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
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@
25	0.001519	0.1943	b2817	amiC	-17.97	0.004427	110 -- 131	1 -- 21	N-acetylmuramoyl-L-alanine amidase	_____________109____________________132\n_____________\|______________________\|\n5'-AGU...UAUUA__________UA__________GCUAA...UCA-3'\n______________GAUGACAGAU__UGCGUCUUUC\n______________\|\|\|:\|\|\|:\|\|__:\|\|\|\|\|\|\|\|\|\n______________CUAUUGUUUA__GCGCAGAAAG\n3'-UUU...UACUA__________C___________-5'\n_____________\|_____________________\|\n_____________22____________________1\n	125 -- 131	1 -- 7	-25.6931 kcal/mol	6.46841 kcal/mol	1.25763 kcal/mol	109 132@LB@ \| \|@LB@5'-AGU...UAUUA UA GCUAA...UCA-3'@LB@ GAUGACAGAU UGCGUCUUUC@LB@ \|\|\|:\|\|\|:\|\| :\|\|\|\|\|\|\|\|\|@LB@ CUAUUGUUUA GCGCAGAAAG@LB@3'-UUU...UACUA C -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -17.97 kcal/mol@LB@Hybridization Energy -25.6931 kcal/mol@LB@Unfolding Energy - mRNA 6.46841 kcal/mol@LB@Unfolding Energy - sRNA 1.25763 kcal/mol@LB@@LB@Position - mRNA 110 -- 131@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 125 -- 131@LB@Position Seed - sRNA 1 -- 7@LB@
79	0.007292	0.3087	b0063	araB	-12.45	0.045578	14 -- 28	6 -- 20	L-ribulokinase	_____________13______________29\n_____________\|_______________\|\n5'-CGG...AAGCC________AA_____AACAA...GGU-3'\n______________AUGACAAA__CGCGU\n______________\|\|:\|\|\|\|\|__\|\|\|\|\|\n______________UAUUGUUU__GCGCA\n3'-UUU...ACUAC________AC_____GAAAG-5'\n_____________\|_______________\|\n_____________21______________5\n	15 -- 21	13 -- 19	-14.5023 kcal/mol	0.813134 kcal/mol	1.24244 kcal/mol	13 29@LB@ \| \|@LB@5'-CGG...AAGCC AA AACAA...GGU-3'@LB@ AUGACAAA CGCGU@LB@ \|\|:\|\|\|\|\| \|\|\|\|\|@LB@ UAUUGUUU GCGCA@LB@3'-UUU...ACUAC AC GAAAG-5'@LB@ \| \|@LB@ 21 5@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -14.5023 kcal/mol@LB@Unfolding Energy - mRNA 0.813134 kcal/mol@LB@Unfolding Energy - sRNA 1.24244 kcal/mol@LB@@LB@Position - mRNA 14 -- 28@LB@Position - sRNA 6 -- 20@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 13 -- 19@LB@
65	0.005951	0.3087	b0064	araC	-16.15	0.009664	167 -- 213	8 -- 48	ara regulon transcriptional activator; autorepressor	_____________166_____________________________________________214\n_____________\|_______________________________________________\|\n5'-GGA...CAAUU______U_________GGU____GU____AAAGUA____U__A____AAAAU...AUU-3'\n______________GGUUUC_UCUCUGAAU___GGGA__AUGA______UGGC_GA_GCGC\n______________::\|\|\|\|_\|\|\|\|\|\|\|\|\|___\|\|\|\|__\|\|\|\|______\|::\|_:\|_\|\|\|\|\n______________UUAAAG_AGAGACUUA___CCCU__UACU______AUUG_UU_CGCG\n3'-UUU...CGGUU______U_________AGU____AC______________U__A____CAGAAAG-5'\n_____________\|_______________________________________________\|\n_____________49______________________________________________7\n	174 -- 180	35 -- 41	-36.5778 kcal/mol	10.9694 kcal/mol	9.45905 kcal/mol	166 214@LB@ \| \|@LB@5'-GGA...CAAUU U GGU GU AAAGUA U A AAAAU...AUU-3'@LB@ GGUUUC UCUCUGAAU GGGA AUGA UGGC GA GCGC@LB@ ::\|\|\|\| \|\|\|\|\|\|\|\|\| \|\|\|\| \|\|\|\| \|::\| :\| \|\|\|\|@LB@ UUAAAG AGAGACUUA CCCU UACU AUUG UU CGCG@LB@3'-UUU...CGGUU U AGU AC U A CAGAAAG-5'@LB@ \| \|@LB@ 49 7@LB@@LB@@LB@Energy -16.15 kcal/mol@LB@Hybridization Energy -36.5778 kcal/mol@LB@Unfolding Energy - mRNA 10.9694 kcal/mol@LB@Unfolding Energy - sRNA 9.45905 kcal/mol@LB@@LB@Position - mRNA 167 -- 213@LB@Position - sRNA 8 -- 48@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 35 -- 41@LB@
