Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
125	0.004538	0.1258	b0951	pqiB	-12.90	0.019327	185 -- 205	37 -- 57	paraquat-inducible SoxRS-regulated MCE domain protein	_____________184___________________206\n_____________\|_____________________\|\n5'-CUG...AGCAU______UCCU___________AUCUA...UUC-3'\n______________GAGGAG____GACAGUAUGGA\n______________:\|\|\|\|:____\|\|\|\|:\|\|\|\|\|\|\n______________UUCCUU____CUGUUAUACCU\n3'-UUU...GUUUU______CAUU___________CGCGU...ACG-5'\n_____________\|_____________________\|\n_____________58____________________36\n	199 -- 205	37 -- 43	-21.8788 kcal/mol	5.24969 kcal/mol	3.68958 kcal/mol	184 206@LB@ \| \|@LB@5'-CUG...AGCAU UCCU AUCUA...UUC-3'@LB@ GAGGAG GACAGUAUGGA@LB@ :\|\|\|\|: \|\|\|\|:\|\|\|\|\|\|@LB@ UUCCUU CUGUUAUACCU@LB@3'-UUU...GUUUU CAUU CGCGU...ACG-5'@LB@ \| \|@LB@ 58 36@LB@@LB@@LB@Energy -12.90 kcal/mol@LB@Hybridization Energy -21.8788 kcal/mol@LB@Unfolding Energy - mRNA 5.24969 kcal/mol@LB@Unfolding Energy - sRNA 3.68958 kcal/mol@LB@@LB@Position - mRNA 185 -- 205@LB@Position - sRNA 37 -- 57@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 37 -- 43@LB@
127	0.004567	0.1258	b2320	pdxB	-8.62	0.223386	291 -- 299	20 -- 28	erythronate-4-phosphate dehydrogenase	_____________290_______300\n_____________\|_________\|\n5'-ACG...CAAUC_________C-3'\n______________CCCGUCGCU\n______________\|\|\|:\|\|\|\|\|\n______________GGGUAGCGA\n3'-UUU...GUUGC_________ACUGC...ACG-5'\n_____________\|_________\|\n_____________29________19\n	293 -- 299	20 -- 26	-15.7186 kcal/mol	1.54056 kcal/mol	5.56153 kcal/mol	290 300@LB@ \| \|@LB@5'-ACG...CAAUC C-3'@LB@ CCCGUCGCU@LB@ \|\|\|:\|\|\|\|\|@LB@ GGGUAGCGA@LB@3'-UUU...GUUGC ACUGC...ACG-5'@LB@ \| \|@LB@ 29 19@LB@@LB@@LB@Energy -8.62 kcal/mol@LB@Hybridization Energy -15.7186 kcal/mol@LB@Unfolding Energy - mRNA 1.54056 kcal/mol@LB@Unfolding Energy - sRNA 5.56153 kcal/mol@LB@@LB@Position - mRNA 291 -- 299@LB@Position - sRNA 20 -- 28@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 20 -- 26@LB@
128	0.004569	0.1258	b3033	yqiB	-9.35	0.155553	90 -- 130	43 -- 87	DUF1249 protein YqiB	_____________89_____________________________________________131\n_____________\|______________________________________________\|\n5'-UGG...GCCGG_____________AUAC______GUA__________AAAUC_____CGCAG...GCG-3'\n______________GAA_CAG____GC____CAGUGG___GAAGAGGGGA_____GACAA\n______________\|\|\|_\|\|:____\|\|____\|\|\|\|::___:\|\|:\|:\|\|:\|_____\|\|\|\|\|\n______________CUU_GUU____CG____GUCAUU___UUUUUUCCUU_____CUGUU\n3'-UUU...GCAUG___A___AACA__AUAC______AAG__________CAUU______AUACC...ACG-5'\n_____________\|______________________________________________\|\n_____________88_____________________________________________42\n	114 -- 120	52 -- 58	-22.1335 kcal/mol	7.07839 kcal/mol	5.71172 kcal/mol	89 131@LB@ \| \|@LB@5'-UGG...GCCGG AUAC GUA AAAUC CGCAG...GCG-3'@LB@ GAA CAG GC CAGUGG GAAGAGGGGA GACAA@LB@ \|\|\| \|\|: \|\| \|\|\|\|:: :\|\|:\|:\|\|:\| \|\|\|\|\|@LB@ CUU GUU CG GUCAUU UUUUUUCCUU CUGUU@LB@3'-UUU...GCAUG A AACA AUAC AAG CAUU AUACC...ACG-5'@LB@ \| \|@LB@ 88 42@LB@@LB@@LB@Energy -9.35 kcal/mol@LB@Hybridization Energy -22.1335 kcal/mol@LB@Unfolding Energy - mRNA 7.07839 kcal/mol@LB@Unfolding Energy - sRNA 5.71172 kcal/mol@LB@@LB@Position - mRNA 90 -- 130@LB@Position - sRNA 43 -- 87@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 52 -- 58@LB@
