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	Additional homologs
91	0.004841	0.1855	b3194	mlaE	-9.16	0.198986	180 -- 189	67 -- 76	ABC transporter maintaining OM lipid asymmetry inner membrane permease protein		_____________179________190\n_____________\|__________\|\n5'-GGA...UCUUU__________UUAAG...GCA-3'\n______________UACCAGGGAG\n______________:\|\|\|\|\|\|\|\|:\n______________GUGGUCCCUU\n3'-UUU...CGGUU__________UAGAA...GUG-5'\n_____________\|__________\|\n_____________77_________66\n	183 -- 189	67 -- 73	-15.9485 kcal/mol	2.86999 kcal/mol	3.9178 kcal/mol	179 190@LB@ \| \|@LB@5'-GGA...UCUUU UUAAG...GCA-3'@LB@ UACCAGGGAG@LB@ :\|\|\|\|\|\|\|\|:@LB@ GUGGUCCCUU@LB@3'-UUU...CGGUU UAGAA...GUG-5'@LB@ \| \|@LB@ 77 66@LB@@LB@@LB@Energy -9.16 kcal/mol@LB@Hybridization Energy -15.9485 kcal/mol@LB@Unfolding Energy - mRNA 2.86999 kcal/mol@LB@Unfolding Energy - sRNA 3.9178 kcal/mol@LB@@LB@Position - mRNA 180 -- 189@LB@Position - sRNA 67 -- 76@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 67 -- 73@LB@
92	0.004911	0.1855	b3732	atpD	-9.01	0.211333	117 -- 128	1 -- 11	F1 sector of membrane-bound ATP synthase beta subunit		_____________116__________129\n_____________\|____________\|\n5'-GGC...GCUCG_______A____UACUC...AAA-3'\n______________UCAGGCC_GCAU\n______________\|\|\|\|\|\|\|_\|\|\|:\n______________AGUCCGG_CGUG\n3'-UUU...CAAAA____________-5'\n_____________\|___________\|\n_____________12__________1\n	117 -- 123	5 -- 11	-17.8068 kcal/mol	3.15312 kcal/mol	5.60325 kcal/mol	116 129@LB@ \| \|@LB@5'-GGC...GCUCG A UACUC...AAA-3'@LB@ UCAGGCC GCAU@LB@ \|\|\|\|\|\|\| \|\|\|:@LB@ AGUCCGG CGUG@LB@3'-UUU...CAAAA -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -17.8068 kcal/mol@LB@Unfolding Energy - mRNA 3.15312 kcal/mol@LB@Unfolding Energy - sRNA 5.60325 kcal/mol@LB@@LB@Position - mRNA 117 -- 128@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 117 -- 123@LB@Position Seed - sRNA 5 -- 11@LB@
93	0.005014	0.1855	b0091	murC	-15.25	0.013117	8 -- 30	73 -- 94	UDP-N-acetylmuramate:L-alanine ligase		_____________7_______________________31\n_____________\|_______________________\|\n____5'-CAGCUUA____________U__________CUGGC...GCG-3'\n______________GCGUGGAUGCUG_CGCCAACACC\n______________\|\|\|:\|:\|\|:\|\|\|_\|\|\|\|\|\|\|\|\|\|\n______________CGCGCUUAUGAC_GCGGUUGUGG\n3'-UUU...CCCCA_______________________UCCCU...GUG-5'\n_____________\|_______________________\|\n_____________95______________________72\n	24 -- 30	73 -- 79	-39.1057 kcal/mol	11.3 kcal/mol	12.5321 kcal/mol	7 31@LB@ \| \|@LB@ 5'-CAGCUUA U CUGGC...GCG-3'@LB@ GCGUGGAUGCUG CGCCAACACC@LB@ \|\|\|:\|:\|\|:\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ CGCGCUUAUGAC GCGGUUGUGG@LB@3'-UUU...CCCCA UCCCU...GUG-5'@LB@ \| \|@LB@ 95 72@LB@@LB@@LB@Energy -15.25 kcal/mol@LB@Hybridization Energy -39.1057 kcal/mol@LB@Unfolding Energy - mRNA 11.3 kcal/mol@LB@Unfolding Energy - sRNA 12.5321 kcal/mol@LB@@LB@Position - mRNA 8 -- 30@LB@Position - sRNA 73 -- 94@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 73 -- 79@LB@
