Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
166	0.01886	0.3812	b3300	secY	-11.48	0.141920	168 -- 177	196 -- 205	preprotein translocase membrane subunit	_____________167_______________178\n_____________\|_________________\|\n5'-CCU...UCGAA____C_G__________CGAGG...UCC-3'\n______________GCUG_U_GCGGUAAAAU\n______________\|\|\|\|_\|_\|\|\|\|\|\|\|\|\|\|\n______________CGAC_A_CGCCAUUUUA\n3'-UUU...UGAAG______G__________UCACG...UAG-5'\n_____________\|_________________\|\n_____________206_______________195\n	177 -- 183	44 -- 50	-20.9884 kcal/mol	6.84834 kcal/mol	6.15722 kcal/mol	167 178@LB@ \| \|@LB@5'-CCU...UCGAA C G CGAGG...UCC-3'@LB@ GCUG U GCGGUAAAAU@LB@ \|\|\|\| \| \|\|\|\|\|\|\|\|\|\|@LB@ CGAC A CGCCAUUUUA@LB@3'-UUU...UGAAG G UCACG...UAG-5'@LB@ \| \|@LB@ 206 195@LB@@LB@@LB@Energy -11.48 kcal/mol@LB@Hybridization Energy -20.9884 kcal/mol@LB@Unfolding Energy - mRNA 6.84834 kcal/mol@LB@Unfolding Energy - sRNA 6.15722 kcal/mol@LB@@LB@Position - mRNA 168 -- 177@LB@Position - sRNA 196 -- 205@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 44 -- 50@LB@
98	0.01073	0.3575	b0424	yajL	-11.45	0.143367	14 -- 29	155 -- 170	oxidative-stress-resistance chaperone	_____________13_______________30\n_____________\|________________\|\n5'-AGA...GUGAU________________UUGAU...CCA-3'\n______________UACGUGAUGCAGGUGA\n______________:\|\|:\|\|\|\|\|\|\|\|\|::\|\n______________GUGUACUACGUCCGUU\n3'-UUU...UCAGU________________CAGUU...UAG-5'\n_____________\|________________\|\n_____________171______________154\n	22 -- 28	156 -- 162	-24.1359 kcal/mol	6.48358 kcal/mol	7.06607 kcal/mol	13 30@LB@ \| \|@LB@5'-AGA...GUGAU UUGAU...CCA-3'@LB@ UACGUGAUGCAGGUGA@LB@ :\|\|:\|\|\|\|\|\|\|\|\|::\|@LB@ GUGUACUACGUCCGUU@LB@3'-UUU...UCAGU CAGUU...UAG-5'@LB@ \| \|@LB@ 171 154@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -24.1359 kcal/mol@LB@Unfolding Energy - mRNA 6.48358 kcal/mol@LB@Unfolding Energy - sRNA 7.06607 kcal/mol@LB@@LB@Position - mRNA 14 -- 29@LB@Position - sRNA 155 -- 170@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 156 -- 162@LB@
103	0.0111	0.3575	b2821	ptrA	-11.45	0.143539	261 -- 295	141 -- 175	protease III	_____________260_______________________________________296\n_____________\|_________________________________________\|\n5'-GCU...GCACC___A_____G______AA____AU_______CGA_______AACCA-3'\n______________CUU_AGUCA_GCA_GA__CGGG__GG_CAGC___UUCAGGA\n______________\|\|:_\|\|\|\|\|_:\|\|_\|\|__\|:\|\|__:\|_\|\|:\|___\|\|\|\|\|:\|\n______________GAG_UCAGU_UGU_CU__GUCC__UC_GUUG___AAGUCUU\n3'-UUU...GUUAU_________G___A__AC____GU__A____A_________AACGC...UAG-5'\n_____________\|_________________________________________\|\n_____________176_______________________________________140\n	289 -- 295	141 -- 147	-30.7779 kcal/mol	8.8583 kcal/mol	8.83168 kcal/mol	260 296@LB@ \| \|@LB@5'-GCU...GCACC A G AA AU CGA AACCA-3'@LB@ CUU AGUCA GCA GA CGGG GG CAGC UUCAGGA@LB@ \|\|: \|\|\|\|\| :\|\| \|\| \|:\|\| :\| \|\|:\| \|\|\|\|\|:\|@LB@ GAG UCAGU UGU CU GUCC UC GUUG AAGUCUU@LB@3'-UUU...GUUAU G A AC GU A A AACGC...UAG-5'@LB@ \| \|@LB@ 176 140@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -30.7779 kcal/mol@LB@Unfolding Energy - mRNA 8.8583 kcal/mol@LB@Unfolding Energy - sRNA 8.83168 kcal/mol@LB@@LB@Position - mRNA 261 -- 295@LB@Position - sRNA 141 -- 175@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 141 -- 147@LB@
