Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
174	0.02096	0.4033	b3929	rraA	-13.95	0.014802	2 -- 21	45 -- 66	ribonuclease E (RNase E) inhibitor protein	_____________1______________________22\n_____________\|______________________\|\n__________5'-A____CC________________CCAAU...GCG-3'\n______________UGGA____CGGUGGCGAUGCGA\n______________\|\|\|\|____\|:\|\|\|\|\|:\|\|\|\|:\|\n______________ACCU____GUCACCGUUACGUU\n3'-UUU...AUACA____UUUA______________ACCGG...UUG-5'\n_____________\|______________________\|\n_____________67_____________________44\n	15 -- 21	45 -- 51	-26.5083 kcal/mol	8.28748 kcal/mol	4.27166 kcal/mol	1 22@LB@ \| \|@LB@ 5'-A CC CCAAU...GCG-3'@LB@ UGGA CGGUGGCGAUGCGA@LB@ \|\|\|\| \|:\|\|\|\|\|:\|\|\|\|:\|@LB@ ACCU GUCACCGUUACGUU@LB@3'-UUU...AUACA UUUA ACCGG...UUG-5'@LB@ \| \|@LB@ 67 44@LB@@LB@@LB@Energy -13.95 kcal/mol@LB@Hybridization Energy -26.5083 kcal/mol@LB@Unfolding Energy - mRNA 8.28748 kcal/mol@LB@Unfolding Energy - sRNA 4.27166 kcal/mol@LB@@LB@Position - mRNA 2 -- 21@LB@Position - sRNA 45 -- 66@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 45 -- 51@LB@
3	3.498e-05	0.03921	b4255	rraB	-13.36	0.020838	142 -- 156	41 -- 54	protein inhibitor of RNase E	_____________141_____________157\n_____________\|_______________\|\n5'-GAG...GUGGA_______U_______GUGUG...CCA-3'\n______________GGCAAUG_CAGUGGU\n______________\|\|\|\|\|\|\|_\|\|:\|\|\|:\n______________CCGUUAC_GUUACCG\n3'-UUU...AGUCA_______________GGUUG...UUG-5'\n_____________\|_______________\|\n_____________55______________40\n	150 -- 156	41 -- 47	-21.65 kcal/mol	4.39843 kcal/mol	3.89026 kcal/mol	141 157@LB@ \| \|@LB@5'-GAG...GUGGA U GUGUG...CCA-3'@LB@ GGCAAUG CAGUGGU@LB@ \|\|\|\|\|\|\| \|\|:\|\|\|:@LB@ CCGUUAC GUUACCG@LB@3'-UUU...AGUCA GGUUG...UUG-5'@LB@ \| \|@LB@ 55 40@LB@@LB@@LB@Energy -13.36 kcal/mol@LB@Hybridization Energy -21.65 kcal/mol@LB@Unfolding Energy - mRNA 4.39843 kcal/mol@LB@Unfolding Energy - sRNA 3.89026 kcal/mol@LB@@LB@Position - mRNA 142 -- 156@LB@Position - sRNA 41 -- 54@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 41 -- 47@LB@
21	0.0009862	0.1579	b2572	rseA	-10.60	0.091224	9 -- 29	44 -- 65	anti-sigma factor	_____________8______________________30\n_____________\|______________________\|\n___5'-UCCCUCCC________UAC____UG_____AACCU...GGG-3'\n______________GGAAGAUU____GCA__GCAAU\n______________\|\|\|\|:\|\|:____\|\|\|__\|\|\|\|\|\n______________CCUUUUAG____CGU__CGUUA\n3'-UUU...UACAA________UCAC___UA_____CCGGG...UUG-5'\n_____________\|______________________\|\n_____________66_____________________43\n	10 -- 16	58 -- 64	-18.0609 kcal/mol	3.14057 kcal/mol	4.32401 kcal/mol	8 30@LB@ \| \|@LB@ 5'-UCCCUCCC UAC UG AACCU...GGG-3'@LB@ GGAAGAUU GCA GCAAU@LB@ \|\|\|\|:\|\|: \|\|\| \|\|\|\|\|@LB@ CCUUUUAG CGU CGUUA@LB@3'-UUU...UACAA UCAC UA CCGGG...UUG-5'@LB@ \| \|@LB@ 66 43@LB@@LB@@LB@Energy -10.60 kcal/mol@LB@Hybridization Energy -18.0609 kcal/mol@LB@Unfolding Energy - mRNA 3.14057 kcal/mol@LB@Unfolding Energy - sRNA 4.32401 kcal/mol@LB@@LB@Position - mRNA 9 -- 29@LB@Position - sRNA 44 -- 65@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 58 -- 64@LB@
