Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
199	0.0124	0.2193	b0128	yadH	-9.95	0.142385	61 -- 79	68 -- 88	putative ABC transporter permease	_____________60____________________80\n_____________\|_____________________\|\n5'-UUA...UUGAA_________G___________UCAAC...UCA-3'\n______________GUGCUGCGU_AGCA__GGGGA\n______________:\|:\|\|\|\|\|:_\|:\|\|__:\|\|\|\|\n______________UAUGACGCG_UUGU__UCCCU\n3'-UUU...GCGCU_________G____GG_____UUAGA...GUG-5'\n_____________\|_____________________\|\n_____________89____________________67\n	61 -- 67	82 -- 88	-26.4707 kcal/mol	9.14335 kcal/mol	7.38144 kcal/mol	60 80@LB@ \| \|@LB@5'-UUA...UUGAA G UCAAC...UCA-3'@LB@ GUGCUGCGU AGCA GGGGA@LB@ :\|:\|\|\|\|\|: \|:\|\| :\|\|\|\|@LB@ UAUGACGCG UUGU UCCCU@LB@3'-UUU...GCGCU G GG UUAGA...GUG-5'@LB@ \| \|@LB@ 89 67@LB@@LB@@LB@Energy -9.95 kcal/mol@LB@Hybridization Energy -26.4707 kcal/mol@LB@Unfolding Energy - mRNA 9.14335 kcal/mol@LB@Unfolding Energy - sRNA 7.38144 kcal/mol@LB@@LB@Position - mRNA 61 -- 79@LB@Position - sRNA 68 -- 88@LB@Position Seed - mRNA 61 -- 67@LB@Position Seed - sRNA 82 -- 88@LB@
63	0.003148	0.1727	b0131	panD	-12.33	0.049519	276 -- 291	70 -- 84	aspartate 1-decarboxylase	_____________275______________292\n_____________\|________________\|\n5'-AUU...GUUCU_______UUG______AUUUU...UUG-3'\n______________UGCGCCA___ACCAGG\n______________\|\|\|\|\|\|\|___\|\|\|\|\|\|\n______________ACGCGGU___UGGUCC\n3'-UUU...UUAUG_______UG_______CUUUA...GUG-5'\n_____________\|________________\|\n_____________85_______________69\n	276 -- 282	78 -- 84	-24.0598 kcal/mol	4.4848 kcal/mol	7.24859 kcal/mol	275 292@LB@ \| \|@LB@5'-AUU...GUUCU UUG AUUUU...UUG-3'@LB@ UGCGCCA ACCAGG@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ ACGCGGU UGGUCC@LB@3'-UUU...UUAUG UG CUUUA...GUG-5'@LB@ \| \|@LB@ 85 69@LB@@LB@@LB@Energy -12.33 kcal/mol@LB@Hybridization Energy -24.0598 kcal/mol@LB@Unfolding Energy - mRNA 4.4848 kcal/mol@LB@Unfolding Energy - sRNA 7.24859 kcal/mol@LB@@LB@Position - mRNA 276 -- 291@LB@Position - sRNA 70 -- 84@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 78 -- 84@LB@
110	0.005921	0.1855	b0156	erpA	-16.74	0.006653	106 -- 166	29 -- 94	iron-sulfur cluster insertion protein	_____________105______________________________________________________________________167\n_____________\|________________________________________________________________________\|\n5'-UAG...AGCCA___A______U__AA_GA__________UAUU____AA_______________________________G__UUUGC...UAC-3'\n______________GCG_GAAUAC_UG__C__AAUACCAGGG____AGAU__UGGC_________GAUUAUUAU__UGGGUUA_AA\n______________\|\|\|_\|\|\|\|\|\|_\|\|__\|__\|\|:\|\|\|\|\|\|\|____\|:\|\|__\|\|\|\|_________:\|\|\|\|\|\|\|\|__\|\|:\|\|\|\|_\|\|\n______________CGC_CUUAUG_AC__G__UUGUGGUCCC____UUUA__ACCG_________UUAAUAAUA__ACUCAAU_UU\n3'-UUU...CCCCA___G_________GC_G___________________GA____ACGCGGCAU_________CU_______G__CCCGU...GUG-5'\n_____________\|________________________________________________________________________\|\n_____________95_______________________________________________________________________28\n	