64	0.005939	0.3087	b3237	argR	-9.39	0.153279	85 -- 104	1 -- 19	l-arginine-responsive arginine metabolism regulon transcriptional regulator	_____________84____________________105\n_____________\|_____________________\|\n5'-ACA...AAAUU_______AUCC__________AUAAC...UGC-3'\n______________UGAUAAA____CGC_UCUUUC\n______________\|:\|:\|\|\|____\|\|\|_\|\|\|\|\|\|\n______________AUUGUUU____GCG_AGAAAG\n3'-UUU...CUACU_______AC_____C______-5'\n_____________\|____________________\|\n_____________20___________________1\n	85 -- 91	13 -- 19	-12.1021 kcal/mol	1.46458 kcal/mol	1.25156 kcal/mol	84 105@LB@ \| \|@LB@5'-ACA...AAAUU AUCC AUAAC...UGC-3'@LB@ UGAUAAA CGC UCUUUC@LB@ \|:\|:\|\|\| \|\|\| \|\|\|\|\|\|@LB@ AUUGUUU GCG AGAAAG@LB@3'-UUU...CUACU AC C -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -9.39 kcal/mol@LB@Hybridization Energy -12.1021 kcal/mol@LB@Unfolding Energy - mRNA 1.46458 kcal/mol@LB@Unfolding Energy - sRNA 1.25156 kcal/mol@LB@@LB@Position - mRNA 85 -- 104@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 13 -- 19@LB@
35	0.002165	0.2094	b2714	ascG	-14.61	0.018547	188 -- 213	10 -- 30	asc operon transcriptional repressor; prpBC operon repressor	_____________187________________________214\n_____________\|__________________________\|\n5'-AAA...UGUAA________AAA_________CG____UGGAA...AAG-3'\n______________AGGGAUGA___UGAUGACGA__AUGC\n______________\|\|\|\|\|\|\|\|___\|\|\|\|:\|\|:\|__\|\|\|\|\n______________UCCCUACU___ACUAUUGUU__UACG\n3'-UUU...UUAAG__________________________CGCAG...AAG-5'\n_____________\|__________________________\|\n_____________31_________________________9\n	201 -- 207	14 -- 20	-25.4703 kcal/mol	3.44882 kcal/mol	7.41066 kcal/mol	187 214@LB@ \| \|@LB@5'-AAA...UGUAA AAA CG UGGAA...AAG-3'@LB@ AGGGAUGA UGAUGACGA AUGC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|:\|\|:\| \|\|\|\|@LB@ UCCCUACU ACUAUUGUU UACG@LB@3'-UUU...UUAAG CGCAG...AAG-5'@LB@ \| \|@LB@ 31 9@LB@@LB@@LB@Energy -14.61 kcal/mol@LB@Hybridization Energy -25.4703 kcal/mol@LB@Unfolding Energy - mRNA 3.44882 kcal/mol@LB@Unfolding Energy - sRNA 7.41066 kcal/mol@LB@@LB@Position - mRNA 188 -- 213@LB@Position - sRNA 10 -- 30@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 14 -- 20@LB@
189	0.01853	0.3104	b3743	asnC	-7.74	0.278830	255 -- 266	5 -- 18	transcriptional activator of asnA; autorepressor	_____________254____________267\n_____________\|______________\|\n5'-AUU...UAAUG______________ACCGC...GCG-3'\n______________GGC_AAUGCGCG_C\n______________::\|_\|\|\|\|\|\|\|\|_\|\n______________UUG_UUACGCGC_G\n3'-UUU...UACUA___U________A_AAAG-5'\n_____________\|______________\|\n_____________19_____________4\n	259 -- 265	7 -- 13	-14.4034 kcal/mol	5.44099 kcal/mol	1.2243 kcal/mol	254 267@LB@ \| \|@LB@5'-AUU...UAAUG ACCGC...GCG-3'@LB@ GGC AAUGCGCG C@LB@ ::\| \|\|\|\|\|\|\|\| \|@LB@ UUG UUACGCGC G@LB@3'-UUU...UACUA U A AAAG-5'@LB@ \| \|@LB@ 19 4@LB@@LB@@LB@Energy -7.74 kcal/mol@LB@Hybridization Energy -14.4034 kcal/mol@LB@Unfolding Energy - mRNA 5.44099 kcal/mol@LB@Unfolding Energy - sRNA 1.2243 kcal/mol@LB@@LB@Position - mRNA 255 -- 266@LB@Position - sRNA 5 -- 18@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 7 -- 13@LB@
