Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
41	0.001644	0.1292	b1918	yecS	-7.37	0.088723	192 -- 214	37 -- 60	ABC family putative inner membrane permease	_____________191_______________________215\n_____________\|_________________________\|\n5'-GGC...CUCCG__________CAU_______A____ACAAC...GCU-3'\n______________GAAAC__GCU___GCAAGAA_GUAU\n______________\|\|\|\|\|__\|\|\|___\|\|\|\|\|\|\|_\|:\|:\n______________CUUUG__CGA___CGUUCUU_CGUG\n3'-UUU...CCCUA_____AA___AUU____________AAUUU...CAA-5'\n_____________\|_________________________\|\n_____________61________________________36\n	203 -- 209	41 -- 47	-18.5053 kcal/mol	4.89056 kcal/mol	6.24651 kcal/mol	191 215@LB@ \| \|@LB@5'-GGC...CUCCG CAU A ACAAC...GCU-3'@LB@ GAAAC GCU GCAAGAA GUAU@LB@ \|\|\|\|\| \|\|\| \|\|\|\|\|\|\| \|:\|:@LB@ CUUUG CGA CGUUCUU CGUG@LB@3'-UUU...CCCUA AA AUU AAUUU...CAA-5'@LB@ \| \|@LB@ 61 36@LB@@LB@@LB@Energy -7.37 kcal/mol@LB@Hybridization Energy -18.5053 kcal/mol@LB@Unfolding Energy - mRNA 4.89056 kcal/mol@LB@Unfolding Energy - sRNA 6.24651 kcal/mol@LB@@LB@Position - mRNA 192 -- 214@LB@Position - sRNA 37 -- 60@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 41 -- 47@LB@
42	0.001686	0.1293	b2733	mutS	-6.21	0.172669	203 -- 222	25 -- 42	methyl-directed mismatch repair protein	_____________202__________________223\n_____________\|____________________\|\n5'-GAU...CCCAU______AA_________U__ACGCC...UGG-3'\n______________GAGUGC__UAGAAAAUU_CG\n______________:\|\|::\|__\|\|:\|\|\|\|\|\|_\|\|\n______________UUCGUG__AUUUUUUAA_GC\n3'-UUU...CGUUC______A_____________AAUGU...CAA-5'\n_____________\|____________________\|\n_____________43___________________24\n	213 -- 219	27 -- 33	-10.4027 kcal/mol	2.54535 kcal/mol	1.64855 kcal/mol	202 223@LB@ \| \|@LB@5'-GAU...CCCAU AA U ACGCC...UGG-3'@LB@ GAGUGC UAGAAAAUU CG@LB@ :\|\|::\| \|\|:\|\|\|\|\|\| \|\|@LB@ UUCGUG AUUUUUUAA GC@LB@3'-UUU...CGUUC A AAUGU...CAA-5'@LB@ \| \|@LB@ 43 24@LB@@LB@@LB@Energy -6.21 kcal/mol@LB@Hybridization Energy -10.4027 kcal/mol@LB@Unfolding Energy - mRNA 2.54535 kcal/mol@LB@Unfolding Energy - sRNA 1.64855 kcal/mol@LB@@LB@Position - mRNA 203 -- 222@LB@Position - sRNA 25 -- 42@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 27 -- 33@LB@
43	0.001794	0.1344	b0631	ybeD	-7.18	0.099343	171 -- 193	16 -- 40	UPF0250 family protein	_____________170________________________194\n_____________\|__________________________\|\n5'-GCU...GAGUU__U______UUA______________AGCUG...AAG-3'\n______________GC_AUUUAA______CGUUACGCCGG\n______________\|\|_\|:\|\|\|\|______\|\|\|\|\|\|:\|\|:\|\n______________CG_UGAAUU______GCAAUGUGGUC\n3'-UUU...UUCUU_________UUUUAA___________CUUUA...CAA-5'\n_____________\|__________________________\|\n_____________41_________________________15\n	