Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
171	0.008374	0.1723	b4485	ytfR	-15.31	0.017344	177 -- 203	32 -- 71	putative sugar ABC transporter ATPase	_____________176_______________________________________204\n_____________\|_________________________________________\|\n5'-CCU...UGGGA_____________________A___________AA______ACGAC...GCC-3'\n______________GCACGC____________UUU_CAC_CGGGGGA___CCAUG\n______________:\|\|\|:\|____________\|\|\|_\|\|\|_\|:\|\|\|\|\|___\|\|\|\|\|\n______________UGUGUG____________AAA_GUG_GUCCCCU___GGUAC\n3'-UUU...UCUGA______UCGUUAAGCAAC_______A_______AAA_____GAAUA...GCA-5'\n_____________\|_________________________________________\|\n_____________72________________________________________31\n	190 -- 196	40 -- 46	-27.8319 kcal/mol	5.2959 kcal/mol	7.22604 kcal/mol	176 204@LB@ \| \|@LB@5'-CCU...UGGGA A AA ACGAC...GCC-3'@LB@ GCACGC UUU CAC CGGGGGA CCAUG@LB@ :\|\|\|:\| \|\|\| \|\|\| \|:\|\|\|\|\| \|\|\|\|\|@LB@ UGUGUG AAA GUG GUCCCCU GGUAC@LB@3'-UUU...UCUGA UCGUUAAGCAAC A AAA GAAUA...GCA-5'@LB@ \| \|@LB@ 72 31@LB@@LB@@LB@Energy -15.31 kcal/mol@LB@Hybridization Energy -27.8319 kcal/mol@LB@Unfolding Energy - mRNA 5.2959 kcal/mol@LB@Unfolding Energy - sRNA 7.22604 kcal/mol@LB@@LB@Position - mRNA 177 -- 203@LB@Position - sRNA 32 -- 71@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 40 -- 46@LB@
172	0.008479	0.1735	b4395	ytjC	-10.99	0.163500	244 -- 268	34 -- 71	phosphatase	_____________243____________________________________269\n_____________\|______________________________________\|\n5'-UCC...GUGGA____CG________________________________GUCUG...AGC-3'\n______________ACGC__AGCGA__CGU______AUUCAGGG_____CCA\n______________\|\|:\|__\|\|\|:\|__\|\|\|______\|:\|\|\|\|\|\|_____\|\|\|\n______________UGUG__UCGUU__GCA______UGAGUCCC_____GGU\n3'-UUU...UCUGA____UG_____AA___ACAAAG________CUAAA___ACGAA...GCA-5'\n_____________\|______________________________________\|\n_____________72_____________________________________33\n	259 -- 265	42 -- 48	-22.1302 kcal/mol	6.3498 kcal/mol	4.79237 kcal/mol	243 269@LB@ \| \|@LB@5'-UCC...GUGGA CG GUCUG...AGC-3'@LB@ ACGC AGCGA CGU AUUCAGGG CCA@LB@ \|\|:\| \|\|\|:\| \|\|\| \|:\|\|\|\|\|\| \|\|\|@LB@ UGUG UCGUU GCA UGAGUCCC GGU@LB@3'-UUU...UCUGA UG AA ACAAAG CUAAA ACGAA...GCA-5'@LB@ \| \|@LB@ 72 33@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -22.1302 kcal/mol@LB@Unfolding Energy - mRNA 6.3498 kcal/mol@LB@Unfolding Energy - sRNA 4.79237 kcal/mol@LB@@LB@Position - mRNA 244 -- 268@LB@Position - sRNA 34 -- 71@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 42 -- 48@LB@
173	0.008582	0.1745	b0060	polB	-11.19	0.150164	8 -- 23	39 -- 51	DNA polymerase II	_____________7________________24\n_____________\|________________\|\n____5'-GAAGAGG_______UAU______AUUCU...AGG-3'\n______________UCGCUUA___GGGGAU\n______________\|\|:\|\|:\|___\|\|\|\|\|\|\n______________AGUGAGU___CCCCUA\n3'-UUU...AACAA________________AAGGU...GCA-5'\n_____________\|________________\|\n_____________52_______________38\n	8 -- 14	45 -- 51	-16.4647 kcal/mol	3.48224 kcal/mol	1.79807 kcal/mol	7 24@LB@ \| \|@LB@ 5'-GAAGAGG UAU AUUCU...AGG-3'@LB@ UCGCUUA GGGGAU@LB@ \|\|:\|\|:\| \|\|\|\|\|\|@LB@ AGUGAGU CCCCUA@LB@3'-UUU...AACAA AAGGU...GCA-5'@LB@ \| \|@LB@ 52 38@LB@@LB@@LB@Energy -11.19 kcal/mol@LB@Hybridization Energy -16.4647 kcal/mol@LB@Unfolding Energy - mRNA 3.48224 kcal/mol@LB@Unfolding Energy - sRNA 1.79807 kcal/mol@LB@@LB@Position - mRNA 8 -- 23@LB@Position - sRNA 39 -- 51@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 45 -- 51@LB@
