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
121	0.01924	0.5155	b0074	leuA	-11.43	0.049038	243 -- 261	39 -- 56	2-isopropylmalate synthase		_____________242_________________262\n_____________\|___________________\|\n5'-CAU...GCGAC______________A____CAAGC...UGG-3'\n______________GGUGAACAGGCGUU_CAGG\n______________\|\|\|:\|\|\|\|\|:\|:\|\|_\|\|\|:\n______________CCAUUUGUCUGUAA_GUCU\n3'-UUU...UAUCC___________________UUACU...UCG-5'\n_____________\|___________________\|\n_____________57__________________38\n	247 -- 253	46 -- 52	-24.0317 kcal/mol	6.35652 kcal/mol	6.24929 kcal/mol	242 262@LB@ \| \|@LB@5'-CAU...GCGAC A CAAGC...UGG-3'@LB@ GGUGAACAGGCGUU CAGG@LB@ \|\|\|:\|\|\|\|\|:\|:\|\| \|\|\|:@LB@ CCAUUUGUCUGUAA GUCU@LB@3'-UUU...UAUCC UUACU...UCG-5'@LB@ \| \|@LB@ 57 38@LB@@LB@@LB@Energy -11.43 kcal/mol@LB@Hybridization Energy -24.0317 kcal/mol@LB@Unfolding Energy - mRNA 6.35652 kcal/mol@LB@Unfolding Energy - sRNA 6.24929 kcal/mol@LB@@LB@Position - mRNA 243 -- 261@LB@Position - sRNA 39 -- 56@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 46 -- 52@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@
123	0.01951	0.5155	b0032	carA	-10.10	0.092857	258 -- 264	55 -- 61	carbamoyl phosphate synthetase small subunit glutamine amidotransferase		_____________257_____265\n_____________\|_______\|\n5'-UUG...GGGCC_______CAACA...AUA-3'\n______________AUAGGGG\n______________\|\|\|\|\|\|\|\n______________UAUCCCC\n3'-UUU...AACUU_______AUUUG...UCG-5'\n_____________\|_______\|\n_____________62______54\n	258 -- 264	55 -- 61	-10.8319 kcal/mol	0.710423 kcal/mol	0.0258473 kcal/mol	257 265@LB@ \| \|@LB@5'-UUG...GGGCC CAACA...AUA-3'@LB@ AUAGGGG@LB@ \|\|\|\|\|\|\|@LB@ UAUCCCC@LB@3'-UUU...AACUU AUUUG...UCG-5'@LB@ \| \|@LB@ 62 54@LB@@LB@@LB@Energy -10.10 kcal/mol@LB@Hybridization Energy -10.8319 kcal/mol@LB@Unfolding Energy - mRNA 0.710423 kcal/mol@LB@Unfolding Energy - sRNA 0.0258473 kcal/mol@LB@@LB@Position - mRNA 258 -- 264@LB@Position - sRNA 55 -- 61@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 55 -- 61@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@
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@
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@
127	0.01998	0.5155	b2922	yggE	-8.69	0.172995	232 -- 253	1 -- 26	oxidative stress defense protein		_____________231________________________254\n_____________\|__________________________\|\n5'-GCA...GGCAU________________C_________AGCGC...CCG-3'\n______________UAAUGGGUA___UUAG_GG_GAUGGC\n______________\|\|\|\|:::\|\|___\|\|\|:_\|:_\|\|\|:\|\|\n______________AUUAUUUAU___AAUU_CU_CUAUCG\n3'-UUU...CUGCC_________UUC____A__A______-5'\n_____________\|_________________________\|\n_____________27________________________1\n	234 -- 240	18 -- 24	-12.7828 kcal/mol	3.51669 kcal/mol	0.580494 kcal/mol	231 254@LB@ \| \|@LB@5'-GCA...GGCAU C AGCGC...CCG-3'@LB@ UAAUGGGUA UUAG GG GAUGGC@LB@ \|\|\|\|:::\|\| \|\|\|: \|: \|\|\|:\|\|@LB@ AUUAUUUAU AAUU CU CUAUCG@LB@3'-UUU...CUGCC UUC A A -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -8.69 kcal/mol@LB@Hybridization Energy -12.7828 kcal/mol@LB@Unfolding Energy - mRNA 3.51669 kcal/mol@LB@Unfolding Energy - sRNA 0.580494 kcal/mol@LB@@LB@Position - mRNA 232 -- 253@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 18 -- 24@LB@
