Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
13	0.0005091	0.1286	b2062	wza	-15.65	0.004784	187 -- 207	5 -- 27	colanic acid export protein; outer membrane auxillary lipoprotein	_____________186_____________________208\n_____________\|_______________________\|\n5'-AAA...CCAAA____________C__________AAUCC...GCA-3'\n______________GUGAUAAAUAAA___AAUGAUGA\n______________\|\|:\|\|\|\|\|\|\|\|\|___\|\|\|\|\|\|\|\|\n______________CAUUAUUUAUUU___UUACUACU\n3'-UUU...ACUGC____________CAA________AUCG-5'\n_____________\|_______________________\|\n_____________28______________________4\n	201 -- 207	5 -- 11	-18.4073 kcal/mol	2.04721 kcal/mol	0.709121 kcal/mol	186 208@LB@ \| \|@LB@5'-AAA...CCAAA C AAUCC...GCA-3'@LB@ GUGAUAAAUAAA AAUGAUGA@LB@ \|\|:\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ CAUUAUUUAUUU UUACUACU@LB@3'-UUU...ACUGC CAA AUCG-5'@LB@ \| \|@LB@ 28 4@LB@@LB@@LB@Energy -15.65 kcal/mol@LB@Hybridization Energy -18.4073 kcal/mol@LB@Unfolding Energy - mRNA 2.04721 kcal/mol@LB@Unfolding Energy - sRNA 0.709121 kcal/mol@LB@@LB@Position - mRNA 187 -- 207@LB@Position - sRNA 5 -- 27@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 5 -- 11@LB@
7	0.0001529	0.07172	b0687	seqA	-15.48	0.005290	212 -- 226	5 -- 19	negative modulator of initiation of replication	_____________211_____________227\n_____________\|_______________\|\n5'-GGA...ACGAU_______________ACUCU...UGA-3'\n______________UGAAGUUGAUGAUGA\n______________\|:\|\|\|\|\|:\|\|\|\|\|\|\|\n______________AUUUCAAUUACUACU\n3'-UUU...UAUUU_______________AUCG-5'\n_____________\|_______________\|\n_____________20______________4\n	220 -- 226	5 -- 11	-18.3215 kcal/mol	2.77487 kcal/mol	0.0620344 kcal/mol	211 227@LB@ \| \|@LB@5'-GGA...ACGAU ACUCU...UGA-3'@LB@ UGAAGUUGAUGAUGA@LB@ \|:\|\|\|\|\|:\|\|\|\|\|\|\|@LB@ AUUUCAAUUACUACU@LB@3'-UUU...UAUUU AUCG-5'@LB@ \| \|@LB@ 20 4@LB@@LB@@LB@Energy -15.48 kcal/mol@LB@Hybridization Energy -18.3215 kcal/mol@LB@Unfolding Energy - mRNA 2.77487 kcal/mol@LB@Unfolding Energy - sRNA 0.0620344 kcal/mol@LB@@LB@Position - mRNA 212 -- 226@LB@Position - sRNA 5 -- 19@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 5 -- 11@LB@
37	0.00362	0.3212	b4479	dgoR	-15.45	0.005416	239 -- 256	41 -- 57	D-galactonate catabolism operon transcriptional repressor	_____________238________________257\n_____________\|__________________\|\n5'-UUU...ACGCU___________U______CGGCA...AAC-3'\n______________GGGUAAACAGA_CGUUCA\n______________\|\|\|\|\|\|\|\|\|\|\|_\|:\|\|\|\|\n______________CCCAUUUGUCU_GUAAGU\n3'-UUU...UUAUC__________________CUUUA...UCG-5'\n_____________\|__________________\|\n_____________58_________________40\n	243 -- 249	47 -- 53	-24.0794 kcal/mol	2.38777 kcal/mol	6.24592 kcal/mol	238 257@LB@ \| \|@LB@5'-UUU...ACGCU U CGGCA...AAC-3'@LB@ GGGUAAACAGA CGUUCA@LB@ \|\|\|\|\|\|\|\|\|\|\| \|:\|\|\|\|@LB@ CCCAUUUGUCU GUAAGU@LB@3'-UUU...UUAUC CUUUA...UCG-5'@LB@ \| \|@LB@ 58 40@LB@@LB@@LB@Energy -15.45 kcal/mol@LB@Hybridization Energy -24.0794 kcal/mol@LB@Unfolding Energy - mRNA 2.38777 kcal/mol@LB@Unfolding Energy - sRNA 6.24592 kcal/mol@LB@@LB@Position - mRNA 239 -- 256@LB@Position - sRNA 41 -- 57@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 47 -- 53@LB@
