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
69	0.002809	0.1417	b1925	fliS	-16.42	0.008504	133 -- 153	57 -- 74	flagellar protein potentiates polymerization	_____________132___________________154\n_____________\|_____________________\|\n5'-UUA...CAGCA_____UUA_____________AAAAC...AUG-3'\n______________GCUAC___ACGCAGCAGUUCG\n______________:\|\|\|\|___\|\|:\|\|\|\|\|:\|\|\|\|\n______________UGAUG___UGUGUCGUUAAGC\n3'-UUU...GUUUC_____________________AACAA...GCA-5'\n_____________\|_____________________\|\n_____________75____________________56\n	147 -- 153	57 -- 63	-25.0139 kcal/mol	5.019 kcal/mol	3.57148 kcal/mol	132 154@LB@ \| \|@LB@5'-UUA...CAGCA UUA AAAAC...AUG-3'@LB@ GCUAC ACGCAGCAGUUCG@LB@ :\|\|\|\| \|\|:\|\|\|\|\|:\|\|\|\|@LB@ UGAUG UGUGUCGUUAAGC@LB@3'-UUU...GUUUC AACAA...GCA-5'@LB@ \| \|@LB@ 75 56@LB@@LB@@LB@Energy -16.42 kcal/mol@LB@Hybridization Energy -25.0139 kcal/mol@LB@Unfolding Energy - mRNA 5.019 kcal/mol@LB@Unfolding Energy - sRNA 3.57148 kcal/mol@LB@@LB@Position - mRNA 133 -- 153@LB@Position - sRNA 57 -- 74@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 57 -- 63@LB@
193	0.0098	0.1776	b0757	galK	-12.45	0.083592	134 -- 176	33 -- 76	galactokinase	_____________133____________________________________________177\n_____________\|______________________________________________\|\n5'-CAU...ACCGC________G_______AG__U___CGCG__G____C____A_____UUUCG...GUG-3'\n______________AGA__ACA_GCAGCAG__CG_UUG____CA_UCAG__GAU_UCCAU\n______________\|\|\|__\|\|\|_:\|\|\|\|\|:__\|\|_\|\|\|____\|\|_\|\|\|\|__\|\|\|_\|\|\|\|\|\n______________UCU__UGU_UGUCGUU__GC_AAC____GU_AGUC__CUA_AGGUA\n3'-UUU...CCGUU___GA___G_______AA______AAA___G____CC___A_____CGAAU...GCA-5'\n_____________\|______________________________________________\|\n_____________77_____________________________________________32\n	141 -- 147	61 -- 67	-31.8657 kcal/mol	14.6029 kcal/mol	4.81602 kcal/mol	133 177@LB@ \| \|@LB@5'-CAU...ACCGC G AG U CGCG G C A UUUCG...GUG-3'@LB@ AGA ACA GCAGCAG CG UUG CA UCAG GAU UCCAU@LB@ \|\|\| \|\|\| :\|\|\|\|\|: \|\| \|\|\| \|\| \|\|\|\| \|\|\| \|\|\|\|\|@LB@ UCU UGU UGUCGUU GC AAC GU AGUC CUA AGGUA@LB@3'-UUU...CCGUU GA G AA AAA G CC A CGAAU...GCA-5'@LB@ \| \|@LB@ 77 32@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -31.8657 kcal/mol@LB@Unfolding Energy - mRNA 14.6029 kcal/mol@LB@Unfolding Energy - sRNA 4.81602 kcal/mol@LB@@LB@Position - mRNA 134 -- 176@LB@Position - sRNA 33 -- 76@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 61 -- 67@LB@
41	0.0008963	0.07693	b1378	pfo	-13.27	0.055135	136 -- 164	58 -- 78	pyruvate-flavodoxin oxidoreductase	_____________135___________________________165\n_____________\|_____________________________\|\n5'-GCU...AAUUG_________UACUGGGC____________CGUGC...CAG-3'\n______________AAAGAUUAC________GCGCAGCAAUUU\n______________\|\|\|\|\|:\|\|\|________:\|:\|\|\|\|\|\|\|\|:\n______________UUUCUGAUG________UGUGUCGUUAAG\n3'-UUU...ACCCG_____________________________CAACA...GCA-5'\n_____________\|_____________________________\|\n_____________79____________________________57\n	158 -- 164	58 -- 64	-22.0871 kcal/mol	5.50788 kcal/mol	3.31018 kcal/mol	135 165@LB@ \| \|@LB@5'-GCU...AAUUG UACUGGGC CGUGC...CAG-3'@LB@ AAAGAUUAC GCGCAGCAAUUU@LB@ \|\|\|\|\|:\|\|\| :\|:\|\|\|\|\|\|\|\|:@LB@ UUUCUGAUG UGUGUCGUUAAG@LB@3'-UUU...ACCCG CAACA...GCA-5'@LB@ \| \|@LB@ 79 57@LB@@LB@@LB@Energy -13.27 kcal/mol@LB@Hybridization Energy -22.0871 kcal/mol@LB@Unfolding Energy - mRNA 5.50788 kcal/mol@LB@Unfolding Energy - sRNA 3.31018 kcal/mol@LB@@LB@Position - mRNA 136 -- 164@LB@Position - sRNA 58 -- 78@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 58 -- 64@LB@
