Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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	Additional homologs
34	0.003196	0.3086	b0896	dmsC	-10.70	0.070045	189 -- 235	4 -- 59	dimethyl sulfoxide reductase anaerobic subunit C		_____________188_______________________________________________________236\n_____________\|_________________________________________________________\|\n5'-CUG...CCCGA___A____UG__________________________________CCGC_________CUUCA...AAG-3'\n______________AGG_GGUG___AGAUG___GGAAGUGGAUGGC____AUGAAUGG______UGAUGAU\n______________\|\|\|_\|\|\|:___\|\|\|::___:\|\|\|:\|\|:\|\|\|:\|____\|\|:\|\|\|::______\|\|\|\|\|\|\|\n______________UCC_CCAU___UCUGU___UCUUUACUUACUG____UAUUUAUU______ACUACUA\n3'-UUU...CUUUA________UUG_____AAG_____________CCAU________UCAAUU_______UCG-5'\n_____________\|_________________________________________________________\|\n_____________60________________________________________________________3\n	229 -- 235	4 -- 10	-34.4804 kcal/mol	17.4476 kcal/mol	6.33761 kcal/mol	188 236@LB@ \| \|@LB@5'-CUG...CCCGA A UG CCGC CUUCA...AAG-3'@LB@ AGG GGUG AGAUG GGAAGUGGAUGGC AUGAAUGG UGAUGAU@LB@ \|\|\| \|\|\|: \|\|\|:: :\|\|\|:\|\|:\|\|\|:\| \|\|:\|\|\|:: \|\|\|\|\|\|\|@LB@ UCC CCAU UCUGU UCUUUACUUACUG UAUUUAUU ACUACUA@LB@3'-UUU...CUUUA UUG AAG CCAU UCAAUU UCG-5'@LB@ \| \|@LB@ 60 3@LB@@LB@@LB@Energy -10.70 kcal/mol@LB@Hybridization Energy -34.4804 kcal/mol@LB@Unfolding Energy - mRNA 17.4476 kcal/mol@LB@Unfolding Energy - sRNA 6.33761 kcal/mol@LB@@LB@Position - mRNA 189 -- 235@LB@Position - sRNA 4 -- 59@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 4 -- 10@LB@
39	0.003905	0.3287	b3541	dppD	-12.54	0.027771	124 -- 154	26 -- 56	dipeptide/heme ABC transporter ATPas		_____________123_______________________________155\n_____________\|_________________________________\|\n5'-UUU...CUGAC_______U________ACCU_____________CUGCG...GCG-3'\n______________GGU__GC_GGCAUUUA____GAUGGGUGACGGU\n______________\|\|\|__:\|_\|:\|\|\|\|:\|____:\|\|\|::\|\|\|\|\|\|\|\n______________CCA__UG_CUGUAAGU____UUACUUACUGCCA\n3'-UUU...UAUCC___UU__U________CU_______________UUAUU...UCG-5'\n_____________\|_________________________________\|\n_____________57________________________________25\n	148 -- 154	26 -- 32	-28.6535 kcal/mol	9.81942 kcal/mol	6.29593 kcal/mol	123 155@LB@ \| \|@LB@5'-UUU...CUGAC U ACCU CUGCG...GCG-3'@LB@ GGU GC GGCAUUUA GAUGGGUGACGGU@LB@ \|\|\| :\| \|:\|\|\|\|:\| :\|\|\|::\|\|\|\|\|\|\|@LB@ CCA UG CUGUAAGU UUACUUACUGCCA@LB@3'-UUU...UAUCC UU U CU UUAUU...UCG-5'@LB@ \| \|@LB@ 57 25@LB@@LB@@LB@Energy -12.54 kcal/mol@LB@Hybridization Energy -28.6535 kcal/mol@LB@Unfolding Energy - mRNA 9.81942 kcal/mol@LB@Unfolding Energy - sRNA 6.29593 kcal/mol@LB@@LB@Position - mRNA 124 -- 154@LB@Position - sRNA 26 -- 56@LB@Position Seed - mRNA 148 -- 154@LB@Position Seed - sRNA 26 -- 32@LB@