145	0.01667	0.3828	b1835	rsmF	-17.85	0.001164	186 -- 211	35 -- 58	16S rRNA m(5)C1407 methyltransferase SAM-dependent	_____________185________________________212\n_____________\|__________________________\|\n5'-CGC...UUUGC________C____UC___________CACCG...GUC-3'\n______________CAGUGGUA_AUGC__GUGGCCCAACA\n______________\|\|\|\|\|\|:\|_\|\|\|\|__:\|\|\|\|\|\|\|\|\|\|\n______________GUCACCGU_UACG__UACCGGGUUGU\n3'-UUU...UUUUA_____________U____________CUUUU...UUG-5'\n_____________\|__________________________\|\n_____________59_________________________34\n	205 -- 211	35 -- 41	-37.9392 kcal/mol	9.33395 kcal/mol	10.7541 kcal/mol	185 212@LB@ \| \|@LB@5'-CGC...UUUGC C UC CACCG...GUC-3'@LB@ CAGUGGUA AUGC GUGGCCCAACA@LB@ \|\|\|\|\|\|:\| \|\|\|\| :\|\|\|\|\|\|\|\|\|\|@LB@ GUCACCGU UACG UACCGGGUUGU@LB@3'-UUU...UUUUA U CUUUU...UUG-5'@LB@ \| \|@LB@ 59 34@LB@@LB@@LB@Energy -17.85 kcal/mol@LB@Hybridization Energy -37.9392 kcal/mol@LB@Unfolding Energy - mRNA 9.33395 kcal/mol@LB@Unfolding Energy - sRNA 10.7541 kcal/mol@LB@@LB@Position - mRNA 186 -- 211@LB@Position - sRNA 35 -- 58@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 35 -- 41@LB@
96	0.009004	0.3118	b3981	secE	-8.82	0.207803	253 -- 270	42 -- 57	preprotein translocase membrane subunit	_____________252________________271\n_____________\|__________________\|\n5'-UAA...GAUGA_____GUCGU________CAUUG...ACU-3'\n______________AGUGG_____UGUGGUGG\n______________\|\|\|\|\|_____\|\|:::\|\|\|\n______________UCACC_____ACGUUACC\n3'-UUU...UUUAG_____GUU__________GGGUU...UUG-5'\n_____________\|__________________\|\n_____________58_________________41\n	264 -- 270	42 -- 48	-15.0916 kcal/mol	2.64473 kcal/mol	3.62906 kcal/mol	252 271@LB@ \| \|@LB@5'-UAA...GAUGA GUCGU CAUUG...ACU-3'@LB@ AGUGG UGUGGUGG@LB@ \|\|\|\|\| \|\|:::\|\|\|@LB@ UCACC ACGUUACC@LB@3'-UUU...UUUAG GUU GGGUU...UUG-5'@LB@ \| \|@LB@ 58 41@LB@@LB@@LB@Energy -8.82 kcal/mol@LB@Hybridization Energy -15.0916 kcal/mol@LB@Unfolding Energy - mRNA 2.64473 kcal/mol@LB@Unfolding Energy - sRNA 3.62906 kcal/mol@LB@@LB@Position - mRNA 253 -- 270@LB@Position - sRNA 42 -- 57@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 42 -- 48@LB@
175	0.02099	0.4033	b2913	serA	-5.57	0.642321	190 -- 257	5 -- 65	D-3-phosphoglycerate dehydrogenase	