62	0.008588	0.4523	b1746	astD	-15.44	0.005443	188 -- 231	17 -- 59	succinylglutamic semialdehyde dehydrogenase	_____________187___________________________________________232\n_____________\|_____________________________________________\|\n5'-GCA...CGCAG___A_A__________GACUUU______UA_______C_______CGGGC...AUG-3'\n______________AGG_G_AAACAG_CAU______AUGGAU__ACGGUGA_UGGAUAA\n______________\|\|\|_\|_\|\|\|\|\|\|_\|\|\|______\|\|\|:\|\|__\|\|\|\|\|:\|_\|::\|\|\|\|\n______________UCC_C_UUUGUC_GUA______UACUUA__UGCCAUU_AUUUAUU\n3'-UUU...CUUUA___C_A______U___AGUCUU______C________________UCAAU...UCG-5'\n_____________\|_____________________________________________\|\n_____________60____________________________________________16\n	217 -- 223	24 -- 30	-28.1653 kcal/mol	6.40491 kcal/mol	6.3229 kcal/mol	187 232@LB@ \| \|@LB@5'-GCA...CGCAG A A GACUUU UA C CGGGC...AUG-3'@LB@ AGG G AAACAG CAU AUGGAU ACGGUGA UGGAUAA@LB@ \|\|\| \| \|\|\|\|\|\| \|\|\| \|\|\|:\|\| \|\|\|\|\|:\| \|::\|\|\|\|@LB@ UCC C UUUGUC GUA UACUUA UGCCAUU AUUUAUU@LB@3'-UUU...CUUUA C A U AGUCUU C UCAAU...UCG-5'@LB@ \| \|@LB@ 60 16@LB@@LB@@LB@Energy -15.44 kcal/mol@LB@Hybridization Energy -28.1653 kcal/mol@LB@Unfolding Energy - mRNA 6.40491 kcal/mol@LB@Unfolding Energy - sRNA 6.3229 kcal/mol@LB@@LB@Position - mRNA 188 -- 231@LB@Position - sRNA 17 -- 59@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 24 -- 30@LB@
24	0.001422	0.1946	b0065	yabI	-15.22	0.006192	70 -- 99	1 -- 29	DedA family inner membrane protein	_____________69______________________________100\n_____________\|_______________________________\|\n5'-UGA...CGUGC____U_____GAA_____G____________CGUCA...GUU-3'\n______________CGGU_GUGAA___AAAGU_AAUGAUG_UAGC\n______________\|\|\|\|_:\|:\|\|___\|\|\|\|\|_\|\|\|\|\|\|\|_\|\|\|\|\n______________GCCA_UAUUU___UUUCA_UUACUAC_AUCG\n3'-UUU...UUACU____U_____A_______A_______U____-5'\n_____________\|______________________________\|\n_____________30_____________________________1\n	89 -- 95	6 -- 12	-22.6746 kcal/mol	5.32597 kcal/mol	2.12711 kcal/mol	69 100@LB@ \| \|@LB@5'-UGA...CGUGC U GAA G CGUCA...GUU-3'@LB@ CGGU GUGAA AAAGU AAUGAUG UAGC@LB@ \|\|\|\| :\|:\|\| \|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|@LB@ GCCA UAUUU UUUCA UUACUAC AUCG@LB@3'-UUU...UUACU U A A U -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -15.22 kcal/mol@LB@Hybridization Energy -22.6746 kcal/mol@LB@Unfolding Energy - mRNA 5.32597 kcal/mol@LB@Unfolding Energy - sRNA 2.12711 kcal/mol@LB@@LB@Position - mRNA 70 -- 99@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 6 -- 12@LB@