129	0.00462	0.126	b1795	yeaQ	-13.29	0.014930	139 -- 150	70 -- 81	UPF0410 family protein	_____________138__________151\n_____________\|____________\|\n5'-AUA...CCGAU____________UUUUU...UCC-3'\n______________GUUGUGCUAUGC\n______________:\|\|\|\|\|\|\|\|\|\|\|\n______________UAACACGAUACG\n3'-UUU...UUAGU____________UCAUU...ACG-5'\n_____________\|____________\|\n_____________82___________69\n	144 -- 150	70 -- 76	-18.6071 kcal/mol	3.49189 kcal/mol	1.8201 kcal/mol	138 151@LB@ \| \|@LB@5'-AUA...CCGAU UUUUU...UCC-3'@LB@ GUUGUGCUAUGC@LB@ :\|\|\|\|\|\|\|\|\|\|\|@LB@ UAACACGAUACG@LB@3'-UUU...UUAGU UCAUU...ACG-5'@LB@ \| \|@LB@ 82 69@LB@@LB@@LB@Energy -13.29 kcal/mol@LB@Hybridization Energy -18.6071 kcal/mol@LB@Unfolding Energy - mRNA 3.49189 kcal/mol@LB@Unfolding Energy - sRNA 1.8201 kcal/mol@LB@@LB@Position - mRNA 139 -- 150@LB@Position - sRNA 70 -- 81@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 70 -- 76@LB@
130	0.00465	0.126	b2916	argP	-9.43	0.148863	238 -- 266	47 -- 73	transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor	_____________237___________________________267\n_____________\|_____________________________\|\n5'-GGC...ACUGG__________ACG____C_____UU____CGCGC...CAG-3'\n______________AUGCGGUGAU___UGAA_GAGGA__UGAG\n______________\|\|\|\|:\|\|:\|\|___::\|\|_:\|\|\|\|__\|:\|\|\n______________UACGUCAUUA___GUUU_UUCCU__AUUC\n3'-UUU...CACGA__________A______U_____UC____UGUUA...ACG-5'\n_____________\|_____________________________\|\n_____________74____________________________46\n	240 -- 246	65 -- 71	-19.9139 kcal/mol	5.97985 kcal/mol	4.50495 kcal/mol	237 267@LB@ \| \|@LB@5'-GGC...ACUGG ACG C UU CGCGC...CAG-3'@LB@ AUGCGGUGAU UGAA GAGGA UGAG@LB@ \|\|\|\|:\|\|:\|\| ::\|\| :\|\|\|\| \|:\|\|@LB@ UACGUCAUUA GUUU UUCCU AUUC@LB@3'-UUU...CACGA A U UC UGUUA...ACG-5'@LB@ \| \|@LB@ 74 46@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -19.9139 kcal/mol@LB@Unfolding Energy - mRNA 5.97985 kcal/mol@LB@Unfolding Energy - sRNA 4.50495 kcal/mol@LB@@LB@Position - mRNA 238 -- 266@LB@Position - sRNA 47 -- 73@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 65 -- 71@LB@
131	0.004841	0.1302	b3242	aaeX	-9.57	0.138370	170 -- 176	1 -- 7	DUF1656 family putative inner membrane efflux pump associated protein	_____________169_____177\n_____________\|_______\|\n5'-GCG...AAUAA_______UCUCU...GGG-3'\n______________CGCCUGC\n______________\|:\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	170 -- 176	1 -- 7	-12.9142 kcal/mol	1.00865 kcal/mol	2.34039 kcal/mol	169 177@LB@ \| \|@LB@5'-GCG...AAUAA UCUCU...GGG-3'@LB@ CGCCUGC@LB@ \|:\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.57 kcal/mol@LB@Hybridization Energy -12.9142 kcal/mol@LB@Unfolding Energy - mRNA 1.00865 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 170 -- 176@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 1 -- 7@LB@
