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
55	0.005617	0.3247	b2829	ptsP	-11.41	0.146041	68 -- 133	122 -- 174	PEP-protein phosphotransferase enzyme I; GAF domain containing protein	______________68____________________________________________________________134\n______________\|_____________________________________________________________\|\n___________5'-_______UACACCAGA__U_____G_______AUG___AAGU_________C______G___GGUGG...UGG-3'\n______________CCAGCAG_________GU_UGA_C_GCUGGCG___GGU____UACUGGUAU_CGGUCA_ACA\n______________\|\|\|\|\|\|\|_________\|\|_\|:\|_\|_\|\|\|\|\|\|\|___\|:\|____:\|\|:::\|\|:_\|:\|\|\|\|_\|\|\|\n______________GGUCGUC_________CA_AUU_G_CGACCGC___CUA____GUGGUUAUG_GUCAGU_UGU\n___3'-UUUUUUUU__________________U___A_A_______CCA___AAAU_________A______G___ACUAC...UAG-5'\n_____________\|______________________________________________________________\|\n_____________175____________________________________________________________121\n	25 -- 31	197 -- 203	-46.8098 kcal/mol	17.4414 kcal/mol	18.4949 kcal/mol	68 134@LB@ \| \|@LB@ 5'- UACACCAGA U G AUG AAGU C G GGUGG...UGG-3'@LB@ CCAGCAG GU UGA C GCUGGCG GGU UACUGGUAU CGGUCA ACA@LB@ \|\|\|\|\|\|\| \|\| \|:\| \| \|\|\|\|\|\|\| \|:\| :\|\|:::\|\|: \|:\|\|\|\| \|\|\|@LB@ GGUCGUC CA AUU G CGACCGC CUA GUGGUUAUG GUCAGU UGU@LB@ 3'-UUUUUUUU U A A CCA AAAU A G ACUAC...UAG-5'@LB@ \| \|@LB@ 175 121@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -46.8098 kcal/mol@LB@Unfolding Energy - mRNA 17.4414 kcal/mol@LB@Unfolding Energy - sRNA 18.4949 kcal/mol@LB@@LB@Position - mRNA 68 -- 133@LB@Position - sRNA 122 -- 174@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 197 -- 203@LB@
34	0.002769	0.2736	b2416	ptsI	-14.05	0.042463	178 -- 225	128 -- 177	PEP-protein phosphotransferase of PTS system (enzyme I)	_____________177_________________________________________226\n_____________\|___________________________________________\|\n5'-GUG...AAAAA_________AGUAAGGUAGGGU______UU______UU_____AUCCC...CCG-3'\n______________UCAGUCACA_____________UAUGAU__CAGGCA__UUAGC\n______________\|\|\|\|\|\|\|\|\|_____________:\|\|\|\|\|__\|\|\|\|\|\|__\|:\|:\|\n______________AGUCAGUGU_____________GUACUA__GUCCGU__AGUUG\n3'-UUU...UUAUG____________________________C_______UC_____AAAGU...UAG-5'\n_____________\|___________________________________________\|\n_____________178_________________________________________127\n	180 -- 186	169 -- 175	-30.6202 kcal/mol	5.78851 kcal/mol	8.17404 kcal/mol	177 226@LB@ \| \|@LB@5'-GUG...AAAAA AGUAAGGUAGGGU UU UU AUCCC...CCG-3'@LB@ UCAGUCACA UAUGAU CAGGCA UUAGC@LB@ \|\|\|\|\|\|\|\|\| :\|\|\|\|\| \|\|\|\|\|\| \|:\|:\|@LB@ AGUCAGUGU GUACUA GUCCGU AGUUG@LB@3'-UUU...UUAUG C UC AAAGU...UAG-5'@LB@ \| \|@LB@ 178 127@LB@@LB@@LB@Energy -14.05 kcal/mol@LB@Hybridization Energy -30.6202 kcal/mol@LB@Unfolding Energy - mRNA 5.78851 kcal/mol@LB@Unfolding Energy - sRNA 8.17404 kcal/mol@LB@@LB@Position - mRNA 178 -- 225@LB@Position - sRNA 128 -- 177@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 169 -- 175@LB@
