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	Additional homologs
141	0.01345	0.3104	b3311	rpsQ	-8.13	0.242987	140 -- 150	8 -- 18	30S ribosomal subunit protein S17		_____________139_________151\n_____________\|___________\|\n5'-GGU...GUUGA___________CGCGA...UCU-3'\n______________AGCAAGUGCGU\n______________\|:\|\|\|:\|\|\|\|:\n______________UUGUUUACGCG\n3'-UUU...UACUA___________CAGAAAG-5'\n_____________\|___________\|\n_____________19__________7\n	144 -- 150	8 -- 14	-14.6725 kcal/mol	5.33741 kcal/mol	1.20363 kcal/mol	139 151@LB@ \| \|@LB@5'-GGU...GUUGA CGCGA...UCU-3'@LB@ AGCAAGUGCGU@LB@ \|:\|\|\|:\|\|\|\|:@LB@ UUGUUUACGCG@LB@3'-UUU...UACUA CAGAAAG-5'@LB@ \| \|@LB@ 19 7@LB@@LB@@LB@Energy -8.13 kcal/mol@LB@Hybridization Energy -14.6725 kcal/mol@LB@Unfolding Energy - mRNA 5.33741 kcal/mol@LB@Unfolding Energy - sRNA 1.20363 kcal/mol@LB@@LB@Position - mRNA 140 -- 150@LB@Position - sRNA 8 -- 18@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 8 -- 14@LB@
142	0.01346	0.3104	b0729	sucD	-11.71	0.061414	39 -- 57	3 -- 21	succinyl-CoA synthetase NAD(P)-binding alpha subunit		_____________38__________________58\n_____________\|___________________\|\n5'-GUU...GGCGC_________A___G__G__AACGU...CUA-3'\n______________GGUAGCAGA_GUG_GU_UU\n______________\|:\|\|:\|\|:\|_\|:\|_\|\|_\|\|\n______________CUAUUGUUU_CGC_CA_AA\n3'-UUU...UACUA_________A___G__G__AG-5'\n_____________\|___________________\|\n_____________22__________________2\n	41 -- 47	13 -- 19	-17.4316 kcal/mol	4.46052 kcal/mol	1.257 kcal/mol	38 58@LB@ \| \|@LB@5'-GUU...GGCGC A G G AACGU...CUA-3'@LB@ GGUAGCAGA GUG GU UU@LB@ \|:\|\|:\|\|:\| \|:\| \|\| \|\|@LB@ CUAUUGUUU CGC CA AA@LB@3'-UUU...UACUA A G G AG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -11.71 kcal/mol@LB@Hybridization Energy -17.4316 kcal/mol@LB@Unfolding Energy - mRNA 4.46052 kcal/mol@LB@Unfolding Energy - sRNA 1.257 kcal/mol@LB@@LB@Position - mRNA 39 -- 57@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 13 -- 19@LB@
143	0.01362	0.3104	b3284	smg	-7.50	0.302399	64 -- 82	5 -- 21	DUF494 family putative periplasmic protein		_____________63__________________83\n_____________\|___________________\|\n5'-UUC...GAUGA_______CC__U__A____GUCGC...CAG-3'\n______________GGUAACA__UG_UG_CGUC\n______________\|:\|\|\|\|\|__\|\|_:\|_\|\|\|\|\n______________CUAUUGU__AC_GC_GCAG\n3'-UUU...UACUA_______UU__________AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	64 -- 70	15 -- 21	-13.2614 kcal/mol	4.51132 kcal/mol	1.24955 kcal/mol	63 83@LB@ \| \|@LB@5'-UUC...GAUGA CC U A GUCGC...CAG-3'@LB@ GGUAACA UG UG CGUC@LB@ \|:\|\|\|\|\| \|\| :\| \|\|\|\|@LB@ CUAUUGU AC GC GCAG@LB@3'-UUU...UACUA UU AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -7.50 kcal/mol@LB@Hybridization Energy -13.2614 kcal/mol@LB@Unfolding Energy - mRNA 4.51132 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 64 -- 82@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 15 -- 21@LB@
