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
86	0.002341	0.09591	b0144	gluQ	-7.21	0.411815	221 -- 264	26 -- 65	glutamyl-Q tRNA(Asp) synthetase	_____________220__________________________________________265\n_____________\|____________________________________________\|\n5'-AGA...UUUUU__________AU__C__ACAC_______AUU__C___UU_____CCUCU...UGA-3'\n______________GUUCAAAGAG__GA_AG____ACAGUAU___GG_CGC__CGCCC\n______________:\|\|\|\|\|\|:\|:__\|\|_\|\|____\|\|\|:\|\|\|___:\|_\|\|\|__\|\|\|\|\|\n______________UAAGUUUUUU__CU_UC____UGUUAUA___UC_GCG__GCGGG\n3'-UUU...GUCAU__________C______AUUC_______CC_______UU_____UAGCG...ACG-5'\n_____________\|____________________________________________\|\n_____________66___________________________________________25\n	242 -- 248	40 -- 46	-28.4973 kcal/mol	7.75098 kcal/mol	13.5387 kcal/mol	220 265@LB@ \| \|@LB@5'-AGA...UUUUU AU C ACAC AUU C UU CCUCU...UGA-3'@LB@ GUUCAAAGAG GA AG ACAGUAU GG CGC CGCCC@LB@ :\|\|\|\|\|\|:\|: \|\| \|\| \|\|\|:\|\|\| :\| \|\|\| \|\|\|\|\|@LB@ UAAGUUUUUU CU UC UGUUAUA UC GCG GCGGG@LB@3'-UUU...GUCAU C AUUC CC UU UAGCG...ACG-5'@LB@ \| \|@LB@ 66 25@LB@@LB@@LB@Energy -7.21 kcal/mol@LB@Hybridization Energy -28.4973 kcal/mol@LB@Unfolding Energy - mRNA 7.75098 kcal/mol@LB@Unfolding Energy - sRNA 13.5387 kcal/mol@LB@@LB@Position - mRNA 221 -- 264@LB@Position - sRNA 26 -- 65@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 40 -- 46@LB@
54	0.0007167	0.04676	b0147	ligT	-15.11	0.004153	163 -- 244	1 -- 81	2'-5' RNA ligase	_____________162_________________________________________________________________________________________245\n_____________\|___________________________________________________________________________________________\|\n5'-CCA...GCCAC_____A__AUC___________UAACC_______CCU__C____CU__AC_____________CUUU___AUC__________________AGAAA...CGG-3'\n______________AUUGU_GC___GCGGUAAUUCA_______GAGUG___CA_AUGU__GA__CGCAACGUCUGUU____GCU___GAC_______UUACCUGC\n______________\|\|\|\|\|_\|\|___\|\|:\|\|\|\|\|\|\|\|_______:\|\|\|:___\|\|_\|\|:\|__\|\|__\|\|\|\|\|\|\|:\|::\|:____\|\|\|___\|\|\|_______\|:\|\|\|\|\|\|\n______________UAACA_CG___CGUCAUUAAGU_______UUCAU___GU_UAUA__CU__GCGUUGCGGGUAG____CGA___CUG_______AGUGGACG\n3'-UUU...UUAGU________AUA___________UUUUUCC_____UCU_______C___C_____________________A_____CAACGUA________-5'\n_____________\|__________________________________________________________________________________________\|\n_____________82_________________________________________________________________________________________1\n	238 -- 244	1 -- 7	-55.1488 kcal/mol	19.3452 kcal/mol	20.694 kcal/mol	162 245@LB@ \| \|@LB@5'-CCA...GCCAC A AUC UAACC CCU C CU AC CUUU AUC AGAAA...CGG-3'@LB@ AUUGU GC GCGGUAAUUCA GAGUG CA AUGU GA CGCAACGUCUGUU GCU GAC UUACCUGC@LB@ \|\|\|\|\| \|\| \|\|:\|\|\|\|\|\|\|\| :\|\|\|: \|\| \|\|:\| \|\| \|\|\|\|\|\|\|:\|::\|: \|\|\| \|\|\| \|:\|\|\|\|\|\|@LB@ UAACA CG CGUCAUUAAGU UUCAU GU UAUA CU GCGUUGCGGGUAG CGA CUG AGUGGACG@LB@3'-UUU...UUAGU AUA UUUUUCC UCU C C A CAACGUA -5'@LB@ \| \|@LB@ 82 1@LB@@LB@@LB@Energy -15.11 kcal/mol@LB@Hybridization Energy -55.1488 kcal/mol@LB@Unfolding Energy - mRNA 19.3452 kcal/mol@LB@Unfolding Energy - sRNA 20.694 kcal/mol@LB@@LB@Position - mRNA 163 -- 244@LB@Position - sRNA 1 -- 81@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 1 -- 7@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@