168	0.01937	0.3812	b4354	yjiY	-11.43	0.145336	99 -- 125	132 -- 159	putative transporter	_____________98__________________________________________________126\n_____________\|___________________________________________________\|\n5'-CUU...UACCU_____UACG_______AACUCU_____CA______A_______A_______AUUUA...ACA-3'\n______________UACUU____CGCGCGU______GGCAA__UC_ACU__CAGGAU_GCGGUCA\n______________\|\|\|\|:____\|:\|:\|:\|______\|\|\|\|\|__\|\|_\|\|\|__\|\|\|:\|\|_\|\|\|\|\|\|\|\n______________AUGAG____GUGUGUA______CCGUU__AG_UGA__GUCUUA_CGCCAGU\n3'-UUU...UGGUU_____UCA________CUACGU_____C___U___AA______A_______AGGGU...UAG-5'\n_____________\|___________________________________________________\|\n_____________160_________________________________________________131\n	119 -- 125	132 -- 138	-39.8751 kcal/mol	13.2469 kcal/mol	12.8104 kcal/mol	98 126@LB@ \| \|@LB@5'-CUU...UACCU UACG AACUCU CA A A AUUUA...ACA-3'@LB@ UACUU CGCGCGU GGCAA UC ACU CAGGAU GCGGUCA@LB@ \|\|\|\|: \|:\|:\|:\| \|\|\|\|\| \|\| \|\|\| \|\|\|:\|\| \|\|\|\|\|\|\|@LB@ AUGAG GUGUGUA CCGUU AG UGA GUCUUA CGCCAGU@LB@3'-UUU...UGGUU UCA CUACGU C U AA A AGGGU...UAG-5'@LB@ \| \|@LB@ 160 131@LB@@LB@@LB@Energy -11.43 kcal/mol@LB@Hybridization Energy -39.8751 kcal/mol@LB@Unfolding Energy - mRNA 13.2469 kcal/mol@LB@Unfolding Energy - sRNA 12.8104 kcal/mol@LB@@LB@Position - mRNA 99 -- 125@LB@Position - sRNA 132 -- 159@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 132 -- 138@LB@
55	0.005617	0.3247	b2829	ptsP	-11.41	0.146041	68 -- 133	122 -- 174	PEP-protein phosphotransferase enzyme I; GAF domain containing protein	______________68____________________________________________________________134\n______________\|_____________________________________________________________\|\n___________5'-_______UACACCAGA__U_____G_______AUG___AAGU_________C______G___GGUGG...UGG-3'\n______________CCAGCAG_________GU_UGA_C_GCUGGCG___GGU____UACUGGUAU_CGGUCA_ACA\n______________\|\|\|\|\|\|\|_________\|\|_\|:\|_\|_\|\|\|\|\|\|\|___\|:\|____:\|\|:::\|\|:_\|:\|\|\|\|_\|\|\|\n______________GGUCGUC_________CA_AUU_G_CGACCGC___CUA____GUGGUUAUG_GUCAGU_UGU\n___3'-UUUUUUUU__________________U___A_A_______CCA___AAAU_________A______G___ACUAC...UAG-5'\n_____________\|______________________________________________________________\|\n_____________175____________________________________________________________121\n	25 -- 31	197 -- 203	-46.8098 kcal/mol	17.4414 kcal/mol	18.4949 kcal/mol	68 134@LB@ \| \|@LB@ 5'- UACACCAGA U G AUG AAGU C G GGUGG...UGG-3'@LB@ CCAGCAG GU UGA C GCUGGCG GGU UACUGGUAU CGGUCA ACA@LB@ \|\|\|\|\|\|\| \|\| \|:\| \| \|\|\|\|\|\|\| \|:\| :\|\|:::\|\|: \|:\|\|\|\| \|\|\|@LB@ GGUCGUC CA AUU G CGACCGC CUA GUGGUUAUG GUCAGU UGU@LB@ 3'-UUUUUUUU U A A CCA AAAU A G ACUAC...UAG-5'@LB@ \| \|@LB@ 175 121@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -46.8098 kcal/mol@LB@Unfolding Energy - mRNA 17.4414 kcal/mol@LB@Unfolding Energy - sRNA 18.4949 kcal/mol@LB@@LB@Position - mRNA 68 -- 133@LB@Position - sRNA 122 -- 174@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 197 -- 203@LB@
96	0.01055	0.3575	b1953	yodD	-11.39	0.147949	264 -- 273	196 -- 205	uncharacterized protein	_____________263_____274\n_____________\|_______\|\n5'-CCA...UUCAC_______GUUUU...AAG-3'\n______________CUUCAUC\n______________\|\|\|\|\|\|\|\n______________GAAGUAG\n3'-UUU...GGAAC_______-5'\n_____________\|______\|\n_____________206____196\n	33 -- 39	1 -- 7	-8.82286 kcal/mol	0.690587 kcal/mol	0.701705 kcal/mol	263 274@LB@ \| \|@LB@5'-CCA...UUCAC GUUUU...AAG-3'@LB@ CUUCAUC@LB@ \|\|\|\|\|\|\|@LB@ GAAGUAG@LB@3'-UUU...GGAAC -5'@LB@ \| \|@LB@ 206 196@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -8.82286 kcal/mol@LB@Unfolding Energy - mRNA 0.690587 kcal/mol@LB@Unfolding Energy - sRNA 0.701705 kcal/mol@LB@@LB@Position - mRNA 264 -- 273@LB@Position - sRNA 196 -- 205@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 1 -- 7@LB@
164	0.01856	0.3808	b0715	abrB	-11.36	0.150074	79 -- 113	125 -- 160	regulator of aidB expression; inner membrane protein	_____________78_____________114\n_____________\|______________\|\n5'-GGC...CGGCG______U_______GCCGA-3'\n______________GCGCUA_UACUUGG\n______________:\|:\|:\|_\|\|\|\|::\|\n______________UGUGGU_AUGAGUC\n3'-UUU...UAAAA______U_______AGUGU...UAG-5'\n_____________\|______________\|\n_____________161____________124\n	289 -- 295	174 -- 180	-13.5584 kcal/mol	1.79119 kcal/mol	3.6661 kcal/mol	78 114@LB@ \| \|@LB@5'-GGC...CGGCG U GCCGA-3'@LB@ GCGCUA UACUUGG@LB@ :\|:\|:\| \|\|\|\|::\|@LB@ UGUGGU AUGAGUC@LB@3'-UUU...UAAAA U AGUGU...UAG-5'@LB@ \| \|@LB@ 161 124@LB@@LB@@LB@Energy -11.36 kcal/mol@LB@Hybridization Energy -13.5584 kcal/mol@LB@Unfolding Energy - mRNA 1.79119 kcal/mol@LB@Unfolding Energy - sRNA 3.6661 kcal/mol@LB@@LB@Position - mRNA 79 -- 113@LB@Position - sRNA 125 -- 160@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 174 -- 180@LB@
5	0.0001254	0.08442	b4481	wecF	-11.27	0.155862	165 -- 206	62 -- 99	TDP-Fuc4NAc:lipidIIFuc4NAc transferase	_____________164_____________________________________207\n_____________\|_______________________________________\|\n5'-UUU...GCGUC___G_____U_____UC__GC___________CAG____CUUUA...ACG-3'\n______________ACU_CGGUU_UAUAU__UG__GG_AAGUCAGC___UUCA\n______________\|\|\|_\|:\|\|:_:\|:\|\|__\|\|__\|\|_\|\|\|\|\|\|:\|___\|\|\|\|\n______________UGA_GUCAG_GUGUA__AC__CC_UUCAGUUG___AAGU\n3'-UUU...GGUUA_________U_____CU__GU__G________A______CUUAA...UAG-5'\n_____________\|_______________________________________\|\n_____________100_____________________________________61\n	54 -- 60	149 -- 155	-25.8626 