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
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@
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@
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@
58	0.005664	0.3247	b1878	flhE	-13.77	0.048330	266 -- 286	140 -- 162	proton seal during flagellar secretion	_____________265_____________________287\n_____________\|_______________________\|\n5'-CGU...AUGUG__________AGUGUA_______UACGC...AUC-3'\n______________GCAGGCAAGU________GGAAU\n______________\|\|\|\|\|\|\|\|\|\|________:\|\|\|\|\n______________CGUCCGUUCA________UCUUA\n3'-UUU...UACUA__________GUUGAAAG_____ACGCC...UAG-5'\n_____________\|_______________________\|\n_____________163_____________________139\n	269 -- 275	153 -- 159	-20.7539 kcal/mol	2.26514 kcal/mol	7.696 kcal/mol	265 287@LB@ \| \|@LB@5'-CGU...AUGUG AGUGUA UACGC...AUC-3'@LB@ GCAGGCAAGU GGAAU@LB@ \|\|\|\|\|\|\|\|\|\| :\|\|\|\|@LB@ CGUCCGUUCA UCUUA@LB@3'-UUU...UACUA GUUGAAAG ACGCC...UAG-5'@LB@ \| \|@LB@ 163 139@LB@@LB@@LB@Energy -13.77 kcal/mol@LB@Hybridization Energy -20.7539 kcal/mol@LB@Unfolding Energy - mRNA 2.26514 kcal/mol@LB@Unfolding Energy - sRNA 7.696 kcal/mol@LB@@LB@Position - mRNA 266 -- 286@LB@Position - sRNA 140 -- 162@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 153 -- 159@LB@
48	0.004626	0.3205	b3462	ftsX	-13.20	0.063258	14 -- 27	192 -- 205	putative ABC transporter permease	_____________13_____________28\n_____________\|______________\|\n5'-CAA...CGGUA__________AC__ACCGA...ACG-3'\n______________CUGCUGGCGG__GA\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\n______________GACGACCGCC__CU\n3'-UUU...UAUUA__________CA__AAAAU...UAG-5'\n_____________\|______________\|\n_____________206____________191\n	17 -- 23	196 -- 202	-23.0043 kcal/mol	4.65554 kcal/mol	9.06563 kcal/mol	13 28@LB@ \| \|@LB@5'-CAA...CGGUA AC ACCGA...ACG-3'@LB@ CUGCUGGCGG GA@LB@ \|\|\|\|\|\|\|\|\|\| \|\|@LB@ GACGACCGCC CU@LB@3'-UUU...UAUUA CA AAAAU...UAG-5'@LB@ \| \|@LB@ 206 191@LB@@LB@@LB@Energy -13.20 kcal/mol@LB@Hybridization Energy -23.0043 kcal/mol@LB@Unfolding Energy - mRNA 4.65554 kcal/mol@LB@Unfolding Energy - sRNA 9.06563 kcal/mol@LB@@LB@Position - mRNA 14 -- 27@LB@Position - sRNA 192 -- 205@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 196 -- 202@LB@
66	0.006473	0.3261	b0712	ybgK	-17.58	0.008094	217 -- 255	130 -- 164	putative allophanate hydrolase subunit 2	_____________216________________________________________________________256\n_____________\|__________________________________________________________\|\n5'-CGC...GGAGU_____GA__A____U_____________U__AUACC___GUG______G_________ACGGU...AUA-3'\n______________AUGCU__AG_UUAU_C___GUGCGGGCA_GU_____ACU___CAGGAU_GCGGUCGUC\n______________\|\|:\|\|__\|\|_\|:\|:_\|___:\|\|\|:\|\|\|\|_\|\|_____\|\|\|___\|\|\|:\|\|_\|\|\|\|\|\|:\|\|\n______________UAUGA__UC_AGUG_G___UACGUCCGU_CA_____UGA___GUCUUA_CGCCAGUAG\n3'-UUU...GUGGU_____G________U_UAC_________U__GU______AA_______A_________GGUGA...UAG-5'\n_____________\|__________________________________________________________\|\n_____________165________________________________________________________129\n	