Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
58	0.004088	0.237	b0998	torD	-12.26	0.038501	93 -- 144	1 -- 57	TorA-maturation chaperone	_____________92__________________________________________________________145\n_____________\|___________________________________________________________\|\n5'-GGU...ACGCU_____AAAU__AGAA___A________C_______CAG________________U____GGCCC...CCA-3'\n______________GGUGG____UG_____GU_CAACGGAA_AGUGGAG___GUGAC______GGCGU_UAAC\n______________:\|\|\|\|____\|\|_____\|:_\|\|\|\|:\|\|\|_\|:\|::\|:___\|\|\|\|\|______\|\|\|:\|_\|\|\|\|\n______________UCACC____AC_____CG_GUUGUCUU_UUAUUUU___CACUG______CCGUA_AUUG\n3'-UUU...UUUAG_____GUU___GUUAC__G________________AGA_____UUAUUU_____U____-5'\n_____________\|__________________________________________________________\|\n_____________58_________________________________________________________1\n	111 -- 117	33 -- 39	-35.8821 kcal/mol	11.4978 kcal/mol	12.1233 kcal/mol	92 145@LB@ \| \|@LB@5'-GGU...ACGCU AAAU AGAA A C CAG U GGCCC...CCA-3'@LB@ GGUGG UG GU CAACGGAA AGUGGAG GUGAC GGCGU UAAC@LB@ :\|\|\|\| \|\| \|: \|\|\|\|:\|\|\| \|:\|::\|: \|\|\|\|\| \|\|\|:\| \|\|\|\|@LB@ UCACC AC CG GUUGUCUU UUAUUUU CACUG CCGUA AUUG@LB@3'-UUU...UUUAG GUU GUUAC G AGA UUAUUU U -5'@LB@ \| \|@LB@ 58 1@LB@@LB@@LB@Energy -12.26 kcal/mol@LB@Hybridization Energy -35.8821 kcal/mol@LB@Unfolding Energy - mRNA 11.4978 kcal/mol@LB@Unfolding Energy - sRNA 12.1233 kcal/mol@LB@@LB@Position - mRNA 93 -- 144@LB@Position - sRNA 1 -- 57@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 33 -- 39@LB@
133	0.01445	0.3654	b1260	trpA	-8.36	0.252100	71 -- 77	38 -- 44	tryptophan synthase alpha subunit	_____________70______78\n_____________\|_______\|\n5'-GCC...CGCCC_______UGCGU...CAU-3'\n______________UGGCCCA\n______________\|\|\|\|\|\|\|\n______________ACCGGGU\n3'-UUU...ACGUU_______UGUCU...UUG-5'\n_____________\|_______\|\n_____________45______37\n	71 -- 77	38 -- 44	-13.3519 kcal/mol	1.05946 kcal/mol	3.93445 kcal/mol	70 78@LB@ \| \|@LB@5'-GCC...CGCCC UGCGU...CAU-3'@LB@ UGGCCCA@LB@ \|\|\|\|\|\|\|@LB@ ACCGGGU@LB@3'-UUU...ACGUU UGUCU...UUG-5'@LB@ \| \|@LB@ 45 37@LB@@LB@@LB@Energy -8.36 kcal/mol@LB@Hybridization Energy -13.3519 kcal/mol@LB@Unfolding Energy - mRNA 1.05946 kcal/mol@LB@Unfolding Energy - sRNA 3.93445 kcal/mol@LB@@LB@Position - mRNA 71 -- 77@LB@Position - sRNA 38 -- 44@LB@Position Seed - mRNA 71 -- 77@LB@Position Seed - sRNA 38 -- 44@LB@