187 -- 193	16 -- 22	-19.4847 kcal/mol	3.10673 kcal/mol	9.1996 kcal/mol	170 194@LB@ \| \|@LB@5'-GCU...GAGUU U UUA AGCUG...AAG-3'@LB@ GC AUUUAA CGUUACGCCGG@LB@ \|\| \|:\|\|\|\| \|\|\|\|\|\|:\|\|:\|@LB@ CG UGAAUU GCAAUGUGGUC@LB@3'-UUU...UUCUU UUUUAA CUUUA...CAA-5'@LB@ \| \|@LB@ 41 15@LB@@LB@@LB@Energy -7.18 kcal/mol@LB@Hybridization Energy -19.4847 kcal/mol@LB@Unfolding Energy - mRNA 3.10673 kcal/mol@LB@Unfolding Energy - sRNA 9.1996 kcal/mol@LB@@LB@Position - mRNA 171 -- 193@LB@Position - sRNA 16 -- 40@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 16 -- 22@LB@
44	0.001875	0.1369	b4485	ytfR	-11.10	0.007490	215 -- 227	10 -- 22	putative sugar ABC transporter ATPase	_____________214___________228\n_____________\|_____________\|\n5'-CCU...GACCA_____________CUCCG...GCC-3'\n______________ACACCAGGAGAUC\n______________\|\|\|\|\|\|\|\|\|:\|\|\|\n______________UGUGGUCCUUUAG\n3'-UUU...AGCAA_____________ACUAC...CAA-5'\n_____________\|_____________\|\n_____________23____________9\n	221 -- 227	10 -- 16	-21.5971 kcal/mol	2.94097 kcal/mol	7.55838 kcal/mol	214 228@LB@ \| \|@LB@5'-CCU...GACCA CUCCG...GCC-3'@LB@ ACACCAGGAGAUC@LB@ \|\|\|\|\|\|\|\|\|:\|\|\|@LB@ UGUGGUCCUUUAG@LB@3'-UUU...AGCAA ACUAC...CAA-5'@LB@ \| \|@LB@ 23 9@LB@@LB@@LB@Energy -11.10 kcal/mol@LB@Hybridization Energy -21.5971 kcal/mol@LB@Unfolding Energy - mRNA 2.94097 kcal/mol@LB@Unfolding Energy - sRNA 7.55838 kcal/mol@LB@@LB@Position - mRNA 215 -- 227@LB@Position - sRNA 10 -- 22@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 10 -- 16@LB@
45	0.001912	0.1369	b0080	cra	-5.81	0.213706	183 -- 197	38 -- 52	transcriptional repressor-activator for carbon metabolism	_____________182_____________198\n_____________\|_______________\|\n5'-GGC...UACAU____C__________AUUGU...AAA-3'\n______________UUUA_GCAAGGGGCA\n______________:\|\|\|_\|\|\|\|\|::\|\|\|\n______________GAAU_CGUUCUUCGU\n3'-UUU...UGAAC____U__________GAAUU...CAA-5'\n_____________\|_______________\|\n_____________53______________37\n	191 -- 197	38 -- 44	-16.0644 kcal/mol	4.16124 kcal/mol	6.09169 kcal/mol	182 198@LB@ \| \|@LB@5'-GGC...UACAU C AUUGU...AAA-3'@LB@ UUUA GCAAGGGGCA@LB@ :\|\|\| \|\|\|\|\|::\|\|\|@LB@ GAAU CGUUCUUCGU@LB@3'-UUU...UGAAC U GAAUU...CAA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -5.81 kcal/mol@LB@Hybridization Energy -16.0644 kcal/mol@LB@Unfolding Energy - mRNA 4.16124 kcal/mol@LB@Unfolding Energy - sRNA 6.09169 kcal/mol@LB@@LB@Position - mRNA 183 -- 197@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 38 -- 44@LB@