174	0.008627	0.1745	b1926	fliT	-7.57	0.540698	180 -- 211	31 -- 53	putative flagellar synthesis and assembly chaperone	_____________179______________________________212\n_____________\|________________________________\|\n5'-GUG...CCUUC___G_______ACCCAGUCU___GAA______ACCGC...UCA-3'\n______________UUU_AUUCAGG_________GAU___CCAUGC\n______________\|\|\|_\|:\|\|\|\|\|_________\|\|\|___\|\|\|\|\|\|\n______________AAA_UGAGUCC_________CUA___GGUACG\n3'-UUU...GCAAC___G_______C___________AA_______AAUAU...GCA-5'\n_____________\|________________________________\|\n_____________54_______________________________30\n	184 -- 190	43 -- 49	-18.5651 kcal/mol	6.60729 kcal/mol	4.38339 kcal/mol	179 212@LB@ \| \|@LB@5'-GUG...CCUUC G ACCCAGUCU GAA ACCGC...UCA-3'@LB@ UUU AUUCAGG GAU CCAUGC@LB@ \|\|\| \|:\|\|\|\|\| \|\|\| \|\|\|\|\|\|@LB@ AAA UGAGUCC CUA GGUACG@LB@3'-UUU...GCAAC G C AA AAUAU...GCA-5'@LB@ \| \|@LB@ 54 30@LB@@LB@@LB@Energy -7.57 kcal/mol@LB@Hybridization Energy -18.5651 kcal/mol@LB@Unfolding Energy - mRNA 6.60729 kcal/mol@LB@Unfolding Energy - sRNA 4.38339 kcal/mol@LB@@LB@Position - mRNA 180 -- 211@LB@Position - sRNA 31 -- 53@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 43 -- 49@LB@
175	0.008768	0.1747	b0658	ybeX	-12.37	0.086971	210 -- 256	35 -- 75	putative ion transport	_____________209_____________________________________________257\n_____________\|_______________________________________________\|\n5'-UUA...GCGAC___AAUU___________GACACGAUAAG__ACA__AA_________CUCCC...ACC-3'\n______________GAC____CACACAGUAGU___________CA___AG__GGGAUUUUU\n______________\|\|\|____\|\|\|\|\|\|\|:\|:\|___________\|\|___\|\|__\|\|\|\|\|\|\|::\n______________CUG____GUGUGUCGUUA___________GU___UC__CCCUAAAGG\n3'-UUU...CGUUU___AU_____________AGCAACAAA____GAG_____________UACGA...GCA-5'\n_____________\|_______________________________________________\|\n_____________76______________________________________________34\n	249 -- 255	36 -- 42	-26.9454 kcal/mol	9.77444 kcal/mol	4.80541 kcal/mol	209 257@LB@ \| \|@LB@5'-UUA...GCGAC AAUU GACACGAUAAG ACA AA CUCCC...ACC-3'@LB@ GAC CACACAGUAGU CA AG GGGAUUUUU@LB@ \|\|\| \|\|\|\|\|\|\|:\|:\| \|\| \|\| \|\|\|\|\|\|\|::@LB@ CUG GUGUGUCGUUA GU UC CCCUAAAGG@LB@3'-UUU...CGUUU AU AGCAACAAA GAG UACGA...GCA-5'@LB@ \| \|@LB@ 76 34@LB@@LB@@LB@Energy -12.37 kcal/mol@LB@Hybridization Energy -26.9454 kcal/mol@LB@Unfolding Energy - mRNA 9.77444 kcal/mol@LB@Unfolding Energy - sRNA 4.80541 kcal/mol@LB@@LB@Position - mRNA 210 -- 256@LB@Position - sRNA 35 -- 75@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 36 -- 42@LB@
