Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
48	0.0005049	0.03706	b2331	smrB	-12.55	0.024312	152 -- 200	43 -- 92	putative DNA endonuclease		_____________151__________________________________________________201\n_____________\|____________________________________________________\|\n5'-UCA...GAUUG__C__________GUAAAC_______GAAAA_______UA___AC_______AUGAA...GAC-3'\n______________CG_UACGAGUCGG________UGUAG_____UUAGAAA__GAG___AGAUAA\n______________\|\|_\|\|\|\|\|:\|\|::________\|\|:\|\|_____\|:\|:\|\|\|__\|\|:___\|\|\|:\|\|\n______________GC_AUGCUUAGUU________ACGUC_____AGUUUUU__CUU___UCUGUU\n3'-UUU...CCGCA_____________AACACGAU_____AUUA________UC___CAU______AUACC...ACG-5'\n_____________\|____________________________________________________\|\n_____________93___________________________________________________42\n	158 -- 164	81 -- 87	-25.319 kcal/mol	6.91043 kcal/mol	5.86211 kcal/mol	151 201@LB@ \| \|@LB@5'-UCA...GAUUG C GUAAAC GAAAA UA AC AUGAA...GAC-3'@LB@ CG UACGAGUCGG UGUAG UUAGAAA GAG AGAUAA@LB@ \|\| \|\|\|\|\|:\|\|:: \|\|:\|\| \|:\|:\|\|\| \|\|: \|\|\|:\|\|@LB@ GC AUGCUUAGUU ACGUC AGUUUUU CUU UCUGUU@LB@3'-UUU...CCGCA AACACGAU AUUA UC CAU AUACC...ACG-5'@LB@ \| \|@LB@ 93 42@LB@@LB@@LB@Energy -12.55 kcal/mol@LB@Hybridization Energy -25.319 kcal/mol@LB@Unfolding Energy - mRNA 6.91043 kcal/mol@LB@Unfolding Energy - sRNA 5.86211 kcal/mol@LB@@LB@Position - mRNA 152 -- 200@LB@Position - sRNA 43 -- 92@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 81 -- 87@LB@
124	0.004441	0.1258	b1656	sodB	-12.34	0.027802	164 -- 220	1 -- 93	superoxide dismutase Fe		_____________163____________________________________________________________________________________________221\n_____________\|______________________________________________________________________________________________\|\n5'-UCU...GGCUA_________________________AAUUAA___U________________________A________AU___AA___________________ACUAC...AGA-3'\n______________UUGUACG____________UAUGCA______UAA_AAAGGA______________GAGU_GCAAUGUC__UCG_____________UUACCUGC\n______________\|:\|\|\|\|\|____________\|\|\|\|\|\|______:\|\|_\|\|\|\|\|\|______________\|\|\|:_\|\|\|\|:\|:\|__\|\|\|_____________\|:\|\|\|\|\|\|\n______________AGCAUGC____________AUACGU______GUU_UUUCCU______________CUCG_CGUUGCGG__AGC_____________AGUGGACG\n3'-UUU...GCCGC_______UUAGUUAACACG______CAUUAA___U______UCAUUCUGUUAUAC_____________GU___GAACUGCAACGUA________-5'\n_____________\|_____________________________________________________________________________________________\|\n_____________94____________________________________________________________________________________________1\n	214 -- 220	1 -- 7	-45.1977 kcal/mol	11.9384 kcal/mol	20.925 kcal/mol	163 221@LB@ \| \|@LB@5'-UCU...GGCUA AAUUAA U A AU AA ACUAC...AGA-3'@LB@ UUGUACG UAUGCA UAA AAAGGA GAGU GCAAUGUC UCG UUACCUGC@LB@ \|:\|\|\|\|\| \|\|\|\|\|\| :\|\| \|\|\|\|\|\| \|\|\|: \|\|\|\|:\|:\| \|\|\| \|:\|\|\|\|\|\|@LB@ AGCAUGC AUACGU GUU UUUCCU CUCG CGUUGCGG AGC AGUGGACG@LB@3'-UUU...GCCGC UUAGUUAACACG CAUUAA U UCAUUCUGUUAUAC GU GAACUGCAACGUA -5'@LB@ \| \|@LB@ 94 1@LB@@LB@@LB@Energy -12.34 kcal/mol@LB@Hybridization Energy -45.1977 kcal/mol@LB@Unfolding Energy - mRNA 11.9384 kcal/mol@LB@Unfolding Energy - sRNA 20.925 kcal/mol@LB@@LB@Position - mRNA 164 -- 220@LB@Position - sRNA 1 -- 93@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 1 -- 7@LB@