180	0.02081	0.3833	b3728	pstS	-9.23	0.378852	18 -- 25	128 -- 135	phosphate ABC transporter periplasmic binding protein	_____________17___________26\n_____________\|____________\|\n5'-AGA...UCCUA____________GUAGC...GUG-3'\n______________UUUUGCUUC_UC\n______________::\|\|\|\|\|\|\|_\|\|\n______________GGAACGAAG_AG\n3'-UUU...GUGGG_________U__-5'\n_____________\|___________\|\n_____________136_________128\n	149 -- 155	4 -- 10	-10.5275 kcal/mol	1.71006 kcal/mol	1.04836 kcal/mol	17 26@LB@ \| \|@LB@5'-AGA...UCCUA GUAGC...GUG-3'@LB@ UUUUGCUUC UC@LB@ ::\|\|\|\|\|\|\| \|\|@LB@ GGAACGAAG AG@LB@3'-UUU...GUGGG U -5'@LB@ \| \|@LB@ 136 128@LB@@LB@@LB@Energy -9.23 kcal/mol@LB@Hybridization Energy -10.5275 kcal/mol@LB@Unfolding Energy - mRNA 1.71006 kcal/mol@LB@Unfolding Energy - sRNA 1.04836 kcal/mol@LB@@LB@Position - mRNA 18 -- 25@LB@Position - sRNA 128 -- 135@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 4 -- 10@LB@
154	0.01719	0.3749	b3726	pstA	-9.04	0.409183	290 -- 297	24 -- 31	phosphate ABC transporter permease	_____________289____________298\n_____________\|______________\|\n5'-CAG...CCGUA_________C____U-3'\n______________UUGCGCUGA_GCUC\n______________\|\|:\|:\|::\|_:\|\|\|\n______________AAUGUGGUU_UGAG\n3'-UUU...ACUAA_________A____UCAGU...UAG-5'\n_____________\|______________\|\n_____________32_____________23\n	288 -- 294	181 -- 187	-13.2096 kcal/mol	2.6708 kcal/mol	3.40409 kcal/mol	289 298@LB@ \| \|@LB@5'-CAG...CCGUA C U-3'@LB@ UUGCGCUGA GCUC@LB@ \|\|:\|:\|::\| :\|\|\|@LB@ AAUGUGGUU UGAG@LB@3'-UUU...ACUAA A UCAGU...UAG-5'@LB@ \| \|@LB@ 32 23@LB@@LB@@LB@Energy -9.04 kcal/mol@LB@Hybridization Energy -13.2096 kcal/mol@LB@Unfolding Energy - mRNA 2.6708 kcal/mol@LB@Unfolding Energy - sRNA 3.40409 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 24 -- 31@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 181 -- 187@LB@
7	0.0005448	0.1842	b1912	pgsA	-14.68	0.031521	247 -- 274	111 -- 134	phosphatidylglycerophosphate synthetase	_____________246__________________________275\n_____________\|____________________________\|\n5'-GUC...CAUCC_________UCUU_______________UCUGC...UUG-3'\n______________UUAUCCCAU____UGUAUUGGUCUUUUA\n______________\|:\|\|\|\|\|\|:____\|\|:\|\|::\|\|\|:\|\|:\|\n______________AGUAGGGUG____ACGUAGUCAGGAAGU\n3'-UUU...ACGCC____________________________UCGUA...UAG-5'\n_____________\|____________________________\|\n_____________135__________________________110\n	268 -- 274	111 -- 117	-27.9222 kcal/mol	