249 -- 255	130 -- 136	-44.2735 kcal/mol	15.0195 kcal/mol	15.1988 kcal/mol	216 256@LB@ \| \|@LB@5'-CGC...GGAGU GA A U U AUACC GUG G ACGGU...AUA-3'@LB@ AUGCU AG UUAU C GUGCGGGCA GU ACU CAGGAU GCGGUCGUC@LB@ \|\|:\|\| \|\| \|:\|: \| :\|\|\|:\|\|\|\| \|\| \|\|\| \|\|\|:\|\| \|\|\|\|\|\|:\|\|@LB@ UAUGA UC AGUG G UACGUCCGU CA UGA GUCUUA CGCCAGUAG@LB@3'-UUU...GUGGU G U UAC U GU AA A GGUGA...UAG-5'@LB@ \| \|@LB@ 165 129@LB@@LB@@LB@Energy -17.58 kcal/mol@LB@Hybridization Energy -44.2735 kcal/mol@LB@Unfolding Energy - mRNA 15.0195 kcal/mol@LB@Unfolding Energy - sRNA 15.1988 kcal/mol@LB@@LB@Position - mRNA 217 -- 255@LB@Position - sRNA 130 -- 164@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 130 -- 136@LB@
10	0.0006004	0.1842	b3656	yicI	-12.42	0.091283	58 -- 101	169 -- 207	putative alpha-glucosidase	_____________57_________102\n_____________\|__________\|\n5'-ACA...GAUAA__________G-3'\n______________UGAAAUGGUG\n______________\|:\|\|\|\|:\|\|\|\n______________AUUUUAUCAC\n3'-UUU...GCGCC__________GACUA...UAG-5'\n_____________\|__________\|\n_____________208________168\n	293 -- 299	40 -- 46	-9.13222 kcal/mol	0.486237 kcal/mol	4.51378 kcal/mol	57 102@LB@ \| \|@LB@5'-ACA...GAUAA G-3'@LB@ UGAAAUGGUG@LB@ \|:\|\|\|\|:\|\|\|@LB@ AUUUUAUCAC@LB@3'-UUU...GCGCC GACUA...UAG-5'@LB@ \| \|@LB@ 208 168@LB@@LB@@LB@Energy -12.42 kcal/mol@LB@Hybridization Energy -9.13222 kcal/mol@LB@Unfolding Energy - mRNA 0.486237 kcal/mol@LB@Unfolding Energy - sRNA 4.51378 kcal/mol@LB@@LB@Position - mRNA 58 -- 101@LB@Position - sRNA 169 -- 207@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 40 -- 46@LB@
91	0.01018	0.3575	b1660	ydhC	-16.12	0.016020	223 -- 255	172 -- 209	putative arabinose efflux transporter	_____________222_____________________________________256\n_____________\|_______________________________________\|\n5'-GAA...AUUUU______G_________________A______________UUCUG...AGG-3'\n______________UAGUCU_GCUGGCGGGU____UUG_GC__GUACUCGGUU\n______________\|\|:\|\|\|_\|\|\|\|\|\|\|\|\|\|____\|\|:_:\|__:\|\|\|\|\|:\|\|:\n______________AUUAGA_CGACCGCCCA____AAU_UG__UAUGAGUCAG\n3'-UUU...UCCAU_________________CUAA___G__GU__________UGUGU...UAG-5'\n_____________\|_______________________________________\|\n_____________210_____________________________________171\n	249 -- 255	172 -- 178	-38.0361 kcal/mol	10.2504 kcal/mol	15.0669 kcal/mol	222 256@LB@ \| \|@LB@5'-GAA...AUUUU G A UUCUG...AGG-3'@LB@ UAGUCU GCUGGCGGGU UUG