Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
88	0.004799	0.1855	b2213	ada	-9.32	0.185618	222 -- 245	63 -- 86	fused DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase	_____________221________________________246\n_____________\|__________________________\|\n5'-GGA...GCUUA____A__A__________C_______GUCUU...CCA-3'\n______________ACUG_CG_UCAACGCUGG___AAUCU\n______________\|\|\|\|_\|\|_:\|\|\|\|:\|::\|___\|\|\|\|\|\n______________UGAC_GC_GGUUGUGGUC___UUAGA\n3'-UUU...GCUUA__________________CCU_____ACCGA...GUG-5'\n_____________\|__________________________\|\n_____________87_________________________62\n	233 -- 239	71 -- 77	-21.7615 kcal/mol	5.05104 kcal/mol	7.38602 kcal/mol	221 246@LB@ \| \|@LB@5'-GGA...GCUUA A A C GUCUU...CCA-3'@LB@ ACUG CG UCAACGCUGG AAUCU@LB@ \|\|\|\| \|\| :\|\|\|\|:\|::\| \|\|\|\|\|@LB@ UGAC GC GGUUGUGGUC UUAGA@LB@3'-UUU...GCUUA CCU ACCGA...GUG-5'@LB@ \| \|@LB@ 87 62@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -21.7615 kcal/mol@LB@Unfolding Energy - mRNA 5.05104 kcal/mol@LB@Unfolding Energy - sRNA 7.38602 kcal/mol@LB@@LB@Position - mRNA 222 -- 245@LB@Position - sRNA 63 -- 86@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 71 -- 77@LB@
87	0.004792	0.1855	b0476	aes	-9.71	0.157345	34 -- 55	56 -- 76	acetyl esterase	_____________33______________________56\n_____________\|_______________________\|\n5'-CGU...ACGUU______________CA_______UUUUA...CAA-3'\n______________UACC_GGGAAAUUU__UGGUUGU\n______________:\|\|\|_\|\|\|\|\|\|\|:\|__\|\|\|:\|\|:\n______________GUGG_CCCUUUAGA__ACCGACG\n3'-UUU...CGGUU____U__________________CGGCA...GUG-5'\n_____________\|_______________________\|\n_____________77______________________55\n	49 -- 55	56 -- 62	-24.1621 kcal/mol	6.04137 kcal/mol	8.40711 kcal/mol	33 56@LB@ \| \|@LB@5'-CGU...ACGUU CA UUUUA...CAA-3'@LB@ UACC GGGAAAUUU UGGUUGU@LB@ :\|\|\| \|\|\|\|\|\|\|:\| \|\|\|:\|\|:@LB@ GUGG CCCUUUAGA ACCGACG@LB@3'-UUU...CGGUU U CGGCA...GUG-5'@LB@ \| \|@LB@ 77 55@LB@@LB@@LB@Energy -9.71 kcal/mol@LB@Hybridization Energy -24.1621 kcal/mol@LB@Unfolding Energy - mRNA 6.04137 kcal/mol@LB@Unfolding Energy - sRNA 8.40711 kcal/mol@LB@@LB@Position - mRNA 34 -- 55@LB@Position - sRNA 56 -- 76@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 56 -- 62@LB@
134	0.007678	0.1993	b3139	agaC	-7.83	0.338422	255 -- 275	57 -- 74	N-acetylgalactosamine-specific enzyme IIC component of PTS	_____________254___________________276\n_____________\|_____________________\|\n5'-AAC...UUGUU_______UUGAU_________GAAGC...CGA-3'\n______________CUGGGGA_____UUUUGGCUG\n______________\|::\|\|\|\|_____\|:\|\|\|\|\|\|\|\n______________GGUCCCU_____AGAACCGAC\n3'-UUU...GUUGU_______UU____________GCGGC...GUG-5'\n_____________\|_____________________\|\n_____________75____________________56\n	269 -- 275	57 -- 63	-21.9136 kcal/mol	6.09668 kcal/mol	7.9843 kcal/mol	254 276@LB@ \| \|@LB@5'-AAC...UUGUU UUGAU GAAGC...CGA-3'@LB@ CUGGGGA UUUUGGCUG@LB@ \|::\|\|\|\| \|:\|\|\|\|\|\|\|@LB@ GGUCCCU AGAACCGAC@LB@3'-UUU...GUUGU UU GCGGC...GUG-5'@LB@ \| \|@LB@ 75 56@LB@@LB@@LB@Energy -7.83 kcal/mol@LB@Hybridization Energy -21.9136 kcal/mol@LB@Unfolding Energy - mRNA 6.09668 kcal/mol@LB@Unfolding Energy - sRNA 7.9843 kcal/mol@LB@@LB@Position - mRNA 255 -- 275@LB@Position - sRNA 57 -- 74@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 57 -- 63@LB@
12	0.0004488	0.1198	b3133	agaV	-20.63	0.001136	94 -- 118	64 -- 86	N-acetylgalactosamine-specific enzyme IIB component of PTS	_____________93________________________119\n_____________\|_________________________\|\n5'-UCA...GGCGA_____A__________C_____C__AUUAU...UAG-3'\n______________GCUGC_GCCAACGCCA_GGGAA_UC\n______________:\|\|\|\|_\|\|\|\|\|\|:\|\|\|_\|\|\|\|\|_\|\|\n______________UGACG_CGGUUGUGGU_CCCUU_AG\n3'-UUU...GCUUA______________________U__AACCG...GUG-5'\n_____________\|_________________________\|\n_____________87________________________63\n	103 -- 109	72 -- 78	-36.2121 kcal/mol	8.19626 kcal/mol	7.38435 kcal/mol	93 119@LB@ \| \|@LB@5'-UCA...GGCGA A C C AUUAU...UAG-3'@LB@ GCUGC GCCAACGCCA GGGAA UC@LB@ :\|\|\|\| \|\|\|\|\|\|:\|\|\| \|\|\|\|\| \|\|@LB@ UGACG CGGUUGUGGU CCCUU AG@LB@3'-UUU...GCUUA U AACCG...GUG-5'@LB@ \| \|@LB@ 87 63@LB@@LB@@LB@Energy -20.63 kcal/mol@LB@Hybridization Energy -36.2121 kcal/mol@LB@Unfolding Energy - mRNA 8.19626 kcal/mol@LB@Unfolding Energy - sRNA 7.38435 kcal/mol@LB@@LB@Position - mRNA 94 -- 118@LB@Position - sRNA 64 -- 86@LB@Position Seed - mRNA 103 -- 109@LB@Position Seed - sRNA 72 -- 78@LB@
75	0.003854	0.1809	b0606	ahpF	-8.17	0.297536	59 -- 82	64 -- 85	alkyl hydroperoxide reductase F52a subunit FAD/NAD(P)-binding	_____________58_______________________83\n_____________\|________________________\|\n5'-UCA...UUGCU___A___GA______UC_______CACCU...CGG-3'\n______________CUG_CGC__AAUACU__GGAAAUU\n______________\|\|\|_\|\|\|__\|\|:\|\|:__\|\|\|\|\|\|:\n______________GAC_GCG__UUGUGG__CCUUUAG\n3'-UUU...CUUAU_______G_______UC_______AACCG...GUG-5'\n_____________\|________________________\|\n_____________86_______________________63\n	76 -- 82	64 -- 70	-19.6667 kcal/mol	4.11652 kcal/mol	7.38387 kcal/mol	58 83@LB@ \| \|@LB@5'-UCA...UUGCU A GA UC CACCU...CGG-3'@LB@ CUG CGC AAUACU GGAAAUU@LB@ \|\|\| \|\|\| \|\|:\|\|: \|\|\|\|\|\|:@LB@ GAC GCG UUGUGG CCUUUAG@LB@3'-UUU...CUUAU G UC AACCG...GUG-5'@LB@ \| \|@LB@ 86 63@LB@@LB@@LB@Energy -8.17 kcal/mol@LB@Hybridization Energy -19.6667 kcal/mol@LB@Unfolding Energy - mRNA 4.11652 kcal/mol@LB@Unfolding Energy - sRNA 7.38387 kcal/mol@LB@@LB@Position - mRNA 59 -- 82@LB@Position - sRNA 64 -- 85@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 64 -- 70@LB@
