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
38	0.003319	0.2912	b3073	patA	-6.81	0.814367	213 -- 222	107 -- 116	putrescine:2-oxoglutaric acid aminotransferase PLP-dependent	_____________212________223\n_____________\|__________\|\n5'-CAU...GGUUA__________CAUCG...CAC-3'\n______________CCUUCGAGCG\n______________\|\|\|\|\|:\|\|\|:\n______________GGAAGUUCGU\n3'-UUU...AGUCA__________ACCAA...UAG-5'\n_____________\|__________\|\n_____________117________106\n	216 -- 222	107 -- 113	-14.0153 kcal/mol	3.04157 kcal/mol	5.58351 kcal/mol	212 223@LB@ \| \|@LB@5'-CAU...GGUUA CAUCG...CAC-3'@LB@ CCUUCGAGCG@LB@ \|\|\|\|\|:\|\|\|:@LB@ GGAAGUUCGU@LB@3'-UUU...AGUCA ACCAA...UAG-5'@LB@ \| \|@LB@ 117 106@LB@@LB@@LB@Energy -6.81 kcal/mol@LB@Hybridization Energy -14.0153 kcal/mol@LB@Unfolding Energy - mRNA 3.04157 kcal/mol@LB@Unfolding Energy - sRNA 5.58351 kcal/mol@LB@@LB@Position - mRNA 213 -- 222@LB@Position - sRNA 107 -- 116@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 107 -- 113@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@
120	0.01317	0.3575	b1158	pinE	-11.56	0.136715	30 -- 59	115 -- 145	e14 prophage; site-specific DNA recombinase	_____________29_____________________60\n_____________\|______________________\|\n5'-AGC...CCGGG______________GUA_____GAGCC...ACA-3'\n______________ACACCAA____CAG___AUGCA\n______________\|\|\|\|\|\|\|____\|\|\|___\|::\|\|\n______________UGUGGUU____GUC___UGUGU\n3'-UUU...UAAAA_______AUGA___AG______ACUAC...UAG-5'\n_____________\|______________________\|\n_____________146____________________114\n	98 -- 104	181 -- 187	-13.8739 kcal/mol	4.34554 kcal/mol	5.05492 kcal/mol	29 60@LB@ \| \|@LB@5'-AGC...CCGGG GUA GAGCC...ACA-3'@LB@ ACACCAA CAG AUGCA@LB@ \|\|\|\|\|\|\| \|\|\| \|::\|\|@LB@ UGUGGUU GUC UGUGU@LB@3'-UUU...UAAAA AUGA AG ACUAC...UAG-5'@LB@ \| \|@LB@ 146 114@LB@@LB@@LB@Energy -11.56 kcal/mol@LB@Hybridization Energy -13.8739 kcal/mol@LB@Unfolding Energy - mRNA 4.34554 kcal/mol@LB@Unfolding Energy - sRNA 5.05492 kcal/mol@LB@@LB@Position - mRNA 30 -- 59@LB@Position - sRNA 115 -- 145@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 181 -- 187@LB@
160	0.01787	0.3749	b3935	priA	-8.27	0.542824	222 -- 250	110 -- 140	Primosome factor n' (replication factor Y)	_____________221_________________________251\n_____________\|___________________________\|\n5'-GAA...UAACC______AU___A_____G_________UAUGC...GCG-3'\n______________CACCGA__UUC_AGUCA_G_AUGAUGC\n______________\|\|\|\|:\|__:\|\|_\|\|\|\|\|_:_\|\|\|\|\|\|\|\n______________GUGGUU__GAG_UCAGU_U_UACUACG\n3'-UUU...AAAAU______AU_________G_G_______UCCGU...UAG-5'\n_____________\|___________________________\|\n_____________141_________________________109\n	193 -- 199	161 -- 167	-24.457 kcal/mol	4.47787 kcal/mol	7.72013 kcal/mol	221 251@LB@ \| \|@LB@5'-GAA...UAACC AU A G UAUGC...GCG-3'@LB@ CACCGA UUC AGUCA G AUGAUGC@LB@ \|\|\|\|:\| :\|\| \|\|\|\|\| : \|\|\|\|\|\|\|@LB@ GUGGUU GAG UCAGU U UACUACG@LB@3'-UUU...AAAAU AU G G UCCGU...UAG-5'@LB@ \| \|@LB@ 141 109@LB@@LB@@LB@Energy -8.27 kcal/mol@LB@Hybridization Energy -24.457 kcal/mol@LB@Unfolding Energy - mRNA 4.47787 kcal/mol@LB@Unfolding Energy - sRNA 7.72013 kcal/mol@LB@@LB@Position - mRNA 222 -- 250@LB@Position - sRNA 110 -- 140@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 161 -- 167@LB@
60	0.005924	0.3261	b4201	priB	-15.35	0.022961	159 -- 180	18 -- 40	primosomal protein N	_____________158_____________181\n_____________\|_______________\|\n5'-AGG...GAAAC_______C_______ACGAU...AUC-3'\n______________UACCUUC__GCUUCA\n______________:\|\|\|::\|__\|\|\|\|\|\|\n______________GUGGGGG__CGAAGU\n3'-UUU...ACCCC_______AA______AG-5'\n_____________\|_______________\|\n_____________41______________17\n	26 -- 32	11 -- 17	-15.0598 kcal/mol	3.0465 kcal/mol	7.09151 kcal/mol	158 181@LB@ \| \|@LB@5'-AGG...GAAAC C ACGAU...AUC-3'@LB@ UACCUUC GCUUCA@LB@ :\|\|\|::\| \|\|\|\|\|\|@LB@ GUGGGGG CGAAGU@LB@3'-UUU...ACCCC AA AG-5'@LB@ \| \|@LB@ 41 17@LB@@LB@@LB@Energy -15.35 kcal/mol@LB@Hybridization Energy -15.0598 kcal/mol@LB@Unfolding Energy - mRNA 3.0465 kcal/mol@LB@Unfolding Energy - sRNA 7.09151 kcal/mol@LB@@LB@Position - mRNA 159 -- 180@LB@Position - sRNA 18 -- 40@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 11 -- 17@LB@