199	0.03375	0.5555	b3860	dsbA	-9.14	0.142422	273 -- 281	48 -- 56	periplasmic protein disulfide isomerase I		_____________272_______282\n_____________\|_________\|\n5'-UUU...AAGAU_________UACAC...AAC-3'\n______________GGUAAACAG\n______________\|\|\|\|\|\|\|\|\|\n______________CCAUUUGUC\n3'-UUU...UAUCC_________UGUAA...UCG-5'\n_____________\|_________\|\n_____________57________47\n	275 -- 281	48 -- 54	-12.2563 kcal/mol	1.07557 kcal/mol	2.03935 kcal/mol	272 282@LB@ \| \|@LB@5'-UUU...AAGAU UACAC...AAC-3'@LB@ GGUAAACAG@LB@ \|\|\|\|\|\|\|\|\|@LB@ CCAUUUGUC@LB@3'-UUU...UAUCC UGUAA...UCG-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -12.2563 kcal/mol@LB@Unfolding Energy - mRNA 1.07557 kcal/mol@LB@Unfolding Energy - sRNA 2.03935 kcal/mol@LB@@LB@Position - mRNA 273 -- 281@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 48 -- 54@LB@
189	0.03168	0.5492	b1533	eamA	-9.19	0.139150	178 -- 226	1 -- 49	cysteine and O-acetyl-L-serine efflux system		_____________177_______________________________________________________227\n_____________\|_________________________________________________________\|\n5'-GUU...ACAAA____GAA______________________AAU__CGCGA____A________U____GCUAC...UGA-3'\n______________AGAU___AUUCAGA_______GGCGGUAG___GU_____AAAG_UGG_GGUG_UGGC\n______________\|\|\|:___\|\|\|\|\|\|\|_______\|:\|\|\|\|\|:___:\|_____\|\|\|\|_\|::_\|:\|\|_\|:\|\|\n______________UCUG___UAAGUCU_______CUGCCAUU___UA_____UUUC_AUU_CUAC_AUCG\n3'-UUU...AUUUG______________UUACUUA________AUU___________A___A____U____-5'\n_____________\|________________________________________________________\|\n_____________50_______________________________________________________1\n	193 -- 199	24 -- 30	-25.3484 kcal/mol	9.82981 kcal/mol	6.32371 kcal/mol	177 227@LB@ \| \|@LB@5'-GUU...ACAAA GAA AAU CGCGA A U GCUAC...UGA-3'@LB@ AGAU AUUCAGA GGCGGUAG GU AAAG UGG GGUG UGGC@LB@ \|\|\|: \|\|\|\|\|\|\| \|:\|\|\|\|\|: :\| \|\|\|\| \|:: \|:\|\| \|:\|\|@LB@ UCUG UAAGUCU CUGCCAUU UA UUUC AUU CUAC AUCG@LB@3'-UUU...AUUUG UUACUUA AUU A A U -5'@LB@ \| \|@LB@ 50 1@LB@@LB@@LB@Energy -9.19 kcal/mol@LB@Hybridization Energy -25.3484 kcal/mol@LB@Unfolding Energy - mRNA 9.82981 kcal/mol@LB@Unfolding Energy - sRNA 6.32371 kcal/mol@LB@@LB@Position - mRNA 178 -- 226@LB@Position - sRNA 1 -- 49@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 24 -- 30@LB@
190	0.03178	0.5492	b2266	elaB	-7.52	0.274944	163 -- 222	3 -- 61	putative membrane-anchored DUF883 family ribosome-binding protein		_____________162_____________________________________________________________223\n_____________\|_______________________________________________________________\|\n5'-ACU...UGUCU____UUAGU______U_____C_C_______GA___AG____UC___UC______________CACGU...AUC-3'\n______________AUAG_____GACAGG__UUUA_G_AAAUGGA__ACG__AAUG__UAA__AGUU__UGGUGAUA\n______________\|\|\|\|_____:\|\|\|\|:__\|\|:\|_\|_\|\|\|\|\|:\|__\|\|\|__\|\|\|:__\|\|\|__\|\|\|\|__\|\|:\|\|\|\|\|\n______________UAUC_____UUGUCU__AAGU_C_UUUACUU__UGC__UUAU__AUU__UCAA__ACUACUAU\n3'-UUU...AACUU____CCCAU______GU______________AC___CA____UU_________UU________CG-5'\n_____________\|_______________________________________________________________\|\n_____________62______________________________________________________________2\n	