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
6	9.655e-05	0.04801	b4175	hflC	-9.47	0.148653	186 -- 211	5 -- 32	HflB protease modulator specific for phage lambda cII repressor	_____________185____________________________212\n_____________\|______________________________\|\n5'-UUA...CAGCG_________________________AA___AGUUA...GUU-3'\n______________UCAGGGG_GA__AUAAC_GAUGCGU__GUC\n______________\|\|\|\|\|\|:_\|\|__\|\|\|\|\|_:\|\|\|\|\|:__\|\|\|\n______________AGUCCCU_CU__UAUUG_UUACGCG__CAG\n3'-UUU...ACUUA_______A__AC_____U____________AAAG-5'\n_____________\|______________________________\|\n_____________33_____________________________4\n	200 -- 206	8 -- 14	-26.2754 kcal/mol	8.97237 kcal/mol	7.8362 kcal/mol	185 212@LB@ \| \|@LB@5'-UUA...CAGCG AA AGUUA...GUU-3'@LB@ UCAGGGG GA AUAAC GAUGCGU GUC@LB@ \|\|\|\|\|\|: \|\| \|\|\|\|\| :\|\|\|\|\|: \|\|\|@LB@ AGUCCCU CU UAUUG UUACGCG CAG@LB@3'-UUU...ACUUA A AC U AAAG-5'@LB@ \| \|@LB@ 33 4@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -26.2754 kcal/mol@LB@Unfolding Energy - mRNA 8.97237 kcal/mol@LB@Unfolding Energy - sRNA 7.8362 kcal/mol@LB@@LB@Position - mRNA 186 -- 211@LB@Position - sRNA 5 -- 32@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 8 -- 14@LB@
94	0.009498	0.3104	b4198	ulaF	-10.74	0.090813	136 -- 150	6 -- 20	L-ribulose 5-phosphate 4-epimerase	_____________135_____________151\n_____________\|_______________\|\n5'-GUC...CAGAA________A______GAUUG...GCG-3'\n______________GUGGCGAA_GCGCGU\n______________:\|::\|:\|\|_\|\|\|\|\|\|\n______________UAUUGUUU_CGCGCA\n3'-UUU...ACUAC________A______GAAAG-5'\n_____________\|_______________\|\n_____________21______________5\n	137 -- 143	13 -- 19	-18.1084 kcal/mol	6.12954 kcal/mol	1.24244 kcal/mol	135 151@LB@ \| \|@LB@5'-GUC...CAGAA A GAUUG...GCG-3'@LB@ GUGGCGAA GCGCGU@LB@ :\|::\|:\|\| \|\|\|\|\|\|@LB@ UAUUGUUU CGCGCA@LB@3'-UUU...ACUAC A GAAAG-5'@LB@ \| \|@LB@ 21 5@LB@@LB@@LB@Energy -10.74 kcal/mol@LB@Hybridization Energy -18.1084 kcal/mol@LB@Unfolding Energy - mRNA 6.12954 kcal/mol@LB@Unfolding Energy - sRNA 1.24244 kcal/mol@LB@@LB@Position - mRNA 136 -- 150@LB@Position - sRNA 6 -- 20@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 13 -- 19@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@
76	0.007084	0.3087	b4214	cysQ	-5.34	0.578728	11 -- 17	26 -- 32	3'(2') 5'-bisphosphate nucleotidase	_____________10______18\n_____________\|_______\|\n5'-AAC...AAUCA_______CAUCC...ACA-3'\n______________UCAGGGA\n______________\|\|\|\|\|\|\|\n______________AGUCCCU\n3'-UUU...ACUUA_______ACUAC...AAG-5'\n_____________\|_______\|\n_____________33______25\n	11 -- 17	26 -- 32	-11.6237 kcal/mol	0.931861 kcal/mol	5.35475 kcal/mol	10 18@LB@ \| \|@LB@5'-AAC...AAUCA CAUCC...ACA-3'@LB@ UCAGGGA@LB@ \|\|\|\|\|\|\|@LB@ AGUCCCU@LB@3'-UUU...ACUUA ACUAC...AAG-5'@LB@ \| \|@LB@ 33 25@LB@@LB@@LB@Energy -5.34 kcal/mol@LB@Hybridization Energy -11.6237 kcal/mol@LB@Unfolding Energy - mRNA 0.931861 kcal/mol@LB@Unfolding Energy - sRNA 5.35475 kcal/mol@LB@@LB@Position - mRNA 11 -- 17@LB@Position - sRNA 26 -- 32@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 26 -- 32@LB@
