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
6	0.0001423	0.07172	b3183	obgE	-17.58	0.001399	174 -- 220	1 -- 51	GTPase involved in cell partioning and DNA repair	_____________173____________________________________________________221\n_____________\|______________________________________________________\|\n5'-UUU...CCCGC__________________UUU____AG___A__________UGU__________AUCGA...GCC-3'\n______________GCAGGC______GAAUGA___ACGG__AAU_AAAUGAAGUU___UGAUGA_AGC\n______________:\|\|\|:\|______:\|\|\|\|\|___\|\|\|\|__\|\|\|_\|\|\|\|:\|\|\|\|\|___\|\|\|\|\|\|_\|\|\|\n______________UGUCUG______UUUACU___UGCC__UUA_UUUAUUUCAA___ACUACU_UCG\n3'-UUU...CCAUU______UAAGUC______UAC____A_______________UU_______A___-5'\n_____________\|_____________________________________________________\|\n_____________52____________________________________________________1\n	202 -- 208	13 -- 19	-33.7182 kcal/mol	9.79823 kcal/mol	6.33528 kcal/mol	173 221@LB@ \| \|@LB@5'-UUU...CCCGC UUU AG A UGU AUCGA...GCC-3'@LB@ GCAGGC GAAUGA ACGG AAU AAAUGAAGUU UGAUGA AGC@LB@ :\|\|\|:\| :\|\|\|\|\| \|\|\|\| \|\|\| \|\|\|\|:\|\|\|\|\| \|\|\|\|\|\| \|\|\|@LB@ UGUCUG UUUACU UGCC UUA UUUAUUUCAA ACUACU UCG@LB@3'-UUU...CCAUU UAAGUC UAC A UU A -5'@LB@ \| \|@LB@ 52 1@LB@@LB@@LB@Energy -17.58 kcal/mol@LB@Hybridization Energy -33.7182 kcal/mol@LB@Unfolding Energy - mRNA 9.79823 kcal/mol@LB@Unfolding Energy - sRNA 6.33528 kcal/mol@LB@@LB@Position - mRNA 174 -- 220@LB@Position - sRNA 1 -- 51@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 13 -- 19@LB@
26	0.001686	0.211	b0091	murC	-10.53	0.075719	174 -- 220	1 -- 48	UDP-N-acetylmuramate:L-alanine ligase	_____________173______________________________________________221\n_____________\|________________________________________________\|\n5'-CAG...CGUAU__AUUUA______U___________A_______UACACAACAAU____AAAAC...GCG-3'\n______________GA_____AGAAGU_AAUGGC_GUAA_GAAUGAA___________UGGC\n______________\|\|_____\|\|\|\|:\|_\|\|\|\|:\|_\|\|\|\|_:\|\|\|:\|\|___________\|:\|\|\n______________CU_____UCUUUA_UUACUG_CAUU_UUUAUUU___________AUCG\n3'-UUU...UUUGU__GUAAG______C______C____A_______CAAUUACUACU____-5'\n_____________\|_______________________________________________\|\n_____________49______________________________________________1\n	199 -- 205	16 -- 22	-22.2946 kcal/mol	5.44296 kcal/mol	6.32011 kcal/mol	173 221@LB@ \| \|@LB@5'-CAG...CGUAU AUUUA U A UACACAACAAU AAAAC...GCG-3'@LB@ GA AGAAGU AAUGGC GUAA GAAUGAA UGGC@LB@ \|\| \|\|\|\|:\| \|\|\|\|:\| \|\|\|\| :\|\|\|:\|\| \|:\|\|@LB@ CU UCUUUA UUACUG CAUU UUUAUUU AUCG@LB@3'-UUU...UUUGU GUAAG C C A CAAUUACUACU -5'@LB@ \| \|@LB@ 49 1@LB@@LB@@LB@Energy -10.53 kcal/mol@LB@Hybridization Energy -22.2946 kcal/mol@LB@Unfolding Energy - mRNA 5.44296 kcal/mol@LB@Unfolding Energy - sRNA 6.32011 kcal/mol@LB@@LB@Position - mRNA 174 -- 220@LB@Position - sRNA 1 -- 48@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 16 -- 22@LB@
28	0.00198	0.2275	b2821	ptrA	-8.02	0.226801	174 -- 191	5 -- 22	protease III	_____________173________________192\n_____________\|__________________\|\n5'-GCU...ACAGA____U________U____GGUCC...CCA-3'\n______________AAAU_AAGUUGAU_AUGA\n______________\|\|\|\|_\|\|\|\|\|:\|\|_\|\|\|\|\n______________UUUA_UUCAAUUA_UACU\n3'-UUU...CAUUA____U________C____AUCG-5'\n_____________\|__________________\|\n_____________23_________________4\n	180 -- 186	10 -- 16	-10.4485 kcal/mol	2.32937 kcal/mol	0.0977783 kcal/mol	173 192@LB@ \| \|@LB@5'-GCU...ACAGA U U GGUCC...CCA-3'@LB@ AAAU AAGUUGAU AUGA@LB@ \|\|\|\| \|\|\|\|\|:\|\| \|\|\|\|@LB@ UUUA UUCAAUUA UACU@LB@3'-UUU...CAUUA U C AUCG-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -8.02 kcal/mol@LB@Hybridization Energy -10.4485 kcal/mol@LB@Unfolding Energy - mRNA 2.32937 kcal/mol@LB@Unfolding Energy - sRNA 0.0977783 kcal/mol@LB@@LB@Position - mRNA 174 -- 191@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 10 -- 16@LB@
70	0.01004	0.4523	b1658	purR	-15.06	0.006831	174 -- 223	1 -- 65	transcriptional repressor hypoxanthine-binding	_____________173________________________________________________________________224\n_____________\|__________________________________________________________________\|\n5'-UUU...GGAGC______UA____C______GU_________G_______AAC______A__________________GAAAC...GCA-3'\n______________UGAAGU__GGGU___UGGA______GAAAU_GAAUGGC___AAUAAA__________GAUG_UAGC\n______________\|\|\|\|:\|__\|\|\|\|___::\|\|______\|\|\|\|\|_\|\|\|\|\|:\|___\|\|\|\|\|\|__________\|\|\|\|_\|\|\|\|\n______________ACUUUA__CCCA___GUCU______CUUUA_CUUACUG___UUAUUU__________CUAC_AUCG\n3'-UUU...GGCCA______UC____UUU____GUAAGU_____________CCA______AUUUCAAUUA____U____-5'\n_____________\|_________________________________________________________________\|\n_____________66________________________________________________________________1\n	199 -- 205	29 -- 35	-29.7477 kcal/mol	7.45199 kcal/mol	7.23987 kcal/mol	173 224@LB@ \| \|@LB@5'-UUU...GGAGC UA C GU G AAC A GAAAC...GCA-3'@LB@ UGAAGU GGGU UGGA GAAAU GAAUGGC AAUAAA GAUG UAGC@LB@ \|\|\|\|:\| \|\|\|\| ::\|\| \|\|\|\|\| \|\|\|\|\|:\| \|\|\|\|\|\| \|\|\|\| \|\|\|\|@LB@ ACUUUA CCCA GUCU CUUUA CUUACUG UUAUUU CUAC AUCG@LB@3'-UUU...GGCCA UC UUU GUAAGU CCA AUUUCAAUUA U -5'@LB@ \| \|@LB@ 66 1@LB@@LB@@LB@Energy -15.06 kcal/mol@LB@Hybridization Energy -29.7477 kcal/mol@LB@Unfolding Energy - mRNA 7.45199 kcal/mol@LB@Unfolding Energy - sRNA 7.23987 kcal/mol@LB@@LB@Position - mRNA 174 -- 223@LB@Position - sRNA 1 -- 65@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 29 -- 35@LB@
114	0.01806	0.5155	b3033	yqiB	-9.53	0.119911	174 -- 206	15 -- 50	DUF1249 protein YqiB	_____________173__________________________________207\n_____________\|____________________________________\|\n5'-UGG...AUCAU__A_____AAA_____________C___________CGUUA...GCG-3'\n______________CA_GCGUU___AAAUGAGUG__GG__AUAAAUGAAG\n______________\|\|_:\|:\|\|___\|\|\|\|\|\|:\|\|__\|\|__\|\|\|\|\|\|:\|\|\|\n______________GU_UGUAA___UUUACUUAC__CC__UAUUUAUUUC\n3'-UUU...CAUUU__C_____GUC_________UG__AU__________AAUUA...UCG-5'\n_____________\|____________________________________\|\n_____________51___________________________________14\n	200 -- 206	15 -- 21	-20.8588 kcal/mol	5.00376 kcal/mol	6.32253 kcal/mol	173 207@LB@ \| \|@LB@5'-UGG...AUCAU A AAA C CGUUA...GCG-3'@LB@ CA GCGUU AAAUGAGUG GG AUAAAUGAAG@LB@ \|\| :\|:\|\| \|\|\|\|\|\|:\|\| \|\| \|\|\|\|\|\|:\|\|\|@LB@ GU UGUAA UUUACUUAC CC UAUUUAUUUC@LB@3'-UUU...CAUUU C GUC UG AU AAUUA...UCG-5'@LB@ \| \|@LB@ 51 14@LB@@LB@@LB@Energy -9.53 kcal/mol@LB@Hybridization Energy -20.8588 kcal/mol@LB@Unfolding Energy - mRNA 5.00376 kcal/mol@LB@Unfolding Energy - sRNA 6.32253 kcal/mol@LB@@LB@Position - mRNA 174 -- 206@LB@Position - sRNA 15 -- 50@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 15 -- 21@LB@
41	0.004182	0.3349	b3771	ilvD	-12.17	0.033695	175 -- 200	14 -- 53	dihydroxyacid dehydratase	_____________174______________________________________201\n_____________\|________________________________________\|\n5'-GCG...UUACG_________C_________________GA___________AUGCC...GUA-3'\n______________AGACAGACA_______________UGG__GUAAAUAAAGU\n______________\|:\|\|\|\|\|\|\|_______________:\|\|__:\|\|\|\|\|\|\|\|\|\|\n______________UUUGUCUGU_______________GCC__UAUUUAUUUCA\n3'-UUU...CCCCA_________AAGUCUUUACUUACU___AU___________AUUAC...UCG-5'\n_____________\|________________________________________\|\n_____________54_______________________________________13\n	194 -- 200	14 -- 20	-22.054 kcal/mol	3.56189 kcal/mol	6.32552 kcal/mol	174 201@LB@ \| \|@LB@5'-GCG...UUACG C GA AUGCC...GUA-3'@LB@ AGACAGACA UGG GUAAAUAAAGU@LB@ \|:\|\|\|\|\|\|\| :\|\| :\|\|\|\|\|\|\|\|\|\|@LB@ UUUGUCUGU GCC UAUUUAUUUCA@LB@3'-UUU...CCCCA AAGUCUUUACUUACU AU AUUAC...UCG-5'@LB@ \| \|@LB@ 54 13@LB@@LB@@LB@Energy -12.17 kcal/mol@LB@Hybridization Energy -22.054 kcal/mol@LB@Unfolding Energy - mRNA 3.56189 kcal/mol@LB@Unfolding Energy - sRNA 6.32552 kcal/mol@LB@@LB@Position - mRNA 175 -- 200@LB@Position - sRNA 14 -- 53@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 14 -- 20@LB@