132	0.004965	0.1313	b0876	ybjD	-10.35	0.091015	20 -- 74	49 -- 93	putative OLD family ATP-dependent endonuclease; DUF2813 family protein	_____________19______________________________________________________75\n_____________\|_______________________________________________________\|\n5'-CGU...AUUUA__A___U_____U___AUUU_____UUUU_____ACUUA____C___________UAACG...GGG-3'\n______________UC_UGC_AAUUA_UUG____UGUUG____UGCAG_____UCAG_AAGAGGGAGUA\n______________\|\|_\|:\|_\|\|\|:\|_\|\|\|____\|\|:\|:____\|\|\|\|\|_____\|\|\|:_\|\|:\|\|\|:\|\|\|\|\n______________AG_AUG_UUAGU_AAC____ACGAU____ACGUC_____AGUU_UUUUCCUUCAU\n3'-UUU...GCCGC__C___C_____U_____________________AUUA_________________UCUGU...ACG-5'\n_____________\|_______________________________________________________\|\n_____________94______________________________________________________48\n	68 -- 74	49 -- 55	-28.5607 kcal/mol	13.348 kcal/mol	4.86987 kcal/mol	19 75@LB@ \| \|@LB@5'-CGU...AUUUA A U U AUUU UUUU ACUUA C UAACG...GGG-3'@LB@ UC UGC AAUUA UUG UGUUG UGCAG UCAG AAGAGGGAGUA@LB@ \|\| \|:\| \|\|\|:\| \|\|\| \|\|:\|: \|\|\|\|\| \|\|\|: \|\|:\|\|\|:\|\|\|\|@LB@ AG AUG UUAGU AAC ACGAU ACGUC AGUU UUUUCCUUCAU@LB@3'-UUU...GCCGC C C U AUUA UCUGU...ACG-5'@LB@ \| \|@LB@ 94 48@LB@@LB@@LB@Energy -10.35 kcal/mol@LB@Hybridization Energy -28.5607 kcal/mol@LB@Unfolding Energy - mRNA 13.348 kcal/mol@LB@Unfolding Energy - sRNA 4.86987 kcal/mol@LB@@LB@Position - mRNA 20 -- 74@LB@Position - sRNA 49 -- 93@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 49 -- 55@LB@
133	0.004969	0.1313	b0148	hrpB	-12.31	0.028366	190 -- 234	2 -- 40	putative ATP-dependent helicase	_____________189___________________________________________235\n_____________\|_____________________________________________\|\n5'-GCA...CCCUC________UU___G________GCC______UGCCGUC_______AAUUA...AAU-3'\n______________UGGAGCGU__UGU_UCGUCGUU___CGUUGC_______UUACCUG\n______________\|\|\|\|\|\|\|:__:\|:_:\|:\|\|\|:\|___\|\|\|\|\|\|_______\|:\|\|\|\|\|\n______________ACCUCGCG__GCG_GGUAGCGA___GCAACG_______AGUGGAC\n3'-UUU...GUUAU________UU____________ACU______UA____________G-5'\n_____________\|_____________________________________________\|\n_____________41____________________________________________1\n	228 -- 234	2 -- 8	-41.1674 kcal/mol	13.5737 kcal/mol	15.2914 kcal/mol	189 235@LB@ \| \|@LB@5'-GCA...CCCUC UU G GCC UGCCGUC AAUUA...AAU-3'@LB@ UGGAGCGU UGU UCGUCGUU CGUUGC UUACCUG@LB@ \|\|\|\|\|\|\|: :\|: :\|:\|\|\|:\| \|\|\|\|\|\| \|:\|\|\|\|\|@LB@ ACCUCGCG GCG GGUAGCGA GCAACG AGUGGAC@LB@3'-UUU...GUUAU UU ACU UA G-5'@LB@ \| \|@LB@ 41 1@LB@@LB@@LB@Energy -12.31 kcal/mol@LB@Hybridization Energy -41.1674 kcal/mol@LB@Unfolding Energy - mRNA 13.5737 kcal/mol@LB@Unfolding Energy - sRNA 15.2914 kcal/mol@LB@@LB@Position - mRNA 190 -- 234@LB@Position - sRNA 2 -- 40@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 2 -- 8@LB@