157 -- 163	32 -- 38	-45.8064 kcal/mol	11.5894 kcal/mol	17.4809 kcal/mol	105 167@LB@ \| \|@LB@5'-UAG...AGCCA A U AA GA UAUU AA G UUUGC...UAC-3'@LB@ GCG GAAUAC UG C AAUACCAGGG AGAU UGGC GAUUAUUAU UGGGUUA AA@LB@ \|\|\| \|\|\|\|\|\| \|\| \| \|\|:\|\|\|\|\|\|\| \|:\|\| \|\|\|\| :\|\|\|\|\|\|\|\| \|\|:\|\|\|\| \|\|@LB@ CGC CUUAUG AC G UUGUGGUCCC UUUA ACCG UUAAUAAUA ACUCAAU UU@LB@3'-UUU...CCCCA G GC G GA ACGCGGCAU CU G CCCGU...GUG-5'@LB@ \| \|@LB@ 95 28@LB@@LB@@LB@Energy -16.74 kcal/mol@LB@Hybridization Energy -45.8064 kcal/mol@LB@Unfolding Energy - mRNA 11.5894 kcal/mol@LB@Unfolding Energy - sRNA 17.4809 kcal/mol@LB@@LB@Position - mRNA 106 -- 166@LB@Position - sRNA 29 -- 94@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 32 -- 38@LB@
118	0.006444	0.1913	b0189	rof	-9.63	0.163299	226 -- 241	29 -- 45	modulator of Rho-dependent transcription termination	_____________225_______________242\n_____________\|_________________\|\n5'-AGG...AAUCA_________________UAAUC...GCG-3'\n______________AUUGUGAUGA_UUACGA\n______________\|\|\|:\|\|\|\|\|\|_\|\|\|\|:\|\n______________UAAUACUACU_AAUGUU\n3'-UUU...UUUAA__________C______CCCGU...GUG-5'\n_____________\|_________________\|\n_____________46________________28\n	229 -- 235	36 -- 42	-15.4032 kcal/mol	3.82623 kcal/mol	1.94966 kcal/mol	225 242@LB@ \| \|@LB@5'-AGG...AAUCA UAAUC...GCG-3'@LB@ AUUGUGAUGA UUACGA@LB@ \|\|\|:\|\|\|\|\|\| \|\|\|\|:\|@LB@ UAAUACUACU AAUGUU@LB@3'-UUU...UUUAA C CCCGU...GUG-5'@LB@ \| \|@LB@ 46 28@LB@@LB@@LB@Energy -9.63 kcal/mol@LB@Hybridization Energy -15.4032 kcal/mol@LB@Unfolding Energy - mRNA 3.82623 kcal/mol@LB@Unfolding Energy - sRNA 1.94966 kcal/mol@LB@@LB@Position - mRNA 226 -- 241@LB@Position - sRNA 29 -- 45@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 36 -- 42@LB@
139	0.008022	0.2031	b0311	betA	-9.91	0.144745	36 -- 54	64 -- 80	choline dehydrogenase a flavoprotein	_____________35__________________55\n_____________\|___________________\|\n5'-CGU...CUGGA________U____C_____CCCGG...AAG-3'\n______________UCAACACC_GGGG_GAAUC\n______________:\|\|\|\|\|\|\|_:\|\|\|_:\|\|\|\|\n______________GGUUGUGG_UCCC_UUUAG\n3'-UUU...GACGC___________________AACCG...GUG-5'\n_____________\|___________________\|\n_____________81__________________63\n	37 -- 43	73 -- 79	-20.9821 kcal/mol	4.03056 kcal/mol	7.04361 kcal/mol	35 55@LB@ \| \|@LB@5'-CGU...CUGGA U C CCCGG...AAG-3'@LB@ UCAACACC GGGG GAAUC@LB@ :\|\|\|\|\|\|\| :\|\|\| :\|\|\|\|@LB@ GGUUGUGG UCCC UUUAG@LB@3'-UUU...GACGC AACCG...GUG-5'@LB@ \| \|@LB@ 81 63@LB@@LB@@LB@Energy -9.91 kcal/mol@LB@Hybridization Energy -20.9821 kcal/mol@LB@Unfolding Energy - mRNA 4.03056 kcal/mol@LB@Unfolding Energy - sRNA 7.04361 kcal/mol@LB@@LB@Position - mRNA 36 -- 54@LB@Position - sRNA 64 -- 80@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 73 -- 79@LB@
182	0.01083	0.2089	b0314	betT	-9.44	0.176432	217 -- 228	66 -- 77	choline transporter of high affinity	_____________216__________229\n_____________\|____________\|\n5'-UUC...UUCAC___G________AGGAC...UCC-3'\n______________ACA_CAGGGAAA\n______________\|\|\|_\|\|\|\|\|\|\|\|\n______________UGU_GUCCCUUU\n3'-UUU...GCGGU___G________AGAAC...GUG-5'\n_____________\|____________\|\n_____________78___________65\n	222 -- 228	66 -- 72	-15.8835 kcal/mol	1.82432 kcal/mol	4.61119 kcal/mol	216 229@LB@ \| \|@LB@5'-UUC...UUCAC G AGGAC...UCC-3'@LB@ ACA CAGGGAAA@LB@ \|\|\| \|\|\|\|\|\|\|\|@LB@ UGU GUCCCUUU@LB@3'-UUU...GCGGU G AGAAC...GUG-5'@LB@ \| \|@LB@ 78 65@LB@@LB@@LB@Energy -9.44 kcal/mol@LB@Hybridization Energy -15.8835 kcal/mol@LB@Unfolding Energy - mRNA 1.82432 kcal/mol@LB@Unfolding Energy - sRNA 4.61119 kcal/mol@LB@@LB@Position - mRNA 217 -- 228@LB@Position - sRNA 66 -- 77@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 66 -- 72@LB@
76	0.003978	0.182	b0336	codB	-6.71	0.504284	39 -- 48	1 -- 11	cytosine transporter	_____________38__________49\n_____________\|___________\|\n5'-CCA...UCUUA___________CCACU...UUU-3'\n______________UCAGGCC_UAC\n______________\|\|\|\|\|\|\|_:\|\|\n______________AGUCCGG_GUG\n3'-UUU...CAAAA_______C___-5'\n_____________\|__________\|\n_____________12_________1\n	39 -- 45	5 -- 11	-14.8291 kcal/mol	2.46298 kcal/mol	5.60325 kcal/mol	38 49@LB@ \| \|@LB@5'-CCA...UCUUA CCACU...UUU-3'@LB@ UCAGGCC UAC@LB@ \|\|\|\|\|\|\| :\|\|@LB@ AGUCCGG GUG@LB@3'-UUU...CAAAA C -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -6.71 kcal/mol@LB@Hybridization Energy -14.8291 kcal/mol@LB@Unfolding Energy - mRNA 2.46298 kcal/mol@LB@Unfolding Energy - sRNA 5.60325 kcal/mol@LB@@LB@Position - mRNA 39 -- 48@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 5 -- 11@LB@
167	0.009922	0.2071	b0367	tauC	-5.98	0.628340	152 -- 162	85 -- 95	taurine ABC transporter permease	_____________151_________163\n_____________\|___________\|\n5'-AUA...CGCCA___________GUUUU...UUU-3'\n______________UGCGCGAAUAU\n______________\|\|\|\|\|\|\|\|\|\|:\n______________ACGCGCUUAUG\n3'-UUU...GCCCC___________ACGCG...GUG-5'\n_____________\|___________\|\n_____________96__________84\n	154 -- 160	87 -- 93	-16.0697 kcal/mol	4.17782 kcal/mol	5.90856 kcal/mol	151 163@LB@ \| \|@LB@5'-AUA...CGCCA GUUUU...UUU-3'@LB@ UGCGCGAAUAU@LB@ \|\|\|\|\|\|\|\|\|\|:@LB@ ACGCGCUUAUG@LB@3'-UUU...GCCCC ACGCG...GUG-5'@LB@ \| \|@LB@ 96 84@LB@@LB@@LB@Energy -5.98 kcal/mol@LB@Hybridization Energy -16.0697 kcal/mol@LB@Unfolding Energy - mRNA 4.17782 kcal/mol@LB@Unfolding Energy - sRNA 5.90856 kcal/mol@LB@@LB@Position - mRNA 152 -- 162@LB@Position - sRNA 85 -- 95@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 87 -- 93@LB@