167	0.01599	0.3104	b4220	tamA	-9.57	0.142740	193 -- 207	4 -- 21	translocation and assembly module for autotransporter export outer membrane subunit	_____________192________________208\n_____________\|__________________\|\n5'-CGC...UUCAG__GA______________AUAUC...GAC-3'\n______________GA____AAAUGUGCG_CU\n______________\|\|____\|\|\|\|\|:\|\|\|_\|\|\n______________CU____UUUACGCGC_GA\n3'-UUU...UACUA__AUUG_________A__AAG-5'\n_____________\|__________________\|\n_____________22_________________3\n	199 -- 205	7 -- 13	-13.0971 kcal/mol	2.26836 kcal/mol	1.2552 kcal/mol	192 208@LB@ \| \|@LB@5'-CGC...UUCAG GA AUAUC...GAC-3'@LB@ GA AAAUGUGCG CU@LB@ \|\| \|\|\|\|\|:\|\|\| \|\|@LB@ CU UUUACGCGC GA@LB@3'-UUU...UACUA AUUG A AAG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -9.57 kcal/mol@LB@Hybridization Energy -13.0971 kcal/mol@LB@Unfolding Energy - mRNA 2.26836 kcal/mol@LB@Unfolding Energy - sRNA 1.2552 kcal/mol@LB@@LB@Position - mRNA 193 -- 207@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 7 -- 13@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@
158	0.01496	0.3104	b4278	insG	-10.00	0.121023	32 -- 48	3 -- 20	IS4 transposase	_____________31_________________49\n_____________\|__________________\|\n5'-GUU...UCCAC________A_________GUUAC...CUC-3'\n______________AUAACAAA__CGCGUUUU\n______________\|\|\|\|\|\|\|\|__\|\|\|\|\|:\|\|\n______________UAUUGUUU__GCGCAGAA\n3'-UUU...ACUAC________AC________AG-5'\n_____________\|__________________\|\n_____________21_________________2\n	42 -- 48	3 -- 9	-15.3953 kcal/mol	4.13684 kcal/mol	1.25547 kcal/mol	31 49@LB@ \| \|@LB@5'-GUU...UCCAC A GUUAC...CUC-3'@LB@ AUAACAAA CGCGUUUU@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|:\|\|@LB@ UAUUGUUU GCGCAGAA@LB@3'-UUU...ACUAC AC AG-5'@LB@ \| \|@LB@ 21 2@LB@@LB@@LB@Energy -10.00 kcal/mol@LB@Hybridization Energy -15.3953 kcal/mol@LB@Unfolding Energy - mRNA 4.13684 kcal/mol@LB@Unfolding Energy - sRNA 1.25547 kcal/mol@LB@@LB@Position - mRNA 32 -- 48@LB@Position - sRNA 3 -- 20@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 3 -- 9@LB@
