Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
52	0.005023	0.3217	b0403	malZ	-9.64	0.320537	253 -- 286	155 -- 185	maltodextrin glucosidase	_____________252___________________________287\n_____________\|_____________________________\|\n5'-UUU...UCAAC_____________U____C__A_______AGACC...AGC-3'\n______________UGCUCA_UUACAC_GUGG_UG_CGGGCGA\n______________\|:\|\|\|\|_\|:\|\|\|\|_:\|\|:_\|\|_\|:\|\|\|:\|\n______________AUGAGU_AGUGUG_UACU_AC_GUCCGUU\n3'-UUU...UGGUU______C______________________CAGUU...UAG-5'\n_____________\|_____________________________\|\n_____________186___________________________154\n	280 -- 286	155 -- 161	-27.4446 kcal/mol	6.9929 kcal/mol	7.82707 kcal/mol	252 287@LB@ \| \|@LB@5'-UUU...UCAAC U C A AGACC...AGC-3'@LB@ UGCUCA UUACAC GUGG UG CGGGCGA@LB@ \|:\|\|\|\| \|:\|\|\|\| :\|\|: \|\| \|:\|\|\|:\|@LB@ AUGAGU AGUGUG UACU AC GUCCGUU@LB@3'-UUU...UGGUU C CAGUU...UAG-5'@LB@ \| \|@LB@ 186 154@LB@@LB@@LB@Energy -9.64 kcal/mol@LB@Hybridization Energy -27.4446 kcal/mol@LB@Unfolding Energy - mRNA 6.9929 kcal/mol@LB@Unfolding Energy - sRNA 7.82707 kcal/mol@LB@@LB@Position - mRNA 253 -- 286@LB@Position - sRNA 155 -- 185@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 155 -- 161@LB@
56	0.005619	0.3247	b2781	mazG	-9.54	0.334798	182 -- 193	141 -- 152	nucleoside triphosphate pyrophosphohydrolase	_____________181__________194\n_____________\|____________\|\n5'-UGA...ACCCG____________CAAUU...CGC-3'\n______________CAAUUUUCAGGA\n______________\|\|\|:\|\|\|\|\|\|:\|\n______________GUUGAAAGUCUU\n3'-UUU...GUUCA____________AACGC...UAG-5'\n_____________\|____________\|\n_____________153__________140\n	187 -- 193	141 -- 147	-13.182 kcal/mol	1.77322 kcal/mol	1.81388 kcal/mol	181 194@LB@ \| \|@LB@5'-UGA...ACCCG CAAUU...CGC-3'@LB@ CAAUUUUCAGGA@LB@ \|\|\|:\|\|\|\|\|\|:\|@LB@ GUUGAAAGUCUU@LB@3'-UUU...GUUCA AACGC...UAG-5'@LB@ \| \|@LB@ 153 140@LB@@LB@@LB@Energy -9.54 kcal/mol@LB@Hybridization Energy -13.182 kcal/mol@LB@Unfolding Energy - mRNA 1.77322 kcal/mol@LB@Unfolding Energy - sRNA 1.81388 kcal/mol@LB@@LB@Position - mRNA 182 -- 193@LB@Position - sRNA 141 -- 152@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 141 -- 147@LB@
89	0.009985	0.3575	b0477	gsk	-9.51	0.338446	88 -- 115	123 -- 150	inosine/guanosine kinase	_____________87_____________116\n_____________\|______________\|\n5'-UUU...UCGCC_________AC___CCGUA...CUG-3'\n______________GCUCAGUUA__CAC\n______________:\|\|\|\|\|\|:\|__\|\|\|\n______________UGAGUCAGU__GUG\n3'-UUU...GGUUA______________UACUA...UAG-5'\n_____________\|______________\|\n_____________151____________122\n	175 -- 181	171 -- 177	-13.3754 kcal/mol	2.68541 kcal/mol	0.283892 kcal/mol	87 116@LB@ \| \|@LB@5'-UUU...UCGCC AC CCGUA...CUG-3'@LB@ GCUCAGUUA CAC@LB@ :\|\|\|\|\|\|:\| \|\|\|@LB@ UGAGUCAGU GUG@LB@3'-UUU...GGUUA UACUA...UAG-5'@LB@ \| \|@LB@ 151 122@LB@@LB@@LB@Energy -9.51 kcal/mol@LB@Hybridization Energy -13.3754 kcal/mol@LB@Unfolding Energy - mRNA 2.68541 kcal/mol@LB@Unfolding Energy - sRNA 0.283892 kcal/mol@LB@@LB@Position - mRNA 88 -- 115@LB@Position - sRNA 123 -- 150@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 171 -- 177@LB@
