Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
179	0.02973	0.5424	b2812	tcdA	-11.60	0.044907	209 -- 228	1 -- 28	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA	_____________208___________________________229\n_____________\|_____________________________\|\n5'-GUG...UCUGU_______________________C_____GUCAG...UUU-3'\n______________GGUAAU_________UAGUGAUG_AUGGC\n______________\|\|\|\|\|\|_________\|\|:\|\|\|\|\|_\|\|:\|\|\n______________CCAUUA_________AUUACUAC_UAUCG\n3'-UUU...UACUG______UUUAUUUCA______________-5'\n_____________\|____________________________\|\n_____________29___________________________1\n	216 -- 222	6 -- 12	-16.3639 kcal/mol	3.995 kcal/mol	0.766821 kcal/mol	208 229@LB@ \| \|@LB@5'-GUG...UCUGU C GUCAG...UUU-3'@LB@ GGUAAU UAGUGAUG AUGGC@LB@ \|\|\|\|\|\| \|\|:\|\|\|\|\| \|\|:\|\|@LB@ CCAUUA AUUACUAC UAUCG@LB@3'-UUU...UACUG UUUAUUUCA -5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -11.60 kcal/mol@LB@Hybridization Energy -16.3639 kcal/mol@LB@Unfolding Energy - mRNA 3.995 kcal/mol@LB@Unfolding Energy - sRNA 0.766821 kcal/mol@LB@@LB@Position - mRNA 209 -- 228@LB@Position - sRNA 1 -- 28@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 6 -- 12@LB@
184	0.03077	0.549	b1101	ptsG	-13.95	0.012872	39 -- 58	1 -- 19	fused glucose-specific PTS enzymes: IIB component/IIC component	_____________38___________________59\n_____________\|____________________\|\n5'-CAU...UGAUC_________AAC________CGUCA...GUU-3'\n______________UGAAGUUGA___GUGAUAGC\n______________\|:\|\|\|\|\|:\|___:\|\|\|\|\|\|\|\n______________AUUUCAAUU___UACUAUCG\n3'-UUU...UAUUU_________AC_________-5'\n_____________\|___________________\|\n_____________20__________________1\n	52 -- 58	1 -- 7	-17.415 kcal/mol	3.39679 kcal/mol	0.0638423 kcal/mol	38 59@LB@ \| \|@LB@5'-CAU...UGAUC AAC CGUCA...GUU-3'@LB@ UGAAGUUGA GUGAUAGC@LB@ \|:\|\|\|\|\|:\| :\|\|\|\|\|\|\|@LB@ AUUUCAAUU UACUAUCG@LB@3'-UUU...UAUUU AC -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -13.95 kcal/mol@LB@Hybridization Energy -17.415 kcal/mol@LB@Unfolding Energy - mRNA 3.39679 kcal/mol@LB@Unfolding Energy - sRNA 0.0638423 kcal/mol@LB@@LB@Position - mRNA 39 -- 58@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 1 -- 7@LB@
187	0.03165	0.5492	b2717	hycI	-9.48	0.123006	243 -- 251	1 -- 9	protease involved in processing C-terminal end of HycE	_____________242_______252\n_____________\|_________\|\n5'-AGC...UGGGC_________GCAGG...ACU-3'\n______________GAUGAUGGC\n______________\|\|\|\|\|\|:\|\|\n______________CUACUAUCG\n3'-UUU...AAUUA_________-5'\n_____________\|________\|\n_____________10_______1\n	245 -- 251	1 -- 7	-13.2104 kcal/mol	3.71514 kcal/mol	0.0200155 kcal/mol	242 252@LB@ \| \|@LB@5'-AGC...UGGGC GCAGG...ACU-3'@LB@ GAUGAUGGC@LB@ \|\|\|\|\|\|:\|\|@LB@ CUACUAUCG@LB@3'-UUU...AAUUA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -13.2104 kcal/mol@LB@Unfolding Energy - mRNA 3.71514 kcal/mol@LB@Unfolding Energy - sRNA 0.0200155 kcal/mol@LB@@LB@Position - mRNA 243 -- 251@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 1 -- 7@LB@