83	0.001966	0.08273	b1584	speG	-9.79	0.123144	169 -- 214	25 -- 77	spermidine N(1)-acetyltransferase		_____________168_____________________________________________________215\n_____________\|_______________________________________________________\|\n5'-UCU...UAACC__________________________U____G____CGUUAU___CA________CAGUG...GGU-3'\n______________UGUUAU____UGAUUUA____AGGAA_GUAA_GACA_______GC__AGCGCCCA\n______________\|\|:\|\|\|____\|:\|\|\|:\|____\|\|\|\|\|_\|\|\|\|_\|\|\|\|_______\|\|__\|:\|\|\|\|\|\|\n______________ACGAUA____AUUAAGU____UCCUU_CAUU_CUGU_______CG__UUGCGGGU\n3'-UUU...UUAAC______CGUC_______UUUU_______________UAUACCU__CG________AGCGA...ACG-5'\n_____________\|_______________________________________________________\|\n_____________78______________________________________________________24\n	208 -- 214	25 -- 31	-32.6914 kcal/mol	9.23779 kcal/mol	13.6641 kcal/mol	168 215@LB@ \| \|@LB@5'-UCU...UAACC U G CGUUAU CA CAGUG...GGU-3'@LB@ UGUUAU UGAUUUA AGGAA GUAA GACA GC AGCGCCCA@LB@ \|\|:\|\|\| \|:\|\|\|:\| \|\|\|\|\| \|\|\|\| \|\|\|\| \|\| \|:\|\|\|\|\|\|@LB@ ACGAUA AUUAAGU UCCUU CAUU CUGU CG UUGCGGGU@LB@3'-UUU...UUAAC CGUC UUUU UAUACCU CG AGCGA...ACG-5'@LB@ \| \|@LB@ 78 24@LB@@LB@@LB@Energy -9.79 kcal/mol@LB@Hybridization Energy -32.6914 kcal/mol@LB@Unfolding Energy - mRNA 9.23779 kcal/mol@LB@Unfolding Energy - sRNA 13.6641 kcal/mol@LB@@LB@Position - mRNA 169 -- 214@LB@Position - sRNA 25 -- 77@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 25 -- 31@LB@
179	0.007631	0.1495	b3229	sspA	-8.36	0.252415	276 -- 298	54 -- 83	stringent starvation protein A phage P1 late gene activator RNAP-associated acid-resistance protein inactive glutathione S-transferase homolog		_____________275_____________________________299\n_____________\|_______________________________\|\n5'-CCA...AGGUC__C____________________________UG-3'\n______________CG_AUUGUGCUG_GC_______UGAGAAAGG\n______________\|:_\|\|\|\|\|\|\|\|:_\|\|_______::\|:\|\|\|\|\|\n______________GU_UAACACGAU_CG_______GUUUUUUCC\n3'-UUU...GCUUA____________A__UCAUUAA_________UUCAU...ACG-5'\n_____________\|_______________________________\|\n_____________84______________________________53\n	292 -- 298	54 -- 60	-18.0489 kcal/mol	5.94535 kcal/mol	3.74667 kcal/mol	275 299@LB@ \| \|@LB@5'-CCA...AGGUC C UG-3'@LB@ CG AUUGUGCUG GC UGAGAAAGG@LB@ \|: \|\|\|\|\|\|\|\|: \|\| ::\|:\|\|\|\|\|@LB@ GU UAACACGAU CG GUUUUUUCC@LB@3'-UUU...GCUUA A UCAUUAA UUCAU...ACG-5'@LB@ \| \|@LB@ 84 53@LB@@LB@@LB@Energy -8.36 kcal/mol@LB@Hybridization Energy -18.0489 kcal/mol@LB@Unfolding Energy - mRNA 5.94535 kcal/mol@LB@Unfolding Energy - sRNA 3.74667 kcal/mol@LB@@LB@Position - mRNA 276 -- 298@LB@Position - sRNA 54 -- 83@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 54 -- 60@LB@
