Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
14	2.236e-05	0.005627	b3306	rpsH	-12.22	0.029933	187 -- 206	35 -- 55	30S ribosomal subunit protein S8		_____________186____________________207\n_____________\|______________________\|\n5'-AGC...AUCAC______A_______________AUGCA...AAG-3'\n______________GGGAGU_AAGACAG_AU_GAGC\n______________\|\|:\|\|\|_\|\|\|\|\|\|:_\|\|_\|\|\|\|\n______________CCUUCA_UUCUGUU_UA_CUCG\n3'-UUU...UUUUU______________A__C____CGUUG...ACG-5'\n_____________\|______________________\|\n_____________56_____________________34\n	194 -- 200	43 -- 49	-20.142 kcal/mol	3.78995 kcal/mol	4.0932 kcal/mol	186 207@LB@ \| \|@LB@5'-AGC...AUCAC A AUGCA...AAG-3'@LB@ GGGAGU AAGACAG AU GAGC@LB@ \|\|:\|\|\| \|\|\|\|\|\|: \|\| \|\|\|\|@LB@ CCUUCA UUCUGUU UA CUCG@LB@3'-UUU...UUUUU A C CGUUG...ACG-5'@LB@ \| \|@LB@ 56 34@LB@@LB@@LB@Energy -12.22 kcal/mol@LB@Hybridization Energy -20.142 kcal/mol@LB@Unfolding Energy - mRNA 3.78995 kcal/mol@LB@Unfolding Energy - sRNA 4.0932 kcal/mol@LB@@LB@Position - mRNA 187 -- 206@LB@Position - sRNA 35 -- 55@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 43 -- 49@LB@
21	6.29e-05	0.01049	b4040	ubiA	-12.44	0.026053	187 -- 207	35 -- 59	p-hydroxybenzoate octaprenyltransferase		_____________186_______________________208\n_____________\|_________________________\|\n5'-AGC...GUACU________AAA______________GGAGU...UAU-3'\n______________AAGAGGAA_______AAUAUGGAGU\n______________\|\|:\|\|\|\|\|_______\|\|\|\|\|\|\|\|\|:\n______________UUUUCCUU_______UUAUACCUCG\n3'-UUU...AAGUU________CAUUCUG__________CGUUG...ACG-5'\n_____________\|_________________________\|\n_____________60________________________34\n	201 -- 207	35 -- 41	-18.3412 kcal/mol	1.63668 kcal/mol	4.22714 kcal/mol	186 208@LB@ \| \|@LB@5'-AGC...GUACU AAA GGAGU...UAU-3'@LB@ AAGAGGAA AAUAUGGAGU@LB@ \|\|:\|\|\|\|\| \|\|\|\|\|\|\|\|\|:@LB@ UUUUCCUU UUAUACCUCG@LB@3'-UUU...AAGUU CAUUCUG CGUUG...ACG-5'@LB@ \| \|@LB@ 60 34@LB@@LB@@LB@Energy -12.44 kcal/mol@LB@Hybridization Energy -18.3412 kcal/mol@LB@Unfolding Energy - mRNA 1.63668 kcal/mol@LB@Unfolding Energy - sRNA 4.22714 kcal/mol@LB@@LB@Position - mRNA 187 -- 207@LB@Position - sRNA 35 -- 59@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 35 -- 41@LB@
44	0.0004181	0.03347	b3429	glgA	-12.00	0.034422	173 -- 196	35 -- 55	glycogen synthase		_____________172______________________197\n_____________\|________________________\|\n5'-GUA...GCUAC_____U_______UAAACA_____GAUAA...ACG-3'\n______________GGAAG_UAGGGCA______GGAGC\n______________\|\|\|\|\|_\|\|:\|:\|\|______\|\|\|\|\|\n______________CCUUC_AUUCUGU______CCUCG\n3'-UUU...UUUUU_____________UAUA_______CGUUG...ACG-5'\n_____________\|________________________\|\n_____________56_______________________34\n	179 -- 185	44 -- 50	-21.7083 kcal/mol	5.57994 kcal/mol	4.0932 kcal/mol	172 197@LB@ \| \|@LB@5'-GUA...GCUAC U UAAACA GAUAA...ACG-3'@LB@ GGAAG UAGGGCA GGAGC@LB@ \|\|\|\|\| \|\|:\|:\|\| \|\|\|\|\|@LB@ CCUUC AUUCUGU CCUCG@LB@3'-UUU...UUUUU UAUA CGUUG...ACG-5'@LB@ \| \|@LB@ 56 34@LB@@LB@@LB@Energy -12.00 kcal/mol@LB@Hybridization Energy -21.7083 kcal/mol@LB@Unfolding Energy - mRNA 5.57994 kcal/mol@LB@Unfolding Energy - sRNA 4.0932 kcal/mol@LB@@LB@Position - mRNA 173 -- 196@LB@Position - sRNA 35 -- 55@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 44 -- 50@LB@
66	0.001137	0.05992	b0076	leuO	-9.90	0.116504	167 -- 195	35 -- 60	global transcription factor		_____________166_____________________________196\n_____________\|_______________________________\|\n5'-UAU...AUAAG___________UAAGUGU_____________UAAGU...UGA-3'\n______________GGAAAGGGAGU_______GACA__GUGGAGU\n______________::\|\|\|\|\|:\|\|\|_______\|\|\|\|__:\|\|\|\|\|:\n______________UUUUUCCUUCA_______CUGU__UACCUCG\n3'-UUU...UAAGU___________UU_________UA_______CGUUG...ACG-5'\n_____________\|_______________________________\|\n_____________61______________________________34\n	189 -- 195	35 -- 41	-23.1584 kcal/mol	8.98888 kcal/mol	4.23745 kcal/mol	166 196@LB@ \| \|@LB@5'-UAU...AUAAG UAAGUGU UAAGU...UGA-3'@LB@ GGAAAGGGAGU GACA GUGGAGU@LB@ ::\|\|\|\|\|:\|\|\| \|\|\|\| :\|\|\|\|\|:@LB@ UUUUUCCUUCA CUGU UACCUCG@LB@3'-UUU...UAAGU UU UA CGUUG...ACG-5'@LB@ \| \|@LB@ 61 34@LB@@LB@@LB@Energy -9.90 kcal/mol@LB@Hybridization Energy -23.1584 kcal/mol@LB@Unfolding Energy - mRNA 8.98888 kcal/mol@LB@Unfolding Energy - sRNA 4.23745 kcal/mol@LB@@LB@Position - mRNA 167 -- 195@LB@Position - sRNA 35 -- 60@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 35 -- 41@LB@
77	0.00185	0.08273	b2325	yfcL	-11.04	0.061434	190 -- 213	35 -- 57	uncharacterized protein		_____________189______________________214\n_____________\|________________________\|\n5'-AAC...ACAAU______AG________CGC_____UUGAA...GCC-3'\n______________GAGGAA__AAGAUGAU___GGAGU\n______________:\|\|\|\|\|__\|\|\|\|::\|\|___\|\|\|\|:\n______________UUCCUU__UUCUGUUA___CCUCG\n3'-UUU...GUUUU______CA________UA______CGUUG...ACG-5'\n_____________\|________________________\|\n_____________58_______________________34\n	199 -- 205	42 -- 48	-19.5886 kcal/mol	4.3321 kcal/mol	4.1846 kcal/mol	189 214@LB@ \| \|@LB@5'-AAC...ACAAU AG CGC UUGAA...GCC-3'@LB@ GAGGAA AAGAUGAU GGAGU@LB@ :\|\|\|\|\| \|\|\|\|::\|\| \|\|\|\|:@LB@ UUCCUU UUCUGUUA CCUCG@LB@3'-UUU...GUUUU CA UA CGUUG...ACG-5'@LB@ \| \|@LB@ 58 34@LB@@LB@@LB@Energy -11.04 kcal/mol@LB@Hybridization Energy -19.5886 kcal/mol@LB@Unfolding Energy - mRNA 4.3321 kcal/mol@LB@Unfolding Energy - sRNA 4.1846 kcal/mol@LB@@LB@Position - mRNA 190 -- 213@LB@Position - sRNA 35 -- 57@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 42 -- 48@LB@