GC GUACUCGGUU@LB@ \|\|:\|\|\| \|\|\|\|\|\|\|\|\|\| \|\|: :\| :\|\|\|\|\|:\|\|:@LB@ AUUAGA CGACCGCCCA AAU UG UAUGAGUCAG@LB@3'-UUU...UCCAU CUAA G GU UGUGU...UAG-5'@LB@ \| \|@LB@ 210 171@LB@@LB@@LB@Energy -16.12 kcal/mol@LB@Hybridization Energy -38.0361 kcal/mol@LB@Unfolding Energy - mRNA 10.2504 kcal/mol@LB@Unfolding Energy - sRNA 15.0669 kcal/mol@LB@@LB@Position - mRNA 223 -- 255@LB@Position - sRNA 172 -- 209@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 172 -- 178@LB@
124	0.0136	0.3575	b4065	yjcE	-10.85	0.188871	258 -- 289	125 -- 174	putative cation/proton antiporter	_____________257___________290\n_____________\|_____________\|\n5'-UAU...UGGUC_____U_______CCUUU...UGC-3'\n______________ACUCG_GUCAUGC\n______________\|\|\|\|:_\|\|\|\|::\|\n______________UGAGU_CAGUGUG\n3'-UUU...GGUUA_____________UACUA...UAG-5'\n_____________\|_____________\|\n_____________175___________124\n	267 -- 273	168 -- 174	-13.2629 kcal/mol	3.88311 kcal/mol	0.283892 kcal/mol	257 290@LB@ \| \|@LB@5'-UAU...UGGUC U CCUUU...UGC-3'@LB@ ACUCG GUCAUGC@LB@ \|\|\|\|: \|\|\|\|::\|@LB@ UGAGU CAGUGUG@LB@3'-UUU...GGUUA UACUA...UAG-5'@LB@ \| \|@LB@ 175 124@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -13.2629 kcal/mol@LB@Unfolding Energy - mRNA 3.88311 kcal/mol@LB@Unfolding Energy - sRNA 0.283892 kcal/mol@LB@@LB@Position - mRNA 258 -- 289@LB@Position - sRNA 125 -- 174@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 168 -- 174@LB@
145	0.01541	0.3575	b1191	cvrA	-14.91	0.028165	61 -- 91	128 -- 160	putative cation/proton antiporter	_____________60___________________________________92\n_____________\|____________________________________\|\n5'-UGA...CGGGA_____CUC_______GA___________________GUUCU...CUA-3'\n______________AGGCA___AGUUGAC__UUA_____GCGGUCAUCCU\n______________\|\|\|\|\|___\|\|\|::\|\|__\|:\|_____\|\|\|\|\|\|\|\|\|\|:\n______________UCCGU___UCAGUUG__AGU_____CGCCAGUAGGG\n3'-UUU...CUACG_______________AA___CUUAA___________UGACG...UAG-5'\n_____________\|____________________________________\|\n_____________161__________________________________127\n	85 -- 91	128 -- 134	-32.547 kcal/mol	9.03914 kcal/mol	12.2557 kcal/mol	60 92@LB@ \| \|@LB@5'-UGA...CGGGA CUC GA GUUCU...CUA-3'@LB@ AGGCA AGUUGAC UUA GCGGUCAUCCU@LB@ \|\|\|\|\| \|\|\|::\|\| \|:\| \|\|\|\|\|\|\|\|\|\|:@LB@ UCCGU UCAGUUG AGU CGCCAGUAGGG@LB@3'-UUU...CUACG AA CUUAA UGACG...UAG-5'@LB@ \| \|@LB@ 161 127@LB@@LB@@LB@Energy -14.91 kcal/mol@LB@Hybridization Energy -32.547 kcal/mol@LB@Unfolding Energy - mRNA 9.03914 kcal/mol@LB@Unfolding Energy - sRNA 12.2557 kcal/mol@LB@@LB@Position - mRNA 61 -- 91@LB@Position - sRNA 128 -- 160@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 128 -- 134@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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