46	0.002046	0.1433	b3106	yhaK	-10.10	0.015122	97 -- 120	7 -- 28	redox-sensitive bicupin	_____________96_______________________121\n_____________\|________________________\|\n5'-UCC...GCCAU______CU__U_____________ACAUA...AAU-3'\n______________UUCGUU__CA_UCAGGAAAUUUGA\n______________\|\|\|\|\|\|__\|\|_:\|\|\|\|\|\|\|\|:\|\|\|\n______________AAGCAA__GU_GGUCCUUUAGACU\n3'-UUU...UUUUU______U_________________ACACAA-5'\n_____________\|________________________\|\n_____________29_______________________6\n	111 -- 117	10 -- 16	-23.1033 kcal/mol	4.40095 kcal/mol	8.59864 kcal/mol	96 121@LB@ \| \|@LB@5'-UCC...GCCAU CU U ACAUA...AAU-3'@LB@ UUCGUU CA UCAGGAAAUUUGA@LB@ \|\|\|\|\|\| \|\| :\|\|\|\|\|\|\|\|:\|\|\|@LB@ AAGCAA GU GGUCCUUUAGACU@LB@3'-UUU...UUUUU U ACACAA-5'@LB@ \| \|@LB@ 29 6@LB@@LB@@LB@Energy -10.10 kcal/mol@LB@Hybridization Energy -23.1033 kcal/mol@LB@Unfolding Energy - mRNA 4.40095 kcal/mol@LB@Unfolding Energy - sRNA 8.59864 kcal/mol@LB@@LB@Position - mRNA 97 -- 120@LB@Position - sRNA 7 -- 28@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 10 -- 16@LB@
47	0.002119	0.1452	b0694	kdpE	-6.96	0.113004	177 -- 189	26 -- 38	response regulator in two-component regulatory system with KdpD	_____________176___________190\n_____________\|_____________\|\n5'-ACG...CCUGA_____________CAUGA...CGC-3'\n______________ACUUGAAGAAUUU\n______________\|\|\|\|:\|\|:\|\|\|\|:\n______________UGAAUUUUUUAAG\n3'-UUU...CUUCG_____________CAAUG...CAA-5'\n_____________\|_____________\|\n_____________39____________25\n	179 -- 185	30 -- 36	-10.6038 kcal/mol	2.21135 kcal/mol	1.43364 kcal/mol	176 190@LB@ \| \|@LB@5'-ACG...CCUGA CAUGA...CGC-3'@LB@ ACUUGAAGAAUUU@LB@ \|\|\|\|:\|\|:\|\|\|\|:@LB@ UGAAUUUUUUAAG@LB@3'-UUU...CUUCG CAAUG...CAA-5'@LB@ \| \|@LB@ 39 25@LB@@LB@@LB@Energy -6.96 kcal/mol@LB@Hybridization Energy -10.6038 kcal/mol@LB@Unfolding Energy - mRNA 2.21135 kcal/mol@LB@Unfolding Energy - sRNA 1.43364 kcal/mol@LB@@LB@Position - mRNA 177 -- 189@LB@Position - sRNA 26 -- 38@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 30 -- 36@LB@
48	0.002202	0.1465	b3209	elbB	-11.61	0.005163	95 -- 137	2 -- 41	isoprenoid biosynthesis protein with amidotransferase-like domain	_____________94__________________________________________138\n_____________\|___________________________________________\|\n5'-GCG...AAGAU___AAA_______U____________G_AUC____AA______GAUGC...GUG-3'\n______________AGC___ACUUAAA_GAUUUGUUACAU_A___AGUU__AUGUGU\n______________\|\|\|___\|\|\|\|\|\|\|_:\|\|\|:\|\|\|\|\|\|:_\|___\|:\|:__\|\|\|\|\|\|\n______________UCG___UGAAUUU_UUAAGCAAUGUG_U___UUAG__UACACA\n3'-UUU...GUUCU_____________U____________G_CCU____AC______A-5'\n_____________\|___________________________________________\|\n_____________42__________________________________________1\n	101 -- 107	32 -- 38	-29.0989 kcal/mol	8.27062 kcal/mol	9.22136 kcal/mol	94 138@LB@ \| \|@LB@5'-GCG...AAGAU