44	0.002732	0.2088	b3450	ugpC	-10.48	0.096645	106 -- 116	47 -- 57	sn-glycerol-3-phosphate ABC transporter ATPase	_____________105_________117\n_____________\|___________\|\n5'-GUG...GUGAU___________UGUUA...UCG-3'\n______________GGUGGCGAUGU\n______________:\|\|\|\|\|:\|\|\|:\n______________UCACCGUUACG\n3'-UUU...UUUAG___________UUACC...UUG-5'\n_____________\|___________\|\n_____________58__________46\n	110 -- 116	47 -- 53	-17.083 kcal/mol	3.56469 kcal/mol	3.03952 kcal/mol	105 117@LB@ \| \|@LB@5'-GUG...GUGAU UGUUA...UCG-3'@LB@ GGUGGCGAUGU@LB@ :\|\|\|\|\|:\|\|\|:@LB@ UCACCGUUACG@LB@3'-UUU...UUUAG UUACC...UUG-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -10.48 kcal/mol@LB@Hybridization Energy -17.083 kcal/mol@LB@Unfolding Energy - mRNA 3.56469 kcal/mol@LB@Unfolding Energy - sRNA 3.03952 kcal/mol@LB@@LB@Position - mRNA 106 -- 116@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 110 -- 116@LB@Position Seed - sRNA 47 -- 53@LB@
57	0.004077	0.237	b4198	ulaF	-9.90	0.127727	21 -- 37	42 -- 55	L-ribulose 5-phosphate 4-epimerase	_____________20________________38\n_____________\|_________________\|\n5'-GUC...CCGUU_____AAG_________AUUUC...GCG-3'\n______________UGGCG___GUGUAGUGG\n______________\|\|\|\|:___:\|\|:\|:\|\|\|\n______________ACCGU___UACGUUACC\n3'-UUU...UAGUC_________________GGGUU...UUG-5'\n_____________\|_________________\|\n_____________56________________41\n	31 -- 37	42 -- 48	-17.0201 kcal/mol	3.6214 kcal/mol	3.50097 kcal/mol	20 38@LB@ \| \|@LB@5'-GUC...CCGUU AAG AUUUC...GCG-3'@LB@ UGGCG GUGUAGUGG@LB@ \|\|\|\|: :\|\|:\|:\|\|\|@LB@ ACCGU UACGUUACC@LB@3'-UUU...UAGUC GGGUU...UUG-5'@LB@ \| \|@LB@ 56 41@LB@@LB@@LB@Energy -9.90 kcal/mol@LB@Hybridization Energy -17.0201 kcal/mol@LB@Unfolding Energy - mRNA 3.6214 kcal/mol@LB@Unfolding Energy - sRNA 3.50097 kcal/mol@LB@@LB@Position - mRNA 21 -- 37@LB@Position - sRNA 42 -- 55@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 42 -- 48@LB@
99	0.009334	0.3118	b0675	umpH	-9.49	0.153954	143 -- 172	39 -- 66	UMP phosphatase	_____________142____________________________173\n_____________\|______________________________\|\n5'-AGC...UUUGC__________A__U__UUUUA_______G_UUAUU...AUA-3'\n______________UGGAAAAUUA_UG_GC_____UAGUGGC_C\n______________\|\|\|\|\|\|\|\|:\|_\|\|_\|\|_____:\|:\|\|\|\|_\|\n______________ACCUUUUAGU_AC_CG_____GUUACCG_G\n3'-UUU...AUACA__________C_____UUAC________G_UUGUC...UUG-5'\n_____________\|______________________________\|\n_____________67_____________________________38\n	145 -- 151	58 -- 64	-25.171 kcal/mol	9.00393 kcal/mol	6.67256 kcal/mol	142 173@LB@ \| \|@LB@5'-AGC...UUUGC A U UUUUA G UUAUU...AUA-3'@LB@ UGGAAAAUUA UG GC UAGUGGC C@LB@ \|\|\|\|\|\|\|\|:\| \|\| \|\| :\|:\|\|\|\| \|@LB@ ACCUUUUAGU AC CG GUUACCG G@LB@3'-UUU...AUACA C UUAC G UUGUC...UUG-5'@LB@ \| \|@LB@ 67 38@LB@@LB@@LB@Energy -9.49 kcal/mol@LB@Hybridization Energy -25.171 kcal/mol@LB@Unfolding Energy - mRNA 9.00393 kcal/mol@LB@Unfolding Energy - sRNA 6.67256 kcal/mol@LB@@LB@Position - mRNA 143 -- 172@LB@Position - sRNA 39 -- 66@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 58 -- 64@LB@