189	0.03168	0.5492	b1533	eamA	-9.19	0.139150	178 -- 226	1 -- 49	cysteine and O-acetyl-L-serine efflux system	_____________177_______________________________________________________227\n_____________\|_________________________________________________________\|\n5'-GUU...ACAAA____GAA______________________AAU__CGCGA____A________U____GCUAC...UGA-3'\n______________AGAU___AUUCAGA_______GGCGGUAG___GU_____AAAG_UGG_GGUG_UGGC\n______________\|\|\|:___\|\|\|\|\|\|\|_______\|:\|\|\|\|\|:___:\|_____\|\|\|\|_\|::_\|:\|\|_\|:\|\|\n______________UCUG___UAAGUCU_______CUGCCAUU___UA_____UUUC_AUU_CUAC_AUCG\n3'-UUU...AUUUG______________UUACUUA________AUU___________A___A____U____-5'\n_____________\|________________________________________________________\|\n_____________50_______________________________________________________1\n	193 -- 199	24 -- 30	-25.3484 kcal/mol	9.82981 kcal/mol	6.32371 kcal/mol	177 227@LB@ \| \|@LB@5'-GUU...ACAAA GAA AAU CGCGA A U GCUAC...UGA-3'@LB@ AGAU AUUCAGA GGCGGUAG GU AAAG UGG GGUG UGGC@LB@ \|\|\|: \|\|\|\|\|\|\| \|:\|\|\|\|\|: :\| \|\|\|\| \|:: \|:\|\| \|:\|\|@LB@ UCUG UAAGUCU CUGCCAUU UA UUUC AUU CUAC AUCG@LB@3'-UUU...AUUUG UUACUUA AUU A A U -5'@LB@ \| \|@LB@ 50 1@LB@@LB@@LB@Energy -9.19 kcal/mol@LB@Hybridization Energy -25.3484 kcal/mol@LB@Unfolding Energy - mRNA 9.82981 kcal/mol@LB@Unfolding Energy - sRNA 6.32371 kcal/mol@LB@@LB@Position - mRNA 178 -- 226@LB@Position - sRNA 1 -- 49@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 24 -- 30@LB@
192	0.03268	0.5507	b3532	bcsB	-10.41	0.080313	186 -- 199	1 -- 12	regulator of cellulose synthase cyclic di-GMP binding	_____________185____________200\n_____________\|______________\|\n5'-AAG...UCAAC__________AC__GAUGA...UCA-3'\n______________AAUGAUGAUA__GC\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\n______________UUACUACUAU__CG\n3'-UUU...UUCAA______________-5'\n_____________\|_____________\|\n_____________13____________1\n	189 -- 195	3 -- 9	-11.9692 kcal/mol	1.52301 kcal/mol	0.0394463 kcal/mol	185 200@LB@ \| \|@LB@5'-AAG...UCAAC AC GAUGA...UCA-3'@LB@ AAUGAUGAUA GC@LB@ \|\|\|\|\|\|\|\|\|\| \|\|@LB@ UUACUACUAU CG@LB@3'-UUU...UUCAA -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -11.9692 kcal/mol@LB@Unfolding Energy - mRNA 1.52301 kcal/mol@LB@Unfolding Energy - sRNA 0.0394463 kcal/mol@LB@@LB@Position - mRNA 186 -- 199@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 3 -- 9@LB@
194	0.03269	0.5507	b2049	cpsB	-9.94	0.099932	179 -- 235	1 -- 54	mannose-1-phosphate guanyltransferase	_____________178________________________________________________________236\n_____________\|__________________________________________________________\|\n5'-ACA...AUUUA___________________AAUU______CA__CGAAACUCUAUCC___U________AGGUG...GCC-3'\n______________UAAAU_GAUAUUCGGGGAU____AUGGCG__GU_____________AGU_GUGAUGGC\n______________\|\|\|\|:_\|\|:\|\|\|\|:\|::\|\|____\|\|\|:\|\|__\|\|_____________\|:\|_:\|\|\|\|:\|\|\n______________AUUUG_CUGUAAGUCUUUA____UACUGC__CA_____________UUA_UACUAUCG\n3'-UUU...UCCCC_____U_____________CU____________UUAUUUAUUUCAA___C________-5'\n_____________\|_________________________________________________________\|\n_____________55________________________________________________________1\n	