1.79949 kcal/mol	14.1586 kcal/mol	246 275@LB@ \| \|@LB@5'-GUC...CAUCC UCUU UCUGC...UUG-3'@LB@ UUAUCCCAU UGUAUUGGUCUUUUA@LB@ \|:\|\|\|\|\|\|: \|\|:\|\|::\|\|\|:\|\|:\|@LB@ AGUAGGGUG ACGUAGUCAGGAAGU@LB@3'-UUU...ACGCC UCGUA...UAG-5'@LB@ \| \|@LB@ 135 110@LB@@LB@@LB@Energy -14.68 kcal/mol@LB@Hybridization Energy -27.9222 kcal/mol@LB@Unfolding Energy - mRNA 1.79949 kcal/mol@LB@Unfolding Energy - sRNA 14.1586 kcal/mol@LB@@LB@Position - mRNA 247 -- 274@LB@Position - sRNA 111 -- 134@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 111 -- 117@LB@
140	0.01495	0.3575	b2415	ptsH	-9.89	0.288161	112 -- 122	24 -- 34	phosphohistidinoprotein-hexose phosphotransferase component of PTS system (Hpr)	_____________111____________123\n_____________\|______________\|\n5'-UUG...CAAUA_____UA_______ACCGC...UUA-3'\n______________CAGGC__AAGUCGA\n______________\|\|\|\|\|__\|\|\|\|\|:\|\n______________GUCCG__UUCAGUU\n3'-UUU...ACUAC______________GAAAG...UAG-5'\n_____________\|______________\|\n_____________35_____________23\n	138 -- 144	150 -- 156	-14.4294 kcal/mol	3.35524 kcal/mol	6.54796 kcal/mol	111 123@LB@ \| \|@LB@5'-UUG...CAAUA UA ACCGC...UUA-3'@LB@ CAGGC AAGUCGA@LB@ \|\|\|\|\| \|\|\|\|\|:\|@LB@ GUCCG UUCAGUU@LB@3'-UUU...ACUAC GAAAG...UAG-5'@LB@ \| \|@LB@ 35 23@LB@@LB@@LB@Energy -9.89 kcal/mol@LB@Hybridization Energy -14.4294 kcal/mol@LB@Unfolding Energy - mRNA 3.35524 kcal/mol@LB@Unfolding Energy - sRNA 6.54796 kcal/mol@LB@@LB@Position - mRNA 112 -- 122@LB@Position - sRNA 24 -- 34@LB@Position Seed - mRNA 138 -- 144@LB@Position Seed - sRNA 150 -- 156@LB@
90	0.01008	0.3575	b3994	thiC	-11.53	0.138483	145 -- 158	1 -- 14	phosphomethylpyrimidine synthase	_____________144_________159\n_____________\|___________\|\n5'-AUG...CGUCU___________CGUCG...UUU-3'\n______________CUUGCUUCAUC\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________GAACGAAGUAG\n3'-UUU...UGGGG___________-5'\n_____________\|__________\|\n_____________15_________1\n	152 -- 158	1 -- 7	-17.5294 kcal/mol	1.22878 kcal/mol	1.03329 kcal/mol	144 159@LB@ \| \|@LB@5'-AUG...CGUCU CGUCG...UUU-3'@LB@ CUUGCUUCAUC@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ GAACGAAGUAG@LB@3'-UUU...UGGGG -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -11.53 kcal/mol@LB@Hybridization Energy -17.5294 kcal/mol@LB@Unfolding Energy - mRNA 1.22878 kcal/mol@LB@Unfolding Energy - sRNA 1.03329 kcal/mol@LB@@LB@Position - mRNA 145 -- 158@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 1 -- 7@LB@