80	0.006956	0.2822	b1914	uvrY	-9.02	0.189987	260 -- 281	5 -- 24	response regulator in two-component regulatory system with BarA	_____________259____________________282\n_____________\|______________________\|\n5'-UUC...CGCAU____GAA____UA_________AAAGU...CAU-3'\n______________UCUG___GAUA__AAGGGUAUA\n______________\|\|\|\|___\|\|:\|__\|\|:\|\|:\|\|\|\n______________AGAC___CUGU__UUUCCGUAU\n3'-UUU...AUUUU____A______UA_________AUUG-5'\n_____________\|______________________\|\n_____________25_____________________4\n	275 -- 281	5 -- 11	-15.9126 kcal/mol	2.27135 kcal/mol	4.61703 kcal/mol	259 282@LB@ \| \|@LB@5'-UUC...CGCAU GAA UA AAAGU...CAU-3'@LB@ UCUG GAUA AAGGGUAUA@LB@ \|\|\|\| \|\|:\| \|\|:\|\|:\|\|\|@LB@ AGAC CUGU UUUCCGUAU@LB@3'-UUU...AUUUU A UA AUUG-5'@LB@ \| \|@LB@ 25 4@LB@@LB@@LB@Energy -9.02 kcal/mol@LB@Hybridization Energy -15.9126 kcal/mol@LB@Unfolding Energy - mRNA 2.27135 kcal/mol@LB@Unfolding Energy - sRNA 4.61703 kcal/mol@LB@@LB@Position - mRNA 260 -- 281@LB@Position - sRNA 5 -- 24@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 5 -- 11@LB@
181	0.02239	0.4143	b2894	xerD	-11.89	0.046874	147 -- 194	9 -- 61	site-specific tyrosine recombinase	_____________146_____________________________________________________195\n_____________\|_______________________________________________________\|\n5'-ACC...GCUUU_____C____________AA___A_______UC_______GA_____C_______GCGCA...UGU-3'\n______________AGUCA__GGCA___CAAU__GGC_UAAUGGA_____AAAU__GUGAC_AUAAGGG\n______________\|:\|\|\|__\|\|\|\|___\|\|\|\|__\|\|\|_:\|\|::\|\|_____\|\|\|\|__\|\|\|\|\|_\|\|\|\|:\|\|\n______________UUAGU__CCGU___GUUA__CCG_GUUGUCU_____UUUA__CACUG_UAUUUCC\n3'-UUU...ACCUU_____CA____UAC_________G_______UUUAU____GA_____U_______GUAUAUUG-5'\n_____________\|_______________________________________________________\|\n_____________62______________________________________________________8\n	188 -- 194	9 -- 15	-33.0704 kcal/mol	10.0398 kcal/mol	11.1358 kcal/mol	146 195@LB@ \| \|@LB@5'-ACC...GCUUU C AA A UC GA C GCGCA...UGU-3'@LB@ AGUCA GGCA CAAU GGC UAAUGGA AAAU GUGAC AUAAGGG@LB@ \|:\|\|\| \|\|\|\| \|\|\|\| \|\|\| :\|\|::\|\| \|\|\|\| \|\|\|\|\| \|\|\|\|:\|\|@LB@ UUAGU CCGU GUUA CCG GUUGUCU UUUA CACUG UAUUUCC@LB@3'-UUU...ACCUU CA UAC G UUUAU GA U GUAUAUUG-5'@LB@ \| \|@LB@ 62 8@LB@@LB@@LB@Energy -11.89 kcal/mol@LB@Hybridization Energy -33.0704 kcal/mol@LB@Unfolding Energy - mRNA 10.0398 kcal/mol@LB@Unfolding Energy - sRNA 11.1358 kcal/mol@LB@@LB@Position - mRNA 147 -- 194@LB@Position - sRNA 9 -- 61@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 9 -- 15@LB@
140	0.01599	0.3828	b0119	yacL	-11.32	0.063485	266 -- 299	25 -- 57	UPF0231 family protein	_____________265_________________________________300\n_____________\|___________________________________\|\n5'-GGU...CAUGA______CGG___C_________GA___________G-3'\n______________AGUGGU___GCA_UGGUUUAAU__AGA_GGUGAAA\n______________\|\|\|\|\|:___\|\|\|_\|\|\|:::\|\|:__\|\|\|_::\|:\|\|\|\n______________UCACCG___CGU_ACCGGGUUG__UCU_UUAUUUU\n3'-UUU...UUUAG______UUA___U______________U_______AGACA...UUG-5'\n_____________\|___________________________________\|\n_____________58__________________________________24\n	