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
57	0.002848	0.1727	b2059	wcaA	-10.75	0.100075	282 -- 295	72 -- 85	putative glycosyl transferase	_____________281____________296\n_____________\|______________\|\n5'-AAC...CGGUU_________G____CAGCA-3'\n______________UUGCGCCAG_ACUA\n______________:\|\|\|\|\|\|\|:_\|\|:\|\n______________GACGCGGUU_UGGU\n3'-UUU...CUUAU_________G____CCCUU...GUG-5'\n_____________\|______________\|\n_____________86_____________71\n	284 -- 290	77 -- 83	-19.8604 kcal/mol	1.87274 kcal/mol	7.23443 kcal/mol	281 296@LB@ \| \|@LB@5'-AAC...CGGUU G CAGCA-3'@LB@ UUGCGCCAG ACUA@LB@ :\|\|\|\|\|\|\|: \|\|:\|@LB@ GACGCGGUU UGGU@LB@3'-UUU...CUUAU G CCCUU...GUG-5'@LB@ \| \|@LB@ 86 71@LB@@LB@@LB@Energy -10.75 kcal/mol@LB@Hybridization Energy -19.8604 kcal/mol@LB@Unfolding Energy - mRNA 1.87274 kcal/mol@LB@Unfolding Energy - sRNA 7.23443 kcal/mol@LB@@LB@Position - mRNA 282 -- 295@LB@Position - sRNA 72 -- 85@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 77 -- 83@LB@
114	0.006011	0.1855	b0422	xseB	-10.73	0.101337	104 -- 119	73 -- 87	exonuclease VII small subunit	_____________103______________120\n_____________\|________________\|\n5'-CAA...CGCUU________A__U____UUACC...AAG-3'\n______________UGCUGUGC_CA_CACC\n______________\|:\|\|\|:\|\|_\|\|_\|\|\|\|\n______________AUGACGCG_GU_GUGG\n3'-UUU...CGCUU___________U____UCCCU...GUG-5'\n_____________\|________________\|\n_____________88_______________72\n	105 -- 111	80 -- 86	-20.3088 kcal/mol	2.628 kcal/mol	6.95602 kcal/mol	103 120@LB@ \| \|@LB@5'-CAA...CGCUU A U UUACC...AAG-3'@LB@ UGCUGUGC CA CACC@LB@ \|:\|\|\|:\|\| \|\| \|\|\|\|@LB@ AUGACGCG GU GUGG@LB@3'-UUU...CGCUU U UCCCU...GUG-5'@LB@ \| \|@LB@ 88 72@LB@@LB@@LB@Energy -10.73 kcal/mol@LB@Hybridization Energy -20.3088 kcal/mol@LB@Unfolding Energy - mRNA 2.628 kcal/mol@LB@Unfolding Energy - sRNA 6.95602 kcal/mol@LB@@LB@Position - mRNA 104 -- 119@LB@Position - sRNA 73 -- 87@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 80 -- 86@LB@
72	0.00375	0.1804	b0386	proC	-10.69	0.102749	216 -- 233	53 -- 70	pyrroline-5-carboxylate reductase NAD(P)-binding	_____________215________________234\n_____________\|__________________\|\n5'-CAU...AAAUC__UUUUA_________G_AAUAU...GGG-3'\n______________GG_____UUGGCUGCG_C\n______________\|\|_____\|\|\|\|\|\|\|\|\|_\|\n______________CC_____AACCGACGC_G\n3'-UUU...UGGUC__UUUAG_________G_CAUUU...GUG-5'\n_____________\|__________________\|\n_____________71_________________52\n	225 -- 231	55 -- 61	-21.889 kcal/mol	4.36146 kcal/mol	6.83419 kcal/mol	215 234@LB@ \| \|@LB@5'-CAU...AAAUC UUUUA G AAUAU...GGG-3'@LB@ GG UUGGCUGCG C@LB@ \|\| \|\|\|\|\|\|\|\|\| \|@LB@ CC AACCGACGC G@LB@3'-UUU...UGGUC UUUAG G CAUUU...GUG-5'@LB@ \| \|@LB@ 71 52@LB@@LB@@LB@Energy -10.69 kcal/mol@LB@Hybridization Energy -21.889 kcal/mol@LB@Unfolding Energy - mRNA 4.36146 kcal/mol@LB@Unfolding Energy - sRNA 6.83419 kcal/mol@LB@@LB@Position - mRNA 216 -- 233@LB@Position - sRNA 53 -- 70@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 55 -- 61@LB@
68	0.00345	0.1727	b3168	infB	-10.64	0.105292	126 -- 148	49 -- 77	translation initiation factor IF-2	_____________125___________________________149\n_____________\|_____________________________\|\n5'-AAG...CCGGA______________A______________UAUUU...CUG-3'\n______________GCACU_____GAUU_UGGCUGC_CCGUAA\n______________:\|\|\|:_____:\|\|:_\|\|\|\|\|\|\|_\|\|\|\|\|\|\n______________UGUGG_____UUAG_ACCGACG_GGCAUU\n3'-UUU...GCGGU_____UCCCU____A_______C______UAAUA...GUG-5'\n_____________\|_____________________________\|\n_____________78____________________________48\n	136 -- 142	56 -- 62	-27.6009 kcal/mol	7.61735 kcal/mol	9.34562 kcal/mol	125 149@LB@ \| \|@LB@5'-AAG...CCGGA A UAUUU...CUG-3'@LB@ GCACU GAUU UGGCUGC CCGUAA@LB@ :\|\|\|: :\|\|: \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ UGUGG UUAG ACCGACG GGCAUU@LB@3'-UUU...GCGGU UCCCU A C UAAUA...GUG-5'@LB@ \| \|@LB@ 78 48@LB@@LB@@LB@Energy -10.64 kcal/mol@LB@Hybridization Energy -27.6009 kcal/mol@LB@Unfolding Energy - mRNA 7.61735 kcal/mol@LB@Unfolding Energy - sRNA 9.34562 kcal/mol@LB@@LB@Position - mRNA 126 -- 148@LB@Position - sRNA 49 -- 77@LB@Position Seed - mRNA 136 -- 142@LB@Position Seed - sRNA 56 -- 62@LB@
127	0.007097	0.1961	b4065	yjcE	-10.62	0.105957	81 -- 91	51 -- 62	putative cation/proton antiporter	_____________80___________92\n_____________\|____________\|\n5'-UAU...GGCAA____________UUUUA...UGC-3'\n______________UGGCUGC_CCGU\n______________\|\|\|\|\|\|\|_\|\|\|\|\n______________ACCGACG_GGCA\n3'-UUU...UUAGA_______C____UUUAA...GUG-5'\n_____________\|____________\|\n_____________63___________50\n	81 -- 87	56 -- 62	-18.8543 kcal/mol	3.34811 kcal/mol	4.8826 kcal/mol	80 92@LB@ \| \|@LB@5'-UAU...GGCAA UUUUA...UGC-3'@LB@ UGGCUGC CCGU@LB@ \|\|\|\|\|\|\| \|\|\|\|@LB@ ACCGACG GGCA@LB@3'-UUU...UUAGA C UUUAA...GUG-5'@LB@ \| \|@LB@ 63 50@LB@@LB@@LB@Energy -10.62 kcal/mol@LB@Hybridization Energy -18.8543 kcal/mol@LB@Unfolding Energy - mRNA 3.34811 kcal/mol@LB@Unfolding Energy - sRNA 4.8826 kcal/mol@LB@@LB@Position - mRNA 81 -- 91@LB@Position - sRNA 51 -- 62@LB@Position Seed - mRNA 81 -- 87@LB@Position Seed - sRNA 56 -- 62@LB@
79	0.004357	0.1855	b0008	talB	-10.61	0.106795	240 -- 280	50 -- 88	transaldolase B	_____________239________________________________________281\n_____________\|__________________________________________\|\n5'-AGG...CCACC___G_________________C___GC___AAUGAA______UCAAC...CAA-3'\n______________GUA_UG_GCCGACACUGGGGA_AUC__GGC______GCUGUA\n______________:\|\|_\|\|_\|\|\|:\|\|\|\|::\|\|\|\|_\|\|\|__\|\|\|______\|\|:\|\|\|\n______________UAU_AC_CGGUUGUGGUCCCU_UAG__CCG______CGGCAU\n3'-UUU...GCGCU___G__G______________U___AA___ACG_________UUAAU...GUG-5'\n_____________\|__________________________________________\|\n_____________89_________________________________________49\n	253 -- 259	68 -- 74	-44.9099 kcal/mol	17.4497 kcal/mol	16.8544 kcal/mol	239 281@LB@ \| \|@LB@5'-AGG...CCACC G C GC AAUGAA UCAAC...CAA-3'@LB@ GUA UG GCCGACACUGGGGA AUC GGC GCUGUA@LB@ :\|\| \|\| \|\|\|:\|\|\|\|::\|\|\|\| \|\|\| \|\|\| \|\|:\|\|\|@LB@ UAU AC CGGUUGUGGUCCCU UAG CCG CGGCAU@LB@3'-UUU...GCGCU G G U AA ACG UUAAU...GUG-5'@LB@ \| \|@LB@ 89 49@LB@@LB@@LB@Energy -10.61 kcal/mol@LB@Hybridization Energy -44.9099 kcal/mol@LB@Unfolding Energy - mRNA 17.4497 kcal/mol@LB@Unfolding Energy - sRNA 16.8544 kcal/mol@LB@@LB@Position - mRNA 240 -- 280@LB@Position - sRNA 50 -- 88@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 68 -- 74@LB@
60	0.003031	0.1727	b3432	glgB	-10.57	0.108575	114 -- 123	51 -- 60	1 4-alpha-glucan branching enzyme	_____________113________124\n_____________\|__________\|\n5'-CAU...AGAGU__________UCAGG...GAC-3'\n______________GCUGCGCCGU\n______________\|\|\|\|\|\|\|\|\|\|\n______________CGACGCGGCA\n3'-UUU...AGAAC__________UUUAA...GUG-5'\n_____________\|__________\|\n_____________61_________50\n	117 -- 123	51 -- 57	-20.705 kcal/mol	5.26394 kcal/mol	4.87294 kcal/mol	113 124@LB@ \| \|@LB@5'-CAU...AGAGU UCAGG...GAC-3'@LB@ GCUGCGCCGU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CGACGCGGCA@LB@3'-UUU...AGAAC UUUAA...GUG-5'@LB@ \| \|@LB@ 61 50@LB@@LB@@LB@Energy -10.57 kcal/mol@LB@Hybridization Energy -20.705 kcal/mol@LB@Unfolding Energy - mRNA 5.26394 kcal/mol@LB@Unfolding Energy - sRNA 4.87294 kcal/mol@LB@@LB@Position - mRNA 114 -- 123@LB@Position - sRNA 51 -- 60@LB@Position Seed - mRNA 117 -- 123@LB@Position Seed - sRNA 51 -- 57@LB@
105	0.005654	0.1855	b0004	thrC	-10.56	0.108775	227 -- 299	1 -- 79	L-threonine synthase	_____________226_____________________________________________________________________________________300\n_____________\|_______________________________________________________________________________________\|\n5'-CGC...GAUCA____G_G____UCAG____U__GCAA_______CCCAG____________________AAAAU___GG___________________G-3'\n______________CAAC_A_CAGG_____CUU_GC____GCCGUAA___________GGGUU____GGGCA_____CAG__GCUGUUUUUU___CCGCAC\n______________\|\|\|\|_\|_\|\|\|\|_____\|\|\|_\|\|____\|\|\|\|\|\|\|___________\|:\|\|\|____\|\|\|\|\|_____\|\|\|__:\|\|\|\|\|\|\|\|:___\|\|\|\|\|\|\n______________GUUG_U_GUCC_____GAA_CG____CGGCAUU___________CUCAA____CCCGU_____GUC__UGACAAAAAG___GGCGUG\n3'-UUU...ACGCG______G____CUUUA___C__ACG________UAAUAAUACUA_____UGUU_____________G___________UCC______-5'\n_____________\|______________________________________________________________________________________\|\n_____________80_____________________________________________________________________________________1\n	287 -- 293	10 -- 16	-55.9039 kcal/mol	22.5864 kcal/mol	22.7537 kcal/mol	226 300@LB@ \| \|@LB@5'-CGC...GAUCA G G UCAG U GCAA CCCAG AAAAU GG G-3'@LB@ CAAC A CAGG CUU GC GCCGUAA GGGUU GGGCA CAG GCUGUUUUUU CCGCAC@LB@ \|\|\|\| \| \|\|\|\| \|\|\| \|\| \|\|\|\|\|\|\| \|:\|\|\| \|\|\|\|\| \|\|\| :\|\|\|\|\|\|\|\|: \|\|\|\|\|\|@LB@ GUUG U GUCC GAA CG CGGCAUU CUCAA CCCGU GUC UGACAAAAAG GGCGUG@LB@3'-UUU...ACGCG G CUUUA C ACG UAAUAAUACUA UGUU G UCC -5'@LB@ \| \|@LB@ 80 1@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -55.9039 kcal/mol@LB@Unfolding Energy - mRNA 22.5864 kcal/mol@LB@Unfolding Energy - sRNA 22.7537 kcal/mol@LB@@LB@Position - mRNA 227 -- 299@LB@Position - sRNA 1 -- 79@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 10 -- 16@LB@
184	0.01102	0.2089	b1033	ghrA	-10.56	0.108938	6 -- 15	64 -- 73	glyoxylate/hydroxypyruvate reductase A	_____________5__________16\n_____________\|__________\|\n______5'-UAAUU__________AUGAC...GCG-3'\n______________UAGGGAAAUC\n______________:\|\|\|\|\|\|\|\|\|\n______________GUCCCUUUAG\n3'-UUU...UUGUG__________AACCG...GUG-5'\n_____________\|__________\|\n_____________74_________63\n	9 -- 15	64 -- 70	-14.6499 kcal/mol	0.954451 kcal/mol	3.13463 kcal/mol	5 16@LB@ \| \|@LB@ 5'-UAAUU AUGAC...GCG-3'@LB@ UAGGGAAAUC@LB@ :\|\|\|\|\|\|\|\|\|@LB@ GUCCCUUUAG@LB@3'-UUU...UUGUG AACCG...GUG-5'@LB@ \| \|@LB@ 74 63@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -14.6499 kcal/mol@LB@Unfolding Energy - mRNA 0.954451 kcal/mol@LB@Unfolding Energy - sRNA 3.13463 kcal/mol@LB@@LB@Position - mRNA 6 -- 15@LB@Position - sRNA 64 -- 73@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 64 -- 70@LB@
158	0.009324	0.2062	b3574	yiaJ	-10.56	0.109206	175 -- 190	70 -- 85	transcriptional repressor for the yiaKLMNO-lyxK-sgbHUE operon	_____________174______________191\n_____________\|________________\|\n5'-CCC...ACACU________C_______ACGCG...UUG-3'\n______________UUGCGCUA_CAUCAGG\n______________:\|\|\|\|\|:\|_\|\|:\|\|\|\|\n______________GACGCGGU_GUGGUCC\n3'-UUU...CUUAU________U_______CUUUA...GUG-5'\n_____________\|________________\|\n_____________86_______________69\n	184 -- 190	70 -- 76	-22.9924 kcal/mol	5.16069 kcal/mol	7.27689 kcal/mol	174 191@LB@ \| \|@LB@5'-CCC...ACACU C ACGCG...UUG-3'@LB@ UUGCGCUA CAUCAGG@LB@ :\|\|\|\|\|:\| \|\|:\|\|\|\|@LB@ GACGCGGU GUGGUCC@LB@3'-UUU...CUUAU U CUUUA...GUG-5'@LB@ \| \|@LB@ 86 69@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -22.9924 kcal/mol@LB@Unfolding Energy - mRNA 5.16069 kcal/mol@LB@Unfolding Energy - sRNA 7.27689 kcal/mol@LB@@LB@Position - mRNA 175 -- 190@LB@Position - sRNA 70 -- 85@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 70 -- 76@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)

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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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