_____________189_____________________________________________________________________258\n_____________\|_______________________________________________________________________\|\n5'-UGU...AGACA___UU____AAA______AG___UCGC___AGAAA________U____UU____C________________CACCA...CCA-3'\n______________GGA__GGGU___UGGCAA__GUA____UGG_____GACA_AGA_UAAG__UCUG_UGGUA__GAAGGCGUG\n______________\|\|\|__:::\|___\|\|\|\|\|\|__\|:\|____\|\|\|_____:\|\|\|_\|:\|_\|\|\|:__\|\|\|\|_\|\|::\|__:\|\|\|\|\|:\|:\n______________CCU__UUUA___ACCGUU__CGU____ACC_____UUGU_UUU_AUUU__AGAC_ACUGU__UUUCCGUAU\n3'-UUU...UACAA_________GUC______A____U______GGG______C___U____U___________UA_________AUUG-5'\n_____________\|_______________________________________________________________________\|\n_____________66______________________________________________________________________4\n	251 -- 257	5 -- 11	-32.5395 kcal/mol	14.8085 kcal/mol	12.157 kcal/mol	189 258@LB@ \| \|@LB@5'-UGU...AGACA UU AAA AG UCGC AGAAA U UU C CACCA...CCA-3'@LB@ GGA GGGU UGGCAA GUA UGG GACA AGA UAAG UCUG UGGUA GAAGGCGUG@LB@ \|\|\| :::\| \|\|\|\|\|\| \|:\| \|\|\| :\|\|\| \|:\| \|\|\|: \|\|\|\| \|\|::\| :\|\|\|\|\|:\|:@LB@ CCU UUUA ACCGUU CGU ACC UUGU UUU AUUU AGAC ACUGU UUUCCGUAU@LB@3'-UUU...UACAA GUC A U GGG C U U UA AUUG-5'@LB@ \| \|@LB@ 66 4@LB@@LB@@LB@Energy -5.57 kcal/mol@LB@Hybridization Energy -32.5395 kcal/mol@LB@Unfolding Energy - mRNA 14.8085 kcal/mol@LB@Unfolding Energy - sRNA 12.157 kcal/mol@LB@@LB@Position - mRNA 190 -- 257@LB@Position - sRNA 5 -- 65@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 5 -- 11@LB@
130	0.01417	0.3654	b3188	sfsB	-12.77	0.029182	125 -- 158	30 -- 65	malPQ operon transcriptional activator	_____________124__________________________________159\n_____________\|____________________________________\|\n5'-CGG...CAAUA__CC______GA___UA___________________AGUGU...UGA-3'\n______________GG___AUCAG__GUA__GUGAU_GCUCGACAGAAGA\n______________\|\|___\|\|\|\|\|__\|:\|__\|::\|\|_\|\|:\|:\|\|\|\|\|\|:\|\n______________CC___UAGUC__CGU__CGUUA_CGGGUUGUCUUUU\n3'-UUU...UACAA__UUU_____AC___UA_____C_____________AUUUU...UUG-5'\n_____________\|____________________________________\|\n_____________66___________________________________29\n	152 -- 158	30 -- 36	-32.1455 kcal/mol	8.39464 kcal/mol	10.9856 kcal/mol	124 159@LB@ \| \|@LB@5'-CGG...CAAUA CC GA UA AGUGU...UGA-3'@LB@ GG AUCAG GUA GUGAU GCUCGACAGAAGA@LB@ \|\| \|\|\|\|\| \|:\| \|::\|\| \|\|:\|:\|\|\|\|\|\|:\|@LB@ CC UAGUC CGU CGUUA CGGGUUGUCUUUU@LB@3'-UUU...UACAA UUU AC UA C AUUUU...UUG-5'@LB@ \| \|@LB@ 66 29@LB@@LB@@LB@Energy -12.77 kcal/mol@LB@Hybridization Energy -32.1455 kcal/mol@LB@Unfolding Energy - mRNA 8.39464 kcal/mol@LB@Unfolding Energy - sRNA 10.9856 kcal/mol@LB@@LB@Position - mRNA 125 -- 158@LB@Position - sRNA 30 -- 65@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 30 -- 36@LB@
