471 kcal/mol@LB@Unfolding Energy - mRNA 4.22429 kcal/mol@LB@Unfolding Energy - sRNA 3.68465 kcal/mol@LB@@LB@Position - mRNA 159 -- 185@LB@Position - sRNA 49 -- 77@LB@Position Seed - mRNA 159 -- 165@LB@Position Seed - sRNA 71 -- 77@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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