114	0.00366	0.1131	b0162	cdaR	-8.46	0.240590	33 -- 47	64 -- 77	carbohydrate diacid regulon transcriptional regulator; autoregulator	_____________32______________48\n_____________\|_______________\|\n5'-CAA...CUACC____A__________CUCCC...GGC-3'\n______________UGUU_AUGCAGUAAU\n______________\|\|:\|_\|\|\|\|\|\|\|\|\|\|\n______________ACGA_UACGUCAUUA\n3'-UUU...UUAAC_______________AGUUU...ACG-5'\n_____________\|_______________\|\n_____________78______________63\n	41 -- 47	64 -- 70	-14.8052 kcal/mol	3.39589 kcal/mol	2.94867 kcal/mol	32 48@LB@ \| \|@LB@5'-CAA...CUACC A CUCCC...GGC-3'@LB@ UGUU AUGCAGUAAU@LB@ \|\|:\| \|\|\|\|\|\|\|\|\|\|@LB@ ACGA UACGUCAUUA@LB@3'-UUU...UUAAC AGUUU...ACG-5'@LB@ \| \|@LB@ 78 63@LB@@LB@@LB@Energy -8.46 kcal/mol@LB@Hybridization Energy -14.8052 kcal/mol@LB@Unfolding Energy - mRNA 3.39589 kcal/mol@LB@Unfolding Energy - sRNA 2.94867 kcal/mol@LB@@LB@Position - mRNA 33 -- 47@LB@Position - sRNA 64 -- 77@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 64 -- 70@LB@
195	0.008697	0.1548	b0192	nlpE	-11.98	0.034903	167 -- 206	41 -- 78	lipoprotein involved with copper homeostasis and adhesion	_____________166________________________________________207\n_____________\|__________________________________________\|\n5'-UCA...GCAAA____GCA_____CGGG___AA__________U__________AAAAA...CGC-3'\n______________GUGC___GCGGU____AAU__AAAGAAGGAA___GGAUGGUG\n______________\|\|\|\|___\|\|:\|\|____\|\|\|__\|\|\|:\|\|\|\|\|\|___:\|\|:::\|:\n______________CACG___CGUCA____UUA__UUUUUUCCUU___UCUGUUAU\n3'-UUU...GUUAA____AUA____________AG__________CAU________ACCUC...ACG-5'\n_____________\|__________________________________________\|\n_____________79_________________________________________40\n	200 -- 206	41 -- 47	-26.7874 kcal/mol	9.04038 kcal/mol	5.77415 kcal/mol	166 207@LB@ \| \|@LB@5'-UCA...GCAAA GCA CGGG AA U AAAAA...CGC-3'@LB@ GUGC GCGGU AAU AAAGAAGGAA GGAUGGUG@LB@ \|\|\|\| \|\|:\|\| \|\|\| \|\|\|:\|\|\|\|\|\| :\|\|:::\|:@LB@ CACG CGUCA UUA UUUUUUCCUU UCUGUUAU@LB@3'-UUU...GUUAA AUA AG CAU ACCUC...ACG-5'@LB@ \| \|@LB@ 79 40@LB@@LB@@LB@Energy -11.98 kcal/mol@LB@Hybridization Energy -26.7874 kcal/mol@LB@Unfolding Energy - mRNA 9.04038 kcal/mol@LB@Unfolding Energy - sRNA 5.77415 kcal/mol@LB@@LB@Position - mRNA 167 -- 206@LB@Position - sRNA 41 -- 78@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 41 -- 47@LB@
121	0.004137	0.1205	b0353	mhpT	-11.58	0.044392	170 -- 179	1 -- 10	3-hydroxyphenylpropionic transporter	_____________169________180\n_____________\|__________\|\n5'-CGG...UCGCG__________ACUCG...CGG-3'\n______________AUUCACCUGC\n______________\|\|\|\|\|\|\|\|\|\|\n______________UAAGUGGACG\n3'-UUU...CAACG__________-5'\n_____________\|_________\|\n_____________11________1\n	173 -- 179	1 -- 7	-16.6324 kcal/mol	2.26547 kcal/mol	2.7891 kcal/mol	169 180@LB@ \| \|@LB@5'-CGG...UCGCG ACUCG...CGG-3'@LB@ AUUCACCUGC@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UAAGUGGACG@LB@3'-UUU...CAACG -5'@LB@ \| \|@LB@ 11 1@LB@@LB@@LB@Energy -11.58 kcal/mol@LB@Hybridization Energy -16.6324 kcal/mol@LB@Unfolding Energy - mRNA 2.26547 kcal/mol@LB@Unfolding Energy - sRNA 2.7891 kcal/mol@LB@@LB@Position - mRNA 170 -- 179@LB@Position - sRNA 1 -- 10@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 1 -- 7@LB@
