Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
121	0.006643	0.1913	b1813	nudL	-11.92	0.059353	114 -- 132	70 -- 86	putative CoA pyrophosphohydrolase weak 3-phosphohydroxypyruvate phosphatase	_____________113_________________133\n_____________\|___________________\|\n5'-CCU...GUGGA____U________G_____AAGAA...CUG-3'\n______________AUUG_CGCCGAUA_CCAGG\n______________\|:\|\|_\|\|\|\|:\|:\|_\|\|\|\|\|\n______________UGAC_GCGGUUGU_GGUCC\n3'-UUU...GCUUA___________________CUUUA...GUG-5'\n_____________\|___________________\|\n_____________87__________________69\n	120 -- 126	75 -- 81	-24.7024 kcal/mol	5.50013 kcal/mol	7.27772 kcal/mol	113 133@LB@ \| \|@LB@5'-CCU...GUGGA U G AAGAA...CUG-3'@LB@ AUUG CGCCGAUA CCAGG@LB@ \|:\|\| \|\|\|\|:\|:\| \|\|\|\|\|@LB@ UGAC GCGGUUGU GGUCC@LB@3'-UUU...GCUUA CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -24.7024 kcal/mol@LB@Unfolding Energy - mRNA 5.50013 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 114 -- 132@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 75 -- 81@LB@
86	0.004777	0.1855	b3157	yhbT	-11.83	0.061936	277 -- 294	70 -- 85	SCP-2 sterol transfer family protein	_____________276________________295\n_____________\|__________________\|\n5'-CUG...GCCAU________AA________UUCUUG-3'\n______________UUGCGCUA__ACGCCAGG\n______________:\|\|\|\|\|:\|__\|\|:\|\|\|\|\|\n______________GACGCGGU__UGUGGUCC\n3'-UUU...CUUAU__________________CUUUA...GUG-5'\n_____________\|__________________\|\n_____________86_________________69\n	288 -- 294	70 -- 76	-24.8001 kcal/mol	5.69349 kcal/mol	7.27689 kcal/mol	276 295@LB@ \| \|@LB@5'-CUG...GCCAU AA UUCUUG-3'@LB@ UUGCGCUA ACGCCAGG@LB@ :\|\|\|\|\|:\| \|\|:\|\|\|\|\|@LB@ GACGCGGU UGUGGUCC@LB@3'-UUU...CUUAU CUUUA...GUG-5'@LB@ \| \|@LB@ 86 69@LB@@LB@@LB@Energy -11.83 kcal/mol@LB@Hybridization Energy -24.8001 kcal/mol@LB@Unfolding Energy - mRNA 5.69349 kcal/mol@LB@Unfolding Energy - sRNA 7.27689 kcal/mol@LB@@LB@Position - mRNA 277 -- 294@LB@Position - sRNA 70 -- 85@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 70 -- 76@LB@
143	0.008308	0.2033	b2049	cpsB	-11.81	0.062535	184 -- 242	25 -- 78	mannose-1-phosphate guanyltransferase	_____________183_______________________________________________________________243\n_____________\|_________________________________________________________________\|\n5'-ACA...UAAAU____U_______U____A_______A________CUCUAUCCA__________________U___UCCGG...GCC-3'\n______________GAUA_UCGGGGA_AAUU_UGGC_GC_GUCG_AAA_________GUUGUGAUG____GCAGG_GGC\n______________:\|:\|_:\|:\|\|\|\|_\|\|\|:_\|\|\|\|_\|\|_\|:\|\|_\|\|\|_________:\|\|:\|\|\|\|\|____:\|\|:\|_\|\|\|\n______________UUGU_GGUCCCU_UUAG_ACCG_CG_CGGC_UUU_________UAAUACUAC____UGUUC_CCG\n3'-UUU...CGCGG_________________A____A_______A___AA________________UCAA_________UGUCG...GUG-5'\n_____________\|_________________________________________________________________\|\n_____________79________________________________________________________________24\n	