155	0.02521	0.526	b4208	cycA	-8.71	0.171102	175 -- 207	24 -- 51	D-alanine/D-serine/glycine transporter	_____________174________________________________208\n_____________\|__________________________________\|\n5'-AUU...ACAAC_______GGUA__________AAAAAC_______AUCAG...UUG-3'\n______________ACAGACA____CAGGAA_GAA______AUGGUAG\n______________\|\|\|\|\|\|\|____\|\|\|:\|\|_\|\|\|______\|:\|\|\|\|:\n______________UGUCUGU____GUCUUU_CUU______UGCCAUU\n3'-UUU...CCAUU_______AA________A___AC___________AUUUA...UCG-5'\n_____________\|__________________________________\|\n_____________52_________________________________23\n	201 -- 207	24 -- 30	-19.5671 kcal/mol	4.55835 kcal/mol	6.29692 kcal/mol	174 208@LB@ \| \|@LB@5'-AUU...ACAAC GGUA AAAAAC AUCAG...UUG-3'@LB@ ACAGACA CAGGAA GAA AUGGUAG@LB@ \|\|\|\|\|\|\| \|\|\|:\|\| \|\|\| \|:\|\|\|\|:@LB@ UGUCUGU GUCUUU CUU UGCCAUU@LB@3'-UUU...CCAUU AA A AC AUUUA...UCG-5'@LB@ \| \|@LB@ 52 23@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -19.5671 kcal/mol@LB@Unfolding Energy - mRNA 4.55835 kcal/mol@LB@Unfolding Energy - sRNA 6.29692 kcal/mol@LB@@LB@Position - mRNA 175 -- 207@LB@Position - sRNA 24 -- 51@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 24 -- 30@LB@
3	3.826e-06	0.004187	b0090	murG	-16.88	0.002220	177 -- 235	1 -- 51	N-acetylglucosaminyl transferase	_____________176_________________________________________________________236\n_____________\|___________________________________________________________\|\n5'-AUU...AAAGC___________UAC_____UCAC____A_____C___G____CGA______________AGGCG...GUU-3'\n______________GCAGGCGUUUG___GAGGU____GAUG_GUGGU_AAG_AAAG___UUAAUGGUGAUGGC\n______________:\|\|\|:\|:\|\|::___\|\|::\|____\|\|:\|_\|\|::\|_\|\|:_\|\|\|\|___\|\|\|\|\|\|:\|\|\|\|:\|\|\n______________UGUCUGUAAGU___CUUUA____CUGC_CAUUA_UUU_UUUC___AAUUACUACUAUCG\n3'-UUU...CCAUU___________________CUUA______________A_____________________-5'\n_____________\|__________________________________________________________\|\n_____________52_________________________________________________________1\n	229 -- 235	1 -- 7	-39.4015 kcal/mol	16.1862 kcal/mol	6.33528 kcal/mol	176 236@LB@ \| \|@LB@5'-AUU...AAAGC UAC UCAC A C G CGA AGGCG...GUU-3'@LB@ GCAGGCGUUUG GAGGU GAUG GUGGU AAG AAAG UUAAUGGUGAUGGC@LB@ :\|\|\|:\|:\|\|:: \|\|::\| \|\|:\| \|\|::\| \|\|: \|\|\|\| \|\|\|\|\|\|:\|\|\|\|:\|\|@LB@ UGUCUGUAAGU CUUUA CUGC CAUUA UUU UUUC AAUUACUACUAUCG@LB@3'-UUU...CCAUU CUUA A -5'@LB@ \| \|@LB@ 52 1@LB@@LB@@LB@Energy -16.88 kcal/mol@LB@Hybridization Energy -39.4015 kcal/mol@LB@Unfolding Energy - mRNA 16.1862 kcal/mol@LB@Unfolding Energy - sRNA 6.33528 kcal/mol@LB@@LB@Position - mRNA 177 -- 235@LB@Position - sRNA 1 -- 51@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 1 -- 7@LB@
9	0.000223	0.08136	b1826	mgrB	-16.34	0.003128	178 -- 244	1 -- 63	regulatory peptide for PhoPQ feedback inhibition	