98	0.003129	0.1114	b0357	frmR	-9.19	0.168108	184 -- 207	25 -- 48	regulator protein that represses frmRAB operon	_____________183______________________208\n_____________\|________________________\|\n5'-CUG...CAUGC________A__U___AA_______GUACU...CCG-3'\n______________AGAUGAUG_GG_GCG__AUGCCCA\n______________\|\|\|::\|\|:_\|\|_\|\|\|__\|:\|\|\|\|\|\n______________UCUGUUAU_CC_CGC__UGCGGGU\n3'-UUU...UUCAU________A__U___GU_______AGCGA...ACG-5'\n_____________\|________________________\|\n_____________49_______________________24\n	201 -- 207	25 -- 31	-27.7971 kcal/mol	6.33291 kcal/mol	12.271 kcal/mol	183 208@LB@ \| \|@LB@5'-CUG...CAUGC A U AA GUACU...CCG-3'@LB@ AGAUGAUG GG GCG AUGCCCA@LB@ \|\|\|::\|\|: \|\| \|\|\| \|:\|\|\|\|\|@LB@ UCUGUUAU CC CGC UGCGGGU@LB@3'-UUU...UUCAU A U GU AGCGA...ACG-5'@LB@ \| \|@LB@ 49 24@LB@@LB@@LB@Energy -9.19 kcal/mol@LB@Hybridization Energy -27.7971 kcal/mol@LB@Unfolding Energy - mRNA 6.33291 kcal/mol@LB@Unfolding Energy - sRNA 12.271 kcal/mol@LB@@LB@Position - mRNA 184 -- 207@LB@Position - sRNA 25 -- 48@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 25 -- 31@LB@
176	0.007245	0.145	b0397	sbcC	-11.91	0.036282	117 -- 185	1 -- 55	exonuclease dsDNA ATP-dependent	_____________116____________________________________________________________________186\n_____________\|______________________________________________________________________\|\n5'-GAA...GCACU_____AACU______AUCGC___A__________CA__AUCUUUUCACCAC__________A_____C__CGGAG...UUG-3'\n______________GGAAG____GGAUGA_____AGC_GCAACGUCUG__GC_____________GACGUUGCAU_C_CCU_GC\n______________\|\|\|\|\|____:\|\|::\|_____\|\|\|_\|\|\|\|\|\|:\|::__\|\|_____________\|\|\|\|\|\|\|\|\|\|_\|_\|\|\|_\|\|\n______________CCUUC____UCUGUU_____UCG_CGUUGCGGGU__CG_____________CUGCAACGUA_G_GGA_CG\n3'-UUU...UUUUU_____AU________AUACC______________AG__AA_____________________A_U______-5'\n_____________\|_____________________________________________________________________\|\n_____________56____________________________________________________________________1\n	170 -- 176	10 -- 16	-47.2501 kcal/mol	18.5328 kcal/mol	16.8092 kcal/mol	116 186@LB@ \| \|@LB@5'-GAA...GCACU AACU AUCGC A CA AUCUUUUCACCAC A C CGGAG...UUG-3'@LB@ GGAAG GGAUGA AGC GCAACGUCUG GC GACGUUGCAU C CCU GC@LB@ \|\|\|\|\| :\|\|::\| \|\|\| \|\|\|\|\|\|:\|:: \|\| \|\|\|\|\|\|\|\|\|\| \| \|\|\| \|\|@LB@ CCUUC UCUGUU UCG CGUUGCGGGU CG CUGCAACGUA G GGA CG@LB@3'-UUU...UUUUU AU AUACC AG AA A U -5'@LB@ \| \|@LB@ 56 1@LB@@LB@@LB@Energy -11.91 kcal/mol@LB@Hybridization Energy -47.2501 kcal/mol@LB@Unfolding Energy - mRNA 18.5328 kcal/mol@LB@Unfolding Energy - sRNA 16.8092 kcal/mol@LB@@LB@Position - mRNA 117 -- 185@LB@Position - sRNA 1 -- 55@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 10 -- 16@LB@