134	0.004994	0.1313	b1518	lsrG	-14.53	0.006358	14 -- 66	30 -- 79	autoinducer-2 (AI-2) degrading protein LsrG	_____________13_______________________________________________________67\n_____________\|________________________________________________________\|\n5'-GAG...GGAAA____________GCUA____UC____CGCUUCU____UG_________________AUUUU...AAG-3'\n______________UGUGCUG_GCAG____UCGA__AGGG_______GGUG____GAUAUGGGGCGUAAU\n______________\|\|\|\|\|\|:_\|\|\|\|____\|\|:\|__\|:\|\|_______:\|\|:____:\|\|\|\|\|\|:\|\|\|:\|\|:\n______________ACACGAU_CGUC____AGUU__UUCC_______UCAU____UUAUACCUCGCGUUG\n3'-UUU...AGUUA_______A____AUUA____UU____U__________UCUG_______________CGGGU...ACG-5'\n_____________\|________________________________________________________\|\n_____________80_______________________________________________________29\n	58 -- 64	32 -- 38	-43.6874 kcal/mol	15.7058 kcal/mol	13.4555 kcal/mol	13 67@LB@ \| \|@LB@5'-GAG...GGAAA GCUA UC CGCUUCU UG AUUUU...AAG-3'@LB@ UGUGCUG GCAG UCGA AGGG GGUG GAUAUGGGGCGUAAU@LB@ \|\|\|\|\|\|: \|\|\|\| \|\|:\| \|:\|\| :\|\|: :\|\|\|\|\|\|:\|\|\|:\|\|:@LB@ ACACGAU CGUC AGUU UUCC UCAU UUAUACCUCGCGUUG@LB@3'-UUU...AGUUA A AUUA UU U UCUG CGGGU...ACG-5'@LB@ \| \|@LB@ 80 29@LB@@LB@@LB@Energy -14.53 kcal/mol@LB@Hybridization Energy -43.6874 kcal/mol@LB@Unfolding Energy - mRNA 15.7058 kcal/mol@LB@Unfolding Energy - sRNA 13.4555 kcal/mol@LB@@LB@Position - mRNA 14 -- 66@LB@Position - sRNA 30 -- 79@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 32 -- 38@LB@
135	0.00505	0.1318	b0918	kdsB	-10.75	0.072320	21 -- 54	1 -- 42	3-deoxy-manno-octulosonate cytidylyltransferase	_____________20_________________________________________55\n_____________\|__________________________________________\|\n5'-CCC...GGAAC______U____U______________AAU_____________CCGGU...UUC-3'\n______________UAUGGA___CA_CGUC___UGCUUGA_____CAUU_GCCUGC\n______________\|\|\|\|\|\|___\|\|_\|\|:\|___:\|\|\|\|\|\|_____\|\|\|\|_:\|\|\|\|\|\n______________AUACCU___GU_GCGG___GCGAACU_____GUAA_UGGACG\n3'-UUU...CUGUU______CGC__U____GUA_______GCAAC____G______-5'\n_____________\|_________________________________________\|\n_____________43________________________________________1\n	35 -- 41	17 -- 23	-30.6746 kcal/mol	4.6323 kcal/mol	15.293 kcal/mol	20 55@LB@ \| \|@LB@5'-CCC...GGAAC U U AAU CCGGU...UUC-3'@LB@ UAUGGA CA CGUC UGCUUGA CAUU GCCUGC@LB@ \|\|\|\|\|\| \|\| \|\|:\| :\|\|\|\|\|\| \|\|\|\| :\|\|\|\|\|@LB@ AUACCU GU GCGG GCGAACU GUAA UGGACG@LB@3'-UUU...CUGUU CGC U GUA GCAAC G -5'@LB@ \| \|@LB@ 43 1@LB@@LB@@LB@Energy -10.75 kcal/mol@LB@Hybridization Energy -30.6746 kcal/mol@LB@Unfolding Energy - mRNA 4.6323 kcal/mol@LB@Unfolding Energy - sRNA 15.293 kcal/mol@LB@@LB@Position - mRNA 21 -- 54@LB@Position - sRNA 1 -- 42@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 17 -- 23@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching