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
125	0.01993	0.5155	b2347	yfdC	-8.10	0.220050	281 -- 291	15 -- 25	putative inner membrane protein		_____________280_________292\n_____________\|___________\|\n5'-GCA...AUAGA___________ACCGA...UCC-3'\n______________AAUAGAUGAAG\n______________\|\|\|\|:\|\|:\|\|\|\n______________UUAUUUAUUUC\n3'-UUU...UGCCA___________AAUUA...UCG-5'\n_____________\|___________\|\n_____________26__________14\n	285 -- 291	15 -- 21	-8.49349 kcal/mol	0.301625 kcal/mol	0.0943905 kcal/mol	280 292@LB@ \| \|@LB@5'-GCA...AUAGA ACCGA...UCC-3'@LB@ AAUAGAUGAAG@LB@ \|\|\|\|:\|\|:\|\|\|@LB@ UUAUUUAUUUC@LB@3'-UUU...UGCCA AAUUA...UCG-5'@LB@ \| \|@LB@ 26 14@LB@@LB@@LB@Energy -8.10 kcal/mol@LB@Hybridization Energy -8.49349 kcal/mol@LB@Unfolding Energy - mRNA 0.301625 kcal/mol@LB@Unfolding Energy - sRNA 0.0943905 kcal/mol@LB@@LB@Position - mRNA 281 -- 291@LB@Position - sRNA 15 -- 25@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 15 -- 21@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@
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@
103	0.01627	0.5059	b3527	yhjJ	-12.72	0.025178	191 -- 250	1 -- 59	putative periplasmic M16 family chaperone		_____________190_____________________________________________________________________251\n_____________\|_______________________________________________________________________\|\n5'-CUC...UGAUC______UC___U___GGGCACAAAAA____ACUUUUAGCG____________________C__________CACUG...GGC-3'\n______________AGGGGU__ACA_GCA___________UUCG__________GGCGGU___________UUG_UGAUGAUGGC\n______________\|\|\|\|\|\|__\|\|\|_:\|\|___________\|\|\|:__________\|:\|\|\|\|___________\|\|:_\|\|\|\|\|\|\|:\|\|\n______________UCCCCA__UGU_UGU___________AAGU__________CUGCCA___________AAU_ACUACUAUCG\n3'-UUU...CUUUA______UU___C__________________CUUUACUUA_______UUAUUUAUUUC___U__________-5'\n_____________\|______________________________________________________________________\|\n_____________60_____________________________________________________________________1\n	244 -- 250	1 -- 7	-34.0873 kcal/mol	15.0257 kcal/mol	6.33764 kcal/mol	190 251@LB@ \| \|@LB@5'-CUC...UGAUC UC U GGGCACAAAAA ACUUUUAGCG C CACUG...GGC-3'@LB@ AGGGGU ACA GCA UUCG GGCGGU UUG UGAUGAUGGC@LB@ \|\|\|\|\|\| \|\|\| :\|\| \|\|\|: \|:\|\|\|\| \|\|: \|\|\|\|\|\|\|:\|\|@LB@ UCCCCA UGU UGU AAGU CUGCCA AAU ACUACUAUCG@LB@3'-UUU...CUUUA UU C CUUUACUUA UUAUUUAUUUC U -5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -12.72 kcal/mol@LB@Hybridization Energy -34.0873 kcal/mol@LB@Unfolding Energy - mRNA 15.0257 kcal/mol@LB@Unfolding Energy - sRNA 6.33764 kcal/mol@LB@@LB@Position - mRNA 191 -- 250@LB@Position - sRNA 1 -- 59@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 1 -- 7@LB@