75	0.007778	0.3458	b0766	ybhA	-9.49	0.341100	208 -- 245	124 -- 172	pyridoxal phosphate (PLP) phosphatase	_____________207___________________________246\n_____________\|_____________________________\|\n5'-GAA...UGGAA_______UG________________U___UCUCG...GCG-3'\n______________UACGCCA__AC_CA__CACGCGUGA_UGC\n______________\|\|\|:\|\|\|__\|\|_\|\|__\|\|\|:\|:\|\|\|_\|\|\|\n______________AUGUGGU__UG_GU__GUGUGUACU_ACG\n3'-UUU...CUAAA_______UA__A__CA_____________UCCGU...UAG-5'\n_____________\|_____________________________\|\n_____________173___________________________123\n	195 -- 201	182 -- 188	-28.0817 kcal/mol	7.23992 kcal/mol	7.72227 kcal/mol	207 246@LB@ \| \|@LB@5'-GAA...UGGAA UG U UCUCG...GCG-3'@LB@ UACGCCA AC CA CACGCGUGA UGC@LB@ \|\|\|:\|\|\| \|\| \|\| \|\|\|:\|:\|\|\| \|\|\|@LB@ AUGUGGU UG GU GUGUGUACU ACG@LB@3'-UUU...CUAAA UA A CA UCCGU...UAG-5'@LB@ \| \|@LB@ 173 123@LB@@LB@@LB@Energy -9.49 kcal/mol@LB@Hybridization Energy -28.0817 kcal/mol@LB@Unfolding Energy - mRNA 7.23992 kcal/mol@LB@Unfolding Energy - sRNA 7.72227 kcal/mol@LB@@LB@Position - mRNA 208 -- 245@LB@Position - sRNA 124 -- 172@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 182 -- 188@LB@
172	0.01969	0.3812	b0213	yafS	-9.47	0.344290	95 -- 113	1 -- 19	putative S-adenosyl-L-methionine-dependent methyltransferase	_____________94________114\n_____________\|_________\|\n5'-UGG...UCAAA_________CUCCU...UCA-3'\n______________CUGUCGUGG\n______________\|\|\|\|\|\|:\|\|\n______________GACAGCGCC\n3'-UUU...GAAGC_________AUUUU...UAG-5'\n_____________\|_________\|\n_____________20________0\n	228 -- 234	50 -- 56	-16.2917 kcal/mol	2.78861 kcal/mol	4.02 kcal/mol	94 114@LB@ \| \|@LB@5'-UGG...UCAAA CUCCU...UCA-3'@LB@ CUGUCGUGG@LB@ \|\|\|\|\|\|:\|\|@LB@ GACAGCGCC@LB@3'-UUU...GAAGC AUUUU...UAG-5'@LB@ \| \|@LB@ 20 0@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -16.2917 kcal/mol@LB@Unfolding Energy - mRNA 2.78861 kcal/mol@LB@Unfolding Energy - sRNA 4.02 kcal/mol@LB@@LB@Position - mRNA 95 -- 113@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 50 -- 56@LB@
111	0.0122	0.3575	b1813	nudL	-9.44	0.347588	99 -- 131	174 -- 206	putative CoA pyrophosphohydrolase weak 3-phosphohydroxypyruvate phosphatase	_____________98________________________________132\n_____________\|_________________________________\|\n5'-CCU...UCUGC_____G_____UG__A__GU________GC___GAAGA...CUG-3'\n______________UCUGC_GGCGG__GA_UU__CGCCGAUA__CAG\n______________\|\|\|\|\|_\|\|\|\|\|__\|\|_\|\|__\|:\|\|:\|\|\|__\|\|\|\n______________AGACG_CCGCC__CU_AA__GUGGUUAU__GUC\n3'-UUU...AUAUU_____A_____CA__A__AU________GA___AGUGU...UAG-5'\n_____________\|_________________________________\|\n_____________207_______________________________173\n	120 -- 126	179 -- 185	-36.2385 kcal/mol	15.3331 kcal/mol	14.8345 kcal/mol	98 132@LB@ \| \|@LB@5'-CCU...UCUGC G UG A GU GC GAAGA...CUG-3'@LB@ UCUGC GGCGG GA UU CGCCGAUA CAG@LB@ \|\|\|\|\| \|\|\|\|\| \|\| \|\| \|:\|\|:\|\|\| \|\|\|@LB@ AGACG CCGCC CU AA GUGGUUAU GUC@LB@3'-UUU...AUAUU A CA A AU GA AGUGU...UAG-5'@LB@ \| \|@LB@ 207 173@LB@@LB@@LB@Energy -9.44 kcal/mol@LB@Hybridization Energy -36.2385 kcal/mol@LB@Unfolding Energy - mRNA 15.3331 kcal/mol@LB@Unfolding Energy - sRNA 14.8345 kcal/mol@LB@@LB@Position - mRNA 99 -- 131@LB@Position - sRNA 174 -- 206@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 179 -- 185@LB@