168	0.01645	0.3104	b3720	bglH	-8.64	0.202347	15 -- 28	9 -- 22	carbohydrate-specific outer membrane porin cryptic	_____________14_____________29\n_____________\|______________\|\n5'-AUU...GAUCG_________UG___AAGGA...GCC-3'\n______________UGAUGAUAA__GCG\n______________\|\|\|\|:\|:\|\|__\|\|\|\n______________ACUAUUGUU__CGC\n3'-UUU...CUACU_________UA___GCAGAAAG-5'\n_____________\|______________\|\n_____________23_____________8\n	17 -- 23	14 -- 20	-13.7208 kcal/mol	3.8428 kcal/mol	1.23827 kcal/mol	14 29@LB@ \| \|@LB@5'-AUU...GAUCG UG AAGGA...GCC-3'@LB@ UGAUGAUAA GCG@LB@ \|\|\|\|:\|:\|\| \|\|\|@LB@ ACUAUUGUU CGC@LB@3'-UUU...CUACU UA GCAGAAAG-5'@LB@ \| \|@LB@ 23 8@LB@@LB@@LB@Energy -8.64 kcal/mol@LB@Hybridization Energy -13.7208 kcal/mol@LB@Unfolding Energy - mRNA 3.8428 kcal/mol@LB@Unfolding Energy - sRNA 1.23827 kcal/mol@LB@@LB@Position - mRNA 15 -- 28@LB@Position - sRNA 9 -- 22@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 14 -- 20@LB@
131	0.01264	0.3104	b3412	bioH	-11.05	0.080071	12 -- 32	7 -- 31	pimeloyl-ACP methyl ester carboxylesterase	_____________11________________________33\n_____________\|_________________________\|\n5'-GGC...GACCG______A__________________GCGGG...ACG-3'\n______________CAGGGA_GAUGG____GAGUGUGUG\n______________\|\|\|\|\|\|_\|\|\|\|:____:\|:\|\|:\|:\|\n______________GUCCCU_CUACU____UUUACGCGC\n3'-UUU...CUUAA______A_____AUUG_________AGAAAG-5'\n_____________\|_________________________\|\n_____________32________________________6\n	26 -- 32	7 -- 13	-25.3011 kcal/mol	6.49654 kcal/mol	7.75103 kcal/mol	11 33@LB@ \| \|@LB@5'-GGC...GACCG A GCGGG...ACG-3'@LB@ CAGGGA GAUGG GAGUGUGUG@LB@ \|\|\|\|\|\| \|\|\|\|: :\|:\|\|:\|:\|@LB@ GUCCCU CUACU UUUACGCGC@LB@3'-UUU...CUUAA A AUUG AGAAAG-5'@LB@ \| \|@LB@ 32 6@LB@@LB@@LB@Energy -11.05 kcal/mol@LB@Hybridization Energy -25.3011 kcal/mol@LB@Unfolding Energy - mRNA 6.49654 kcal/mol@LB@Unfolding Energy - sRNA 7.75103 kcal/mol@LB@@LB@Position - mRNA 12 -- 32@LB@Position - sRNA 7 -- 31@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 7 -- 13@LB@
176	0.01748	0.3104	b0435	bolA	-9.78	0.131850	202 -- 220	4 -- 22	stationary-phase morphogene transcriptional repressor for mreB; also regulator for dacA dacC and ampC	_____________201_________________221\n_____________\|___________________\|\n5'-UGA...UUUCA________C___A___GA_AGAAG...CCG-3'\n______________UGAUGAUA_GUG_GCG__U\n______________\|\|\|\|:\|:\|_:\|\|_\|\|\|__\|\n______________ACUAUUGU_UAC_CGC__A\n3'-UUU...CUACU________U___G___AG_AAG-5'\n_____________\|___________________\|\n_____________23__________________3\n	203 -- 209	15 -- 21	-14.8727 kcal/mol	3.8346 kcal/mol	1.2572 kcal/mol	201 221@LB@ \| \|@LB@5'-UGA...UUUCA C A GA AGAAG...CCG-3'@LB@ UGAUGAUA GUG GCG U@LB@ \|\|\|\|:\|:\| :\|\| \|\|\| \|@LB@ ACUAUUGU UAC CGC A@LB@3'-UUU...CUACU U G AG AAG-5'@LB@ \| \|@LB@ 23 3@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -14.8727 kcal/mol@LB@Unfolding Energy - mRNA 3.8346 kcal/mol@LB@Unfolding Energy - sRNA 1.2572 kcal/mol@LB@@LB@Position - mRNA 202 -- 220@LB@Position - sRNA 4 -- 22@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 15 -- 21@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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