3	7.57e-07	0.0008889	b1763	topB	-11.97	0.035059	233 -- 258	1 -- 37	DNA topoisomerase III		_____________232___________________________________259\n_____________\|_____________________________________\|\n5'-UCU...AGUCU_____________________________________CCAAA...GUA-3'\n______________GGCGC_GCG_CCAUUGCU_GAUGU________CCUGC\n______________:\|\|\|\|_:\|\|_\|\|\|\|:\|\|\|_\|\|:\|\|________\|\|\|\|\|\n______________UCGCG_UGC_GGUAGCGA_CUGCA________GGACG\n3'-UUU...AUACC_____U___G________A_____ACGUAAGU_____-5'\n_____________\|____________________________________\|\n_____________38___________________________________1\n	242 -- 248	20 -- 26	-35.9728 kcal/mol	8.72127 kcal/mol	15.288 kcal/mol	232 259@LB@ \| \|@LB@5'-UCU...AGUCU CCAAA...GUA-3'@LB@ GGCGC GCG CCAUUGCU GAUGU CCUGC@LB@ :\|\|\|\| :\|\| \|\|\|\|:\|\|\| \|\|:\|\| \|\|\|\|\|@LB@ UCGCG UGC GGUAGCGA CUGCA GGACG@LB@3'-UUU...AUACC U G A ACGUAAGU -5'@LB@ \| \|@LB@ 38 1@LB@@LB@@LB@Energy -11.97 kcal/mol@LB@Hybridization Energy -35.9728 kcal/mol@LB@Unfolding Energy - mRNA 8.72127 kcal/mol@LB@Unfolding Energy - sRNA 15.288 kcal/mol@LB@@LB@Position - mRNA 233 -- 258@LB@Position - sRNA 1 -- 37@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 20 -- 26@LB@
28	0.0001471	0.01851	b0997	torA	-9.78	0.123932	184 -- 203	41 -- 60	trimethylamine N-oxide (TMAO) reductase I catalytic subunit	b3551 b1872	_____________183__________________204\n_____________\|____________________\|\n5'-UAC...GCGAU__________A__A______AACAA...CGC-3'\n______________AAGAAGGAAG_AA_AUAAUG\n______________\|\|:\|\|\|\|\|\|\|_\|\|_\|:\|\|\|:\n______________UUUUUCCUUC_UU_UGUUAU\n3'-UUU...UAAGU__________A__C______ACCUC...ACG-5'\n_____________\|____________________\|\n_____________61___________________40\n	187 -- 193	51 -- 57	-13.1224 kcal/mol	1.37417 kcal/mol	1.96633 kcal/mol	183 204@LB@ \| \|@LB@5'-UAC...GCGAU A A AACAA...CGC-3'@LB@ AAGAAGGAAG AA AUAAUG@LB@ \|\|:\|\|\|\|\|\|\| \|\| \|:\|\|\|:@LB@ UUUUUCCUUC UU UGUUAU@LB@3'-UUU...UAAGU A C ACCUC...ACG-5'@LB@ \| \|@LB@ 61 40@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -13.1224 kcal/mol@LB@Unfolding Energy - mRNA 1.37417 kcal/mol@LB@Unfolding Energy - sRNA 1.96633 kcal/mol@LB@@LB@Position - mRNA 184 -- 203@LB@Position - sRNA 41 -- 60@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 51 -- 57@LB@
145	0.00562	0.1365	b2532	trmJ	-9.44	0.148020	215 -- 233	68 -- 84	tRNA mC32 mU32 2'-O-methyltransferase SAM-dependent		_____________214_________________234\n_____________\|___________________\|\n5'-CGU...AAUAU__G__________G__G__ACGUC...UGU-3'\n______________UC_AAUUGUGCUG_UG_AG\n______________\|\|_\|\|\|\|\|\|\|\|\|:_\|\|_\|\|\n______________AG_UUAACACGAU_AC_UC\n3'-UUU...UGCUU________________G__AUUAA...ACG-5'\n_____________\|___________________\|\n_____________85__________________67\n	221 -- 227	73 -- 79	-16.7979 kcal/mol	3.71432 kcal/mol	3.64047 kcal/mol	214 234@LB@ \| \|@LB@5'-CGU...AAUAU G G G ACGUC...UGU-3'@LB@ UC AAUUGUGCUG UG AG@LB@ \|\| \|\|\|\|\|\|\|\|\|: \|\| \|\|@LB@ AG UUAACACGAU AC UC@LB@3'-UUU...UGCUU G AUUAA...ACG-5'@LB@ \| \|@LB@ 85 67@LB@@LB@@LB@Energy -9.44 kcal/mol@LB@Hybridization Energy -16.7979 kcal/mol@LB@Unfolding Energy - mRNA 3.71432 kcal/mol@LB@Unfolding Energy - sRNA 3.64047 kcal/mol@LB@@LB@Position - mRNA 215 -- 233@LB@Position - sRNA 68 -- 84@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 73 -- 79@LB@