169	0.02775	0.531	b2110	yehC	-5.87	0.481945	191 -- 199	20 -- 28	putative periplasmic pilin chaperone		_____________190_______200\n_____________\|_________\|\n5'-CAG...CUCCA_________CAUGG...CCG-3'\n______________GGUAAUAAA\n______________\|\|\|\|\|\|\|\|\|\n______________CCAUUAUUU\n3'-UUU...UACUG_________AUUUC...UCG-5'\n_____________\|_________\|\n_____________29________19\n	193 -- 199	20 -- 26	-7.96952 kcal/mol	1.36589 kcal/mol	0.737257 kcal/mol	190 200@LB@ \| \|@LB@5'-CAG...CUCCA CAUGG...CCG-3'@LB@ GGUAAUAAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ CCAUUAUUU@LB@3'-UUU...UACUG AUUUC...UCG-5'@LB@ \| \|@LB@ 29 19@LB@@LB@@LB@Energy -5.87 kcal/mol@LB@Hybridization Energy -7.96952 kcal/mol@LB@Unfolding Energy - mRNA 1.36589 kcal/mol@LB@Unfolding Energy - sRNA 0.737257 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 20 -- 28@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 20 -- 26@LB@
100	0.01591	0.5059	b0531	sfmC	-11.86	0.039421	211 -- 227	6 -- 22	putative periplasmic pilus chaperone	b4316	_____________210_______________228\n_____________\|_________________\|\n5'-AAU...GACUA___________U_____CUCAU...GUA-3'\n______________AAAUAAAGUUA_UGAUG\n______________\|\|\|\|\|\|\|\|\|\|\|_\|\|\|\|\|\n______________UUUAUUUCAAU_ACUAC\n3'-UUU...CAUUA___________U_____UAUCG-5'\n_____________\|_________________\|\n_____________23________________5\n	215 -- 221	12 -- 18	-15.888 kcal/mol	3.9302 kcal/mol	0.0976382 kcal/mol	210 228@LB@ \| \|@LB@5'-AAU...GACUA U CUCAU...GUA-3'@LB@ AAAUAAAGUUA UGAUG@LB@ \|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ UUUAUUUCAAU ACUAC@LB@3'-UUU...CAUUA U UAUCG-5'@LB@ \| \|@LB@ 23 5@LB@@LB@@LB@Energy -11.86 kcal/mol@LB@Hybridization Energy -15.888 kcal/mol@LB@Unfolding Energy - mRNA 3.9302 kcal/mol@LB@Unfolding Energy - sRNA 0.0976382 kcal/mol@LB@@LB@Position - mRNA 211 -- 227@LB@Position - sRNA 6 -- 22@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 12 -- 18@LB@
67	0.009794	0.4523	b2823	ppdC	-12.40	0.029910	245 -- 275	3 -- 28	putative prepilin peptidase-dependent protein		_____________244_____________________________276\n_____________\|_______________________________\|\n5'-ACG...CCGGA_______UUGGC_____U_____________AUUGU...UCC-3'\n______________GGUAAUG_____GAUGG_GUUGAUGGUGAUG\n______________\|\|\|\|\|\|:_____:\|\|::_\|\|\|:\|\|\|:\|\|\|\|:\n______________CCAUUAU_____UUAUU_CAAUUACUACUAU\n3'-UUU...UACUG_________________U_____________CG-5'\n_____________\|_______________________________\|\n_____________29______________________________2\n	269 -- 275	3 -- 9	-21.5159 kcal/mol	8.35299 kcal/mol	0.766561 kcal/mol	244 276@LB@ \| \|@LB@5'-ACG...CCGGA UUGGC U AUUGU...UCC-3'@LB@ GGUAAUG GAUGG GUUGAUGGUGAUG@LB@ \|\|\|\|\|\|: :\|\|:: \|\|\|:\|\|\|:\|\|\|\|:@LB@ CCAUUAU UUAUU CAAUUACUACUAU@LB@3'-UUU...UACUG U CG-5'@LB@ \| \|@LB@ 29 2@LB@@LB@@LB@Energy -12.40 kcal/mol@LB@Hybridization Energy -21.5159 kcal/mol@LB@Unfolding Energy - mRNA 8.35299 kcal/mol@LB@Unfolding Energy - sRNA 0.766561 kcal/mol@LB@@LB@Position - mRNA 245 -- 275@LB@Position - sRNA 3 -- 28@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 3 -- 9@LB@