72	0.00375	0.1804	b0386	proC	-10.69	0.102749	216 -- 233	53 -- 70	pyrroline-5-carboxylate reductase NAD(P)-binding	_____________215________________234\n_____________\|__________________\|\n5'-CAU...AAAUC__UUUUA_________G_AAUAU...GGG-3'\n______________GG_____UUGGCUGCG_C\n______________\|\|_____\|\|\|\|\|\|\|\|\|_\|\n______________CC_____AACCGACGC_G\n3'-UUU...UGGUC__UUUAG_________G_CAUUU...GUG-5'\n_____________\|__________________\|\n_____________71_________________52\n	225 -- 231	55 -- 61	-21.889 kcal/mol	4.36146 kcal/mol	6.83419 kcal/mol	215 234@LB@ \| \|@LB@5'-CAU...AAAUC UUUUA G AAUAU...GGG-3'@LB@ GG UUGGCUGCG C@LB@ \|\| \|\|\|\|\|\|\|\|\| \|@LB@ CC AACCGACGC G@LB@3'-UUU...UGGUC UUUAG G CAUUU...GUG-5'@LB@ \| \|@LB@ 71 52@LB@@LB@@LB@Energy -10.69 kcal/mol@LB@Hybridization Energy -21.889 kcal/mol@LB@Unfolding Energy - mRNA 4.36146 kcal/mol@LB@Unfolding Energy - sRNA 6.83419 kcal/mol@LB@@LB@Position - mRNA 216 -- 233@LB@Position - sRNA 53 -- 70@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 55 -- 61@LB@
66	0.003275	0.1727	b0394	mak	-8.12	0.303293	18 -- 92	5 -- 77	manno(fructo)kinase	_____________17_______________________________________________________________________________93\n_____________\|________________________________________________________________________________\|\n5'-GUU...CUUCU____G___C_______CGC____AA_A_G_____CC____AAUUUUUGA_______________GAUAA____CAC____UUGUC...GUG-3'\n______________GCAC_CAG_GAAAUCU___GGCU__G_C_GUAAA__AUUA_________AC_____CACAGCAU_____UUUC___GGCC\n______________:\|\|\|_\|\|\|_\|\|\|\|\|\|\|___\|\|\|\|__\|_\|_\|\|\|\|\|__\|\|\|\|_________\|\|_____\|\|\|\|\|\|\|:_____\|\|\|\|___\|\|\|\|\n______________UGUG_GUC_CUUUAGA___CCGA__C_G_CAUUU__UAAU_________UG_____GUGUCGUG_____AAAG___CCGG\n3'-UUU...GCGGU________C_______A______CG___G_____AA____ACUACUCAA__UUCCC________ACAA_____U______CGUG-5'\n_____________\|________________________________________________________________________________\|\n_____________78_______________________________________________________________________________4\n	70 -- 76	18 -- 24	-46.4183 kcal/mol	15.5654 kcal/mol	22.7286 kcal/mol	17 93@LB@ \| \|@LB@5'-GUU...CUUCU G C CGC AA A G CC AAUUUUUGA GAUAA CAC UUGUC...GUG-3'@LB@ GCAC CAG GAAAUCU GGCU G C GUAAA AUUA AC CACAGCAU UUUC GGCC@LB@ :\|\|\| \|\|\| \|\|\|\|\|\|\| \|\|\|\| \| \| \|\|\|\|\| \|\|\|\| \|\| \|\|\|\|\|\|\|: \|\|\|\| \|\|\|\|@LB@ UGUG GUC CUUUAGA CCGA C G CAUUU UAAU UG GUGUCGUG AAAG CCGG@LB@3'-UUU...GCGGU C A CG G AA ACUACUCAA UUCCC ACAA U CGUG-5'@LB@ \| \|@LB@ 78 4@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -46.4183 kcal/mol@LB@Unfolding Energy - mRNA 15.5654 kcal/mol@LB@Unfolding Energy - sRNA 22.7286 kcal/mol@LB@@LB@Position - mRNA 18 -- 92@LB@Position - sRNA 5 -- 77@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 18 -- 24@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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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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