_____________177______________________________________________________________________245\n_____________\|________________________________________________________________________\|\n5'-UAC...ACAUA_______U_________G_____________AAAGUUUC_____GUCGUUCU_______UC______U____UUGCU...AAU-3'\n______________AGGUAGG_G_AAACGGA_AUU__GGAGUGAA________GAUGG__________GGUUG__GUGGUG_UGGC\n______________\|::\|\|\|\|_\|_\|\|\|\|:\|\|_\|\|\|__\|:\|:\|\|\|\|________\|\|:\|\|__________:\|\|\|:__:\|\|:\|\|_\|:\|\|\n______________UUUAUCC_C_UUUGUCU_UAA__CUUUACUU________CUGCC__________UCAAU__UACUAC_AUCG\n3'-UUU...CCAAC_______C_A_______G___GU________A____________AUUAUUUAUU_____________U____-5'\n_____________\|_______________________________________________________________________\|\n_____________64______________________________________________________________________1\n	187 -- 193	47 -- 53	-38.9165 kcal/mol	16.2325 kcal/mol	6.344 kcal/mol	177 245@LB@ \| \|@LB@5'-UAC...ACAUA U G AAAGUUUC GUCGUUCU UC U UUGCU...AAU-3'@LB@ AGGUAGG G AAACGGA AUU GGAGUGAA GAUGG GGUUG GUGGUG UGGC@LB@ \|::\|\|\|\| \| \|\|\|\|:\|\| \|\|\| \|:\|:\|\|\|\| \|\|:\|\| :\|\|\|: :\|\|:\|\| \|:\|\|@LB@ UUUAUCC C UUUGUCU UAA CUUUACUU CUGCC UCAAU UACUAC AUCG@LB@3'-UUU...CCAAC C A G GU A AUUAUUUAUU U -5'@LB@ \| \|@LB@ 64 1@LB@@LB@@LB@Energy -16.34 kcal/mol@LB@Hybridization Energy -38.9165 kcal/mol@LB@Unfolding Energy - mRNA 16.2325 kcal/mol@LB@Unfolding Energy - sRNA 6.344 kcal/mol@LB@@LB@Position - mRNA 178 -- 244@LB@Position - sRNA 1 -- 63@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 47 -- 53@LB@
140	0.02319	0.526	b3615	waaH	-10.58	0.073933	178 -- 212	1 -- 47	LPS(HepIII)-glucuronic acid glycosyltransferase	_____________177______________________________________________213\n_____________\|________________________________________________\|\n5'-GAU...GGAUA____________C____U_______UU________________AC___ACCAA...GGA-3'\n______________AC_UUCAGAGGU____G_CGGUAAU___________AUGAUGA__AGC\n______________\|\|_\|\|\|\|\|\|::\|____\|_\|\|\|\|\|\|\|___________\|\|\|\|\|\|\|__\|\|\|\n______________UG_AAGUCUUUA____C_GCCAUUA___________UACUACU__UCG\n3'-UUU...UUGUC__U_________CUUA_U_______UUUAUUUCAAU_______A____-5'\n_____________\|_______________________________________________\|\n_____________48______________________________________________1\n	201 -- 207	5 -- 11	-24.9941 kcal/mol	8.09222 kcal/mol	6.32011 kcal/mol	177 213@LB@ \| \|@LB@5'-GAU...GGAUA C U UU AC ACCAA...GGA-3'@LB@ AC UUCAGAGGU G CGGUAAU AUGAUGA AGC@LB@ \|\| \|\|\|\|\|\|::\| \| \|\|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|@LB@ UG AAGUCUUUA C GCCAUUA UACUACU UCG@LB@3'-UUU...UUGUC U CUUA U UUUAUUUCAAU A -5'@LB@ \| \|@LB@ 48 1@LB@@LB@@LB@Energy -10.58 kcal/mol@LB@Hybridization Energy -24.9941 kcal/mol@LB@Unfolding Energy - mRNA 8.09222 kcal/mol@LB@Unfolding Energy - sRNA 6.32011 kcal/mol@LB@@LB@Position - mRNA 178 -- 212@LB@Position - sRNA 1 -- 47@LB@Position Seed - mRNA 201 -- 207@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)

Job resubmission

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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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