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
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@
85	0.01268	0.4896	b1827	kdgR	-11.91	0.038409	291 -- 299	56 -- 64	KDG regulon transcriptional repressor	_____________290_______300\n_____________\|_________\|\n5'-GCC...AGCGC_________A-3'\n______________GAAAUAGGG\n______________\|\|\|\|\|\|\|\|\|\n______________CUUUAUCCC\n3'-UUU...GCCAA_________CAUUU...UCG-5'\n_____________\|_________\|\n_____________65________55\n	293 -- 299	56 -- 62	-12.6296 kcal/mol	0.690209 kcal/mol	0.02823 kcal/mol	290 300@LB@ \| \|@LB@5'-GCC...AGCGC A-3'@LB@ GAAAUAGGG@LB@ \|\|\|\|\|\|\|\|\|@LB@ CUUUAUCCC@LB@3'-UUU...GCCAA CAUUU...UCG-5'@LB@ \| \|@LB@ 65 55@LB@@LB@@LB@Energy -11.91 kcal/mol@LB@Hybridization Energy -12.6296 kcal/mol@LB@Unfolding Energy - mRNA 0.690209 kcal/mol@LB@Unfolding Energy - sRNA 0.02823 kcal/mol@LB@@LB@Position - mRNA 291 -- 299@LB@Position - sRNA 56 -- 64@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 56 -- 62@LB@
122	0.01943	0.5155	b1842	holE	-10.27	0.085496	209 -- 257	4 -- 63	DNA polymerase III theta subunit	_____________208____________________________________________________________258\n_____________\|______________________________________________________________\|\n5'-GUC...CUGAA____CU__C_____U___U__AA_____________________________G____UC___UUGGC...UGC-3'\n______________GAAU__GG_UAAAC_GGA_CA__CAGAAAUG_____________GAUAAAGU_AAUG__GAU\n______________:\|\|\|__\|\|_\|\|\|\|\|_:\|\|_\|\|__\|\|\|\|\|\|\|\|_____________:\|\|\|\|\|\|\|_\|\|\|\|__\|\|\|\n______________UUUA__CC_AUUUG_UCU_GU__GUCUUUAC_____________UUAUUUCA_UUAC__CUA\n3'-UUU...CCAAC____UC__C____________AA________UUACUGCCAUUAU________A____UA___UCG-5'\n_____________\|______________________________________________________________\|\n_____________64_____________________________________________________________3\n	241 -- 247	14 -- 20	-26.5551 kcal/mol	9.93779 kcal/mol	6.34398 kcal/mol	208 258@LB@ \| \|@LB@5'-GUC...CUGAA CU C U U AA G UC UUGGC...UGC-3'@LB@ GAAU GG UAAAC GGA CA CAGAAAUG GAUAAAGU AAUG GAU@LB@ :\|\|\| \|\| \|\|\|\|\| :\|\| \|\| \|\|\|\|\|\|\|\| :\|\|\|\|\|\|\| \|\|\|\| \|\|\|@LB@ UUUA CC AUUUG UCU GU GUCUUUAC UUAUUUCA UUAC CUA@LB@3'-UUU...CCAAC UC C AA UUACUGCCAUUAU A UA UCG-5'@LB@ \| \|@LB@ 64 3@LB@@LB@@LB@Energy -10.27 kcal/mol@LB@Hybridization Energy -26.5551 kcal/mol@LB@Unfolding Energy - mRNA 9.93779 kcal/mol@LB@Unfolding Energy - sRNA 6.34398 kcal/mol@LB@@LB@Position - mRNA 209 -- 257@LB@Position - sRNA 4 -- 63@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 14 -- 20@LB@
36	0.003415	0.3114	b1849	purT	-10.41	0.080237	8 -- 43	29 -- 56	phosphoribosylglycinamide formyltransferase 2	_____________7_____________________________________44\n_____________\|_____________________________________\|\n____5'-UUUUGCU_______________UCUCUUCGCCCUCAC_______UACGU...GUC-3'\n______________GGUAAAC_GACAUUU_______________GAAUGAC\n______________\|\|\|\|\|\|\|_\|\|\|\|\|\|:_______________\|\|\|\|\|\|\|\n______________CCAUUUG_CUGUAAG_______________CUUACUG\n3'-UUU...UAUCC_______U_______UCUUUA________________CCAUU...UCG-5'\n_____________\|_____________________________________\|\n_____________57____________________________________28\n	37 -- 43	29 -- 35	-21.896 kcal/mol	5.20104 kcal/mol	6.28612 kcal/mol	7 44@LB@ \| \|@LB@ 5'-UUUUGCU UCUCUUCGCCCUCAC UACGU...GUC-3'@LB@ GGUAAAC GACAUUU GAAUGAC@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|: \|\|\|\|\|\|\|@LB@ CCAUUUG CUGUAAG CUUACUG@LB@3'-UUU...UAUCC U UCUUUA CCAUU...UCG-5'@LB@ \| \|@LB@ 57 28@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -21.896 kcal/mol@LB@Unfolding Energy - mRNA 5.20104 kcal/mol@LB@Unfolding Energy - sRNA 6.28612 kcal/mol@LB@@LB@Position - mRNA 8 -- 43@LB@Position - sRNA 29 -- 56@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 29 -- 35@LB@