84	0.01184	0.4627	b3101	yqjF	-11.66	0.043663	211 -- 235	1 -- 23	putative quinol oxidase subunit		_____________210_______________________236\n_____________\|_________________________\|\n5'-CAG...AAAAU____A__U_______UAC_______GCGCA...GUA-3'\n______________UAGA_GA_GUUGGUG___UGGUAGC\n______________\|\|:\|_:\|_\|\|\|::\|\|___\|\|:\|\|\|\|\n______________AUUU_UU_CAAUUAC___ACUAUCG\n3'-UUU...CCAUU____A__U_______U_________-5'\n_____________\|________________________\|\n_____________24_______________________1\n	229 -- 235	1 -- 7	-15.9826 kcal/mol	4.21954 kcal/mol	0.105066 kcal/mol	210 236@LB@ \| \|@LB@5'-CAG...AAAAU A U UAC GCGCA...GUA-3'@LB@ UAGA GA GUUGGUG UGGUAGC@LB@ \|\|:\| :\| \|\|\|::\|\| \|\|:\|\|\|\|@LB@ AUUU UU CAAUUAC ACUAUCG@LB@3'-UUU...CCAUU A U U -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -15.9826 kcal/mol@LB@Unfolding Energy - mRNA 4.21954 kcal/mol@LB@Unfolding Energy - sRNA 0.105066 kcal/mol@LB@@LB@Position - mRNA 211 -- 235@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 1 -- 7@LB@
64	0.008913	0.4523	b4231	yjfF	-11.33	0.051476	106 -- 140	1 -- 41	putative sugar ABC transporter permease		_____________105_______________________________________141\n_____________\|_________________________________________\|\n5'-CGG...CCGCC_________CCA_______________C_____________UUUGC...GAG-3'\n______________AGAGAUGAA____GGUGGUGA___AAG__GGUGGUGGU_GC\n______________\|\|\|:\|\|\|\|\|____\|\|\|::\|:\|___\|\|\|__::\|\|:\|\|:\|_\|\|\n______________UCUUUACUU____CCAUUAUU___UUC__UUACUACUA_CG\n3'-UUU...GUAAG_________ACUG________UAU___AA_________U__-5'\n_____________\|________________________________________\|\n_____________42_______________________________________1\n	132 -- 138	4 -- 10	-27.205 kcal/mol	9.83395 kcal/mol	6.043 kcal/mol	105 141@LB@ \| \|@LB@5'-CGG...CCGCC CCA C UUUGC...GAG-3'@LB@ AGAGAUGAA GGUGGUGA AAG GGUGGUGGU GC@LB@ \|\|\|:\|\|\|\|\| \|\|\|::\|:\| \|\|\| ::\|\|:\|\|:\| \|\|@LB@ UCUUUACUU CCAUUAUU UUC UUACUACUA CG@LB@3'-UUU...GUAAG ACUG UAU AA U -5'@LB@ \| \|@LB@ 42 1@LB@@LB@@LB@Energy -11.33 kcal/mol@LB@Hybridization Energy -27.205 kcal/mol@LB@Unfolding Energy - mRNA 9.83395 kcal/mol@LB@Unfolding Energy - sRNA 6.043 kcal/mol@LB@@LB@Position - mRNA 106 -- 140@LB@Position - sRNA 1 -- 41@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 4 -- 10@LB@
46	0.00512	0.3601	b2012	yeeD	-13.46	0.016912	185 -- 206	3 -- 23	putative TusA family sulfurtransferase		_____________184____________________207\n_____________\|______________________\|\n5'-GAU...CAAAU__________G___A_______AUUAA...UAG-3'\n______________UAAGUAAGGU_UAA_GAUGGUG\n______________\|\|\|:\|\|\|:\|\|_\|\|\|_\|\|\|\|:\|:\n______________AUUUAUUUCA_AUU_CUACUAU\n3'-UUU...CCAUU______________A_______CG-5'\n_____________\|______________________\|\n_____________24_____________________2\n	200 -- 206	3 -- 9	-15.4658 kcal/mol	1.89879 kcal/mol	0.104738 kcal/mol	184 207@LB@ \| \|@LB@5'-GAU...CAAAU G A AUUAA...UAG-3'@LB@ UAAGUAAGGU UAA GAUGGUG@LB@ \|\|\|:\|\|\|:\|\| \|\|\| \|\|\|\|:\|:@LB@ AUUUAUUUCA AUU CUACUAU@LB@3'-UUU...CCAUU A CG-5'@LB@ \| \|@LB@ 24 2@LB@@LB@@LB@Energy -13.46 kcal/mol@LB@Hybridization Energy -15.4658 kcal/mol@LB@Unfolding Energy - mRNA 1.89879 kcal/mol@LB@Unfolding Energy - sRNA 0.104738 kcal/mol@LB@@LB@Position - mRNA 185 -- 206@LB@Position - sRNA 3 -- 23@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 3 -- 9@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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