229 -- 235	1 -- 7	-30.0746 kcal/mol	13.8011 kcal/mol	6.33758 kcal/mol	178 236@LB@ \| \|@LB@5'-ACA...AUUUA AAUU CA CGAAACUCUAUCC U AGGUG...GCC-3'@LB@ UAAAU GAUAUUCGGGGAU AUGGCG GU AGU GUGAUGGC@LB@ \|\|\|\|: \|\|:\|\|\|\|:\|::\|\| \|\|\|:\|\| \|\| \|:\| :\|\|\|\|:\|\|@LB@ AUUUG CUGUAAGUCUUUA UACUGC CA UUA UACUAUCG@LB@3'-UUU...UCCCC U CU UUAUUUAUUUCAA C -5'@LB@ \| \|@LB@ 55 1@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -30.0746 kcal/mol@LB@Unfolding Energy - mRNA 13.8011 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 179 -- 235@LB@Position - sRNA 1 -- 54@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 1 -- 7@LB@
198	0.03373	0.5555	b3915	fieF	-7.92	0.235762	278 -- 297	1 -- 19	ferrous iron and zinc transporter	_____________277__________________298\n_____________\|____________________\|\n5'-AAA...CUGAU____A__UU__C________AUA-3'\n______________UAAA_UU__UG_AUGGUGGU\n______________\|\|\|\|_\|\|__\|\|_\|\|\|:\|:\|:\n______________AUUU_AA__AC_UACUAUCG\n3'-UUU...UAUUU____C__UU___________-5'\n_____________\|___________________\|\n_____________20__________________1\n	291 -- 297	1 -- 7	-10.0103 kcal/mol	2.02347 kcal/mol	0.0638423 kcal/mol	277 298@LB@ \| \|@LB@5'-AAA...CUGAU A UU C AUA-3'@LB@ UAAA UU UG AUGGUGGU@LB@ \|\|\|\| \|\| \|\| \|\|\|:\|:\|:@LB@ AUUU AA AC UACUAUCG@LB@3'-UUU...UAUUU C UU -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -7.92 kcal/mol@LB@Hybridization Energy -10.0103 kcal/mol@LB@Unfolding Energy - mRNA 2.02347 kcal/mol@LB@Unfolding Energy - sRNA 0.0638423 kcal/mol@LB@@LB@Position - mRNA 278 -- 297@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 1 -- 7@LB@
19	0.0008973	0.1482	b3964	yijD	-17.08	0.001951	152 -- 223	2 -- 55	DUF1422 family inner membrane protein	_____________151______________________________________________________________________224\n_____________\|________________________________________________________________________\|\n5'-ACU...UCGCC______A___GAAAACCGCAAU_____CG_______UGAAG____A________AC___CA___CAA_____AGGUA...UGC-3'\n______________GUGAAC_AGA____________UAUUC__GGAAAUG_____GACG_GUAAUGAA__AAG__AAU___GAUAG\n______________\|\|:\|\|\|_\|\|\|____________:\|\|\|\|__:\|\|\|\|\|\|_____\|\|\|\|_\|\|\|\|\|:\|\|__\|\|\|__\|\|\|___\|\|\|\|\|\n______________CAUUUG_UCU____________GUAAG__UCUUUAC_____CUGC_CAUUAUUU__UUC__UUA___CUAUC\n3'-UUU...AUCCC____________________________________UUA_______________AU___AA___CUA_____G-5'\n_____________\|________________________________________________________________________\|\n_____________56_______________________________________________________________________1\n	199 -- 205	20 -- 26	-31.4266 kcal/mol	8.00944 kcal/mol	6.33752 kcal/mol	151 224@LB@ \| \|@LB@5'-ACU...UCGCC A GAAAACCGCAAU CG UGAAG A AC CA CAA AGGUA...UGC-3'@LB@ GUGAAC AGA UAUUC