Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
81	0.007385	0.3087	b0736	ybgC	-11.71	0.061637	220 -- 237	4 -- 21	acyl-CoA thioester hydrolase	_____________219________________238\n_____________\|__________________\|\n5'-UUG...GUUUC______C___U_______ACUAU...AAA-3'\n______________GAUGGC_GGU_CGCGUCU\n______________\|\|\|::\|_::\|_\|\|\|\|\|\|\|\n______________CUAUUG_UUA_GCGCAGA\n3'-UUU...UACUA______U___C_______AAG-5'\n_____________\|__________________\|\n_____________22_________________3\n	231 -- 237	4 -- 10	-19.027 kcal/mol	6.06673 kcal/mol	1.2552 kcal/mol	219 238@LB@ \| \|@LB@5'-UUG...GUUUC C U ACUAU...AAA-3'@LB@ GAUGGC GGU CGCGUCU@LB@ \|\|\|::\| ::\| \|\|\|\|\|\|\|@LB@ CUAUUG UUA GCGCAGA@LB@3'-UUU...UACUA U C AAG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -11.71 kcal/mol@LB@Hybridization Energy -19.027 kcal/mol@LB@Unfolding Energy - mRNA 6.06673 kcal/mol@LB@Unfolding Energy - sRNA 1.2552 kcal/mol@LB@@LB@Position - mRNA 220 -- 237@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 4 -- 10@LB@
82	0.007621	0.3104	b3388	damX	-7.48	0.304490	3 -- 13	8 -- 18	cell division protein that binds to the septal ring	_____________2___________14\n_____________\|___________\|\n_________5'-GG__G________UUAAU...AAC-3'\n______________GA_AGAUGCGC\n______________:\|_\|:\|\|\|\|\|\|\n______________UU_UUUACGCG\n3'-UUU...UACUA__G________CAGAAAG-5'\n_____________\|___________\|\n_____________19__________7\n	7 -- 13	8 -- 14	-13.7317 kcal/mol	5.04786 kcal/mol	1.20363 kcal/mol	2 14@LB@ \| \|@LB@ 5'-GG G UUAAU...AAC-3'@LB@ GA AGAUGCGC@LB@ :\| \|:\|\|\|\|\|\|@LB@ UU UUUACGCG@LB@3'-UUU...UACUA G CAGAAAG-5'@LB@ \| \|@LB@ 19 7@LB@@LB@@LB@Energy -7.48 kcal/mol@LB@Hybridization Energy -13.7317 kcal/mol@LB@Unfolding Energy - mRNA 5.04786 kcal/mol@LB@Unfolding Energy - sRNA 1.20363 kcal/mol@LB@@LB@Position - mRNA 3 -- 13@LB@Position - sRNA 8 -- 18@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 8 -- 14@LB@
83	0.007683	0.3104	b4244	pyrI	-7.62	0.290375	210 -- 222	10 -- 21	aspartate carbamoyltransferase regulatory subunit	_____________209___________223\n_____________\|_____________\|\n5'-UUC...CACAC__________U__AGGUU...UCA-3'\n______________GAUAAUAAAU_GC\n______________\|\|\|\|\|:\|\|\|\|_\|\|\n______________CUAUUGUUUA_CG\n3'-UUU...UACUA_____________CGCAG...AAG-5'\n_____________\|_____________\|\n_____________22____________9\n	213 -- 219	12 -- 18	-11.1174 kcal/mol	2.26673 kcal/mol	1.23076 kcal/mol	209 223@LB@ \| \|@LB@5'-UUC...CACAC U AGGUU...UCA-3'@LB@ GAUAAUAAAU GC@LB@ \|\|\|\|\|:\|\|\|\| \|\|@LB@ CUAUUGUUUA CG@LB@3'-UUU...UACUA CGCAG...AAG-5'@LB@ \| \|@LB@ 22 9@LB@@LB@@LB@Energy -7.62 kcal/mol@LB@Hybridization Energy -11.1174 kcal/mol@LB@Unfolding Energy - mRNA 2.26673 kcal/mol@LB@Unfolding Energy - sRNA 1.23076 kcal/mol@LB@@LB@Position - mRNA 210 -- 222@LB@Position - sRNA 10 -- 21@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 12 -- 18@LB@