144	0.01383	0.3104	b1135	rluE	-11.03	0.080673	174 -- 189	5 -- 20	23S rRNA pseudouridine(2457) synthase		_____________173______________190\n_____________\|________________\|\n5'-UGU...CCGUC____A___________AUUAG...AAC-3'\n______________AUGA_AGAUGCGCGUU\n______________\|\|:\|_\|:\|\|\|\|\|\|\|\|:\n______________UAUU_UUUACGCGCAG\n3'-UUU...ACUAC____G___________AAAG-5'\n_____________\|________________\|\n_____________21_______________4\n	183 -- 189	5 -- 11	-17.9797 kcal/mol	5.69694 kcal/mol	1.24804 kcal/mol	173 190@LB@ \| \|@LB@5'-UGU...CCGUC A AUUAG...AAC-3'@LB@ AUGA AGAUGCGCGUU@LB@ \|\|:\| \|:\|\|\|\|\|\|\|\|:@LB@ UAUU UUUACGCGCAG@LB@3'-UUU...ACUAC G AAAG-5'@LB@ \| \|@LB@ 21 4@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -17.9797 kcal/mol@LB@Unfolding Energy - mRNA 5.69694 kcal/mol@LB@Unfolding Energy - sRNA 1.24804 kcal/mol@LB@@LB@Position - mRNA 174 -- 189@LB@Position - sRNA 5 -- 20@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 5 -- 11@LB@
145	0.01404	0.3104	b0721	sdhC	-10.79	0.088833	202 -- 215	9 -- 22	succinate dehydrogenase membrane subunit binds cytochrome b556		_____________201____________216\n_____________\|______________\|\n5'-UCC...AUUCA______G_______AAAAA...CCG-3'\n______________UGAUAA_AAAUGUG\n______________\|\|\|\|\|\|_\|\|\|\|\|:\|\n______________ACUAUU_UUUACGC\n3'-UUU...CUACU______G_______GCAGAAAG-5'\n_____________\|______________\|\n_____________23_____________8\n	209 -- 215	9 -- 15	-14.1232 kcal/mol	2.09271 kcal/mol	1.23827 kcal/mol	201 216@LB@ \| \|@LB@5'-UCC...AUUCA G AAAAA...CCG-3'@LB@ UGAUAA AAAUGUG@LB@ \|\|\|\|\|\| \|\|\|\|\|:\|@LB@ ACUAUU UUUACGC@LB@3'-UUU...CUACU G GCAGAAAG-5'@LB@ \| \|@LB@ 23 8@LB@@LB@@LB@Energy -10.79 kcal/mol@LB@Hybridization Energy -14.1232 kcal/mol@LB@Unfolding Energy - mRNA 2.09271 kcal/mol@LB@Unfolding Energy - sRNA 1.23827 kcal/mol@LB@@LB@Position - mRNA 202 -- 215@LB@Position - sRNA 9 -- 22@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 9 -- 15@LB@
146	0.01406	0.3104	b3831	udp	-7.35	0.318150	153 -- 161	1 -- 9	uridine phosphorylase		_____________152_______162\n_____________\|_________\|\n5'-AUC...GUAAA_________UGCUU...AGA-3'\n______________GUGUCUUUU\n______________\|:\|\|\|\|\|\|:\n______________CGCAGAAAG\n3'-UUU...UUACG_________-5'\n_____________\|________\|\n_____________10_______1\n	155 -- 161	1 -- 7	-10.4616 kcal/mol	1.99462 kcal/mol	1.11751 kcal/mol	152 162@LB@ \| \|@LB@5'-AUC...GUAAA UGCUU...AGA-3'@LB@ GUGUCUUUU@LB@ \|:\|\|\|\|\|\|:@LB@ CGCAGAAAG@LB@3'-UUU...UUACG -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.35 kcal/mol@LB@Hybridization Energy -10.4616 kcal/mol@LB@Unfolding Energy - mRNA 1.99462 kcal/mol@LB@Unfolding Energy - sRNA 1.11751 kcal/mol@LB@@LB@Position - mRNA 153 -- 161@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 155 -- 161@LB@Position Seed - sRNA 1 -- 7@LB@
147	0.01411	0.3104	b0441	ppiD	-10.51	0.099467	81 -- 98	3 -- 21	periplasmic folding chaperone has an inactive PPIase domain		_____________80__________________99\n_____________\|___________________\|\n5'-GUA...UAUUC______UUUC_________GUGGG...ACC-3'\n______________GGUGAC_____UGCGUCUU\n______________\|:\|:\|\|_____:\|\|\|\|\|\|\|\n______________CUAUUG_____GCGCAGAA\n3'-UUU...UACUA______UUUAC________AG-5'\n_____________\|___________________\|\n_____________22__________________2\n	92 -- 98	3 -- 9	-17.0331 kcal/mol	5.27038 kcal/mol	1.257 kcal/mol	80 99@LB@ \| \|@LB@5'-GUA...UAUUC UUUC GUGGG...ACC-3'@LB@ GGUGAC UGCGUCUU@LB@ \|:\|:\|\| :\|\|\|\|\|\|\|@LB@ CUAUUG GCGCAGAA@LB@3'-UUU...UACUA UUUAC AG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -17.0331 kcal/mol@LB@Unfolding Energy - mRNA 5.27038 kcal/mol@LB@Unfolding Energy - sRNA 1.257 kcal/mol@LB@@LB@Position - mRNA 81 -- 98@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 3 -- 9@LB@