216 -- 222	3 -- 9	-26.4945 kcal/mol	12.6276 kcal/mol	6.34398 kcal/mol	162 223@LB@ \| \|@LB@5'-ACU...UGUCU UUAGU U C C GA AG UC UC CACGU...AUC-3'@LB@ AUAG GACAGG UUUA G AAAUGGA ACG AAUG UAA AGUU UGGUGAUA@LB@ \|\|\|\| :\|\|\|\|: \|\|:\| \| \|\|\|\|\|:\| \|\|\| \|\|\|: \|\|\| \|\|\|\| \|\|:\|\|\|\|\|@LB@ UAUC UUGUCU AAGU C UUUACUU UGC UUAU AUU UCAA ACUACUAU@LB@3'-UUU...AACUU CCCAU GU AC CA UU UU CG-5'@LB@ \| \|@LB@ 62 2@LB@@LB@@LB@Energy -7.52 kcal/mol@LB@Hybridization Energy -26.4945 kcal/mol@LB@Unfolding Energy - mRNA 12.6276 kcal/mol@LB@Unfolding Energy - sRNA 6.34398 kcal/mol@LB@@LB@Position - mRNA 163 -- 222@LB@Position - sRNA 3 -- 61@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 3 -- 9@LB@
59	0.008416	0.4523	b0566	envY	-9.46	0.123665	249 -- 263	50 -- 64	porin thermoregulatory transcriptional activator	b1499 b0564 b3515 b4116 b3516	_____________248_____________264\n_____________\|_______________\|\n5'-GGC...AAAAA_______A_______GUCAA...ACU-3'\n______________GAGGUAG_GGUAAGC\n______________\|\|::\|\|\|_\|\|\|\|\|:\|\n______________CUUUAUC_CCAUUUG\n3'-UUU...GCCAA_______C_______UCUGU...UCG-5'\n_____________\|_______________\|\n_____________65______________49\n	257 -- 263	50 -- 56	-15.2892 kcal/mol	5.08919 kcal/mol	0.736811 kcal/mol	248 264@LB@ \| \|@LB@5'-GGC...AAAAA A GUCAA...ACU-3'@LB@ GAGGUAG GGUAAGC@LB@ \|\|::\|\|\| \|\|\|\|\|:\|@LB@ CUUUAUC CCAUUUG@LB@3'-UUU...GCCAA C UCUGU...UCG-5'@LB@ \| \|@LB@ 65 49@LB@@LB@@LB@Energy -9.46 kcal/mol@LB@Hybridization Energy -15.2892 kcal/mol@LB@Unfolding Energy - mRNA 5.08919 kcal/mol@LB@Unfolding Energy - sRNA 0.736811 kcal/mol@LB@@LB@Position - mRNA 249 -- 263@LB@Position - sRNA 50 -- 64@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 50 -- 56@LB@
132	0.0212	0.526	b2455	eutE	-9.17	0.140915	224 -- 235	1 -- 12	aldehyde oxidoreductase ethanolamine utilization protein		_____________223__________236\n_____________\|____________\|\n5'-GGU...GAACA________A___GGUAC...UCG-3'\n______________GGUGGUGA_AGC\n______________::\|\|:\|\|\|_\|\|\|\n______________UUACUACU_UCG\n3'-UUU...UUCAA________A___-5'\n_____________\|___________\|\n_____________13__________1\n	225 -- 231	5 -- 11	-12.5804 kcal/mol	3.3751 kcal/mol	0.0394463 kcal/mol	223 236@LB@ \| \|@LB@5'-GGU...GAACA A GGUAC...UCG-3'@LB@ GGUGGUGA AGC@LB@ ::\|\|:\|\|\| \|\|\|@LB@ UUACUACU UCG@LB@3'-UUU...UUCAA A -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -9.17 kcal/mol@LB@Hybridization Energy -12.5804 kcal/mol@LB@Unfolding Energy - mRNA 3.3751 kcal/mol@LB@Unfolding Energy - sRNA 0.0394463 kcal/mol@LB@@LB@Position - mRNA 224 -- 235@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 5 -- 11@LB@