48	0.005342	0.3653	b3380	yhfW	-15.20	0.006283	218 -- 233	1 -- 15	phosphopentomutase-related metalloenzyme superfamily protein	_____________217______________234\n_____________\|________________\|\n5'-CUC...GUGGU________U_______UUUGG...GUG-3'\n______________GUUAGUGA_UGAUAGC\n______________\|\|\|\|:\|\|\|_\|\|\|\|\|\|\|\n______________CAAUUACU_ACUAUCG\n3'-UUU...UAUUU________________-5'\n_____________\|_______________\|\n_____________16______________1\n	227 -- 233	1 -- 7	-17.7091 kcal/mol	2.46465 kcal/mol	0.0474282 kcal/mol	217 234@LB@ \| \|@LB@5'-CUC...GUGGU U UUUGG...GUG-3'@LB@ GUUAGUGA UGAUAGC@LB@ \|\|\|\|:\|\|\| \|\|\|\|\|\|\|@LB@ CAAUUACU ACUAUCG@LB@3'-UUU...UAUUU -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -15.20 kcal/mol@LB@Hybridization Energy -17.7091 kcal/mol@LB@Unfolding Energy - mRNA 2.46465 kcal/mol@LB@Unfolding Energy - sRNA 0.0474282 kcal/mol@LB@@LB@Position - mRNA 218 -- 233@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 1 -- 7@LB@
70	0.01004	0.4523	b1658	purR	-15.06	0.006831	174 -- 223	1 -- 65	transcriptional repressor hypoxanthine-binding	_____________173________________________________________________________________224\n_____________\|__________________________________________________________________\|\n5'-UUU...GGAGC______UA____C______GU_________G_______AAC______A__________________GAAAC...GCA-3'\n______________UGAAGU__GGGU___UGGA______GAAAU_GAAUGGC___AAUAAA__________GAUG_UAGC\n______________\|\|\|\|:\|__\|\|\|\|___::\|\|______\|\|\|\|\|_\|\|\|\|\|:\|___\|\|\|\|\|\|__________\|\|\|\|_\|\|\|\|\n______________ACUUUA__CCCA___GUCU______CUUUA_CUUACUG___UUAUUU__________CUAC_AUCG\n3'-UUU...GGCCA______UC____UUU____GUAAGU_____________CCA______AUUUCAAUUA____U____-5'\n_____________\|_________________________________________________________________\|\n_____________66________________________________________________________________1\n	199 -- 205	29 -- 35	-29.7477 kcal/mol	7.45199 kcal/mol	7.23987 kcal/mol	173 224@LB@ \| \|@LB@5'-UUU...GGAGC UA C GU G AAC A GAAAC...GCA-3'@LB@ UGAAGU GGGU UGGA GAAAU GAAUGGC AAUAAA GAUG UAGC@LB@ \|\|\|\|:\| \|\|\|\| ::\|\| \|\|\|\|\| \|\|\|\|\|:\| \|\|\|\|\|\| \|\|\|\| \|\|\|\|@LB@ ACUUUA CCCA GUCU CUUUA CUUACUG UUAUUU CUAC AUCG@LB@3'-UUU...GGCCA UC UUU GUAAGU CCA AUUUCAAUUA U -5'@LB@ \| \|@LB@ 66 1@LB@@LB@@LB@Energy -15.06 kcal/mol@LB@Hybridization Energy -29.7477 kcal/mol@LB@Unfolding Energy - mRNA 7.45199 kcal/mol@LB@Unfolding Energy - sRNA 7.23987 kcal/mol@LB@@LB@Position - mRNA 174 -- 223@LB@Position - sRNA 1 -- 65@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 29 -- 35@LB@
142	0.02395	0.526	b0192	nlpE	-14.44	0.009771	167 -- 226	1 -- 55	lipoprotein involved with copper homeostasis and adhesion	_____________166_______________________________________________________________227\n_____________\|_________________________________________________________________\|\n5'-UCA...GCAAA___C_______G________AAAAAGAAG____G________AA_______C____A____C___GAUGG...CGC-3'\n______________GUG_GCAG_CG_UCGGGAAU_________GAAU_GAUGGUGA_____AAAG__GAU_GUGA_AGC\n______________\|\|:_:\|\|\|_\|:_\|\|:\|:\|\|\|_________\|\|\|\|_\|\|:\|\|\|:\|_____\|\|\|\|__:\|\|_:\|\|\|_\|\|\|\n______________CAU_UGUC_GU_AGUCUUUA_________CUUA_CUGCCAUU_____UUUC__UUA_UACU_UCG\n3'-UUU...AUCCC___U____U__A______________________________AUUUA____AA___C____A___-5'\n_____________\|________________________________________________________________\|\n_____________56_______________________________________________________________1\n	