148	0.01421	0.3104	b2379	alaC	-8.54	0.209762	290 -- 297	5 -- 12	glutamate-pyruvate aminotransferase; glutamic-pyruvic transaminase (GPT); alanine transaminase		_____________289______298\n_____________\|________\|\n5'-UGU...AUGGC________GGC-3'\n______________UGCGCGUC\n______________\|\|\|\|\|\|\|\|\n______________ACGCGCAG\n3'-UUU...UGUUU________AAAG-5'\n_____________\|________\|\n_____________13_______4\n	291 -- 297	5 -- 11	-14.909 kcal/mol	5.25295 kcal/mol	1.11508 kcal/mol	289 298@LB@ \| \|@LB@5'-UGU...AUGGC GGC-3'@LB@ UGCGCGUC@LB@ \|\|\|\|\|\|\|\|@LB@ ACGCGCAG@LB@3'-UUU...UGUUU AAAG-5'@LB@ \| \|@LB@ 13 4@LB@@LB@@LB@Energy -8.54 kcal/mol@LB@Hybridization Energy -14.909 kcal/mol@LB@Unfolding Energy - mRNA 5.25295 kcal/mol@LB@Unfolding Energy - sRNA 1.11508 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 5 -- 12@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 5 -- 11@LB@
149	0.01422	0.3104	b0415	ribE	-7.20	0.333957	258 -- 265	4 -- 11	riboflavin synthase beta chain		_____________257______266\n_____________\|________\|\n5'-CGG...CCAUC________CAACA...GUG-3'\n______________GCGCGUUU\n______________\|\|\|\|\|\|:\|\n______________CGCGCAGA\n3'-UUU...GUUUA________AAG-5'\n_____________\|________\|\n_____________12_______3\n	259 -- 265	4 -- 10	-13.1965 kcal/mol	4.83677 kcal/mol	1.15639 kcal/mol	257 266@LB@ \| \|@LB@5'-CGG...CCAUC CAACA...GUG-3'@LB@ GCGCGUUU@LB@ \|\|\|\|\|\|:\|@LB@ CGCGCAGA@LB@3'-UUU...GUUUA AAG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -7.20 kcal/mol@LB@Hybridization Energy -13.1965 kcal/mol@LB@Unfolding Energy - mRNA 4.83677 kcal/mol@LB@Unfolding Energy - sRNA 1.15639 kcal/mol@LB@@LB@Position - mRNA 258 -- 265@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 4 -- 10@LB@
150	0.01436	0.3104	b3951	pflD	-11.87	0.057659	67 -- 75	5 -- 13	putative glycine radical domain-containing pyruvate formate-lyase	b0823	_____________66________76\n_____________\|_________\|\n5'-GAU...CCAUC_________AACAU...AAA-3'\n______________GUGCGCGUC\n______________:\|\|\|\|\|\|\|\|\n______________UACGCGCAG\n3'-UUU...UUGUU_________AAAG-5'\n_____________\|_________\|\n_____________14________4\n	69 -- 75	5 -- 11	-16.8274 kcal/mol	3.80607 kcal/mol	1.15134 kcal/mol	66 76@LB@ \| \|@LB@5'-GAU...CCAUC AACAU...AAA-3'@LB@ GUGCGCGUC@LB@ :\|\|\|\|\|\|\|\|@LB@ UACGCGCAG@LB@3'-UUU...UUGUU AAAG-5'@LB@ \| \|@LB@ 14 4@LB@@LB@@LB@Energy -11.87 kcal/mol@LB@Hybridization Energy -16.8274 kcal/mol@LB@Unfolding Energy - mRNA 3.80607 kcal/mol@LB@Unfolding Energy - sRNA 1.15134 kcal/mol@LB@@LB@Position - mRNA 67 -- 75@LB@Position - sRNA 5 -- 13@LB@Position Seed - mRNA 69 -- 75@LB@Position Seed - sRNA 5 -- 11@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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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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