107	0.003422	0.1114	b0415	ribE	-10.96	0.064092	190 -- 254	4 -- 58	riboflavin synthase beta chain	_____________189_________________________________________________________________255\n_____________\|___________________________________________________________________\|\n5'-CGG...AACCC________AAAAU_A___U___U_A_________UUGCUAC____GA____C_____C__CA_____AUCGC...GUG-3'\n______________GAAGGAAG_____G_ACA_UAU_G_AGC_UAACG_______CCCG__CGCU__GCGU_GC__UCACC\n______________:\|\|\|\|\|\|\|_____\|_\|\|\|_\|\|\|_\|_\|\|\|_:\|\|\|\|_______\|\|\|:__\|\|\|\|__:\|\|\|_\|\|__\|\|\|\|\|\n______________UUUCCUUC_____C_UGU_AUA_C_UCG_GUUGC_______GGGU__GCGA__UGCA_CG__AGUGG\n3'-UUU...AGUUU________AUU_______U___C_____C________________A_____AC____A__UA_____ACG-5'\n_____________\|___________________________________________________________________\|\n_____________59__________________________________________________________________3\n	191 -- 197	51 -- 57	-41.366 kcal/mol	13.5359 kcal/mol	16.8715 kcal/mol	189 255@LB@ \| \|@LB@5'-CGG...AACCC AAAAU A U U A UUGCUAC GA C C CA AUCGC...GUG-3'@LB@ GAAGGAAG G ACA UAU G AGC UAACG CCCG CGCU GCGU GC UCACC@LB@ :\|\|\|\|\|\|\| \| \|\|\| \|\|\| \| \|\|\| :\|\|\|\| \|\|\|: \|\|\|\| :\|\|\| \|\| \|\|\|\|\|@LB@ UUUCCUUC C UGU AUA C UCG GUUGC GGGU GCGA UGCA CG AGUGG@LB@3'-UUU...AGUUU AUU U C C A AC A UA ACG-5'@LB@ \| \|@LB@ 59 3@LB@@LB@@LB@Energy -10.96 kcal/mol@LB@Hybridization Energy -41.366 kcal/mol@LB@Unfolding Energy - mRNA 13.5359 kcal/mol@LB@Unfolding Energy - sRNA 16.8715 kcal/mol@LB@@LB@Position - mRNA 190 -- 254@LB@Position - sRNA 4 -- 58@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 51 -- 57@LB@
166	0.006486	0.1377	b0440	hupB	-11.63	0.043010	149 -- 200	46 -- 93	HU DNA-binding transcriptional regulator beta subunit	_____________148______________________________________________________201\n_____________\|________________________________________________________\|\n5'-CGC...CGCGU______CUUGAAG__U__________GAUAUA______AU__________AG____GUGAA...CUG-3'\n______________UCGUAC_______GA_UCAA__GUGC________AAUU__AAAGAGGAAG__AAGA\n______________\|\|\|\|\|\|_______\|\|_\|\|\|\|__\|\|\|\|________\|\|\|\|__\|\|\|:\|\|\|\|\|\|__\|\|\|\|\n______________AGCAUG_______CU_AGUU__CACG________UUAA__UUUUUCCUUC__UUCU\n3'-UUU...GCCGC_______________U____AA____AUACGUCA____GU__________A_____GUUAU...ACG-5'\n_____________\|________________________________________________________\|\n_____________94_______________________________________________________45\n	188 -- 194	51 -- 57	-29.0191 kcal/mol	11.8112 kcal/mol	5.57675 kcal/mol	148 201@LB@ \| \|@LB@5'-CGC...CGCGU CUUGAAG U GAUAUA AU AG GUGAA...CUG-3'@LB@ UCGUAC GA UCAA GUGC AAUU AAAGAGGAAG AAGA@LB@ \|\|\|\|\|\| \|\| \|\|\|\| \|\|\|\| \|\|\|\| \|\|\|:\|\|\|\|\|\| \|\|\|\|@LB@ AGCAUG CU AGUU CACG UUAA UUUUUCCUUC UUCU@LB@3'-UUU...GCCGC U AA AUACGUCA GU A GUUAU...ACG-5'@LB@ \| \|@LB@ 94 45@LB@@LB@@LB@Energy -11.63 kcal/mol@LB@Hybridization Energy -29.0191 kcal/mol@LB@Unfolding Energy - mRNA 11.8112 kcal/mol@LB@Unfolding Energy - sRNA 5.57675 kcal/mol@LB@@LB@Position - mRNA 149 -- 200@LB@Position - sRNA 46 -- 93@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 51 -- 57@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:

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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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