81	0.003429	0.1462	b0413	nrdR	-16.32	0.009130	136 -- 177	33 -- 64	Nrd regulon repressor	_____________135_________________________________________178\n_____________\|___________________________________________\|\n5'-AGG...GUUGC__C_________A___UCAG_______UAAAAUA_________UAACC...UGU-3'\n______________GC__UUUGUUGU_UCG____UUCAGGG_______GAUUUCCGU\n______________\|\|__\|\|:\|\|\|\|\|_\|\|:____:\|\|\|\|\|\|_______\|\|\|\|\|\|\|:\|\n______________CG__AAGCAACA_AGU____GAGUCCC_______CUAAAGGUA\n3'-UUU...UGUGU__UU________A______________________________CGAAU...GCA-5'\n_____________\|___________________________________________\|\n_____________65__________________________________________32\n	171 -- 177	33 -- 39	-28.4719 kcal/mol	7.3911 kcal/mol	4.76435 kcal/mol	135 178@LB@ \| \|@LB@5'-AGG...GUUGC C A UCAG UAAAAUA UAACC...UGU-3'@LB@ GC UUUGUUGU UCG UUCAGGG GAUUUCCGU@LB@ \|\| \|\|:\|\|\|\|\| \|\|: :\|\|\|\|\|\| \|\|\|\|\|\|\|:\|@LB@ CG AAGCAACA AGU GAGUCCC CUAAAGGUA@LB@3'-UUU...UGUGU UU A CGAAU...GCA-5'@LB@ \| \|@LB@ 65 32@LB@@LB@@LB@Energy -16.32 kcal/mol@LB@Hybridization Energy -28.4719 kcal/mol@LB@Unfolding Energy - mRNA 7.3911 kcal/mol@LB@Unfolding Energy - sRNA 4.76435 kcal/mol@LB@@LB@Position - mRNA 136 -- 177@LB@Position - sRNA 33 -- 64@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 33 -- 39@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@
137	0.006282	0.1605	b0123	cueO	-13.57	0.047118	144 -- 176	48 -- 78	multicopper oxidase (laccase)	_____________143________________________________177\n_____________\|__________________________________\|\n5'-CUG...AGGGG___________U__A_______AUU_________CUGCU...CGU-3'\n______________AAGGACUAUGC_CA_C_GUUUG___UUGUUUCGC\n______________\|\|:\|\|\|\|\|::\|_\|\|_\|_:\|\|:\|___\|\|\|\|\|\|\|:\|\n______________UUUCUGAUGUG_GU_G_UAAGC___AACAAAGUG\n3'-UUU...ACCCG___________U__C_U_________________AGUCC...GCA-5'\n_____________\|__________________________________\|\n_____________79_________________________________47\n	170 -- 176	48 -- 54	-24.1368 kcal/mol	6.88378 kcal/mol	3.68736 kcal/mol	143 177@LB@ \| \|@LB@5'-CUG...AGGGG U A AUU CUGCU...CGU-3'@LB@ AAGGACUAUGC CA C GUUUG UUGUUUCGC@LB@ \|\|:\|\|\|\|\|::\| \|\| \| :\|\|:\| \|\|\|\|\|\|\|:\|@LB@ UUUCUGAUGUG GU G UAAGC AACAAAGUG@LB@3'-UUU...ACCCG U C U AGUCC...GCA-5'@LB@ \| \|@LB@ 79 47@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -24.1368 kcal/mol@LB@Unfolding Energy - mRNA 6.88378 kcal/mol@LB@Unfolding Energy - sRNA 3.68736 kcal/mol@LB@@LB@Position - mRNA 144 -- 176@LB@Position - sRNA 48 -- 78@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 48 -- 54@LB@
95	0.004386	0.1538	b1083	flgL	-11.72	0.118200	146 -- 194	40 -- 76	flagellar hook-filament junction protein	_____________145_________________________________________________195\n_____________\|___________________________________________________\|\n5'-UUG...UCUGC____G___A______________AUGCGCUGAUUAACA______A______GAUAA...GUA-3'\n______________AGAC_GCA_AC_GCGAUUU_UUG_______________UUCGCU_AGGGGA\n______________\|\|\|\|_:\|\|_\|\|_\|\|:\|\|\|:_\|\|\|_______________\|\|\|:\|\|_\|\|\|\|\|\|\n______________UCUG_UGU_UG_CGUUAAG_AAC_______________AAGUGA_UCCCCU\n3'-UUU...CCGUU____A___G__U_______C___A____________________G______AAAGG...GCA-5'\n_____________\|___________________________________________________\|\n_____________77__________________________________________________39\n	