109	0.003466	0.1114	b4485	ytfR	-10.51	0.083206	29 -- 56	35 -- 61	putative sugar ABC transporter ATPase		_____________28____________________________57\n_____________\|_____________________________\|\n5'-CCU...AAGAA___UU__A_________AA__________AUUGA...GCC-3'\n______________GAA__AG_GAAG_AAGA__AAUAUGGGGU\n______________:\|\|__\|\|_\|\|\|\|_\|\|\|\|__\|\|\|\|\|\|\|:\|:\n______________UUU__UC_CUUC_UUCU__UUAUACCUCG\n3'-UUU...UUAAG___UU_______A____G___________CGUUG...ACG-5'\n_____________\|_____________________________\|\n_____________62____________________________34\n	50 -- 56	35 -- 41	-20.6661 kcal/mol	5.51365 kcal/mol	4.61294 kcal/mol	28 57@LB@ \| \|@LB@5'-CCU...AAGAA UU A AA AUUGA...GCC-3'@LB@ GAA AG GAAG AAGA AAUAUGGGGU@LB@ :\|\| \|\| \|\|\|\| \|\|\|\| \|\|\|\|\|\|\|:\|:@LB@ UUU UC CUUC UUCU UUAUACCUCG@LB@3'-UUU...UUAAG UU A G CGUUG...ACG-5'@LB@ \| \|@LB@ 62 34@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -20.6661 kcal/mol@LB@Unfolding Energy - mRNA 5.51365 kcal/mol@LB@Unfolding Energy - sRNA 4.61294 kcal/mol@LB@@LB@Position - mRNA 29 -- 56@LB@Position - sRNA 35 -- 61@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 35 -- 41@LB@
147	0.005701	0.1366	b1622	malY	-7.52	0.364460	44 -- 91	35 -- 85	PLP-dependent beta-cystathionase and maltose regulon regulator		_____________43____________________________________________________92\n_____________\|_____________________________________________________\|\n5'-UCG...GAUAU____C____UAA_______GCACU__________CAAUC___________C__AGUAC...UCA-3'\n______________GUCG_UUGU___UGUGCAG_________GAAGGA_____GGGCAAU_UGG_GU\n______________:\|\|:_\|\|\|\|___\|:\|\|\|\|\|_________:\|\|\|\|\|_____:\|:\|\|\|\|_\|\|\|_\|:\n______________UAGU_AACA___AUACGUC_________UUUCCU_____UCUGUUA_ACC_CG\n3'-UUU...AUGCU____U____CG________AUUAAGUUU______UCAU________U___U__CGUUG...ACG-5'\n_____________\|_____________________________________________________\|\n_____________86____________________________________________________34\n	79 -- 85	42 -- 48	-29.3049 kcal/mol	13.5755 kcal/mol	8.20283 kcal/mol	43 92@LB@ \| \|@LB@5'-UCG...GAUAU C UAA GCACU CAAUC C AGUAC...UCA-3'@LB@ GUCG UUGU UGUGCAG GAAGGA GGGCAAU UGG GU@LB@ :\|\|: \|\|\|\| \|:\|\|\|\|\| :\|\|\|\|\| :\|:\|\|\|\| \|\|\| \|:@LB@ UAGU AACA AUACGUC UUUCCU UCUGUUA ACC CG@LB@3'-UUU...AUGCU U CG AUUAAGUUU UCAU U U CGUUG...ACG-5'@LB@ \| \|@LB@ 86 34@LB@@LB@@LB@Energy -7.52 kcal/mol@LB@Hybridization Energy -29.3049 kcal/mol@LB@Unfolding Energy - mRNA 13.5755 kcal/mol@LB@Unfolding Energy - sRNA 8.20283 kcal/mol@LB@@LB@Position - mRNA 44 -- 91@LB@Position - sRNA 35 -- 85@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 42 -- 48@LB@