227 -- 233	37 -- 43	-41.0645 kcal/mol	15.3492 kcal/mol	13.8987 kcal/mol	183 243@LB@ \| \|@LB@5'-ACA...UAAAU U U A A CUCUAUCCA U UCCGG...GCC-3'@LB@ GAUA UCGGGGA AAUU UGGC GC GUCG AAA GUUGUGAUG GCAGG GGC@LB@ :\|:\| :\|:\|\|\|\| \|\|\|: \|\|\|\| \|\| \|:\|\| \|\|\| :\|\|:\|\|\|\|\| :\|\|:\| \|\|\|@LB@ UUGU GGUCCCU UUAG ACCG CG CGGC UUU UAAUACUAC UGUUC CCG@LB@3'-UUU...CGCGG A A A AA UCAA UGUCG...GUG-5'@LB@ \| \|@LB@ 79 24@LB@@LB@@LB@Energy -11.81 kcal/mol@LB@Hybridization Energy -41.0645 kcal/mol@LB@Unfolding Energy - mRNA 15.3492 kcal/mol@LB@Unfolding Energy - sRNA 13.8987 kcal/mol@LB@@LB@Position - mRNA 184 -- 242@LB@Position - sRNA 25 -- 78@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 37 -- 43@LB@
179	0.01058	0.208	b1325	ycjG	-11.81	0.062523	258 -- 297	32 -- 77	L-Ala-D/L-Glu epimerase	_____________257_______________________________________________298\n_____________\|_________________________________________________\|\n5'-AAG...UGAUU______________GCA__GAA____G______________________AAC-3'\n______________GC_CCGGGGAAGUC___GU___GCGC_CGUG_______GUGGUG_GUUG\n______________:\|_\|\|:\|\|\|\|\|:\|\|___\|:___\|\|\|\|_\|\|\|:_______:\|\|:\|\|_\|\|\|:\n______________UG_GGUCCCUUUAG___CG___CGCG_GCAU_______UACUAC_CAAU\n3'-UUU...GCGGU__U___________AAC__A___________UUAAUAA______U____GUUCC...GUG-5'\n_____________\|_________________________________________________\|\n_____________78________________________________________________31\n	264 -- 270	64 -- 70	-38.4326 kcal/mol	17.2613 kcal/mol	9.36253 kcal/mol	257 298@LB@ \| \|@LB@5'-AAG...UGAUU GCA GAA G AAC-3'@LB@ GC CCGGGGAAGUC GU GCGC CGUG GUGGUG GUUG@LB@ :\| \|\|:\|\|\|\|\|:\|\| \|: \|\|\|\| \|\|\|: :\|\|:\|\| \|\|\|:@LB@ UG GGUCCCUUUAG CG CGCG GCAU UACUAC CAAU@LB@3'-UUU...GCGGU U AAC A UUAAUAA U GUUCC...GUG-5'@LB@ \| \|@LB@ 78 31@LB@@LB@@LB@Energy -11.81 kcal/mol@LB@Hybridization Energy -38.4326 kcal/mol@LB@Unfolding Energy - mRNA 17.2613 kcal/mol@LB@Unfolding Energy - sRNA 9.36253 kcal/mol@LB@@LB@Position - mRNA 258 -- 297@LB@Position - sRNA 32 -- 77@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 64 -- 70@LB@
62	0.003053	0.1727	b3812	yigB	-11.80	0.062766	182 -- 199	65 -- 83	5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase; pyrimidine phosphatase; riboflavin synthesis	_____________181_________________200\n_____________\|___________________\|\n5'-CUG...UCCAC__________G________AAUGC...GAG-3'\n______________GCGCCAA_AC_GGGGAAAU\n______________\|\|\|\|\|\|\|_\|\|_:\|\|\|\|\|\|\|\n______________CGCGGUU_UG_UCCCUUUA\n3'-UUU...UAUGA_______G__G________GAACC...GUG-5'\n_____________\|___________________\|\n_____________84__________________64\n	193 -- 199	65 -- 71	-28.1563 kcal/mol	8.99645 kcal/mol	7.35968 kcal/mol	181 200@LB@ \| \|@LB@5'-CUG...UCCAC G AAUGC...GAG-3'@LB@ GCGCCAA AC GGGGAAAU@LB@ \|\|\|\|\|\|\| \|\| :\|\|\|\|\|\|\|@LB@ CGCGGUU UG UCCCUUUA@LB@3'-UUU...UAUGA G G GAACC...GUG-5'@LB@ \| \|@LB@ 84 64@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -28.1563 kcal/mol@LB@Unfolding Energy - mRNA 8.99645 kcal/mol@LB@Unfolding Energy - sRNA 7.35968 kcal/mol@LB@@LB@Position - mRNA 182 -- 199@LB@Position - sRNA 65 -- 83@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 65 -- 71@LB@