171	0.01011	0.2071	b4086	alsC	-10.38	0.118114	189 -- 207	53 -- 70	D-allose ABC transporter permease	_____________188_________________208\n_____________\|___________________\|\n5'-CGC...GAAGA_______A____A__G___UUACC...CGA-3'\n______________GGAGAUU_UGGC_UG_GCU\n______________\|\|\|:\|\|:_\|\|\|\|_\|\|_\|\|:\n______________CCUUUAG_ACCG_AC_CGG\n3'-UUU...UGGUC_______A_______G___CAUUU...GUG-5'\n_____________\|___________________\|\n_____________71__________________52\n	189 -- 195	64 -- 70	-21.9341 kcal/mol	4.72392 kcal/mol	6.83419 kcal/mol	188 208@LB@ \| \|@LB@5'-CGC...GAAGA A A G UUACC...CGA-3'@LB@ GGAGAUU UGGC UG GCU@LB@ \|\|\|:\|\|: \|\|\|\| \|\| \|\|:@LB@ CCUUUAG ACCG AC CGG@LB@3'-UUU...UGGUC A G CAUUU...GUG-5'@LB@ \| \|@LB@ 71 52@LB@@LB@@LB@Energy -10.38 kcal/mol@LB@Hybridization Energy -21.9341 kcal/mol@LB@Unfolding Energy - mRNA 4.72392 kcal/mol@LB@Unfolding Energy - sRNA 6.83419 kcal/mol@LB@@LB@Position - mRNA 189 -- 207@LB@Position - sRNA 53 -- 70@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 64 -- 70@LB@
149	0.008735	0.2059	b3088	alx	-8.37	0.274530	278 -- 288	25 -- 35	putative membrane-bound redox modulator	_____________277_________289\n_____________\|___________\|\n5'-GGG...CUGUU___________GUCGU...CAC-3'\n______________GUUGCAGGGGC\n______________\|\|\|:\|\|:\|\|\|\|\n______________CAAUGUUCCCG\n3'-UUU...CUACU___________UGUCG...GUG-5'\n_____________\|___________\|\n_____________36__________24\n	282 -- 288	25 -- 31	-18.295 kcal/mol	6.20791 kcal/mol	3.71635 kcal/mol	277 289@LB@ \| \|@LB@5'-GGG...CUGUU GUCGU...CAC-3'@LB@ GUUGCAGGGGC@LB@ \|\|\|:\|\|:\|\|\|\|@LB@ CAAUGUUCCCG@LB@3'-UUU...CUACU UGUCG...GUG-5'@LB@ \| \|@LB@ 36 24@LB@@LB@@LB@Energy -8.37 kcal/mol@LB@Hybridization Energy -18.295 kcal/mol@LB@Unfolding Energy - mRNA 6.20791 kcal/mol@LB@Unfolding Energy - sRNA 3.71635 kcal/mol@LB@@LB@Position - mRNA 278 -- 288@LB@Position - sRNA 25 -- 35@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 25 -- 31@LB@
106	0.005731	0.1855	b0867	amiD	-15.82	0.010089	39 -- 60	64 -- 86	1 6-anhydro-N-acetylmuramyl-L-alanine amidase Zn-dependent; OM lipoprotein	_____________38_______________________61\n_____________\|________________________\|\n5'-GAU...AAAGA_______AA_______________GCCUU...CCC-3'\n______________ACUGCGU__AGCAC__GGGAGAUC\n______________\|\|\|\|\|\|:__\|:\|\|\|__\|\|\|\|:\|\|\|\n______________UGACGCG__UUGUG__CCCUUUAG\n3'-UUU...GCUUA_______G______GU________AACCG...GUG-5'\n_____________\|________________________\|\n_____________87_______________________63\n	54 -- 60	64 -- 70	-27.7093 kcal/mol	4.50209 kcal/mol	7.38435 kcal/mol	38 61@LB@ \| \|@LB@5'-GAU...AAAGA AA GCCUU...CCC-3'@LB@ ACUGCGU AGCAC GGGAGAUC@LB@ \|\|\|\|\|\|: \|:\|\|\| \|\|\|\|:\|\|\|@LB@ UGACGCG UUGUG CCCUUUAG@LB@3'-UUU...GCUUA G GU AACCG...GUG-5'@LB@ \| \|@LB@ 87 63@LB@@LB@@LB@Energy -15.82 kcal/mol@LB@Hybridization Energy -27.7093 kcal/mol@LB@Unfolding Energy - mRNA 4.50209 kcal/mol@LB@Unfolding Energy - sRNA 7.38435 kcal/mol@LB@@LB@Position - mRNA 39 -- 60@LB@Position - sRNA 64 -- 86@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 64 -- 70@LB@