94	0.005015	0.1855	b2703	srlE	-7.35	0.404948	254 -- 271	70 -- 86	glucitol/sorbitol-specific enzyme IIB component of PTS		_____________253_________________272\n_____________\|___________________\|\n5'-GAA...CUUGA____AAA____________AAAAA...GUA-3'\n______________GCUG___GCC_ACGCCGGG\n______________:\|\|\|___\|\|\|_\|\|:\|\|:\|\|\n______________UGAC___CGG_UGUGGUCC\n3'-UUU...GCUUA____G_____U________CUUUA...GUG-5'\n_____________\|___________________\|\n_____________87__________________69\n	265 -- 271	70 -- 76	-23.089 kcal/mol	8.46506 kcal/mol	7.27772 kcal/mol	253 272@LB@ \| \|@LB@5'-GAA...CUUGA AAA AAAAA...GUA-3'@LB@ GCUG GCC ACGCCGGG@LB@ :\|\|\| \|\|\| \|\|:\|\|:\|\|@LB@ UGAC CGG UGUGGUCC@LB@3'-UUU...GCUUA G U CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -7.35 kcal/mol@LB@Hybridization Energy -23.089 kcal/mol@LB@Unfolding Energy - mRNA 8.46506 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 254 -- 271@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 70 -- 76@LB@
95	0.005084	0.1855	b3182	dacB	-12.18	0.052827	253 -- 263	2 -- 12	D-alanyl-D-alanine carboxypeptidase		_____________252_________264\n_____________\|___________\|\n5'-CCG...CAGUG___________AAUGU...GUG-3'\n______________UUCAGGCCGCA\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________AAGUCCGGCGU\n3'-UUU...ACAAA___________G-5'\n_____________\|___________\|\n_____________13__________1\n	257 -- 263	2 -- 8	-21.5619 kcal/mol	3.68722 kcal/mol	5.66926 kcal/mol	252 264@LB@ \| \|@LB@5'-CCG...CAGUG AAUGU...GUG-3'@LB@ UUCAGGCCGCA@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ AAGUCCGGCGU@LB@3'-UUU...ACAAA G-5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -12.18 kcal/mol@LB@Hybridization Energy -21.5619 kcal/mol@LB@Unfolding Energy - mRNA 3.68722 kcal/mol@LB@Unfolding Energy - sRNA 5.66926 kcal/mol@LB@@LB@Position - mRNA 253 -- 263@LB@Position - sRNA 2 -- 12@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 2 -- 8@LB@
96	0.005105	0.1855	b0870	ltaE	-12.99	0.036706	93 -- 116	68 -- 88	L-allo-threonine aldolase PLP-dependent		_____________92_______________________117\n_____________\|________________________\|\n5'-GUC...UGUAU_________G___U______C___CGCGG...ACC-3'\n______________AUGCUGCGC_CAA_CAUCAG_GGA\n______________\|\|:\|\|\|\|\|\|_\|\|\|_\|\|:\|\|\|_\|\|\|\n______________UAUGACGCG_GUU_GUGGUC_CCU\n3'-UUU...GCGCU________________________UUAGA...GUG-5'\n_____________\|________________________\|\n_____________89_______________________67\n	95 -- 101	80 -- 86	-29.0922 kcal/mol	8.72289 kcal/mol	7.38144 kcal/mol	92 117@LB@ \| \|@LB@5'-GUC...UGUAU G U C CGCGG...ACC-3'@LB@ AUGCUGCGC CAA CAUCAG GGA@LB@ \|\|:\|\|\|\|\|\| \|\|\| \|\|:\|\|\| \|\|\|@LB@ UAUGACGCG GUU GUGGUC CCU@LB@3'-UUU...GCGCU UUAGA...GUG-5'@LB@ \| \|@LB@ 89 67@LB@@LB@@LB@Energy -12.99 kcal/mol@LB@Hybridization Energy -29.0922 kcal/mol@LB@Unfolding Energy - mRNA 8.72289 kcal/mol@LB@Unfolding Energy - sRNA 7.38144 kcal/mol@LB@@LB@Position - mRNA 93 -- 116@LB@Position - sRNA 68 -- 88@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 80 -- 86@LB@
97	0.005188	0.1855	b3060	ttdR	-16.80	0.006462	125 -- 147	67 -- 90	transcriptional activator of ttdABT	b1799	_____________124______________________148\n_____________\|________________________\|\n5'-UCC...AGAAU________________G_______UGGCA...CGC-3'\n______________GAAUAUUGCGCCAG_A_CAGGGAA\n______________\|\|\|\|\|:\|\|\|\|\|\|\|:_\|_\|\|\|\|\|\|\|\n______________CUUAUGACGCGGUU_U_GUCCCUU\n3'-UUU...ACGCG______________G_G_______UAGAA...GUG-5'\n_____________\|________________________\|\n_____________91_______________________66\n	141 -- 147	67 -- 73	-34.0784 kcal/mol	7.10756 kcal/mol	10.1694 kcal/mol	124 148@LB@ \| \|@LB@5'-UCC...AGAAU G UGGCA...CGC-3'@LB@ GAAUAUUGCGCCAG A CAGGGAA@LB@ \|\|\|\|\|:\|\|\|\|\|\|\|: \| \|\|\|\|\|\|\|@LB@ CUUAUGACGCGGUU U GUCCCUU@LB@3'-UUU...ACGCG G G UAGAA...GUG-5'@LB@ \| \|@LB@ 91 66@LB@@LB@@LB@Energy -16.80 kcal/mol@LB@Hybridization Energy -34.0784 kcal/mol@LB@Unfolding Energy - mRNA 7.10756 kcal/mol@LB@Unfolding Energy - sRNA 10.1694 kcal/mol@LB@@LB@Position - mRNA 125 -- 147@LB@Position - sRNA 67 -- 90@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 67 -- 73@LB@