98	0.01586	0.5059	b1860	ruvB	-8.95	0.154425	184 -- 211	1 -- 30	ATP-dependent DNA helicase component of RuvABC resolvasome	_____________183_____________________________212\n_____________\|_______________________________\|\n5'-ACG...GCGCC___U__UG_______________U_______AGACC...GUC-3'\n______________GCG_UA__AGGUAAAG__GAUGA_UGA_AGC\n______________:\|\|_\|\|__\|::\|\|\|\|\|__:\|\|\|\|_\|\|\|_\|\|\|\n______________UGC_AU__UUUAUUUC__UUACU_ACU_UCG\n3'-UUU...CUUAC___C__UA________AA_________A___-5'\n_____________\|______________________________\|\n_____________31_____________________________1\n	193 -- 199	15 -- 21	-17.0174 kcal/mol	5.93551 kcal/mol	2.12822 kcal/mol	183 212@LB@ \| \|@LB@5'-ACG...GCGCC U UG U AGACC...GUC-3'@LB@ GCG UA AGGUAAAG GAUGA UGA AGC@LB@ :\|\| \|\| \|::\|\|\|\|\| :\|\|\|\| \|\|\| \|\|\|@LB@ UGC AU UUUAUUUC UUACU ACU UCG@LB@3'-UUU...CUUAC C UA AA A -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -8.95 kcal/mol@LB@Hybridization Energy -17.0174 kcal/mol@LB@Unfolding Energy - mRNA 5.93551 kcal/mol@LB@Unfolding Energy - sRNA 2.12822 kcal/mol@LB@@LB@Position - mRNA 184 -- 211@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 15 -- 21@LB@
136	0.02238	0.526	b1883	cheB	-10.46	0.078180	185 -- 206	1 -- 23	fused chemotaxis regulator: protein-glutamate methylesterase in two-component regulatory system with CheA	_____________184______________________207\n_____________\|________________________\|\n5'-GGG...UGCGC_________A____C_________AAAAU...CGA-3'\n______________UAAGUAAGG_UUAA_GAUGA__GC\n______________\|\|\|:\|\|\|:\|_\|\|\|\|_\|\|\|\|\|__\|\|\n______________AUUUAUUUC_AAUU_CUACU__CG\n3'-UUU...CCAUU______________A_____AU__-5'\n_____________\|_______________________\|\n_____________24______________________1\n	187 -- 193	15 -- 21	-15.1436 kcal/mol	4.57462 kcal/mol	0.105066 kcal/mol	184 207@LB@ \| \|@LB@5'-GGG...UGCGC A C AAAAU...CGA-3'@LB@ UAAGUAAGG UUAA GAUGA GC@LB@ \|\|\|:\|\|\|:\| \|\|\|\| \|\|\|\|\| \|\|@LB@ AUUUAUUUC AAUU CUACU CG@LB@3'-UUU...CCAUU A AU -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -15.1436 kcal/mol@LB@Unfolding Energy - mRNA 4.57462 kcal/mol@LB@Unfolding Energy - sRNA 0.105066 kcal/mol@LB@@LB@Position - mRNA 185 -- 206@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 15 -- 21@LB@
162	0.02632	0.526	b1886	tar	-10.00	0.096892	244 -- 251	53 -- 60	methyl-accepting chemotaxis protein II	_____________243______252\n_____________\|________\|\n5'-UGC...GGUGC________UUCGC...UUC-3'\n______________UGGGGGUA\n______________\|:\|\|\|\|\|\|\n______________AUCCCCAU\n3'-UUU...ACUUU________UUGUC...UCG-5'\n_____________\|________\|\n_____________61_______52\n	245 -- 251	53 -- 59	-12.2006 kcal/mol	2.12623 kcal/mol	0.0710089 kcal/mol	243 252@LB@ \| \|@LB@5'-UGC...GGUGC UUCGC...UUC-3'@LB@ UGGGGGUA@LB@ \|:\|\|\|\|\|\|@LB@ AUCCCCAU@LB@3'-UUU...ACUUU UUGUC...UCG-5'@LB@ \| \|@LB@ 61 52@LB@@LB@@LB@Energy -10.00 kcal/mol@LB@Hybridization Energy -12.2006 kcal/mol@LB@Unfolding Energy - mRNA 2.12623 kcal/mol@LB@Unfolding Energy - sRNA 0.0710089 kcal/mol@LB@@LB@Position - mRNA 244 -- 251@LB@Position - sRNA 53 -- 60@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 53 -- 59@LB@