84	0.008129	0.3104	b2579	grcA	-9.71	0.135356	279 -- 291	5 -- 18	autonomous glycyl radical cofactor	_____________278____________292\n_____________\|______________\|\n5'-UUG...AAAAA______________GCAUC...UUG-3'\n______________GGCGAA_GCGCGUU\n______________::\|:\|\|_\|\|\|\|\|\|:\n______________UUGUUU_CGCGCAG\n3'-UUU...UACUA______A_______AAAG-5'\n_____________\|______________\|\n_____________19_____________4\n	285 -- 291	5 -- 11	-16.0784 kcal/mol	5.14159 kcal/mol	1.2243 kcal/mol	278 292@LB@ \| \|@LB@5'-UUG...AAAAA GCAUC...UUG-3'@LB@ GGCGAA GCGCGUU@LB@ ::\|:\|\| \|\|\|\|\|\|:@LB@ UUGUUU CGCGCAG@LB@3'-UUU...UACUA A AAAG-5'@LB@ \| \|@LB@ 19 4@LB@@LB@@LB@Energy -9.71 kcal/mol@LB@Hybridization Energy -16.0784 kcal/mol@LB@Unfolding Energy - mRNA 5.14159 kcal/mol@LB@Unfolding Energy - sRNA 1.2243 kcal/mol@LB@@LB@Position - mRNA 279 -- 291@LB@Position - sRNA 5 -- 18@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 5 -- 11@LB@
85	0.008151	0.3104	b0914	msbA	-12.09	0.052799	181 -- 198	1 -- 18	lipid ABC transporter permease/ATPase	_____________180________________199\n_____________\|__________________\|\n5'-AGC...AUUUC_________UG_______GAAUG...CGU-3'\n______________AACAAAUGC__GUUUUUU\n______________\|\|\|\|\|\|\|\|\|__\|\|:\|\|\|:\n______________UUGUUUACG__CAGAAAG\n3'-UUU...UACUA_________CG_______-5'\n_____________\|_________________\|\n_____________19________________1\n	192 -- 198	1 -- 7	-16.7201 kcal/mol	3.39277 kcal/mol	1.24077 kcal/mol	180 199@LB@ \| \|@LB@5'-AGC...AUUUC UG GAAUG...CGU-3'@LB@ AACAAAUGC GUUUUUU@LB@ \|\|\|\|\|\|\|\|\| \|\|:\|\|\|:@LB@ UUGUUUACG CAGAAAG@LB@3'-UUU...UACUA CG -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -12.09 kcal/mol@LB@Hybridization Energy -16.7201 kcal/mol@LB@Unfolding Energy - mRNA 3.39277 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 181 -- 198@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 1 -- 7@LB@
86	0.008729	0.3104	b4213	cpdB	-12.03	0.054140	68 -- 81	8 -- 21	2':3'-cyclic-nucleotide 2'-phosphodiesterase	_____________67_____________82\n_____________\|______________\|\n5'-UGA...CUAUC_U____________CAACU...AUA-3'\n______________G_UAAUGAAUGCGC\n______________\|_\|\|\|::\|\|\|\|\|\|\|\n______________C_AUUGUUUACGCG\n3'-UUU...UACUA_U____________CAGAAAG-5'\n_____________\|______________\|\n_____________22_____________7\n	75 -- 81	8 -- 14	-15.4826 kcal/mol	2.2212 kcal/mol	1.23638 kcal/mol	67 82@LB@ \| \|@LB@5'-UGA...CUAUC U CAACU...AUA-3'@LB@ G UAAUGAAUGCGC@LB@ \| \|\|\|::\|\|\|\|\|\|\|@LB@ C AUUGUUUACGCG@LB@3'-UUU...UACUA U CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -12.03 kcal/mol@LB@Hybridization Energy -15.4826 kcal/mol@LB@Unfolding Energy - mRNA 2.2212 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 68 -- 81@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 8 -- 14@LB@
87	0.008927	0.3104	b0195	tsaA	-8.24	0.234029	220 -- 237	1 -- 18	tRNA-Thr(GGU) m(6)t(6)A37 methyltransferase SAM-dependent	_____________219________________238\n_____________\|__________________\|\n5'-GAA...GUUCG_______AG_____A___GCUCG...ACG-3'\n______________AGCAAAU__GCGUU_UUC\n______________\|:\|\|\|\|\|__\|\|\|\|:_\|\|\|\n______________UUGUUUA__CGCAG_AAG\n3'-UUU...UACUA_______CG_____A___-5'\n_____________\|_________________\|\n_____________19________________1\n	220 -- 226	12 -- 18	-15.6275 kcal/mol	6.14962 kcal/mol	1.24077 kcal/mol	219 238@LB@ \| \|@LB@5'-GAA...GUUCG AG A GCUCG...ACG-3'@LB@ AGCAAAU GCGUU UUC@LB@ \|:\|\|\|\|\| \|\|\|\|: \|\|\|@LB@ UUGUUUA CGCAG AAG@LB@3'-UUU...UACUA CG A -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -8.24 kcal/mol@LB@Hybridization Energy -15.6275 kcal/mol@LB@Unfolding Energy - mRNA 6.14962 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 220 -- 237@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 12 -- 18@LB@