98	0.005208	0.1855	b4174	hflK	-10.42	0.116019	265 -- 284	65 -- 83	modulator for HflB protease specific for phage lambda cII repressor		_____________264__________________285\n_____________\|____________________\|\n5'-AGA...ACCUG___G____U__G________GGAAA...GUC-3'\n______________GCG_CAAC_CU_AGGGAAAU\n______________\|\|\|_\|\|\|\|_\|:_\|\|\|\|\|\|\|\|\n______________CGC_GUUG_GG_UCCCUUUA\n3'-UUU...UAUGA___G____U___________GAACC...GUG-5'\n_____________\|____________________\|\n_____________84___________________64\n	278 -- 284	65 -- 71	-24.0318 kcal/mol	6.25533 kcal/mol	7.35968 kcal/mol	264 285@LB@ \| \|@LB@5'-AGA...ACCUG G U G GGAAA...GUC-3'@LB@ GCG CAAC CU AGGGAAAU@LB@ \|\|\| \|\|\|\| \|: \|\|\|\|\|\|\|\|@LB@ CGC GUUG GG UCCCUUUA@LB@3'-UUU...UAUGA G U GAACC...GUG-5'@LB@ \| \|@LB@ 84 64@LB@@LB@@LB@Energy -10.42 kcal/mol@LB@Hybridization Energy -24.0318 kcal/mol@LB@Unfolding Energy - mRNA 6.25533 kcal/mol@LB@Unfolding Energy - sRNA 7.35968 kcal/mol@LB@@LB@Position - mRNA 265 -- 284@LB@Position - sRNA 65 -- 83@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 65 -- 71@LB@
99	0.005465	0.1855	b0767	pgl	-9.37	0.182441	275 -- 291	70 -- 86	6-phosphogluconolactonase		_____________274________________292\n_____________\|__________________\|\n5'-UCA...GGCGC____A_____________UUGUC...AUG-3'\n______________ACUG_CGCUGACA_CAGG\n______________\|\|\|\|_\|\|\|::\|\|\|_\|\|\|\|\n______________UGAC_GCGGUUGU_GUCC\n3'-UUU...GCUUA_____________G____CUUUA...GUG-5'\n_____________\|__________________\|\n_____________87_________________69\n	281 -- 287	75 -- 81	-21.4952 kcal/mol	4.85205 kcal/mol	7.27772 kcal/mol	274 292@LB@ \| \|@LB@5'-UCA...GGCGC A UUGUC...AUG-3'@LB@ ACUG CGCUGACA CAGG@LB@ \|\|\|\| \|\|\|::\|\|\| \|\|\|\|@LB@ UGAC GCGGUUGU GUCC@LB@3'-UUU...GCUUA G CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -9.37 kcal/mol@LB@Hybridization Energy -21.4952 kcal/mol@LB@Unfolding Energy - mRNA 4.85205 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 275 -- 291@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 75 -- 81@LB@
100	0.00547	0.1855	b2451	eutA	-10.77	0.099200	8 -- 32	56 -- 86	reactivating factor for ethanolamine ammonia lyase		_____________7_______________________________33\n_____________\|_______________________________\|\n____5'-GUCAUCA________UU______________CC_____UUUCG...UGU-3'\n______________ACUGCGCC__CGCC______GUUU__GCUGC\n______________\|\|\|\|\|\|\|\|__\|:\|\|______:\|:\|__\|\|\|\|\|\n______________UGACGCGG__GUGG______UAGA__CGACG\n3'-UUU...GCUUA________UU____UCCCUU____AC_____CGGCA...GUG-5'\n_____________\|_______________________________\|\n_____________87______________________________55\n	9 -- 15	79 -- 85	-30.9169 kcal/mol	5.09004 kcal/mol	15.0537 kcal/mol	7 33@LB@ \| \|@LB@ 5'-GUCAUCA UU CC UUUCG...UGU-3'@LB@ ACUGCGCC CGCC GUUU GCUGC@LB@ \|\|\|\|\|\|\|\| \|:\|\| :\|:\| \|\|\|\|\|@LB@ UGACGCGG GUGG UAGA CGACG@LB@3'-UUU...GCUUA UU UCCCUU AC CGGCA...GUG-5'@LB@ \| \|@LB@ 87 55@LB@@LB@@LB@Energy -10.77 kcal/mol@LB@Hybridization Energy -30.9169 kcal/mol@LB@Unfolding Energy - mRNA 5.09004 kcal/mol@LB@Unfolding Energy - sRNA 15.0537 kcal/mol@LB@@LB@Position - mRNA 8 -- 32@LB@Position - sRNA 56 -- 86@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 79 -- 85@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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