176	0.008803	0.1747	b1242	ychE	-11.39	0.137124	41 -- 64	45 -- 75	UPF0056 family inner membrane protein	_____________40______________________________65\n_____________\|_______________________________\|\n5'-CAU...UUGGU____________________________A__ACUAG...GCA-3'\n______________GGCUACAU_UAGCA______UGUUUUGC_CA\n______________\|:\|\|\|\|\|:_:\|\|\|\|______\|\|\|\|\|::\|_\|\|\n______________CUGAUGUG_GUCGU______ACAAAGUG_GU\n3'-UUU...CGUUU________U_____UAAGCA________A__CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	55 -- 61	48 -- 54	-19.9041 kcal/mol	4.77357 kcal/mol	3.74078 kcal/mol	40 65@LB@ \| \|@LB@5'-CAU...UUGGU A ACUAG...GCA-3'@LB@ GGCUACAU UAGCA UGUUUUGC CA@LB@ \|:\|\|\|\|\|: :\|\|\|\| \|\|\|\|\|::\| \|\|@LB@ CUGAUGUG GUCGU ACAAAGUG GU@LB@3'-UUU...CGUUU U UAAGCA A CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -19.9041 kcal/mol@LB@Unfolding Energy - mRNA 4.77357 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 41 -- 64@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 55 -- 61@LB@Position Seed - sRNA 48 -- 54@LB@
177	0.008834	0.1747	b0932	pepN	-9.31	0.316043	123 -- 145	58 -- 78	aminopeptidase N	_____________122_____________________146\n_____________\|_______________________\|\n5'-GUA...AAGAU_____UU_______GC_______ACGCA...AGA-3'\n______________GAAGA__CUGCAUA__GCGAUUU\n______________:\|\|\|\|__\|\|:\|\|:\|__\|\|:\|\|\|:\n______________UUUCU__GAUGUGU__CGUUAAG\n3'-UUU...ACCCG______________GU_______CAACA...GCA-5'\n_____________\|_______________________\|\n_____________79______________________57\n	139 -- 145	58 -- 64	-18.0038 kcal/mol	5.38317 kcal/mol	3.31018 kcal/mol	122 146@LB@ \| \|@LB@5'-GUA...AAGAU UU GC ACGCA...AGA-3'@LB@ GAAGA CUGCAUA GCGAUUU@LB@ :\|\|\|\| \|\|:\|\|:\| \|\|:\|\|\|:@LB@ UUUCU GAUGUGU CGUUAAG@LB@3'-UUU...ACCCG GU CAACA...GCA-5'@LB@ \| \|@LB@ 79 57@LB@@LB@@LB@Energy -9.31 kcal/mol@LB@Hybridization Energy -18.0038 kcal/mol@LB@Unfolding Energy - mRNA 5.38317 kcal/mol@LB@Unfolding Energy - sRNA 3.31018 kcal/mol@LB@@LB@Position - mRNA 123 -- 145@LB@Position - sRNA 58 -- 78@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 58 -- 64@LB@
178	0.008884	0.1747	b0051	rsmA	-9.94	0.250586	2 -- 32	30 -- 58	16S rRNA m(6)A1518 m(6)A1519 dimethyltransferase SAM-dependent	_____________1_______________________________33\n_____________\|_______________________________\|\n__________5'-G__A___AC___GA______UC__C_______AAAAU...UUA-3'\n______________CG_UGU__CAC__UCAGGG__UU_CCGUGCU\n______________\|\|_\|\|\|__\|\|\|__\|\|\|\|\|\|__\|\|_\|\|:\|\|\|\|\n______________GC_ACA__GUG__AGUCCC__AA_GGUACGA\n3'-UUU...GUUAA__A___AA___________CU__A_______AUAUU...GCA-5'\n_____________\|_______________________________\|\n_____________59______________________________29\n	26 -- 32	30 -- 36	-26.3106 kcal/mol	10.5715 kcal/mol	5.79877 kcal/mol	1 33@LB@ \| \|@LB@ 5'-G A AC GA UC C AAAAU...UUA-3'@LB@ CG UGU CAC UCAGGG UU CCGUGCU@LB@ \|\| \|\|\| \|\|\| \|\|\|\|\|\| \|\| \|\|:\|\|\|\|@LB@ GC ACA GUG AGUCCC AA GGUACGA@LB@3'-UUU...GUUAA A AA CU A AUAUU...GCA-5'@LB@ \| \|@LB@ 59 29@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -26.3106 kcal/mol@LB@Unfolding Energy - mRNA 10.5715 kcal/mol@LB@Unfolding Energy - sRNA 5.79877 kcal/mol@LB@@LB@Position - mRNA 2 -- 32@LB@Position - sRNA 30 -- 58@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 30 -- 36@LB@