115	0.003699	0.1133	b3343	tusB	-8.43	0.243717	216 -- 222	20 -- 26	mnm(5)-s(2)U34-tRNA synthesis 2-thiolation protein		_____________215_____223\n_____________\|_______\|\n5'-GCU...CAUUA_______CACCC...GCG-3'\n______________CAUCGCU\n______________\|\|\|\|\|\|\|\n______________GUAGCGA\n3'-UUU...UGCGG_______ACUGC...ACG-5'\n_____________\|_______\|\n_____________27______19\n	216 -- 222	20 -- 26	-9.55221 kcal/mol	1.0434 kcal/mol	0.0768517 kcal/mol	215 223@LB@ \| \|@LB@5'-GCU...CAUUA CACCC...GCG-3'@LB@ CAUCGCU@LB@ \|\|\|\|\|\|\|@LB@ GUAGCGA@LB@3'-UUU...UGCGG ACUGC...ACG-5'@LB@ \| \|@LB@ 27 19@LB@@LB@@LB@Energy -8.43 kcal/mol@LB@Hybridization Energy -9.55221 kcal/mol@LB@Unfolding Energy - mRNA 1.0434 kcal/mol@LB@Unfolding Energy - sRNA 0.0768517 kcal/mol@LB@@LB@Position - mRNA 216 -- 222@LB@Position - sRNA 20 -- 26@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 20 -- 26@LB@
21	6.29e-05	0.01049	b4040	ubiA	-12.44	0.026053	187 -- 207	35 -- 59	p-hydroxybenzoate octaprenyltransferase		_____________186_______________________208\n_____________\|_________________________\|\n5'-AGC...GUACU________AAA______________GGAGU...UAU-3'\n______________AAGAGGAA_______AAUAUGGAGU\n______________\|\|:\|\|\|\|\|_______\|\|\|\|\|\|\|\|\|:\n______________UUUUCCUU_______UUAUACCUCG\n3'-UUU...AAGUU________CAUUCUG__________CGUUG...ACG-5'\n_____________\|_________________________\|\n_____________60________________________34\n	201 -- 207	35 -- 41	-18.3412 kcal/mol	1.63668 kcal/mol	4.22714 kcal/mol	186 208@LB@ \| \|@LB@5'-AGC...GUACU AAA GGAGU...UAU-3'@LB@ AAGAGGAA AAUAUGGAGU@LB@ \|\|:\|\|\|\|\| \|\|\|\|\|\|\|\|\|:@LB@ UUUUCCUU UUAUACCUCG@LB@3'-UUU...AAGUU CAUUCUG CGUUG...ACG-5'@LB@ \| \|@LB@ 60 34@LB@@LB@@LB@Energy -12.44 kcal/mol@LB@Hybridization Energy -18.3412 kcal/mol@LB@Unfolding Energy - mRNA 1.63668 kcal/mol@LB@Unfolding Energy - sRNA 4.22714 kcal/mol@LB@@LB@Position - mRNA 187 -- 207@LB@Position - sRNA 35 -- 59@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 35 -- 41@LB@
103	0.003335	0.1114	b3494	uspB	-9.88	0.117554	193 -- 207	43 -- 57	universal stress (ethanol tolerance) protein B		_____________192_____________208\n_____________\|_______________\|\n5'-AAU...CCGGG_________U_____GCACC...UGC-3'\n______________GAGGAGGUA_GAUAA\n______________:\|\|\|\|:\|\|\|_\|\|:\|\|\n______________UUCCUUCAU_CUGUU\n3'-UUU...GUUUU_________U_____AUACC...ACG-5'\n_____________\|_______________\|\n_____________58______________42\n	195 -- 201	49 -- 55	-16.0492 kcal/mol	4.41466 kcal/mol	1.75421 kcal/mol	192 208@LB@ \| \|@LB@5'-AAU...CCGGG U GCACC...UGC-3'@LB@ GAGGAGGUA GAUAA@LB@ :\|\|\|\|:\|\|\| \|\|:\|\|@LB@ UUCCUUCAU CUGUU@LB@3'-UUU...GUUUU U AUACC...ACG-5'@LB@ \| \|@LB@ 58 42@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -16.0492 kcal/mol@LB@Unfolding Energy - mRNA 4.41466 kcal/mol@LB@Unfolding Energy - sRNA 1.75421 kcal/mol@LB@@LB@Position - mRNA 193 -- 207@LB@Position - sRNA 43 -- 57@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 49 -- 55@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)

Job resubmission

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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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