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
147	0.008705	0.2059	b0071	leuD	-8.42	0.269085	76 -- 114	1 -- 54	3-isopropylmalate dehydratase small subunit	_____________75_____________________________________________________115\n_____________\|______________________________________________________\|\n5'-GCC...AGCAA______C_________A__CCGC_________________________G_____GCAUC...AAG-3'\n______________CCGUAA_UU____UGA_GG____CAGGGGCGCGGC___________GG_CGCAC\n______________\|\|\|\|\|\|_\|\|____\|\|\|_\|:____\|\|:\|\|\|\|:\|:\|\|___________\|\|_\|\|\|\|\|\n______________GGCAUU_AA____ACU_CU____GUUCCCGUGUCG___________CC_GCGUG\n3'-UUU...GACGC______U__UAAU___A__CAAU____________UGACAAAAAGU__G_____-5'\n_____________\|_____________________________________________________\|\n_____________55____________________________________________________1\n	98 -- 104	22 -- 28	-40.9174 kcal/mol	15.4198 kcal/mol	17.077 kcal/mol	75 115@LB@ \| \|@LB@5'-GCC...AGCAA C A CCGC G GCAUC...AAG-3'@LB@ CCGUAA UU UGA GG CAGGGGCGCGGC GG CGCAC@LB@ \|\|\|\|\|\| \|\| \|\|\| \|: \|\|:\|\|\|\|:\|:\|\| \|\| \|\|\|\|\|@LB@ GGCAUU AA ACU CU GUUCCCGUGUCG CC GCGUG@LB@3'-UUU...GACGC U UAAU A CAAU UGACAAAAAGU G -5'@LB@ \| \|@LB@ 55 1@LB@@LB@@LB@Energy -8.42 kcal/mol@LB@Hybridization Energy -40.9174 kcal/mol@LB@Unfolding Energy - mRNA 15.4198 kcal/mol@LB@Unfolding Energy - sRNA 17.077 kcal/mol@LB@@LB@Position - mRNA 76 -- 114@LB@Position - sRNA 1 -- 54@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 22 -- 28@LB@
159	0.009346	0.2062	b3661	nlpA	-7.63	0.365650	232 -- 240	1 -- 9	cytoplasmic membrane lipoprotein-28	_____________231_______241\n_____________\|_________\|\n5'-UGU...GACAG_________UAUUG...ACA-3'\n______________GGGCCGCAU\n______________:\|\|\|\|\|\|\|:\n______________UCCGGCGUG\n3'-UUU...AAAAG_________-5'\n_____________\|________\|\n_____________10_______1\n	234 -- 240	1 -- 7	-16.6231 kcal/mol	3.46198 kcal/mol	5.10726 kcal/mol	231 241@LB@ \| \|@LB@5'-UGU...GACAG UAUUG...ACA-3'@LB@ GGGCCGCAU@LB@ :\|\|\|\|\|\|\|:@LB@ UCCGGCGUG@LB@3'-UUU...AAAAG -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -16.6231 kcal/mol@LB@Unfolding Energy - mRNA 3.46198 kcal/mol@LB@Unfolding Energy - sRNA 5.10726 kcal/mol@LB@@LB@Position - mRNA 232 -- 240@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 1 -- 7@LB@
197	0.01211	0.2164	b0495	ybbA	-7.53	0.379415	88 -- 97	1 -- 10	putative ABC transporter ATPase	_____________87_________98\n_____________\|__________\|\n5'-GCC...CAGGC__________UGGCA...UCA-3'\n______________CAGGCCGCGC\n______________\|\|\|\|\|\|\|\|:\|\n______________GUCCGGCGUG\n3'-UUU...AAAAA__________-5'\n_____________\|_________\|\n_____________11________1\n	91 -- 97	1 -- 7	-21.6304 kcal/mol	8.71663 kcal/mol	5.44172 kcal/mol	87 98@LB@ \| \|@LB@5'-GCC...CAGGC UGGCA...UCA-3'@LB@ CAGGCCGCGC@LB@ \|\|\|\|\|\|\|\|:\|@LB@ GUCCGGCGUG@LB@3'-UUU...AAAAA -5'@LB@ \| \|@LB@ 11 1@LB@@LB@@LB@Energy -7.53 kcal/mol@LB@Hybridization Energy -21.6304 kcal/mol@LB@Unfolding Energy - mRNA 8.71663 kcal/mol@LB@Unfolding Energy - sRNA 5.44172 kcal/mol@LB@@LB@Position - mRNA 88 -- 97@LB@Position - sRNA 1 -- 10@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 1 -- 7@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@