75	0.006972	0.3087	b4348	hsdS	-13.63	0.027959	190 -- 211	7 -- 29	specificity determinant for hsdM and hsdR	_____________189_____________________212\n_____________\|_______________________\|\n5'-CUG...UUGGU_______A_____________G_GAAAU...UAA-3'\n______________GGGGUGA_GG_AAUGAGUGCG_G\n______________\|\|\|:\|\|\|_\|:_\|\|::\|:\|\|\|\|_\|\n______________CCCUACU_CU_UUGUUUACGC_C\n3'-UUU...UAAGU_______A__A__________G_AGAAAG-5'\n_____________\|_______________________\|\n_____________30______________________6\n	203 -- 209	9 -- 15	-24.9713 kcal/mol	3.9222 kcal/mol	7.41901 kcal/mol	189 212@LB@ \| \|@LB@5'-CUG...UUGGU A G GAAAU...UAA-3'@LB@ GGGGUGA GG AAUGAGUGCG G@LB@ \|\|\|:\|\|\| \|: \|\|::\|:\|\|\|\| \|@LB@ CCCUACU CU UUGUUUACGC C@LB@3'-UUU...UAAGU A A G AGAAAG-5'@LB@ \| \|@LB@ 30 6@LB@@LB@@LB@Energy -13.63 kcal/mol@LB@Hybridization Energy -24.9713 kcal/mol@LB@Unfolding Energy - mRNA 3.9222 kcal/mol@LB@Unfolding Energy - sRNA 7.41901 kcal/mol@LB@@LB@Position - mRNA 190 -- 211@LB@Position - sRNA 7 -- 29@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 9 -- 15@LB@
126	0.01241	0.3104	b4379	yjjW	-11.82	0.058804	207 -- 217	8 -- 18	putative pyruvate formate lyase activating enzyme	_____________206_________218\n_____________\|___________\|\n5'-CGG...UGAAC___________UUUAG...UGC-3'\n______________AGCAGAUGCGC\n______________\|:\|\|:\|\|\|\|\|\|\n______________UUGUUUACGCG\n3'-UUU...UACUA___________CAGAAAG-5'\n_____________\|___________\|\n_____________19__________7\n	211 -- 217	8 -- 14	-16.9543 kcal/mol	3.92931 kcal/mol	1.20363 kcal/mol	206 218@LB@ \| \|@LB@5'-CGG...UGAAC UUUAG...UGC-3'@LB@ AGCAGAUGCGC@LB@ \|:\|\|:\|\|\|\|\|\|@LB@ UUGUUUACGCG@LB@3'-UUU...UACUA CAGAAAG-5'@LB@ \| \|@LB@ 19 7@LB@@LB@@LB@Energy -11.82 kcal/mol@LB@Hybridization Energy -16.9543 kcal/mol@LB@Unfolding Energy - mRNA 3.92931 kcal/mol@LB@Unfolding Energy - sRNA 1.20363 kcal/mol@LB@@LB@Position - mRNA 207 -- 217@LB@Position - sRNA 8 -- 18@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 8 -- 14@LB@
165	0.01591	0.3104	b4393	trpR	-12.13	0.051953	230 -- 246	5 -- 21	transcriptional repressor tryptophan-binding	_____________229_______________247\n_____________\|_________________\|\n5'-GAG...GCAGC_________ACA_____ACCAG...AUC-3'\n______________GAUGGCAGA___GCGUC\n______________\|\|\|::\|\|:\|___\|\|\|\|\|\n______________CUAUUGUUU___CGCAG\n3'-UUU...UACUA_________ACG_____AAAG-5'\n_____________\|_________________\|\n_____________22________________4\n	232 -- 238	13 -- 19	-18.7652 kcal/mol	5.38929 kcal/mol	1.24955 kcal/mol	229 247@LB@ \| \|@LB@5'-GAG...GCAGC ACA ACCAG...AUC-3'@LB@ GAUGGCAGA GCGUC@LB@ \|\|\|::\|\|:\| \|\|\|\|\|@LB@ CUAUUGUUU CGCAG@LB@3'-UUU...UACUA ACG AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -12.13 kcal/mol@LB@Hybridization Energy -18.7652 kcal/mol@LB@Unfolding Energy - mRNA 5.38929 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 230 -- 246@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 13 -- 19@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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