14	0.0005336	0.1268	b0178	skp	-14.43	0.011083	94 -- 112	46 -- 65	periplasmic chaperone	_____________93___________________113\n_____________\|____________________\|\n5'-CUC...ACAAA____UG______________GCGAU...UCC-3'\n______________GGAA___UAGUGGUAGUGUA\n______________\|\|\|\|___:\|\|\|\|\|:\|:\|\|:\|\n______________CCUU___GUCACCGUUACGU\n3'-UUU...UACAA____UUA_____________UACCG...UUG-5'\n_____________\|____________________\|\n_____________66___________________45\n	105 -- 111	47 -- 53	-21.6303 kcal/mol	3.11688 kcal/mol	4.07994 kcal/mol	93 113@LB@ \| \|@LB@5'-CUC...ACAAA UG GCGAU...UCC-3'@LB@ GGAA UAGUGGUAGUGUA@LB@ \|\|\|\| :\|\|\|\|\|:\|:\|\|:\|@LB@ CCUU GUCACCGUUACGU@LB@3'-UUU...UACAA UUA UACCG...UUG-5'@LB@ \| \|@LB@ 66 45@LB@@LB@@LB@Energy -14.43 kcal/mol@LB@Hybridization Energy -21.6303 kcal/mol@LB@Unfolding Energy - mRNA 3.11688 kcal/mol@LB@Unfolding Energy - sRNA 4.07994 kcal/mol@LB@@LB@Position - mRNA 94 -- 112@LB@Position - sRNA 46 -- 65@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 47 -- 53@LB@
9	0.0003848	0.1262	b2708	srlQ	-10.45	0.097910	5 -- 28	40 -- 60	D-arabinose 5-phosphate isomerase	_____________4_________________________29\n_____________\|_________________________\|\n_______5'-UACC______AA____AU___________GCGCG...GCG-3'\n______________GUCAGU__GGCA__GUGCAAUG_CC\n______________:\|\|\|\|\|__\|\|\|\|__:\|\|\|\|\|\|\|_\|\|\n______________UAGUCA__CCGU__UACGUUAC_GG\n3'-UUU...CCUUU______________________C__GUUGU...UUG-5'\n_____________\|_________________________\|\n_____________61________________________39\n	20 -- 26	43 -- 49	-23.8159 kcal/mol	7.25851 kcal/mol	6.10522 kcal/mol	4 29@LB@ \| \|@LB@ 5'-UACC AA AU GCGCG...GCG-3'@LB@ GUCAGU GGCA GUGCAAUG CC@LB@ :\|\|\|\|\| \|\|\|\| :\|\|\|\|\|\|\| \|\|@LB@ UAGUCA CCGU UACGUUAC GG@LB@3'-UUU...CCUUU C GUUGU...UUG-5'@LB@ \| \|@LB@ 61 39@LB@@LB@@LB@Energy -10.45 kcal/mol@LB@Hybridization Energy -23.8159 kcal/mol@LB@Unfolding Energy - mRNA 7.25851 kcal/mol@LB@Unfolding Energy - sRNA 6.10522 kcal/mol@LB@@LB@Position - mRNA 5 -- 28@LB@Position - sRNA 40 -- 60@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 43 -- 49@LB@
106	0.009895	0.3118	b3962	sthA	-8.25	0.262922	71 -- 97	8 -- 33	pyridine nucleotide transhydrogenase soluble	_____________70___________________________98\n_____________\|____________________________\|\n5'-UAC...GGGCA_________AACA______AGC______CGCUC...CAG-3'\n______________AAAGUAAGA_____GACAA___AAAGGC\n______________\|\|\|:\|\|\|:\|_____\|\|\|\|\|___\|\|\|\|\|\|\n______________UUUUAUUUU_____CUGUU___UUUCCG\n3'-UUU...UUGUC_________AGACA_____A________UAUAUUG-5'\n_____________\|____________________________\|\n_____________34___________________________7\n	73 -- 79	25 -- 31	-15.3826 kcal/mol	2.09876 kcal/mol	5.02883 kcal/mol	70 98@LB@ \| \|@LB@5'-UAC...GGGCA AACA AGC CGCUC...CAG-3'@LB@ AAAGUAAGA GACAA AAAGGC@LB@ \|\|\|:\|\|\|:\| \|\|\|\|\| \|\|\|\|\|\|@LB@ UUUUAUUUU CUGUU UUUCCG@LB@3'-UUU...UUGUC AGACA A UAUAUUG-5'@LB@ \| \|@LB@ 34 7@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -15.3826 kcal/mol@LB@Unfolding Energy - mRNA 2.09876 kcal/mol@LB@Unfolding Energy - sRNA 5.02883 kcal/mol@LB@@LB@Position - mRNA 71 -- 97@LB@Position - sRNA 8 -- 33@LB@Position Seed - mRNA 73 -- 79@LB@Position Seed - sRNA 25 -- 31@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