142	0.00825	0.2033	b3457	livH	-8.25	0.287512	56 -- 64	3 -- 11	branched-chain amino acid ABC transporter permease	_____________55________65\n_____________\|_________\|\n5'-GAU...CGUGA_________UGAAC...ACG-3'\n______________UUGGGCCGC\n______________\|::\|\|\|\|\|\|\n______________AGUCCGGCG\n3'-UUU...CAAAA_________UG-5'\n_____________\|_________\|\n_____________12________2\n	58 -- 64	3 -- 9	-16.0849 kcal/mol	2.23282 kcal/mol	5.54194 kcal/mol	55 65@LB@ \| \|@LB@5'-GAU...CGUGA UGAAC...ACG-3'@LB@ UUGGGCCGC@LB@ \|::\|\|\|\|\|\|@LB@ AGUCCGGCG@LB@3'-UUU...CAAAA UG-5'@LB@ \| \|@LB@ 12 2@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -16.0849 kcal/mol@LB@Unfolding Energy - mRNA 2.23282 kcal/mol@LB@Unfolding Energy - sRNA 5.54194 kcal/mol@LB@@LB@Position - mRNA 56 -- 64@LB@Position - sRNA 3 -- 11@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 3 -- 9@LB@
186	0.01109	0.2089	b3234	degQ	-11.96	0.058310	267 -- 277	3 -- 13	serine endoprotease periplasmic	_____________266_________278\n_____________\|___________\|\n5'-CUG...CGUCA___________CGCGU...UUG-3'\n______________UUUCAGGCCGU\n______________\|\|\|\|\|\|\|\|\|\|:\n______________AAAGUCCGGCG\n3'-UUU...GACAA___________UG-5'\n_____________\|___________\|\n_____________14__________2\n	271 -- 277	3 -- 9	-19.4081 kcal/mol	1.79109 kcal/mol	5.63489 kcal/mol	266 278@LB@ \| \|@LB@5'-CUG...CGUCA CGCGU...UUG-3'@LB@ UUUCAGGCCGU@LB@ \|\|\|\|\|\|\|\|\|\|:@LB@ AAAGUCCGGCG@LB@3'-UUU...GACAA UG-5'@LB@ \| \|@LB@ 14 2@LB@@LB@@LB@Energy -11.96 kcal/mol@LB@Hybridization Energy -19.4081 kcal/mol@LB@Unfolding Energy - mRNA 1.79109 kcal/mol@LB@Unfolding Energy - sRNA 5.63489 kcal/mol@LB@@LB@Position - mRNA 267 -- 277@LB@Position - sRNA 3 -- 13@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 3 -- 9@LB@
66	0.003275	0.1727	b0394	mak	-8.12	0.303293	18 -- 92	5 -- 77	manno(fructo)kinase	_____________17_______________________________________________________________________________93\n_____________\|________________________________________________________________________________\|\n5'-GUU...CUUCU____G___C_______CGC____AA_A_G_____CC____AAUUUUUGA_______________GAUAA____CAC____UUGUC...GUG-3'\n______________GCAC_CAG_GAAAUCU___GGCU__G_C_GUAAA__AUUA_________AC_____CACAGCAU_____UUUC___GGCC\n______________:\|\|\|_\|\|\|_\|\|\|\|\|\|\|___\|\|\|\|__\|_\|_\|\|\|\|\|__\|\|\|\|_________\|\|_____\|\|\|\|\|\|\|:_____\|\|\|\|___\|\|\|\|\n______________UGUG_GUC_CUUUAGA___CCGA__C_G_CAUUU__UAAU_________UG_____GUGUCGUG_____AAAG___CCGG\n3'-UUU...GCGGU________C_______A______CG___G_____AA____ACUACUCAA__UUCCC________ACAA_____U______CGUG-5'\n_____________\|________________________________________________________________________________\|\n_____________78_______________________________________________________________________________4\n	70 -- 76	18 -- 24	-46.4183 kcal/mol	15.5654 kcal/mol	22.7286 kcal/mol	17 93@LB@ \| \|@LB@5'-GUU...CUUCU G C CGC AA A G CC AAUUUUUGA GAUAA CAC UUGUC...GUG-3'@LB@ GCAC CAG GAAAUCU GGCU G C GUAAA AUUA AC CACAGCAU UUUC GGCC@LB@ :\|\|\| \|\|\| \|\|\|\|\|\|\| \|\|\|\| \| \| \|\|\|\|\| \|\|\|\| \|\| \|\|\|\|\|\|\|: \|\|\|\| \|\|\|\|@LB@ UGUG GUC CUUUAGA CCGA C G CAUUU UAAU UG GUGUCGUG AAAG CCGG@LB@3'-UUU...GCGGU C A CG G AA ACUACUCAA UUCCC ACAA U CGUG-5'@LB@ \| \|@LB@ 78 4@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -46.4183 kcal/mol@LB@Unfolding Energy - mRNA 15.5654 kcal/mol@LB@Unfolding Energy - sRNA 22.7286 kcal/mol@LB@@LB@Position - mRNA 18 -- 92@LB@Position - sRNA 5 -- 77@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 18 -- 24@LB@
157	0.009216	0.2062	b3361	fic	-9.77	0.153316	103 -- 112	5 -- 14	stationary phase-induced protein putative toxin	_____________102________113\n_____________\|__________\|\n5'-CGC...CGUAA__________AGUCG...AAC-3'\n______________UUUUCAGGCC\n______________\|\|\|\|\|\|\|\|\|\|\n______________AAAAGUCCGG\n3'-UUU...UGACA__________CGUG-5'\n_____________\|__________\|\n_____________15_________4\n	106 -- 112	5 -- 11	-15.6889 kcal/mol	1.64573 kcal/mol	4.24834 kcal/mol	102 113@LB@ \| \|@LB@5'-CGC...CGUAA AGUCG...AAC-3'@LB@ UUUUCAGGCC@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ AAAAGUCCGG@LB@3'-UUU...UGACA CGUG-5'@LB@ \| \|@LB@ 15 4@LB@@LB@@LB@Energy -9.77 kcal/mol@LB@Hybridization Energy -15.6889 kcal/mol@LB@Unfolding Energy - mRNA 1.64573 kcal/mol@LB@Unfolding Energy - sRNA 4.24834 kcal/mol@LB@@LB@Position - mRNA 103 -- 112@LB@Position - sRNA 5 -- 14@LB@Position Seed - mRNA 106 -- 112@LB@Position Seed - sRNA 5 -- 11@LB@
177	0.01048	0.208	b2416	ptsI	-10.21	0.127224	180 -- 212	6 -- 36	PEP-protein phosphotransferase of PTS system (enzyme I)	_____________179________________________________213\n_____________\|__________________________________\|\n5'-GUG...AAAUC___C_____UAA____G___UA__A_________AUUUU...CCG-3'\n______________AGU_ACAAG___GGUA_GGU__UG__UUUCAGGC\n______________\|\|\|_\|\|\|\|\|___\|\|:\|_:\|:__\|\|__\|\|\|\|\|\|\|\|\n______________UCA_UGUUC___CCGU_UCG__AC__AAAGUCCG\n3'-UUU...ACUAC___A____________G___UG__AA________GCGUG-5'\n_____________\|__________________________________\|\n_____________37_________________________________5\n	206 -- 212	6 -- 12	-27.3223 kcal/mol	5.11839 kcal/mol	11.9979 kcal/mol	179 213@LB@ \| \|@LB@5'-GUG...AAAUC C UAA G UA A AUUUU...CCG-3'@LB@ AGU ACAAG GGUA GGU UG UUUCAGGC@LB@ \|\|\| \|\|\|\|\| \|\|:\| :\|: \|\| \|\|\|\|\|\|\|\|@LB@ UCA UGUUC CCGU UCG AC AAAGUCCG@LB@3'-UUU...ACUAC A G UG AA GCGUG-5'@LB@ \| \|@LB@ 37 5@LB@@LB@@LB@Energy -10.21 kcal/mol@LB@Hybridization Energy -27.3223 kcal/mol@LB@Unfolding Energy - mRNA 5.11839 kcal/mol@LB@Unfolding Energy - sRNA 11.9979 kcal/mol@LB@@LB@Position - mRNA 180 -- 212@LB@Position - sRNA 6 -- 36@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 6 -- 12@LB@
185	0.01108	0.2089	b0662	ubiF	-8.33	0.279302	272 -- 292	6 -- 27	2-octaprenyl-3-methyl-6-methoxy-1 4-benzoquinol oxygenase	_____________271____________________293\n_____________\|______________________\|\n5'-AAU...GGGCU____________GA___GC___AACGGUGA-3'\n______________GGCACAGCAC_G__UUU__GGU\n______________\|\|\|\|\|\|\|\|\|\|_\|__\|\|\|__\|\|:\n______________CCGUGUCGUG_C__AAA__CCG\n3'-UUU...UGUUC__________A_AA___GU___GCGUG-5'\n_____________\|______________________\|\n_____________28_____________________5\n	275 -- 281	18 -- 24	-24.5826 kcal/mol	6.14687 kcal/mol	10.1088 kcal/mol	271 293@LB@ \| \|@LB@5'-AAU...GGGCU GA GC AACGGUGA-3'@LB@ GGCACAGCAC G UUU GGU@LB@ \|\|\|\|\|\|\|\|\|\| \| \|\|\| \|\|:@LB@ CCGUGUCGUG C AAA CCG@LB@3'-UUU...UGUUC A AA GU GCGUG-5'@LB@ \| \|@LB@ 28 5@LB@@LB@@LB@Energy -8.33 kcal/mol@LB@Hybridization Energy -24.5826 kcal/mol@LB@Unfolding Energy - mRNA 6.14687 kcal/mol@LB@Unfolding Energy - sRNA 10.1088 kcal/mol@LB@@LB@Position - mRNA 272 -- 292@LB@Position - sRNA 6 -- 27@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 18 -- 24@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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