88	0.008928	0.3104	b0405	queA	-8.89	0.184414	201 -- 209	5 -- 13	S-adenosylmethionine:tRNA ribosyltransferase-isomerase	_____________200_______210\n_____________\|_________\|\n5'-GGG...GUGUC_________ACCGA...GGC-3'\n______________AUGCGCGUU\n______________\|\|\|\|\|\|\|\|:\n______________UACGCGCAG\n3'-UUU...UUGUU_________AAAG-5'\n_____________\|_________\|\n_____________14________4\n	203 -- 209	5 -- 11	-14.1161 kcal/mol	4.07268 kcal/mol	1.15134 kcal/mol	200 210@LB@ \| \|@LB@5'-GGG...GUGUC ACCGA...GGC-3'@LB@ AUGCGCGUU@LB@ \|\|\|\|\|\|\|\|:@LB@ UACGCGCAG@LB@3'-UUU...UUGUU AAAG-5'@LB@ \| \|@LB@ 14 4@LB@@LB@@LB@Energy -8.89 kcal/mol@LB@Hybridization Energy -14.1161 kcal/mol@LB@Unfolding Energy - mRNA 4.07268 kcal/mol@LB@Unfolding Energy - sRNA 1.15134 kcal/mol@LB@@LB@Position - mRNA 201 -- 209@LB@Position - sRNA 5 -- 13@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 5 -- 11@LB@
89	0.009028	0.3104	b0529	folD	-8.62	0.203566	239 -- 251	4 -- 17	bifunctional 5 10-methylene-tetrahydrofolate dehydrogenase/ 5 10-methylene-tetrahydrofolate cyclohydrolase	_____________238____________252\n_____________\|______________\|\n5'-CAA...GCGCA______________GAAGU...CAC-3'\n______________GCAGGUGCGC_UCU\n______________:\|\|::\|\|\|\|\|_\|\|\|\n______________UGUUUACGCG_AGA\n3'-UUU...ACUAU__________C___AAG-5'\n_____________\|______________\|\n_____________18_____________3\n	242 -- 248	8 -- 14	-17.587 kcal/mol	7.73476 kcal/mol	1.22888 kcal/mol	238 252@LB@ \| \|@LB@5'-CAA...GCGCA GAAGU...CAC-3'@LB@ GCAGGUGCGC UCU@LB@ :\|\|::\|\|\|\|\| \|\|\|@LB@ UGUUUACGCG AGA@LB@3'-UUU...ACUAU C AAG-5'@LB@ \| \|@LB@ 18 3@LB@@LB@@LB@Energy -8.62 kcal/mol@LB@Hybridization Energy -17.587 kcal/mol@LB@Unfolding Energy - mRNA 7.73476 kcal/mol@LB@Unfolding Energy - sRNA 1.22888 kcal/mol@LB@@LB@Position - mRNA 239 -- 251@LB@Position - sRNA 4 -- 17@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 8 -- 14@LB@
90	0.009145	0.3104	b1079	flgH	-6.81	0.379144	179 -- 204	10 -- 38	flagellar protein of basal-body outer-membrane L ring	_____________178___________________________205\n_____________\|_____________________________\|\n5'-ACU...GUUUA____U___U____A_________C_____AAAAA...GGG-3'\n______________CUGA_UUU___GA_GAUGAUAGC__AUGC\n______________\|\|\|\|_\|\|:___\|\|_\|\|\|\|\|\|\|:\|__\|\|\|\|\n______________GACU_AAG___CU_CUACUAUUG__UACG\n3'-UUU...GUAGA____U___UCC__A_________UU____CGCAG...AAG-5'\n_____________\|_____________________________\|\n_____________39____________________________9\n	193 -- 199	16 -- 22	-21.1251 kcal/mol	4.97135 kcal/mol	9.34299 kcal/mol	178 205@LB@ \| \|@LB@5'-ACU...GUUUA U U A C AAAAA...GGG-3'@LB@ CUGA UUU GA GAUGAUAGC AUGC@LB@ \|\|\|\| \|\|: \|\| \|\|\|\|\|\|\|:\| \|\|\|\|@LB@ GACU AAG CU CUACUAUUG UACG@LB@3'-UUU...GUAGA U UCC A UU CGCAG...AAG-5'@LB@ \| \|@LB@ 39 9@LB@@LB@@LB@Energy -6.81 kcal/mol@LB@Hybridization Energy -21.1251 kcal/mol@LB@Unfolding Energy - mRNA 4.97135 kcal/mol@LB@Unfolding Energy - sRNA 9.34299 kcal/mol@LB@@LB@Position - mRNA 179 -- 204@LB@Position - sRNA 10 -- 38@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 16 -- 22@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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