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	Additional homologs
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@
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@
128	0.01397	0.3575	b2440	eutC	-11.59	0.134682	23 -- 48	126 -- 153	ethanolamine ammonia-lyase small subunit (light chain)		_____________22______________________________49\n_____________\|_______________________________\|\n______5'-CCGCU_______G_______________AC______GACCA...ACU-3'\n______________GGGUGAU___ACAUC_AUGCUCA__UAC_CA\n______________\|\|\|\|\|\|\|___\|\|\|:\|_\|\|:\|\|\|\|__:\|\|_\|\|\n______________CCCACUA___UGUGG_UAUGAGU__GUG_GU\n3'-UUU...GACCG_______AAA_____U_______CA___U__ACUAC...UAG-5'\n_____________\|_______________________________\|\n_____________154_____________________________125\n	19 -- 25	175 -- 181	-25.4577 kcal/mol	6.00586 kcal/mol	5.22711 kcal/mol	22 49@LB@ \| \|@LB@ 5'-CCGCU G AC GACCA...ACU-3'@LB@ GGGUGAU ACAUC AUGCUCA UAC CA@LB@ \|\|\|\|\|\|\| \|\|\|:\| \|\|:\|\|\|\| :\|\| \|\|@LB@ CCCACUA UGUGG UAUGAGU GUG GU@LB@3'-UUU...GACCG AAA U CA U ACUAC...UAG-5'@LB@ \| \|@LB@ 154 125@LB@@LB@@LB@Energy -11.59 kcal/mol@LB@Hybridization Energy -25.4577 kcal/mol@LB@Unfolding Energy - mRNA 6.00586 kcal/mol@LB@Unfolding Energy - sRNA 5.22711 kcal/mol@LB@@LB@Position - mRNA 23 -- 48@LB@Position - sRNA 126 -- 153@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 175 -- 181@LB@
151	0.01691	0.3749	b2442	intZ	-12.49	0.088679	278 -- 291	17 -- 31	CPZ-55 prophage; putative phage integrase	b2349	_____________277_________________292\n_____________\|___________________\|\n5'-ACA...AAACU____________C_G____CGGGG...UGC-3'\n______________CACCGAU__UCA_U_ACGC\n______________\|\|\|\|:\|\|__\|\|\|_\|_\|\|:\|\n______________GUGGUUA__AGU_A_UGUG\n3'-UUU...AAAAU_______UG___C_G____UACUA...UAG-5'\n_____________\|___________________\|\n_____________32__________________16\n	269 -- 275	180 -- 186	-14.1411 kcal/mol	1.5591 kcal/mol	4.88042 kcal/mol	277 292@LB@ \| \|@LB@5'-ACA...AAACU C G CGGGG...UGC-3'@LB@ CACCGAU UCA U ACGC@LB@ \|\|\|\|:\|\| \|\|\| \| \|\|:\|@LB@ GUGGUUA AGU A UGUG@LB@3'-UUU...AAAAU UG C G UACUA...UAG-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -12.49 kcal/mol@LB@Hybridization Energy -14.1411 kcal/mol@LB@Unfolding Energy - mRNA 1.5591 kcal/mol@LB@Unfolding Energy - sRNA 4.88042 kcal/mol@LB@@LB@Position - mRNA 278 -- 291@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 180 -- 186@LB@
46	0.004081	0.2985	b2466	ypfG	-10.37	0.233995	256 -- 280	68 -- 95	DUF1176 family protein		_____________255_____281\n_____________\|_______\|\n5'-AAA...CAAAC_______UUAAU...UCA-3'\n______________GUCACAU\n______________\|\|\|\|\|\|:\n______________CAGUGUG\n3'-UUU...UGAGU_______UACUA...UAG-5'\n_____________\|_______\|\n_____________96______67\n	57 -- 63	168 -- 174	-9.42181 kcal/mol	2.13246 kcal/mol	0.260649 kcal/mol	255 281@LB@ \| \|@LB@5'-AAA...CAAAC UUAAU...UCA-3'@LB@ GUCACAU@LB@ \|\|\|\|\|\|:@LB@ CAGUGUG@LB@3'-UUU...UGAGU UACUA...UAG-5'@LB@ \| \|@LB@ 96 67@LB@@LB@@LB@Energy -10.37 kcal/mol@LB@Hybridization Energy -9.42181 kcal/mol@LB@Unfolding Energy - mRNA 2.13246 kcal/mol@LB@Unfolding Energy - sRNA 0.260649 kcal/mol@LB@@LB@Position - mRNA 256 -- 280@LB@Position - sRNA 68 -- 95@LB@Position Seed - mRNA 57 -- 63@LB@Position Seed - sRNA 168 -- 174@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@