126	0.01995	0.5155	b2452	eutH	-9.16	0.141344	190 -- 206	5 -- 22	ethanolamine transporter		_____________189________________207\n_____________\|__________________\|\n5'-UUG...ACAGG________GC________AUUAA...UCC-3'\n______________GAGUAAAG__GAUGG_GA\n______________:\|:\|\|\|\|\|__:\|\|\|:_\|\|\n______________UUUAUUUC__UUACU_CU\n3'-UUU...CAUUA________AA_____A__AUCG-5'\n_____________\|__________________\|\n_____________23_________________4\n	191 -- 197	15 -- 21	-11.7395 kcal/mol	2.48279 kcal/mol	0.0977783 kcal/mol	189 207@LB@ \| \|@LB@5'-UUG...ACAGG GC AUUAA...UCC-3'@LB@ GAGUAAAG GAUGG GA@LB@ :\|:\|\|\|\|\| :\|\|\|: \|\|@LB@ UUUAUUUC UUACU CU@LB@3'-UUU...CAUUA AA A AUCG-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -9.16 kcal/mol@LB@Hybridization Energy -11.7395 kcal/mol@LB@Unfolding Energy - mRNA 2.48279 kcal/mol@LB@Unfolding Energy - sRNA 0.0977783 kcal/mol@LB@@LB@Position - mRNA 190 -- 206@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 15 -- 21@LB@
176	0.02871	0.5353	b0518	fdrA	-11.39	0.049925	288 -- 297	6 -- 15	putative NAD(P)-binding acyl-CoA synthetase	b0320	_____________287________298\n_____________\|__________\|\n5'-CGC...AAAAU__________UUU-3'\n______________GUUGAUGAUG\n______________\|\|\|:\|\|\|\|\|\|\n______________CAAUUACUAC\n3'-UUU...UAUUU__________UAUCG-5'\n_____________\|__________\|\n_____________16_________5\n	291 -- 297	6 -- 12	-11.8608 kcal/mol	0.426728 kcal/mol	0.0442104 kcal/mol	287 298@LB@ \| \|@LB@5'-CGC...AAAAU UUU-3'@LB@ GUUGAUGAUG@LB@ \|\|\|:\|\|\|\|\|\|@LB@ CAAUUACUAC@LB@3'-UUU...UAUUU UAUCG-5'@LB@ \| \|@LB@ 16 5@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -11.8608 kcal/mol@LB@Unfolding Energy - mRNA 0.426728 kcal/mol@LB@Unfolding Energy - sRNA 0.0442104 kcal/mol@LB@@LB@Position - mRNA 288 -- 297@LB@Position - sRNA 6 -- 15@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 6 -- 12@LB@
168	0.02737	0.531	b1385	feaB	-11.89	0.038862	180 -- 210	1 -- 28	phenylacetaldehyde dehydrogenase		_____________179_____________________________211\n_____________\|_______________________________\|\n5'-UUG...CACUG_____AU_______AAA________CAG___CGCAU...GUG-3'\n______________GGUAA__AAUAAGG___AGUGAUGA___AGC\n______________\|\|\|\|\|__\|\|\|\|\|:\|___\|:\|\|\|\|\|\|___\|\|\|\n______________CCAUU__UUAUUUC___UUACUACU___UCG\n3'-UUU...UACUG_____AU_______AA_________A_____-5'\n_____________\|______________________________\|\n_____________29_____________________________1\n	198 -- 204	5 -- 11	-19.4278 kcal/mol	6.77275 kcal/mol	0.766821 kcal/mol	179 211@LB@ \| \|@LB@5'-UUG...CACUG AU AAA CAG CGCAU...GUG-3'@LB@ GGUAA AAUAAGG AGUGAUGA AGC@LB@ \|\|\|\|\| \|\|\|\|\|:\| \|:\|\|\|\|\|\| \|\|\|@LB@ CCAUU UUAUUUC UUACUACU UCG@LB@3'-UUU...UACUG AU AA A -5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -11.89 kcal/mol@LB@Hybridization Energy -19.4278 kcal/mol@LB@Unfolding Energy - mRNA 6.77275 kcal/mol@LB@Unfolding Energy - sRNA 0.766821 kcal/mol@LB@@LB@Position - mRNA 180 -- 210@LB@Position - sRNA 1 -- 28@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 5 -- 11@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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