AAA U G AUC AA GAUGC...GUG-3'@LB@ AGC ACUUAAA GAUUUGUUACAU A AGUU AUGUGU@LB@ \|\|\| \|\|\|\|\|\|\| :\|\|\|:\|\|\|\|\|\|: \| \|:\|: \|\|\|\|\|\|@LB@ UCG UGAAUUU UUAAGCAAUGUG U UUAG UACACA@LB@3'-UUU...GUUCU U G CCU AC A-5'@LB@ \| \|@LB@ 42 1@LB@@LB@@LB@Energy -11.61 kcal/mol@LB@Hybridization Energy -29.0989 kcal/mol@LB@Unfolding Energy - mRNA 8.27062 kcal/mol@LB@Unfolding Energy - sRNA 9.22136 kcal/mol@LB@@LB@Position - mRNA 95 -- 137@LB@Position - sRNA 2 -- 41@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 32 -- 38@LB@
49	0.002267	0.1465	b0592	fepB	-6.35	0.159662	143 -- 160	24 -- 40	ferrienterobactin ABC transporter periplasmic binding protein	_____________142________________161\n_____________\|__________________\|\n5'-AUA...AUUGU______UGUC________CAUUA...UUA-3'\n______________GCGCUU____GAAUUUGU\n______________\|\|:\|\|\|____:\|\|\|\|:\|\|\n______________CGUGAA____UUUAAGCA\n3'-UUU...UUCUU______UUU_________AUGUG...CAA-5'\n_____________\|__________________\|\n_____________41_________________23\n	154 -- 160	24 -- 30	-12.773 kcal/mol	4.77335 kcal/mol	1.64869 kcal/mol	142 161@LB@ \| \|@LB@5'-AUA...AUUGU UGUC CAUUA...UUA-3'@LB@ GCGCUU GAAUUUGU@LB@ \|\|:\|\|\| :\|\|\|\|:\|\|@LB@ CGUGAA UUUAAGCA@LB@3'-UUU...UUCUU UUU AUGUG...CAA-5'@LB@ \| \|@LB@ 41 23@LB@@LB@@LB@Energy -6.35 kcal/mol@LB@Hybridization Energy -12.773 kcal/mol@LB@Unfolding Energy - mRNA 4.77335 kcal/mol@LB@Unfolding Energy - sRNA 1.64869 kcal/mol@LB@@LB@Position - mRNA 143 -- 160@LB@Position - sRNA 24 -- 40@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 24 -- 30@LB@
50	0.002273	0.1465	b4159	mscM	-6.32	0.162358	72 -- 90	16 -- 34	mechanosensitive channel protein miniconductance	_____________71__________________91\n_____________\|___________________\|\n5'-AAG...CUACC____CC_____________ACGCU...AGC-3'\n______________GAAA__UUUGUUACGCCAG\n______________:\|\|\|__\|\|:\|\|\|\|\|:\|\|\|\|\n______________UUUU__AAGCAAUGUGGUC\n3'-UUU...GUGAA____UU_____________CUUUA...CAA-5'\n_____________\|___________________\|\n_____________35__________________15\n	84 -- 90	16 -- 22	-19.9467 kcal/mol	4.98786 kcal/mol	8.63814 kcal/mol	71 91@LB@ \| \|@LB@5'-AAG...CUACC CC ACGCU...AGC-3'@LB@ GAAA UUUGUUACGCCAG@LB@ :\|\|\| \|\|:\|\|\|\|\|:\|\|\|\|@LB@ UUUU AAGCAAUGUGGUC@LB@3'-UUU...GUGAA UU CUUUA...CAA-5'@LB@ \| \|@LB@ 35 15@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -19.9467 kcal/mol@LB@Unfolding Energy - mRNA 4.98786 kcal/mol@LB@Unfolding Energy - sRNA 8.63814 kcal/mol@LB@@LB@Position - mRNA 72 -- 90@LB@Position - sRNA 16 -- 34@LB@Position Seed - mRNA 84 -- 90@LB@Position Seed - sRNA 16 -- 22@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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