159	0.01779	0.3749	b2504	yfgG	-11.18	0.162405	230 -- 250	168 -- 187	uncharacterized protein		_____________229___________________251\n_____________\|_____________________\|\n5'-CCU...AAACG________UUAA_________GACCC...UUA-3'\n______________ACACCGAU____CAGUCGCAU\n______________\|\|\|\|\|:\|\|____\|\|\|\|\|:\|\|:\n______________UGUGGUUA____GUCAGUGUG\n3'-UUU...UAAAA________UGA__________UACUA...UAG-5'\n_____________\|_____________________\|\n_____________188___________________167\n	244 -- 250	168 -- 174	-22.7597 kcal/mol	5.28018 kcal/mol	4.88067 kcal/mol	229 251@LB@ \| \|@LB@5'-CCU...AAACG UUAA GACCC...UUA-3'@LB@ ACACCGAU CAGUCGCAU@LB@ \|\|\|\|\|:\|\| \|\|\|\|\|:\|\|:@LB@ UGUGGUUA GUCAGUGUG@LB@3'-UUU...UAAAA UGA UACUA...UAG-5'@LB@ \| \|@LB@ 188 167@LB@@LB@@LB@Energy -11.18 kcal/mol@LB@Hybridization Energy -22.7597 kcal/mol@LB@Unfolding Energy - mRNA 5.28018 kcal/mol@LB@Unfolding Energy - sRNA 4.88067 kcal/mol@LB@@LB@Position - mRNA 230 -- 250@LB@Position - sRNA 168 -- 187@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 168 -- 174@LB@
179	0.02059	0.3833	b2535	csiE	-10.55	0.216292	103 -- 142	58 -- 90	stationary phase inducible protein		_____________102___________143\n_____________\|_____________\|\n5'-GCA...GAUUA__________C__CAUUU...UGG-3'\n______________GCAUUCCCUU_GC\n______________\|\|\|::\|\|\|\|\|_\|\|\n______________CGUGGGGGAA_CG\n3'-UUU...UACCC_____________AAGUAG-5'\n_____________\|_____________\|\n_____________91____________57\n	133 -- 139	9 -- 15	-16.9052 kcal/mol	2.85301 kcal/mol	6.64496 kcal/mol	102 143@LB@ \| \|@LB@5'-GCA...GAUUA C CAUUU...UGG-3'@LB@ GCAUUCCCUU GC@LB@ \|\|\|::\|\|\|\|\| \|\|@LB@ CGUGGGGGAA CG@LB@3'-UUU...UACCC AAGUAG-5'@LB@ \| \|@LB@ 91 57@LB@@LB@@LB@Energy -10.55 kcal/mol@LB@Hybridization Energy -16.9052 kcal/mol@LB@Unfolding Energy - mRNA 2.85301 kcal/mol@LB@Unfolding Energy - sRNA 6.64496 kcal/mol@LB@@LB@Position - mRNA 103 -- 142@LB@Position - sRNA 58 -- 90@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 9 -- 15@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@
22	0.001812	0.2633	b2566	era	-10.12	0.260747	283 -- 292	16 -- 26	membrane-associated 16S rRNA-binding GTPase		_____________282________________293\n_____________\|__________________\|\n5'-UUG...AAUGA_________AA_______UGCGG...UCU-3'\n______________GCAUCGAUA___AGUUAC\n______________:\|\|:\|:\|\|\|___\|\|\|:\|\|\n______________UGUGGUUAU___UCAGUG\n3'-UUU...UAAAA_________GAG______UGUAC...UAG-5'\n_____________\|__________________\|\n_____________27_________________15\n	205 -- 211	181 -- 187	-15.5423 kcal/mol	3.87874 kcal/mol	4.86686 kcal/mol	282 293@LB@ \| \|@LB@5'-UUG...AAUGA AA UGCGG...UCU-3'@LB@ GCAUCGAUA AGUUAC@LB@ :\|\|:\|:\|\|\| \|\|\|:\|\|@LB@ UGUGGUUAU UCAGUG@LB@3'-UUU...UAAAA GAG UGUAC...UAG-5'@LB@ \| \|@LB@ 27 15@LB@@LB@@LB@Energy -10.12 kcal/mol@LB@Hybridization Energy -15.5423 kcal/mol@LB@Unfolding Energy - mRNA 3.87874 kcal/mol@LB@Unfolding Energy - sRNA 4.86686 kcal/mol@LB@@LB@Position - mRNA 283 -- 292@LB@Position - sRNA 16 -- 26@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 181 -- 187@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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