33	0.002591	0.2642	b0331	prpB	-22.44	0.000909	137 -- 159	1 -- 22	2-methylisocitrate lyase	_____________136__________________160\n_____________\|____________________\|\n5'-GUC...AUUGU_____A______________UUUAU...UGG-3'\n______________GGCAC_CCCCUUGCUUUGUC\n______________\|\|\|\|\|_\|\|\|\|\|\|\|\|\|\|::\|\|\n______________CCGUG_GGGGAACGAAGUAG\n3'-UUU...GUACC____________________-5'\n_____________\|___________________\|\n_____________23__________________1\n	153 -- 159	1 -- 7	-33.844 kcal/mol	4.2272 kcal/mol	8.43224 kcal/mol	136 160@LB@ \| \|@LB@5'-GUC...AUUGU A UUUAU...UGG-3'@LB@ GGCAC CCCCUUGCUUUGUC@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|\|\|::\|\|@LB@ CCGUG GGGGAACGAAGUAG@LB@3'-UUU...GUACC -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -22.44 kcal/mol@LB@Hybridization Energy -33.844 kcal/mol@LB@Unfolding Energy - mRNA 4.2272 kcal/mol@LB@Unfolding Energy - sRNA 8.43224 kcal/mol@LB@@LB@Position - mRNA 137 -- 159@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 1 -- 7@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@
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@
103	0.0111	0.3575	b2821	ptrA	-11.45	0.143539	261 -- 295	141 -- 175	protease III	_____________260_______________________________________296\n_____________\|_________________________________________\|\n5'-GCU...GCACC___A_____G______AA____AU_______CGA_______AACCA-3'\n______________CUU_AGUCA_GCA_GA__CGGG__GG_CAGC___UUCAGGA\n______________\|\|:_\|\|\|\|\|_:\|\|_\|\|__\|:\|\|__:\|_\|\|:\|___\|\|\|\|\|:\|\n______________GAG_UCAGU_UGU_CU__GUCC__UC_GUUG___AAGUCUU\n3'-UUU...GUUAU_________G___A__AC____GU__A____A_________AACGC...UAG-5'\n_____________\|_________________________________________\|\n_____________176_______________________________________140\n	289 -- 295	141 -- 147	-30.7779 kcal/mol	8.8583 kcal/mol	8.83168 kcal/mol	260 296@LB@ \| \|@LB@5'-GCU...GCACC A G AA AU CGA AACCA-3'@LB@ CUU AGUCA GCA GA CGGG GG CAGC UUCAGGA@LB@ \|\|: \|\|\|\|\| :\|\| \|\| \|:\|\| :\| \|\|:\| \|\|\|\|\|:\|@LB@ GAG UCAGU UGU CU GUCC UC GUUG AAGUCUU@LB@3'-UUU...GUUAU G A AC GU A A AACGC...UAG-5'@LB@ \| \|@LB@ 176 140@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -30.7779 kcal/mol@LB@Unfolding Energy - mRNA 8.8583 kcal/mol@LB@Unfolding Energy - sRNA 8.83168 kcal/mol@LB@@LB@Position - mRNA 261 -- 295@LB@Position - sRNA 141 -- 175@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 141 -- 147@LB@
12	0.0007005	0.1842	b1101	ptsG	-16.86	0.011310	173 -- 192	168 -- 187	fused glucose-specific PTS enzymes: IIB component/IIC component	_____________172__________________193\n_____________\|____________________\|\n5'-CAU...AAAAA_____C________GA____UCUCA...GUU-3'\n______________GCACC_AUACUCAG__GCAC\n______________:\|\|\|\|_\|\|\|\|\|\|\|\|__:\|\|\|\n______________UGUGG_UAUGAGUC__UGUG\n3'-UUU...UAAAA_____U________AG____UACUA...UAG-5'\n_____________\|____________________\|\n_____________188__________________167\n	180 -- 186	174 -- 180	-27.3381 kcal/mol	3.90127 kcal/mol	4.88067 kcal/mol	172 193@LB@ \| \|@LB@5'-CAU...AAAAA C GA UCUCA...GUU-3'@LB@ GCACC AUACUCAG GCAC@LB@ :\|\|\|\| \|\|\|\|\|\|\|\| :\|\|\|@LB@ UGUGG UAUGAGUC UGUG@LB@3'-UUU...UAAAA U AG UACUA...UAG-5'@LB@ \| \|@LB@ 188 167@LB@@LB@@LB@Energy -16.86 kcal/mol@LB@Hybridization Energy -27.3381 kcal/mol@LB@Unfolding Energy - mRNA 3.90127 kcal/mol@LB@Unfolding Energy - sRNA 4.88067 kcal/mol@LB@@LB@Position - mRNA 173 -- 192@LB@Position - sRNA 168 -- 187@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 174 -- 180@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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