154	0.005979	0.1368	b4136	dsbD	-7.81	0.321864	41 -- 58	35 -- 56	thiol:disulfide interchange protein and activator of DsbC		_____________40______________________59\n_____________\|_______________________\|\n5'-UGC...UUACU___A___________________AAGAA...CGG-3'\n______________GGG_AGGUAAG_C____UGGAGC\n______________:\|\|_\|:\|\|\|\|\|_\|____\|\|\|\|\|\|\n______________UCC_UUCAUUC_G____ACCUCG\n3'-UUU...UUUUU___________U_UUAU______CGUUG...ACG-5'\n_____________\|_______________________\|\n_____________57______________________34\n	45 -- 51	47 -- 53	-17.7247 kcal/mol	5.71782 kcal/mol	4.15888 kcal/mol	40 59@LB@ \| \|@LB@5'-UGC...UUACU A AAGAA...CGG-3'@LB@ GGG AGGUAAG C UGGAGC@LB@ :\|\| \|:\|\|\|\|\| \| \|\|\|\|\|\|@LB@ UCC UUCAUUC G ACCUCG@LB@3'-UUU...UUUUU U UUAU CGUUG...ACG-5'@LB@ \| \|@LB@ 57 34@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -17.7247 kcal/mol@LB@Unfolding Energy - mRNA 5.71782 kcal/mol@LB@Unfolding Energy - sRNA 4.15888 kcal/mol@LB@@LB@Position - mRNA 41 -- 58@LB@Position - sRNA 35 -- 56@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 47 -- 53@LB@
174	0.007207	0.145	b1034	ycdX	-9.36	0.154134	94 -- 120	35 -- 63	alkaline phosphatase		_____________93_____________________________121\n_____________\|______________________________\|\n5'-GGC...CCAGC__________________G___C__C____AAGUC...AAC-3'\n______________UCGAAAAAGGG___GAGA_GGU_UG_GGGC\n______________\|\|:\|\|\|\|\|\|\|:___:\|\|\|_::\|_\|\|_\|:\|\|\n______________AGUUUUUUCCU___UUCU_UUA_AC_CUCG\n3'-UUU...CAUUA___________UCA____G___U_______CGUUG...ACG-5'\n_____________\|______________________________\|\n_____________64_____________________________34\n	98 -- 104	53 -- 59	-21.9855 kcal/mol	6.52956 kcal/mol	6.08557 kcal/mol	93 121@LB@ \| \|@LB@5'-GGC...CCAGC G C C AAGUC...AAC-3'@LB@ UCGAAAAAGGG GAGA GGU UG GGGC@LB@ \|\|:\|\|\|\|\|\|\|: :\|\|\| ::\| \|\| \|:\|\|@LB@ AGUUUUUUCCU UUCU UUA AC CUCG@LB@3'-UUU...CAUUA UCA G U CGUUG...ACG-5'@LB@ \| \|@LB@ 64 34@LB@@LB@@LB@Energy -9.36 kcal/mol@LB@Hybridization Energy -21.9855 kcal/mol@LB@Unfolding Energy - mRNA 6.52956 kcal/mol@LB@Unfolding Energy - sRNA 6.08557 kcal/mol@LB@@LB@Position - mRNA 94 -- 120@LB@Position - sRNA 35 -- 63@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 53 -- 59@LB@
181	0.007702	0.1499	b3145	yraK	-8.82	0.202558	266 -- 280	35 -- 49	putative fimbrial-like adhesin protein	b0533 b0941	_____________265_____________281\n_____________\|_______________\|\n5'-CGA...UCCUC____G__________CGACA...CGA-3'\n______________AGGA_GGUGUGGAGC\n______________\|:\|\|_::\|:\|\|\|\|\|\|\n______________UUCU_UUAUACCUCG\n3'-UUU...CUUCA____G__________CGUUG...ACG-5'\n_____________\|_______________\|\n_____________50______________34\n	274 -- 280	35 -- 41	-19.5909 kcal/mol	7.00879 kcal/mol	3.74396 kcal/mol	265 281@LB@ \| \|@LB@5'-CGA...UCCUC G CGACA...CGA-3'@LB@ AGGA GGUGUGGAGC@LB@ \|:\|\| ::\|:\|\|\|\|\|\|@LB@ UUCU UUAUACCUCG@LB@3'-UUU...CUUCA G CGUUG...ACG-5'@LB@ \| \|@LB@ 50 34@LB@@LB@@LB@Energy -8.82 kcal/mol@LB@Hybridization Energy -19.5909 kcal/mol@LB@Unfolding Energy - mRNA 7.00879 kcal/mol@LB@Unfolding Energy - sRNA 3.74396 kcal/mol@LB@@LB@Position - mRNA 266 -- 280@LB@Position - sRNA 35 -- 49@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 35 -- 41@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