179	0.009001	0.1747	b2725	hycA	-11.58	0.125812	239 -- 264	43 -- 70	regulator of the transcriptional regulator FhlA	_____________238_____________________________265\n_____________\|_______________________________\|\n5'-UUA...UACAU__________CA____________CUA____ACCAG...AGG-3'\n______________CGCACAGCGG__UCG_____UCGC___CAGG\n______________\|:\|\|\|\|\|\|::__\|\|\|_____\|\|:\|___\|\|\|\|\n______________GUGUGUCGUU__AGC_____AGUG___GUCC\n3'-UUU...CUGAU__________A____AACAA____A______CCUAA...GCA-5'\n_____________\|_______________________________\|\n_____________71______________________________42\n	242 -- 248	61 -- 67	-23.0547 kcal/mol	7.15003 kcal/mol	4.32399 kcal/mol	238 265@LB@ \| \|@LB@5'-UUA...UACAU CA CUA ACCAG...AGG-3'@LB@ CGCACAGCGG UCG UCGC CAGG@LB@ \|:\|\|\|\|\|\|:: \|\|\| \|\|:\| \|\|\|\|@LB@ GUGUGUCGUU AGC AGUG GUCC@LB@3'-UUU...CUGAU A AACAA A CCUAA...GCA-5'@LB@ \| \|@LB@ 71 42@LB@@LB@@LB@Energy -11.58 kcal/mol@LB@Hybridization Energy -23.0547 kcal/mol@LB@Unfolding Energy - mRNA 7.15003 kcal/mol@LB@Unfolding Energy - sRNA 4.32399 kcal/mol@LB@@LB@Position - mRNA 239 -- 264@LB@Position - sRNA 43 -- 70@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 61 -- 67@LB@
180	0.009034	0.1747	b3146	rsmI	-12.76	0.071583	191 -- 238	34 -- 76	16S rRNA C1402 2'-O-ribose methyltransferase SAM-dependent	_____________190____________________________________________________239\n_____________\|______________________________________________________\|\n5'-CAG...AAUAC____G____AAUGAAACA___C_______GC_GAUAAUU_______________GCUUU...AGG-3'\n______________GGAC_ACAC_________ACA_CAA_UCG__G_______CUCAGGG_____CCA\n______________:\|\|\|_\|\|\|\|_________\|\|\|_\|\|\|_\|\|\|__\|_______\|\|\|\|\|\|\|_____\|\|\|\n______________UCUG_UGUG_________UGU_GUU_AGC__C_______GAGUCCC_____GGU\n3'-UUU...CCGUU____A________________C___A___AA_AAAGU_________CUAAA___ACGAA...GCA-5'\n_____________\|______________________________________________________\|\n_____________77_____________________________________________________33\n	229 -- 235	42 -- 48	-25.3144 kcal/mol	7.73901 kcal/mol	4.816 kcal/mol	190 239@LB@ \| \|@LB@5'-CAG...AAUAC G AAUGAAACA C GC GAUAAUU GCUUU...AGG-3'@LB@ GGAC ACAC ACA CAA UCG G CUCAGGG CCA@LB@ :\|\|\| \|\|\|\| \|\|\| \|\|\| \|\|\| \| \|\|\|\|\|\|\| \|\|\|@LB@ UCUG UGUG UGU GUU AGC C GAGUCCC GGU@LB@3'-UUU...CCGUU A C A AA AAAGU CUAAA ACGAA...GCA-5'@LB@ \| \|@LB@ 77 33@LB@@LB@@LB@Energy -12.76 kcal/mol@LB@Hybridization Energy -25.3144 kcal/mol@LB@Unfolding Energy - mRNA 7.73901 kcal/mol@LB@Unfolding Energy - sRNA 4.816 kcal/mol@LB@@LB@Position - mRNA 191 -- 238@LB@Position - sRNA 34 -- 76@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 42 -- 48@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:

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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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