128	0.0201	0.5155	b2782	mazF	-10.78	0.067406	32 -- 50	1 -- 23	mRNA interferase toxin antitoxin is MazE	b4225	_____________31______________________51\n_____________\|_______________________\|\n5'-AUC...CAAUC_______________________GAAGA...UCC-3'\n______________UGAAUA___UUGAUGAUGA_AGU\n______________\|:\|\|\|\|___\|\|:\|\|\|\|\|\|\|_\|\|:\n______________AUUUAU___AAUUACUACU_UCG\n3'-UUU...CCAUU______UUC__________A___-5'\n_____________\|______________________\|\n_____________24_____________________1\n	41 -- 47	5 -- 11	-13.6359 kcal/mol	2.75565 kcal/mol	0.105066 kcal/mol	31 51@LB@ \| \|@LB@5'-AUC...CAAUC GAAGA...UCC-3'@LB@ UGAAUA UUGAUGAUGA AGU@LB@ \|:\|\|\|\| \|\|:\|\|\|\|\|\|\| \|\|:@LB@ AUUUAU AAUUACUACU UCG@LB@3'-UUU...CCAUU UUC A -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -10.78 kcal/mol@LB@Hybridization Energy -13.6359 kcal/mol@LB@Unfolding Energy - mRNA 2.75565 kcal/mol@LB@Unfolding Energy - sRNA 0.105066 kcal/mol@LB@@LB@Position - mRNA 32 -- 50@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 5 -- 11@LB@
129	0.02061	0.5217	b0633	rlpA	-9.57	0.117965	261 -- 273	1 -- 12	septal ring protein suppressor of prc minor lipoprotein		_____________260___________274\n_____________\|_____________\|\n5'-CGG...CAAGC_________C___AACAG...CUG-3'\n______________GAUGAUGGU_AGC\n______________:\|\|\|\|\|\|:\|_\|\|\|\n______________UUACUACUA_UCG\n3'-UUU...UUCAA_____________-5'\n_____________\|____________\|\n_____________13___________1\n	263 -- 269	4 -- 10	-13.3317 kcal/mol	3.7231 kcal/mol	0.0394463 kcal/mol	260 274@LB@ \| \|@LB@5'-CGG...CAAGC C AACAG...CUG-3'@LB@ GAUGAUGGU AGC@LB@ :\|\|\|\|\|\|:\| \|\|\|@LB@ UUACUACUA UCG@LB@3'-UUU...UUCAA -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -9.57 kcal/mol@LB@Hybridization Energy -13.3317 kcal/mol@LB@Unfolding Energy - mRNA 3.7231 kcal/mol@LB@Unfolding Energy - sRNA 0.0394463 kcal/mol@LB@@LB@Position - mRNA 261 -- 273@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 4 -- 10@LB@
130	0.02079	0.5217	b3455	livG	-10.98	0.060940	96 -- 122	4 -- 29	branched-chain amino acid ABC transporter ATPase		_____________95__________________________123\n_____________\|___________________________\|\n5'-AUG...AUGCU_______UU_____U_C__________CUGGC...UCG-3'\n______________CGGUGGU__GAUGG_G_UGAUGAUGAU\n______________\|\|\|\|::\|__:\|\|::_\|_\|:\|\|\|\|\|\|\|\|\n______________GCCAUUA__UUAUU_C_AUUACUACUA\n3'-UUU...UUACU_______U______U_A__________UCG-5'\n_____________\|___________________________\|\n_____________30__________________________3\n	116 -- 122	4 -- 10	-20.0623 kcal/mol	6.95142 kcal/mol	2.12698 kcal/mol	95 123@LB@ \| \|@LB@5'-AUG...AUGCU UU U C CUGGC...UCG-3'@LB@ CGGUGGU GAUGG G UGAUGAUGAU@LB@ \|\|\|\|::\| :\|\|:: \| \|:\|\|\|\|\|\|\|\|@LB@ GCCAUUA UUAUU C AUUACUACUA@LB@3'-UUU...UUACU U U A UCG-5'@LB@ \| \|@LB@ 30 3@LB@@LB@@LB@Energy -10.98 kcal/mol@LB@Hybridization Energy -20.0623 kcal/mol@LB@Unfolding Energy - mRNA 6.95142 kcal/mol@LB@Unfolding Energy - sRNA 2.12698 kcal/mol@LB@@LB@Position - mRNA 96 -- 122@LB@Position - sRNA 4 -- 29@LB@Position Seed - mRNA 116 -- 122@LB@Position Seed - sRNA 4 -- 10@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:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching