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
93	0.008233	0.2977	b2669	stpA	-8.51	0.236304	244 -- 255	39 -- 50	DNA binding protein nucleoid-associated	_____________243__________256\n_____________\|____________\|\n5'-UUC...CCUCC____________GCGAA...UCA-3'\n______________GUGCGAUGGCUC\n______________:\|\|\|:\|\|\|\|\|:\|\n______________UACGUUACCGGG\n3'-UUU...ACCGU____________UUGUC...UUG-5'\n_____________\|____________\|\n_____________51___________38\n	249 -- 255	39 -- 45	-19.1222 kcal/mol	5.86982 kcal/mol	4.73799 kcal/mol	243 256@LB@ \| \|@LB@5'-UUC...CCUCC GCGAA...UCA-3'@LB@ GUGCGAUGGCUC@LB@ :\|\|\|:\|\|\|\|\|:\|@LB@ UACGUUACCGGG@LB@3'-UUU...ACCGU UUGUC...UUG-5'@LB@ \| \|@LB@ 51 38@LB@@LB@@LB@Energy -8.51 kcal/mol@LB@Hybridization Energy -19.1222 kcal/mol@LB@Unfolding Energy - mRNA 5.86982 kcal/mol@LB@Unfolding Energy - sRNA 4.73799 kcal/mol@LB@@LB@Position - mRNA 244 -- 255@LB@Position - sRNA 39 -- 50@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 39 -- 45@LB@
89	0.007733	0.2889	b3426	glpD	-8.48	0.239884	186 -- 234	7 -- 64	sn-glycerol-3-phosphate dehydrogenase aerobic FAD/NAD(P)-binding	_____________185__________________________________________________________235\n_____________\|____________________________________________________________\|\n5'-AAC...CGAAA_U____G________________AAA________UCU_______________________GCAUC...AGG-3'\n______________G_GAAU_AG_GGCA__GC_AUGG___CCAA_AGA______GA_UUGUGAUAG__GGGGCG\n______________\|_:\|\|\|_\|\|_\|\|\|\|__\|\|_\|\|\|\|___\|\|\|\|_\|\|\|______:\|_:\|\|\|\|\|:\|:__::\|\|\|:\n______________C_UUUA_UC_CCGU__CG_UACC___GGUU_UCU______UU_GACACUGUU__UUCCGU\n3'-UUU...ACAAC_U____G__A____UA__U____G______G___UUUAUU__A_________AU______AUAUUG-5'\n_____________\|____________________________________________________________\|\n_____________65___________________________________________________________6\n	222 -- 228	15 -- 21	-34.508 kcal/mol	13.8761 kcal/mol	12.1536 kcal/mol	185 235@LB@ \| \|@LB@5'-AAC...CGAAA U G AAA UCU GCAUC...AGG-3'@LB@ G GAAU AG GGCA GC AUGG CCAA AGA GA UUGUGAUAG GGGGCG@LB@ \| :\|\|\| \|\| \|\|\|\| \|\| \|\|\|\| \|\|\|\| \|\|\| :\| :\|\|\|\|\|:\|: ::\|\|\|:@LB@ C UUUA UC CCGU CG UACC GGUU UCU UU GACACUGUU UUCCGU@LB@3'-UUU...ACAAC U G A UA U G G UUUAUU A AU AUAUUG-5'@LB@ \| \|@LB@ 65 6@LB@@LB@@LB@Energy -8.48 kcal/mol@LB@Hybridization Energy -34.508 kcal/mol@LB@Unfolding Energy - mRNA 13.8761 kcal/mol@LB@Unfolding Energy - sRNA 12.1536 kcal/mol@LB@@LB@Position - mRNA 186 -- 234@LB@Position - sRNA 7 -- 64@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 15 -- 21@LB@
45	0.002879	0.2151	b3319	rplD	-8.41	0.246804	191 -- 204	42 -- 54	50S ribosomal subunit protein L4	_____________190____________205\n_____________\|______________\|\n5'-UCA...CGUAA__A___A_______AAUUA...UUG-3'\n______________GG_GAU_GCAAUGG\n______________\|\|_:\|\|_\|\|\|\|\|\|\|\n______________CC_UUA_CGUUACC\n3'-UUU...AGUCA__G___________GGGUU...UUG-5'\n_____________\|______________\|\n_____________55_____________41\n	198 -- 204	42 -- 48	-13.9027 kcal/mol	1.99374 kcal/mol	3.49932 kcal/mol	190 205@LB@ \| \|@LB@5'-UCA...CGUAA A A AAUUA...UUG-3'@LB@ GG GAU GCAAUGG@LB@ \|\| :\|\| \|\|\|\|\|\|\|@LB@ CC UUA CGUUACC@LB@3'-UUU...AGUCA G GGGUU...UUG-5'@LB@ \| \|@LB@ 55 41@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -13.9027 kcal/mol@LB@Unfolding Energy - mRNA 1.99374 kcal/mol@LB@Unfolding Energy - sRNA 3.49932 kcal/mol@LB@@LB@Position - mRNA 191 -- 204@LB@Position - sRNA 42 -- 54@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 42 -- 48@LB@
189	0.02329	0.4145	b1823	cspC	-8.37	0.250499	214 -- 248	8 -- 63	stress protein member of the CspA-family	_____________213______________________________________________________249\n_____________\|________________________________________________________\|\n5'-UAU...GAUUA____________UA__________________________________________UUUGG...UCU-3'\n______________AAGGUCA__GGU_____AGUGGUUCAAC________GAGUC________UAAAGGU\n______________\|\|::\|\|\|__\|\|:_____\|:\|\|\|::\|\|\|\|________:\|:\|\|________\|\|\|\|\|\|:\n______________UUUUAGU__CCG_____UUACCGGGUUG________UUUAG________AUUUCCG\n3'-UUU...CAACC_______CA___UUACG___________UCUUUUAU_____ACACUGUU_______UAUAUUG-5'\n_____________\|________________________________________________________\|\n_____________64_______________________________________________________7\n	242 -- 248	8 -- 14	-25.9028 kcal/mol	5.39828 kcal/mol	12.1311 kcal/mol	213 249@LB@ \| \|@LB@5'-UAU...GAUUA UA UUUGG...UCU-3'@LB@ AAGGUCA GGU AGUGGUUCAAC GAGUC UAAAGGU@LB@ \|\|::\|\|\| \|\|: \|:\|\|\|::\|\|\|\| :\|:\|\| \|\|\|\|\|\|:@LB@ UUUUAGU CCG UUACCGGGUUG UUUAG AUUUCCG@LB@3'-UUU...CAACC CA UUACG UCUUUUAU ACACUGUU UAUAUUG-5'@LB@ \| \|@LB@ 64 7@LB@@LB@@LB@Energy -8.37 kcal/mol@LB@Hybridization Energy -25.9028 kcal/mol@LB@Unfolding Energy - mRNA 5.39828 kcal/mol@LB@Unfolding Energy - sRNA 12.1311 kcal/mol@LB@@LB@Position - mRNA 214 -- 248@LB@Position - sRNA 8 -- 63@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 8 -- 14@LB@
133	0.01445	0.3654	b1260	trpA	-8.36	0.252100	71 -- 77	38 -- 44	tryptophan synthase alpha subunit	_____________70______78\n_____________\|_______\|\n5'-GCC...CGCCC_______UGCGU...CAU-3'\n______________UGGCCCA\n______________\|\|\|\|\|\|\|\n______________ACCGGGU\n3'-UUU...ACGUU_______UGUCU...UUG-5'\n_____________\|_______\|\n_____________45______37\n	71 -- 77	38 -- 44	-13.3519 kcal/mol	1.05946 kcal/mol	3.93445 kcal/mol	70 78@LB@ \| \|@LB@5'-GCC...CGCCC UGCGU...CAU-3'@LB@ UGGCCCA@LB@ \|\|\|\|\|\|\|@LB@ ACCGGGU@LB@3'-UUU...ACGUU UGUCU...UUG-5'@LB@ \| \|@LB@ 45 37@LB@@LB@@LB@Energy -8.36 kcal/mol@LB@Hybridization Energy -13.3519 kcal/mol@LB@Unfolding Energy - mRNA 1.05946 kcal/mol@LB@Unfolding Energy - sRNA 3.93445 kcal/mol@LB@@LB@Position - mRNA 71 -- 77@LB@Position - sRNA 38 -- 44@LB@Position Seed - mRNA 71 -- 77@LB@Position Seed - sRNA 38 -- 44@LB@
137	0.01537	0.3774	b0952	pqiC	-8.31	0.257066	203 -- 237	17 -- 64	DUF330 family putative lipoprotein	_____________202________________________________________________238\n_____________\|__________________________________________________\|\n5'-ACG...ACAAU_____________U____A_______G_______________________UGGCC...GCG-3'\n______________GAAAA__AGUGGC_AGUG_CGAU__U_CAGCA___________CUGUGGC\n______________\|\|\|\|\|__\|\|\|\|\|\|_\|:\|\|_\|:\|\|__:_\|\|:\|\|___________\|\|\|\|\|:\|\n______________CUUUU__UCACCG_UUAC_GUUA__G_GUUGU___________GACACUG\n3'-UUU...ACAAC_____AG________________CC_G_____CUUUUAUUUUA_______UUAUU...UUG-5'\n_____________\|__________________________________________________\|\n_____________65_________________________________________________16\n	231 -- 237	17 -- 23	-29.1693 kcal/mol	9.7543 kcal/mol	11.1047 kcal/mol	202 238@LB@ \| \|@LB@5'-ACG...ACAAU U A G UGGCC...GCG-3'@LB@ GAAAA AGUGGC AGUG CGAU U CAGCA CUGUGGC@LB@ \|\|\|\|\| \|\|\|\|\|\| \|:\|\| \|:\|\| : \|\|:\|\| \|\|\|\|\|:\|@LB@ CUUUU UCACCG UUAC GUUA G GUUGU GACACUG@LB@3'-UUU...ACAAC AG CC G CUUUUAUUUUA UUAUU...UUG-5'@LB@ \| \|@LB@ 65 16@LB@@LB@@LB@Energy -8.31 kcal/mol@LB@Hybridization Energy -29.1693 kcal/mol@LB@Unfolding Energy - mRNA 9.7543 kcal/mol@LB@Unfolding Energy - sRNA 11.1047 kcal/mol@LB@@LB@Position - mRNA 203 -- 237@LB@Position - sRNA 17 -- 64@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 17 -- 23@LB@
6	0.0002023	0.1081	b1884	cheR	-8.31	0.257615	184 -- 205	1 -- 21	chemotaxis regulator protein-glutamate methyltransferase	_____________183____________________206\n_____________\|______________________\|\n5'-GCC...CUGAA_____UGA_______C______UUCAU...UGA-3'\n______________GUGAU___GAAGGCG_UAUGAC\n______________\|\|\|\|:___:\|\|\|\|\|:_\|\|\|:\|\|\n______________CACUG___UUUCCGU_AUAUUG\n3'-UUU...UUAGA_____UUA______________-5'\n_____________\|_____________________\|\n_____________22____________________1\n	192 -- 198	7 -- 13	-19.9838 kcal/mol	7.26541 kcal/mol	4.41334 kcal/mol	183 206@LB@ \| \|@LB@5'-GCC...CUGAA UGA C UUCAU...UGA-3'@LB@ GUGAU GAAGGCG UAUGAC@LB@ \|\|\|\|: :\|\|\|\|\|: \|\|\|:\|\|@LB@ CACUG UUUCCGU AUAUUG@LB@3'-UUU...UUAGA UUA -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -8.31 kcal/mol@LB@Hybridization Energy -19.9838 kcal/mol@LB@Unfolding Energy - mRNA 7.26541 kcal/mol@LB@Unfolding Energy - sRNA 4.41334 kcal/mol@LB@@LB@Position - mRNA 184 -- 205@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 7 -- 13@LB@
166	0.01968	0.3987	b0784	moaD	-8.29	0.259720	116 -- 144	39 -- 53	molybdopterin synthase small subunit	_____________115___________________________145\n_____________\|_____________________________\|\n5'-GCA...GCAAA_________AAAGAUAUGGUGAU______GGUAC...AGC-3'\n______________GCGGUGCAA______________UGGUCC\n______________\|\|::\|\|\|\|\|______________\|\|\|:\|\|\n______________CGUUACGUU______________ACCGGG\n3'-UUU...GUCAC_____________________________UUGUC...UUG-5'\n_____________\|_____________________________\|\n_____________54____________________________38\n	118 -- 124	45 -- 51	-19.827 kcal/mol	6.7839 kcal/mol	4.75794 kcal/mol	115 145@LB@ \| \|@LB@5'-GCA...GCAAA AAAGAUAUGGUGAU GGUAC...AGC-3'@LB@ GCGGUGCAA UGGUCC@LB@ \|\|::\|\|\|\|\| \|\|\|:\|\|@LB@ CGUUACGUU ACCGGG@LB@3'-UUU...GUCAC UUGUC...UUG-5'@LB@ \| \|@LB@ 54 38@LB@@LB@@LB@Energy -8.29 kcal/mol@LB@Hybridization Energy -19.827 kcal/mol@LB@Unfolding Energy - mRNA 6.7839 kcal/mol@LB@Unfolding Energy - sRNA 4.75794 kcal/mol@LB@@LB@Position - mRNA 116 -- 144@LB@Position - sRNA 39 -- 53@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 45 -- 51@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@
196	0.02524	0.4256	b1805	fadD	-8.19	0.269381	280 -- 298	55 -- 72	acyl-CoA synthetase (long-chain-fatty-acid--CoA ligase)	_____________279_________________299\n_____________\|___________________\|\n5'-UUG...GGUAG_______U___C_______CG-3'\n______________AUAUGUU_GAG_AGUCGGU\n______________\|\|\|\|\|\|\|_\|\|:_\|:\|\|:\|\|\n______________UAUACAA_CUU_UUAGUCA\n3'-UUU...AAAAA_______C___________CCGUU...UUG-5'\n_____________\|___________________\|\n_____________73__________________54\n	292 -- 298	55 -- 61	-14.048 kcal/mol	3.20699 kcal/mol	2.64594 kcal/mol	279 299@LB@ \| \|@LB@5'-UUG...GGUAG U C CG-3'@LB@ AUAUGUU GAG AGUCGGU@LB@ \|\|\|\|\|\|\| \|\|: \|:\|\|:\|\|@LB@ UAUACAA CUU UUAGUCA@LB@3'-UUU...AAAAA C CCGUU...UUG-5'@LB@ \| \|@LB@ 73 54@LB@@LB@@LB@Energy -8.19 kcal/mol@LB@Hybridization Energy -14.048 kcal/mol@LB@Unfolding Energy - mRNA 3.20699 kcal/mol@LB@Unfolding Energy - sRNA 2.64594 kcal/mol@LB@@LB@Position - mRNA 280 -- 298@LB@Position - sRNA 55 -- 72@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 55 -- 61@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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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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