162	0.01805	0.3749	b2499	purM	-13.07	0.067336	182 -- 195	13 -- 27	phosphoribosylaminoimidazole synthetase	_____________181______196\n_____________\|________\|\n__________5'-U________AUGGU...CGC-3'\n______________AUAUUCAG\n______________\|\|\|:\|\|\|\|\n______________UAUGAGUC\n3'-UUU...GUGGU________AGUGU...UAG-5'\n_____________\|________\|\n_____________28_______12\n	3 -- 9	174 -- 180	-7.89877 kcal/mol	1.882 kcal/mol	0.273058 kcal/mol	181 196@LB@ \| \|@LB@ 5'-U AUGGU...CGC-3'@LB@ AUAUUCAG@LB@ \|\|\|:\|\|\|\|@LB@ UAUGAGUC@LB@3'-UUU...GUGGU AGUGU...UAG-5'@LB@ \| \|@LB@ 28 12@LB@@LB@@LB@Energy -13.07 kcal/mol@LB@Hybridization Energy -7.89877 kcal/mol@LB@Unfolding Energy - mRNA 1.882 kcal/mol@LB@Unfolding Energy - sRNA 0.273058 kcal/mol@LB@@LB@Position - mRNA 182 -- 195@LB@Position - sRNA 13 -- 27@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 174 -- 180@LB@
8	0.0005643	0.1842	b2557	purL	-10.01	0.273478	129 -- 143	111 -- 124	phosphoribosylformyl-glycineamide synthetase	_____________128______________144\n_____________\|________________\|\n5'-AGG...UUGGG________AA______AAGAC...UUU-3'\n______________UACACCGA__GCUUAG\n______________\|\|\|\|\|\|:\|__:\|\|:\|\|\n______________AUGUGGUU__UGAGUC\n3'-UUU...CUAAA________A_______AGUGU...UAG-5'\n_____________\|________________\|\n_____________125______________110\n	172 -- 178	181 -- 187	-14.8421 kcal/mol	1.97129 kcal/mol	3.669 kcal/mol	128 144@LB@ \| \|@LB@5'-AGG...UUGGG AA AAGAC...UUU-3'@LB@ UACACCGA GCUUAG@LB@ \|\|\|\|\|\|:\| :\|\|:\|\|@LB@ AUGUGGUU UGAGUC@LB@3'-UUU...CUAAA A AGUGU...UAG-5'@LB@ \| \|@LB@ 125 110@LB@@LB@@LB@Energy -10.01 kcal/mol@LB@Hybridization Energy -14.8421 kcal/mol@LB@Unfolding Energy - mRNA 1.97129 kcal/mol@LB@Unfolding Energy - sRNA 3.669 kcal/mol@LB@@LB@Position - mRNA 129 -- 143@LB@Position - sRNA 111 -- 124@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 181 -- 187@LB@
166	0.01886	0.3812	b3300	secY	-11.48	0.141920	168 -- 177	196 -- 205	preprotein translocase membrane subunit	_____________167_______________178\n_____________\|_________________\|\n5'-CCU...UCGAA____C_G__________CGAGG...UCC-3'\n______________GCUG_U_GCGGUAAAAU\n______________\|\|\|\|_\|_\|\|\|\|\|\|\|\|\|\|\n______________CGAC_A_CGCCAUUUUA\n3'-UUU...UGAAG______G__________UCACG...UAG-5'\n_____________\|_________________\|\n_____________206_______________195\n	177 -- 183	44 -- 50	-20.9884 kcal/mol	6.84834 kcal/mol	6.15722 kcal/mol	167 178@LB@ \| \|@LB@5'-CCU...UCGAA C G CGAGG...UCC-3'@LB@ GCUG U GCGGUAAAAU@LB@ \|\|\|\| \| \|\|\|\|\|\|\|\|\|\|@LB@ CGAC A CGCCAUUUUA@LB@3'-UUU...UGAAG G UCACG...UAG-5'@LB@ \| \|@LB@ 206 195@LB@@LB@@LB@Energy -11.48 kcal/mol@LB@Hybridization Energy -20.9884 kcal/mol@LB@Unfolding Energy - mRNA 6.84834 kcal/mol@LB@Unfolding Energy - sRNA 6.15722 kcal/mol@LB@@LB@Position - mRNA 168 -- 177@LB@Position - sRNA 196 -- 205@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 44 -- 50@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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