183	0.011	0.2089	b0906	ycaP	-11.77	0.063722	48 -- 74	48 -- 75	UPF0702 family putative inner membrane protein	_____________47___________________________75\n_____________\|____________________________\|\n5'-AGU...UCUUU________UAAA___U_______A____AAUCA...UCU-3'\n______________GCCGGGGA_____UG_UUGCGUC_UGAA\n______________:\|\|:\|\|\|\|_____\|\|_:\|\|\|\|:\|_\|:\|\|\n______________UGGUCCCU_____AC_GACGCGG_AUUU\n3'-UUU...GGUUG________UUAGA__C_______C____AAUAA...GUG-5'\n_____________\|____________________________\|\n_____________76___________________________47\n	63 -- 69	53 -- 59	-25.8143 kcal/mol	5.22968 kcal/mol	8.81811 kcal/mol	47 75@LB@ \| \|@LB@5'-AGU...UCUUU UAAA U A AAUCA...UCU-3'@LB@ GCCGGGGA UG UUGCGUC UGAA@LB@ :\|\|:\|\|\|\| \|\| :\|\|\|\|:\| \|:\|\|@LB@ UGGUCCCU AC GACGCGG AUUU@LB@3'-UUU...GGUUG UUAGA C C AAUAA...GUG-5'@LB@ \| \|@LB@ 76 47@LB@@LB@@LB@Energy -11.77 kcal/mol@LB@Hybridization Energy -25.8143 kcal/mol@LB@Unfolding Energy - mRNA 5.22968 kcal/mol@LB@Unfolding Energy - sRNA 8.81811 kcal/mol@LB@@LB@Position - mRNA 48 -- 74@LB@Position - sRNA 48 -- 75@LB@Position Seed - mRNA 63 -- 69@LB@Position Seed - sRNA 53 -- 59@LB@
164	0.009677	0.2068	b1956	yedQ	-11.74	0.064514	187 -- 209	18 -- 41	putative membrane-anchored diguanylate cyclase	_____________186______________________210\n_____________\|________________________\|\n5'-GAG...CAGGU________CGUC____________GAGAC...UAU-3'\n______________UGG_GAGU____AGGGUGCAGCAC\n______________\|\|:_\|\|\|\|____\|\|\|\|::\|\|\|\|\|\|\n______________ACU_CUCA____UCCCGUGUCGUG\n3'-UUU...AUAAU___A____AUGU____________ACAAA...GUG-5'\n_____________\|________________________\|\n_____________42_______________________17\n	203 -- 209	18 -- 24	-27.1151 kcal/mol	6.50018 kcal/mol	8.87585 kcal/mol	186 210@LB@ \| \|@LB@5'-GAG...CAGGU CGUC GAGAC...UAU-3'@LB@ UGG GAGU AGGGUGCAGCAC@LB@ \|\|: \|\|\|\| \|\|\|\|::\|\|\|\|\|\|@LB@ ACU CUCA UCCCGUGUCGUG@LB@3'-UUU...AUAAU A AUGU ACAAA...GUG-5'@LB@ \| \|@LB@ 42 17@LB@@LB@@LB@Energy -11.74 kcal/mol@LB@Hybridization Energy -27.1151 kcal/mol@LB@Unfolding Energy - mRNA 6.50018 kcal/mol@LB@Unfolding Energy - sRNA 8.87585 kcal/mol@LB@@LB@Position - mRNA 187 -- 209@LB@Position - sRNA 18 -- 41@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 18 -- 24@LB@