GGAAAUG GACG GUAAUGAA AAG AAU GAUAG@LB@ \|\|:\|\|\| \|\|\| :\|\|\|\| :\|\|\|\|\|\| \|\|\|\| \|\|\|\|\|:\|\| \|\|\| \|\|\| \|\|\|\|\|@LB@ CAUUUG UCU GUAAG UCUUUAC CUGC CAUUAUUU UUC UUA CUAUC@LB@3'-UUU...AUCCC UUA AU AA CUA G-5'@LB@ \| \|@LB@ 56 1@LB@@LB@@LB@Energy -17.08 kcal/mol@LB@Hybridization Energy -31.4266 kcal/mol@LB@Unfolding Energy - mRNA 8.00944 kcal/mol@LB@Unfolding Energy - sRNA 6.33752 kcal/mol@LB@@LB@Position - mRNA 152 -- 223@LB@Position - sRNA 2 -- 55@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 20 -- 26@LB@
52	0.0063	0.3902	b1473	yddG	-8.84	0.162012	257 -- 264	2 -- 9	aromatic amino acid exporter	_____________256______265\n_____________\|________\|\n5'-GCG...AGCAC________GAUUG...CGG-3'\n______________GAUGGUAG\n______________\|\|\|\|:\|\|\|\n______________CUACUAUC\n3'-UUU...AAUUA________G-5'\n_____________\|________\|\n_____________10_______1\n	258 -- 264	2 -- 8	-10.1209 kcal/mol	1.26064 kcal/mol	0.0191352 kcal/mol	256 265@LB@ \| \|@LB@5'-GCG...AGCAC GAUUG...CGG-3'@LB@ GAUGGUAG@LB@ \|\|\|\|:\|\|\|@LB@ CUACUAUC@LB@3'-UUU...AAUUA G-5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -10.1209 kcal/mol@LB@Unfolding Energy - mRNA 1.26064 kcal/mol@LB@Unfolding Energy - sRNA 0.0191352 kcal/mol@LB@@LB@Position - mRNA 257 -- 264@LB@Position - sRNA 2 -- 9@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 2 -- 8@LB@
61	0.008575	0.4523	b3464	ftsY	-13.38	0.017655	71 -- 119	2 -- 50	Signal Recognition Particle (SRP) receptor	_____________70__________________________________________________120\n_____________\|___________________________________________________\|\n5'-CCC...UCCGC______ACACAUACUUGCA_______AU______U________________ACUAU...CGG-3'\n______________CAGAUA_____________GGCGGUG__GUGAAU_AAGUUAA__GUGAUAG\n______________\|\|\|\|:\|_____________\|:\|\|\|\|:__:\|:\|\|\|_\|\|\|\|\|\|\|__:\|\|\|\|\|\|\n______________GUCUGU_____________CUGCCAU__UAUUUA_UUCAAUU__UACUAUC\n3'-UUU...CAUUU______AAGUCUUUACUUA_______________U_______AC_______G-5'\n_____________\|___________________________________________________\|\n_____________51__________________________________________________1\n	113 -- 119	2 -- 8	-30.4135 kcal/mol	10.695 kcal/mol	6.33478 kcal/mol	70 120@LB@ \| \|@LB@5'-CCC...UCCGC ACACAUACUUGCA AU U ACUAU...CGG-3'@LB@ CAGAUA GGCGGUG GUGAAU AAGUUAA GUGAUAG@LB@ \|\|\|\|:\| \|:\|\|\|\|: :\|:\|\|\| \|\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ GUCUGU CUGCCAU UAUUUA UUCAAUU UACUAUC@LB@3'-UUU...CAUUU AAGUCUUUACUUA U AC G-5'@LB@ \| \|@LB@ 51 1@LB@@LB@@LB@Energy -13.38 kcal/mol@LB@Hybridization Energy -30.4135 kcal/mol@LB@Unfolding Energy - mRNA 10.695 kcal/mol@LB@Unfolding Energy - sRNA 6.33478 kcal/mol@LB@@LB@Position - mRNA 71 -- 119@LB@Position - sRNA 2 -- 50@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 2 -- 8@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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service.

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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