293 -- 299	25 -- 31	-25.5028 kcal/mol	4.248 kcal/mol	9.93955 kcal/mol	265 300@LB@ \| \|@LB@5'-GGU...CAUGA CGG C GA G-3'@LB@ AGUGGU GCA UGGUUUAAU AGA GGUGAAA@LB@ \|\|\|\|\|: \|\|\| \|\|\|:::\|\|: \|\|\| ::\|:\|\|\|@LB@ UCACCG CGU ACCGGGUUG UCU UUAUUUU@LB@3'-UUU...UUUAG UUA U U AGACA...UUG-5'@LB@ \| \|@LB@ 58 24@LB@@LB@@LB@Energy -11.32 kcal/mol@LB@Hybridization Energy -25.5028 kcal/mol@LB@Unfolding Energy - mRNA 4.248 kcal/mol@LB@Unfolding Energy - sRNA 9.93955 kcal/mol@LB@@LB@Position - mRNA 266 -- 299@LB@Position - sRNA 25 -- 57@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 25 -- 31@LB@
26	0.00144	0.1863	b4406	yaeP	-8.75	0.213688	187 -- 204	2 -- 20	UPF0253 family protein	_____________186_________________205\n_____________\|___________________\|\n5'-ACC...AGUGC_____G_____________AAAAA...UGC-3'\n______________UGACA__GAGGGCAUGUGG\n______________\|\|\|\|\|__:\|:\|\|\|\|\|:\|::\n______________ACUGU__UUUCCGUAUAUU\n3'-UUU...UAGAC_____UA____________G-5'\n_____________\|___________________\|\n_____________21__________________1\n	197 -- 203	3 -- 9	-20.0716 kcal/mol	7.09254 kcal/mol	4.22649 kcal/mol	186 205@LB@ \| \|@LB@5'-ACC...AGUGC G AAAAA...UGC-3'@LB@ UGACA GAGGGCAUGUGG@LB@ \|\|\|\|\| :\|:\|\|\|\|\|:\|::@LB@ ACUGU UUUCCGUAUAUU@LB@3'-UUU...UAGAC UA G-5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -8.75 kcal/mol@LB@Hybridization Energy -20.0716 kcal/mol@LB@Unfolding Energy - mRNA 7.09254 kcal/mol@LB@Unfolding Energy - sRNA 4.22649 kcal/mol@LB@@LB@Position - mRNA 187 -- 204@LB@Position - sRNA 2 -- 20@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 3 -- 9@LB@
54	0.003913	0.237	b0387	yaiI	-8.67	0.221647	168 -- 177	9 -- 18	UPF0178 family protein	_____________167________178\n_____________\|__________\|\n5'-CAC...GCGAC__________AUUAC...CAA-3'\n______________ACAAUAGAGG\n______________\|\|\|\|\|\|:\|\|\|\n______________UGUUAUUUCC\n3'-UUU...GACAC__________GUAUAUUG-5'\n_____________\|__________\|\n_____________19_________8\n	171 -- 177	9 -- 15	-10.6786 kcal/mol	1.38452 kcal/mol	0.627418 kcal/mol	167 178@LB@ \| \|@LB@5'-CAC...GCGAC AUUAC...CAA-3'@LB@ ACAAUAGAGG@LB@ \|\|\|\|\|\|:\|\|\|@LB@ UGUUAUUUCC@LB@3'-UUU...GACAC GUAUAUUG-5'@LB@ \| \|@LB@ 19 8@LB@@LB@@LB@Energy -8.67 kcal/mol@LB@Hybridization Energy -10.6786 kcal/mol@LB@Unfolding Energy - mRNA 1.38452 kcal/mol@LB@Unfolding Energy - sRNA 0.627418 kcal/mol@LB@@LB@Position - mRNA 168 -- 177@LB@Position - sRNA 9 -- 18@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 9 -- 15@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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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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