190	0.01143	0.2119	b3233	yhcB	-11.72	0.064941	161 -- 178	66 -- 81	DUF1043 family inner membrane-anchored protein	_____________160________________179\n_____________\|__________________\|\n5'-UUU...CUGAA_________CUAC_____CAAAA...CGU-3'\n______________GCCAACACC____GGAAA\n______________\|\|\|\|\|\|\|\|\|____\|\|\|\|\|\n______________CGGUUGUGG____CCUUU\n3'-UUU...UGACG_________UC_______AGAAC...GUG-5'\n_____________\|__________________\|\n_____________82_________________65\n	163 -- 169	73 -- 79	-21.1167 kcal/mol	2.37182 kcal/mol	7.0207 kcal/mol	160 179@LB@ \| \|@LB@5'-UUU...CUGAA CUAC CAAAA...CGU-3'@LB@ GCCAACACC GGAAA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ CGGUUGUGG CCUUU@LB@3'-UUU...UGACG UC AGAAC...GUG-5'@LB@ \| \|@LB@ 82 65@LB@@LB@@LB@Energy -11.72 kcal/mol@LB@Hybridization Energy -21.1167 kcal/mol@LB@Unfolding Energy - mRNA 2.37182 kcal/mol@LB@Unfolding Energy - sRNA 7.0207 kcal/mol@LB@@LB@Position - mRNA 161 -- 178@LB@Position - sRNA 66 -- 81@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 73 -- 79@LB@
133	0.007533	0.1993	b2194	ccmH	-11.64	0.067570	191 -- 199	1 -- 9	heme lyase CcmH subunit	_____________190_______200\n_____________\|_________\|\n5'-CUG...UAAGG_________AAUGA...AGU-3'\n______________AGGCCGCAC\n______________\|\|\|\|\|\|\|\|\|\n______________UCCGGCGUG\n3'-UUU...AAAAG_________-5'\n_____________\|________\|\n_____________10_______1\n	193 -- 199	1 -- 7	-19.8862 kcal/mol	2.96679 kcal/mol	5.10726 kcal/mol	190 200@LB@ \| \|@LB@5'-CUG...UAAGG AAUGA...AGU-3'@LB@ AGGCCGCAC@LB@ \|\|\|\|\|\|\|\|\|@LB@ UCCGGCGUG@LB@3'-UUU...AAAAG -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -11.64 kcal/mol@LB@Hybridization Energy -19.8862 kcal/mol@LB@Unfolding Energy - mRNA 2.96679 kcal/mol@LB@Unfolding Energy - sRNA 5.10726 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 1 -- 7@LB@
165	0.009721	0.2068	b1475	fdnH	-11.62	0.068172	63 -- 98	41 -- 76	formate dehydrogenase-N Fe-S (beta) subunit nitrate-inducible	_____________62_____________________________________99\n_____________\|______________________________________\|\n5'-CGC...CAAUC________CU___GA__G__U___G______G______AUCGC...UUA-3'\n______________CACUGGGG___UU__GG_UG_CGC_CGUAAA__GUUAU\n______________\|\|\|::\|\|\|___\|:__\|\|_\|\|_\|\|\|_\|\|\|\|\|\|__:\|\|\|\|\n______________GUGGUCCC___AG__CC_AC_GCG_GCAUUU__UAAUA\n3'-UUU...CGGUU________UUU__AA__G_____________AA_____CUACU...GUG-5'\n_____________\|______________________________________\|\n_____________77_____________________________________40\n	64 -- 70	69 -- 75	-31.0903 kcal/mol	10.1186 kcal/mol	9.35565 kcal/mol	62 99@LB@ \| \|@LB@5'-CGC...CAAUC CU GA G U G G AUCGC...UUA-3'@LB@ CACUGGGG UU GG UG CGC CGUAAA GUUAU@LB@ \|\|\|::\|\|\| \|: \|\| \|\| \|\|\| \|\|\|\|\|\| :\|\|\|\|@LB@ GUGGUCCC AG CC AC GCG GCAUUU UAAUA@LB@3'-UUU...CGGUU UUU AA G AA CUACU...GUG-5'@LB@ \| \|@LB@ 77 40@LB@@LB@@LB@Energy -11.62 kcal/mol@LB@Hybridization Energy -31.0903 kcal/mol@LB@Unfolding Energy - mRNA 10.1186 kcal/mol@LB@Unfolding Energy - sRNA 9.35565 kcal/mol@LB@@LB@Position - mRNA 63 -- 98@LB@Position - sRNA 41 -- 76@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 69 -- 75@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

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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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