201 -- 207	24 -- 30	-31.0616 kcal/mol	10.2836 kcal/mol	6.33758 kcal/mol	166 227@LB@ \| \|@LB@5'-UCA...GCAAA C G AAAAAGAAG G AA C A C GAUGG...CGC-3'@LB@ GUG GCAG CG UCGGGAAU GAAU GAUGGUGA AAAG GAU GUGA AGC@LB@ \|\|: :\|\|\| \|: \|\|:\|:\|\|\| \|\|\|\| \|\|:\|\|\|:\| \|\|\|\| :\|\| :\|\|\| \|\|\|@LB@ CAU UGUC GU AGUCUUUA CUUA CUGCCAUU UUUC UUA UACU UCG@LB@3'-UUU...AUCCC U U A AUUUA AA C A -5'@LB@ \| \|@LB@ 56 1@LB@@LB@@LB@Energy -14.44 kcal/mol@LB@Hybridization Energy -31.0616 kcal/mol@LB@Unfolding Energy - mRNA 10.2836 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 167 -- 226@LB@Position - sRNA 1 -- 55@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 24 -- 30@LB@
54	0.006418	0.3902	b0946	zapC	-14.33	0.010402	184 -- 201	47 -- 63	FtsZ stabilizer	_____________183________________202\n_____________\|__________________\|\n5'-AUU...UUAUA_________AG_______UGCGA...GUU-3'\n______________GGGUAGGGG__AGGCAGA\n______________:::\|\|\|\|\|\|__\|::\|\|\|\|\n______________UUUAUCCCC__UUUGUCU\n3'-UUU...CCAAC_________A________GUAAG...UCG-5'\n_____________\|__________________\|\n_____________64_________________46\n	195 -- 201	47 -- 53	-19.5846 kcal/mol	3.17109 kcal/mol	2.08245 kcal/mol	183 202@LB@ \| \|@LB@5'-AUU...UUAUA AG UGCGA...GUU-3'@LB@ GGGUAGGGG AGGCAGA@LB@ :::\|\|\|\|\|\| \|::\|\|\|\|@LB@ UUUAUCCCC UUUGUCU@LB@3'-UUU...CCAAC A GUAAG...UCG-5'@LB@ \| \|@LB@ 64 46@LB@@LB@@LB@Energy -14.33 kcal/mol@LB@Hybridization Energy -19.5846 kcal/mol@LB@Unfolding Energy - mRNA 3.17109 kcal/mol@LB@Unfolding Energy - sRNA 2.08245 kcal/mol@LB@@LB@Position - mRNA 184 -- 201@LB@Position - sRNA 47 -- 63@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 47 -- 53@LB@
184	0.03077	0.549	b1101	ptsG	-13.95	0.012872	39 -- 58	1 -- 19	fused glucose-specific PTS enzymes: IIB component/IIC component	_____________38___________________59\n_____________\|____________________\|\n5'-CAU...UGAUC_________AAC________CGUCA...GUU-3'\n______________UGAAGUUGA___GUGAUAGC\n______________\|:\|\|\|\|\|:\|___:\|\|\|\|\|\|\|\n______________AUUUCAAUU___UACUAUCG\n3'-UUU...UAUUU_________AC_________-5'\n_____________\|___________________\|\n_____________20__________________1\n	52 -- 58	1 -- 7	-17.415 kcal/mol	3.39679 kcal/mol	0.0638423 kcal/mol	38 59@LB@ \| \|@LB@5'-CAU...UGAUC AAC CGUCA...GUU-3'@LB@ UGAAGUUGA GUGAUAGC@LB@ \|:\|\|\|\|\|:\| :\|\|\|\|\|\|\|@LB@ AUUUCAAUU UACUAUCG@LB@3'-UUU...UAUUU AC -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -13.95 kcal/mol@LB@Hybridization Energy -17.415 kcal/mol@LB@Unfolding Energy - mRNA 3.39679 kcal/mol@LB@Unfolding Energy - sRNA 0.0638423 kcal/mol@LB@@LB@Position - mRNA 39 -- 58@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 1 -- 7@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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