6	0.0003621	0.1842	b3242	aaeX	-9.38	0.356280	9 -- 19	125 -- 135	DUF1656 family putative inner membrane efflux pump associated protein	_____________8_________20\n_____________\|_________\|\n5'-GCG...CAUAA_________UAAUA...GGG-3'\n______________CAGUUACGC\n______________\|\|\|\|:\|\|:\|\n______________GUCAGUGUG\n3'-UUU...UAUGA_________UACUA...UAG-5'\n_____________\|_________\|\n_____________136_______124\n	75 -- 81	168 -- 174	-12.5845 kcal/mol	1.53643 kcal/mol	0.276974 kcal/mol	8 20@LB@ \| \|@LB@5'-GCG...CAUAA UAAUA...GGG-3'@LB@ CAGUUACGC@LB@ \|\|\|\|:\|\|:\|@LB@ GUCAGUGUG@LB@3'-UUU...UAUGA UACUA...UAG-5'@LB@ \| \|@LB@ 136 124@LB@@LB@@LB@Energy -9.38 kcal/mol@LB@Hybridization Energy -12.5845 kcal/mol@LB@Unfolding Energy - mRNA 1.53643 kcal/mol@LB@Unfolding Energy - sRNA 0.276974 kcal/mol@LB@@LB@Position - mRNA 9 -- 19@LB@Position - sRNA 125 -- 135@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 168 -- 174@LB@
113	0.01268	0.3575	b2066	udk	-9.33	0.364673	240 -- 253	17 -- 31	uridine/cytidine kinase	_____________239________________254\n_____________\|__________________\|\n5'-CGC...UUCGU_________C__AA____CAGGU...GUG-3'\n______________CGCCCCCUU_CU__CAUC\n______________\|:\|\|\|\|\|\|\|_\|\|__\|\|\|\|\n______________GUGGGGGAA_GA__GUAG\n3'-UUU...ACCCC_________C__A_____-5'\n_____________\|_________________\|\n_____________32________________17\n	161 -- 167	9 -- 15	-20.5437 kcal/mol	3.26859 kcal/mol	7.16879 kcal/mol	239 254@LB@ \| \|@LB@5'-CGC...UUCGU C AA CAGGU...GUG-3'@LB@ CGCCCCCUU CU CAUC@LB@ \|:\|\|\|\|\|\|\| \|\| \|\|\|\|@LB@ GUGGGGGAA GA GUAG@LB@3'-UUU...ACCCC C A -5'@LB@ \| \|@LB@ 32 17@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -20.5437 kcal/mol@LB@Unfolding Energy - mRNA 3.26859 kcal/mol@LB@Unfolding Energy - sRNA 7.16879 kcal/mol@LB@@LB@Position - mRNA 240 -- 253@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 9 -- 15@LB@
71	0.00726	0.3408	b2944	yggI	-9.32	0.365111	156 -- 174	1 -- 18	Zn-dependent metalloprotease-related protein	_____________155_____________175\n_____________\|_______________\|\n5'-GAA...AGCCA________AG_____UUUUC...ACC-3'\n______________CCUCUUGC__UCAUC\n______________\|\|:\|\|\|\|\|__\|\|\|\|\|\n______________GGGGAACG__AGUAG\n3'-UUU...CCGUG________A______-5'\n_____________\|______________\|\n_____________19_____________1\n	161 -- 167	7 -- 13	-18.0684 kcal/mol	1.30619 kcal/mol	6.71812 kcal/mol	155 175@LB@ \| \|@LB@5'-GAA...AGCCA AG UUUUC...ACC-3'@LB@ CCUCUUGC UCAUC@LB@ \|\|:\|\|\|\|\| \|\|\|\|\|@LB@ GGGGAACG AGUAG@LB@3'-UUU...CCGUG A -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -18.0684 kcal/mol@LB@Unfolding Energy - mRNA 1.30619 kcal/mol@LB@Unfolding Energy - sRNA 6.71812 kcal/mol@LB@@LB@Position - mRNA 156 -- 174@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 7 -- 13@LB@
136	0.01456	0.3575	b0369	hemB	-9.31	0.367566	203 -- 221	75 -- 90	5-aminolevulinate dehydratase (porphobilinogen synthase)	_____________202________________222\n_____________\|__________________\|\n5'-CCA...UAAAA_______ACCC_______GGUAU...UGC-3'\n______________CAUCCCU____UGCUUCA\n______________\|\|:\|\|\|:____\|\|\|\|\|\|\|\n______________GUGGGGG____ACGAAGU\n3'-UUU...ACCCC_______A__________AG-5'\n_____________\|__________________\|\n_____________91_________________74\n	153 -- 159	3 -- 9	-17.8942 kcal/mol	1.92924 kcal/mol	7.09151 kcal/mol	202 222@LB@ \| \|@LB@5'-CCA...UAAAA ACCC GGUAU...UGC-3'@LB@ CAUCCCU UGCUUCA@LB@ \|\|:\|\|\|: \|\|\|\|\|\|\|@LB@ GUGGGGG ACGAAGU@LB@3'-UUU...ACCCC A AG-5'@LB@ \| \|@LB@ 91 74@LB@@LB@@LB@Energy -9.31 kcal/mol@LB@Hybridization Energy -17.8942 kcal/mol@LB@Unfolding Energy - mRNA 1.92924 kcal/mol@LB@Unfolding Energy - sRNA 7.09151 kcal/mol@LB@@LB@Position - mRNA 203 -- 221@LB@Position - sRNA 75 -- 90@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 3 -- 9@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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