46	0.002359	0.1727	b4139	aspA	-15.43	0.012067	239 -- 273	37 -- 76	aspartate ammonia-lyase	_____________238_______________________________________274\n_____________\|_________________________________________\|\n5'-GAU...UUGGG_____________CCA____A____________C_______UUCAC...ACU-3'\n______________UACCAGGGAAGUU___GCUG_UGCC______UA_UAUGGUG\n______________:\|\|\|\|\|\|\|\|\|:\|:___\|\|\|\|_:\|\|\|______\|\|_\|\|\|\|:\|\|\n______________GUGGUCCCUUUAG___CGAC_GCGG______AU_AUACUAC\n3'-UUU...CGGUU_____________AAC_________CAUUUA__A_______UCAAU...GUG-5'\n_____________\|_________________________________________\|\n_____________77________________________________________36\n	267 -- 273	37 -- 43	-35.8845 kcal/mol	11.095 kcal/mol	9.35931 kcal/mol	238 274@LB@ \| \|@LB@5'-GAU...UUGGG CCA A C UUCAC...ACU-3'@LB@ UACCAGGGAAGUU GCUG UGCC UA UAUGGUG@LB@ :\|\|\|\|\|\|\|\|\|:\|: \|\|\|\| :\|\|\| \|\| \|\|\|\|:\|\|@LB@ GUGGUCCCUUUAG CGAC GCGG AU AUACUAC@LB@3'-UUU...CGGUU AAC CAUUUA A UCAAU...GUG-5'@LB@ \| \|@LB@ 77 36@LB@@LB@@LB@Energy -15.43 kcal/mol@LB@Hybridization Energy -35.8845 kcal/mol@LB@Unfolding Energy - mRNA 11.095 kcal/mol@LB@Unfolding Energy - sRNA 9.35931 kcal/mol@LB@@LB@Position - mRNA 239 -- 273@LB@Position - sRNA 37 -- 76@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 37 -- 43@LB@
43	0.002187	0.1727	b2222	atoA	-7.38	0.400797	260 -- 273	68 -- 82	acetyl-CoA:acetoacetyl-CoA transferase beta subunit	_____________259_____________274\n_____________\|_______________\|\n5'-CGC...GACAU_______________UCGGU...AUU-3'\n______________CGUUAAC_UUAGGGA\n______________\|\|::\|\|\|_::\|\|\|\|\|\n______________GCGGUUG_GGUCCCU\n3'-UUU...AUGAC_______U_______UUAGA...GUG-5'\n_____________\|_______________\|\n_____________83______________67\n	267 -- 273	68 -- 74	-16.5153 kcal/mol	2.15948 kcal/mol	6.98098 kcal/mol	259 274@LB@ \| \|@LB@5'-CGC...GACAU UCGGU...AUU-3'@LB@ CGUUAAC UUAGGGA@LB@ \|\|::\|\|\| ::\|\|\|\|\|@LB@ GCGGUUG GGUCCCU@LB@3'-UUU...AUGAC U UUAGA...GUG-5'@LB@ \| \|@LB@ 83 67@LB@@LB@@LB@Energy -7.38 kcal/mol@LB@Hybridization Energy -16.5153 kcal/mol@LB@Unfolding Energy - mRNA 2.15948 kcal/mol@LB@Unfolding Energy - sRNA 6.98098 kcal/mol@LB@@LB@Position - mRNA 260 -- 273@LB@Position - sRNA 68 -- 82@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 68 -- 74@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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