157 -- 163	58 -- 64	-28.9648 kcal/mol	12.4692 kcal/mol	4.77843 kcal/mol	145 195@LB@ \| \|@LB@5'-UUG...UCUGC G A AUGCGCUGAUUAACA A GAUAA...GUA-3'@LB@ AGAC GCA AC GCGAUUU UUG UUCGCU AGGGGA@LB@ \|\|\|\| :\|\| \|\| \|\|:\|\|\|: \|\|\| \|\|\|:\|\| \|\|\|\|\|\|@LB@ UCUG UGU UG CGUUAAG AAC AAGUGA UCCCCU@LB@3'-UUU...CCGUU A G U C A G AAAGG...GCA-5'@LB@ \| \|@LB@ 77 39@LB@@LB@@LB@Energy -11.72 kcal/mol@LB@Hybridization Energy -28.9648 kcal/mol@LB@Unfolding Energy - mRNA 12.4692 kcal/mol@LB@Unfolding Energy - sRNA 4.77843 kcal/mol@LB@@LB@Position - mRNA 146 -- 194@LB@Position - sRNA 40 -- 76@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 58 -- 64@LB@
57	0.002011	0.1223	b3057	bacA	-16.67	0.007222	149 -- 193	41 -- 71	undecaprenyl pyrophosphate phosphatase	_____________148___________________________________________194\n_____________\|_____________________________________________\|\n5'-UUC...UGGUC_______________GACAAG_GGUACAUUUUAAUA_________UUUAU...UUG-3'\n______________AUACGCAGUAGUUCG______C______________AUUUAGGGG\n______________\|:\|\|:\|\|\|:\|:\|\|\|\|______\|______________\|:\|:\|\|\|\|\|\n______________UGUGUGUCGUUAAGC______G______________UGAGUCCCC\n3'-UUU...UCUGA_______________AACAAA________________________UAAAG...GCA-5'\n_____________\|_____________________________________________\|\n_____________72____________________________________________40\n	187 -- 193	41 -- 47	-30.087 kcal/mol	8.67993 kcal/mol	4.74226 kcal/mol	148 194@LB@ \| \|@LB@5'-UUC...UGGUC GACAAG GGUACAUUUUAAUA UUUAU...UUG-3'@LB@ AUACGCAGUAGUUCG C AUUUAGGGG@LB@ \|:\|\|:\|\|\|:\|:\|\|\|\| \| \|:\|:\|\|\|\|\|@LB@ UGUGUGUCGUUAAGC G UGAGUCCCC@LB@3'-UUU...UCUGA AACAAA UAAAG...GCA-5'@LB@ \| \|@LB@ 72 40@LB@@LB@@LB@Energy -16.67 kcal/mol@LB@Hybridization Energy -30.087 kcal/mol@LB@Unfolding Energy - mRNA 8.67993 kcal/mol@LB@Unfolding Energy - sRNA 4.74226 kcal/mol@LB@@LB@Position - mRNA 149 -- 193@LB@Position - sRNA 41 -- 71@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 41 -- 47@LB@
10	6.564e-05	0.0231	b3458	livK	-17.14	0.005196	153 -- 196	35 -- 71	leucine transporter subunit	_____________152____________________________________________197\n_____________\|______________________________________________\|\n5'-UGU...UGUUA______AAAAACAA_____CACAACA______GAAU__________GACUA...CGA-3'\n______________ACACAU________AGCAA_________UCAC____GGGGAUUUUU\n______________\|\|\|\|\|:________\|\|\|\|\|_________\|\|\|\|____\|\|\|\|\|\|\|\|::\n______________UGUGUG________UCGUU_________AGUG____CCCCUAAAGG\n3'-UUU...UCUGA___________________AAGCAACAA____AGU___________UACGA...GCA-5'\n_____________\|______________________________________________\|\n_____________72_____________________________________________34\n	190 -- 196	35 -- 41	-26.3585 kcal/mol	4.43917 kcal/mol	4.78171 kcal/mol	152 197@LB@ \| \|@LB@5'-UGU...UGUUA AAAAACAA CACAACA GAAU GACUA...CGA-3'@LB@ ACACAU AGCAA UCAC GGGGAUUUUU@LB@ \|\|\|\|\|: \|\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|::@LB@ UGUGUG UCGUU AGUG CCCCUAAAGG@LB@3'-UUU...UCUGA AAGCAACAA AGU UACGA...GCA-5'@LB@ \| \|@LB@ 72 34@LB@@LB@@LB@Energy -17.14 kcal/mol@LB@Hybridization Energy -26.3585 kcal/mol@LB@Unfolding Energy - mRNA 4.43917 kcal/mol@LB@Unfolding Energy - sRNA 4.78171 kcal/mol@LB@@LB@Position - mRNA 153 -- 196@LB@Position - sRNA 35 -- 71@LB@Position Seed - mRNA 190 -- 196@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@

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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