kcal/mol	10.7241 kcal/mol	8.38318 kcal/mol	164 207@LB@ \| \|@LB@5'-UUU...GCGUC G U UC GC CAG CUUUA...ACG-3'@LB@ ACU CGGUU UAUAU UG GG AAGUCAGC UUCA@LB@ \|\|\| \|:\|\|: :\|:\|\| \|\| \|\| \|\|\|\|\|\|:\| \|\|\|\|@LB@ UGA GUCAG GUGUA AC CC UUCAGUUG AAGU@LB@3'-UUU...GGUUA U CU GU G A CUUAA...UAG-5'@LB@ \| \|@LB@ 100 61@LB@@LB@@LB@Energy -11.27 kcal/mol@LB@Hybridization Energy -25.8626 kcal/mol@LB@Unfolding Energy - mRNA 10.7241 kcal/mol@LB@Unfolding Energy - sRNA 8.38318 kcal/mol@LB@@LB@Position - mRNA 165 -- 206@LB@Position - sRNA 62 -- 99@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 149 -- 155@LB@
134	0.01437	0.3575	b1798	leuE	-11.20	0.161096	19 -- 44	168 -- 191	leucine efflux protein	_____________18_________________________45\n_____________\|__________________________\|\n5'-UGC...AGAAU________________UGCCGA____UACCC...AAA-3'\n______________UUUUACGCCAGUAUUU______GCAC\n______________\|\|\|\|\|\|:\|\|\|:\|\|:\|:______:\|\|\|\n______________AAAAUGUGGUUAUGAG______UGUG\n3'-UUU...CCACU________________UCAG______UACUA...UAG-5'\n_____________\|__________________________\|\n_____________192________________________167\n	26 -- 32	178 -- 184	-22.4094 kcal/mol	4.02149 kcal/mol	4.92826 kcal/mol	18 45@LB@ \| \|@LB@5'-UGC...AGAAU UGCCGA UACCC...AAA-3'@LB@ UUUUACGCCAGUAUUU GCAC@LB@ \|\|\|\|\|\|:\|\|\|:\|\|:\|: :\|\|\|@LB@ AAAAUGUGGUUAUGAG UGUG@LB@3'-UUU...CCACU UCAG UACUA...UAG-5'@LB@ \| \|@LB@ 192 167@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -22.4094 kcal/mol@LB@Unfolding Energy - mRNA 4.02149 kcal/mol@LB@Unfolding Energy - sRNA 4.92826 kcal/mol@LB@@LB@Position - mRNA 19 -- 44@LB@Position - sRNA 168 -- 191@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 178 -- 184@LB@
159	0.01779	0.3749	b2504	yfgG	-11.18	0.162405	230 -- 250	168 -- 187	uncharacterized protein	_____________229___________________251\n_____________\|_____________________\|\n5'-CCU...AAACG________UUAA_________GACCC...UUA-3'\n______________ACACCGAU____CAGUCGCAU\n______________\|\|\|\|\|:\|\|____\|\|\|\|\|:\|\|:\n______________UGUGGUUA____GUCAGUGUG\n3'-UUU...UAAAA________UGA__________UACUA...UAG-5'\n_____________\|_____________________\|\n_____________188___________________167\n	244 -- 250	168 -- 174	-22.7597 kcal/mol	5.28018 kcal/mol	4.88067 kcal/mol	229 251@LB@ \| \|@LB@5'-CCU...AAACG UUAA GACCC...UUA-3'@LB@ ACACCGAU CAGUCGCAU@LB@ \|\|\|\|\|:\|\| \|\|\|\|\|:\|\|:@LB@ UGUGGUUA GUCAGUGUG@LB@3'-UUU...UAAAA UGA UACUA...UAG-5'@LB@ \| \|@LB@ 188 167@LB@@LB@@LB@Energy -11.18 kcal/mol@LB@Hybridization Energy -22.7597 kcal/mol@LB@Unfolding Energy - mRNA 5.28018 kcal/mol@LB@Unfolding Energy - sRNA 4.88067 kcal/mol@LB@@LB@Position - mRNA 230 -- 250@LB@Position - sRNA 168 -- 187@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 168 -- 174@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)

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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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