92	0.01497	0.5059	b1902	ftnB	-10.62	0.072498	12 -- 36	1 -- 25	ferritin B putative ferrous iron reservoir	_____________11________________________37\n_____________\|_________________________\|\n5'-UGA...GUAAA____U_____C________UUA___AUUUU...AAC-3'\n______________AAUA_AUAAA_UUGAUGAU___AGC\n______________\|\|\|\|_\|\|\|\|\|_\|\|:\|\|\|\|\|___\|\|\|\n______________UUAU_UAUUU_AAUUACUA___UCG\n3'-UUU...UGCCA____U_____C________CUA___-5'\n_____________\|________________________\|\n_____________26_______________________1\n	24 -- 30	7 -- 13	-13.6335 kcal/mol	2.89836 kcal/mol	0.112205 kcal/mol	11 37@LB@ \| \|@LB@5'-UGA...GUAAA U C UUA AUUUU...AAC-3'@LB@ AAUA AUAAA UUGAUGAU AGC@LB@ \|\|\|\| \|\|\|\|\| \|\|:\|\|\|\|\| \|\|\|@LB@ UUAU UAUUU AAUUACUA UCG@LB@3'-UUU...UGCCA U C CUA -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -10.62 kcal/mol@LB@Hybridization Energy -13.6335 kcal/mol@LB@Unfolding Energy - mRNA 2.89836 kcal/mol@LB@Unfolding Energy - sRNA 0.112205 kcal/mol@LB@@LB@Position - mRNA 12 -- 36@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 7 -- 13@LB@
172	0.02805	0.531	b1912	pgsA	-10.33	0.083391	160 -- 169	52 -- 61	phosphatidylglycerophosphate synthetase	_____________159________170\n_____________\|__________\|\n5'-GUC...GCAAC__________UCUUA...UUG-3'\n______________AUAGGGGUAA\n______________\|\|\|\|\|\|\|\|\|\|\n______________UAUCCCCAUU\n3'-UUU...AACUU__________UGUCU...UCG-5'\n_____________\|__________\|\n_____________62_________51\n	163 -- 169	52 -- 58	-13.9577 kcal/mol	3.55629 kcal/mol	0.0747282 kcal/mol	159 170@LB@ \| \|@LB@5'-GUC...GCAAC UCUUA...UUG-3'@LB@ AUAGGGGUAA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UAUCCCCAUU@LB@3'-UUU...AACUU UGUCU...UCG-5'@LB@ \| \|@LB@ 62 51@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -13.9577 kcal/mol@LB@Unfolding Energy - mRNA 3.55629 kcal/mol@LB@Unfolding Energy - sRNA 0.0747282 kcal/mol@LB@@LB@Position - mRNA 160 -- 169@LB@Position - sRNA 52 -- 61@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 52 -- 58@LB@
124	0.01977	0.5155	b1920	fliY	-11.21	0.054671	192 -- 201	49 -- 58	cystine transporter subunit	_____________191________202\n_____________\|__________\|\n5'-CCA...CAUUC__________UGAAA...UGC-3'\n______________GGGGUGAAUA\n______________\|\|\|\|\|:\|\|:\|\n______________CCCCAUUUGU\n3'-UUU...UUUAU__________CUGUA...UCG-5'\n_____________\|__________\|\n_____________59_________48\n	195 -- 201	49 -- 55	-14.4557 kcal/mol	2.52037 kcal/mol	0.729386 kcal/mol	191 202@LB@ \| \|@LB@5'-CCA...CAUUC UGAAA...UGC-3'@LB@ GGGGUGAAUA@LB@ \|\|\|\|\|:\|\|:\|@LB@ CCCCAUUUGU@LB@3'-UUU...UUUAU CUGUA...UCG-5'@LB@ \| \|@LB@ 59 48@LB@@LB@@LB@Energy -11.21 kcal/mol@LB@Hybridization Energy -14.4557 kcal/mol@LB@Unfolding Energy - mRNA 2.52037 kcal/mol@LB@Unfolding Energy - sRNA 0.729386 kcal/mol@LB@@LB@Position - mRNA 192 -- 201@LB@Position - sRNA 49 -- 58@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 49 -- 55@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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