Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
161	0.01797	0.3749	b1921	fliZ	-13.03	0.068461	73 -- 137	125 -- 204	RpoS antagonist; putative regulator of FliA activity	_____________72__________________________________________138\n_____________\|___________________________________________\|\n5'-UGC...GAGGU_______AU______G___C_G___________GC________UAUUA...AUC-3'\n______________CGGG_GA_____CGC_GGU_A_UCAGUUACACA_____CAGGC\n______________\|\|\|\|_\|\|_____\|:\|_::\|_\|_\|\|\|\|\|:\|\|\|\|\|_____\|\|\|\|\|\n______________GCCC_CU_____GUG_UUA_U_AGUCAGUGUGU_____GUCCG\n3'-UUU...CGACC____A__AAAAU___G_____G___________ACUAC_____UUCAG...UAG-5'\n_____________\|___________________________________________\|\n_____________205_________________________________________124\n	105 -- 111	167 -- 173	-36.0631 kcal/mol	8.93512 kcal/mol	13.9606 kcal/mol	72 138@LB@ \| \|@LB@5'-UGC...GAGGU AU G C G GC UAUUA...AUC-3'@LB@ CGGG GA CGC GGU A UCAGUUACACA CAGGC@LB@ \|\|\|\| \|\| \|:\| ::\| \| \|\|\|\|\|:\|\|\|\|\| \|\|\|\|\|@LB@ GCCC CU GUG UUA U AGUCAGUGUGU GUCCG@LB@3'-UUU...CGACC A AAAAU G G ACUAC UUCAG...UAG-5'@LB@ \| \|@LB@ 205 124@LB@@LB@@LB@Energy -13.03 kcal/mol@LB@Hybridization Energy -36.0631 kcal/mol@LB@Unfolding Energy - mRNA 8.93512 kcal/mol@LB@Unfolding Energy - sRNA 13.9606 kcal/mol@LB@@LB@Position - mRNA 73 -- 137@LB@Position - sRNA 125 -- 204@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 167 -- 173@LB@
102	0.01106	0.3575	b0647	ybeT	-15.01	0.026876	192 -- 264	115 -- 176	Sel1 family TPR-like repeat protein	_____________191___________265\n_____________\|_____________\|\n5'-AUA...CGAAG__U__________AUAAA...UGG-3'\n______________CA_UCACACAUGA\n______________\|\|_\|\|\|\|\|\|\|\|\|\|\n______________GU_AGUGUGUACU\n3'-UUU...UAUGA__C__________ACGUC...UAG-5'\n_____________\|_____________\|\n_____________177___________114\n	198 -- 204	164 -- 170	-15.9732 kcal/mol	2.87622 kcal/mol	4.17773 kcal/mol	191 265@LB@ \| \|@LB@5'-AUA...CGAAG U AUAAA...UGG-3'@LB@ CA UCACACAUGA@LB@ \|\| \|\|\|\|\|\|\|\|\|\|@LB@ GU AGUGUGUACU@LB@3'-UUU...UAUGA C ACGUC...UAG-5'@LB@ \| \|@LB@ 177 114@LB@@LB@@LB@Energy -15.01 kcal/mol@LB@Hybridization Energy -15.9732 kcal/mol@LB@Unfolding Energy - mRNA 2.87622 kcal/mol@LB@Unfolding Energy - sRNA 4.17773 kcal/mol@LB@@LB@Position - mRNA 192 -- 264@LB@Position - sRNA 115 -- 176@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 164 -- 170@LB@
170	0.01941	0.3812	b3911	cpxA	-13.13	0.065341	265 -- 299	168 -- 204	sensory histidine kinase in two-component regulatory system with CpxR	_____________264______300\n_____________\|________\|\n5'-UAU...GUUUC________GAUAG...GCC-3'\n______________UGCUUCAU\n______________\|\|\|\|\|\|\|\|\n______________ACGAAGUA\n3'-UUU...GGGGA________G-5'\n_____________\|________\|\n_____________205______167\n	196 -- 202	2 -- 8	-10.3801 kcal/mol	3.0426 kcal/mol	0.709873 kcal/mol	264 300@LB@ \| \|@LB@5'-UAU...GUUUC GAUAG...GCC-3'@LB@ UGCUUCAU@LB@ \|\|\|\|\|\|\|\|@LB@ ACGAAGUA@LB@3'-UUU...GGGGA G-5'@LB@ \| \|@LB@ 205 167@LB@@LB@@LB@Energy -13.13 kcal/mol@LB@Hybridization Energy -10.3801 kcal/mol@LB@Unfolding Energy - mRNA 3.0426 kcal/mol@LB@Unfolding Energy - sRNA 0.709873 kcal/mol@LB@@LB@Position - mRNA 265 -- 299@LB@Position - sRNA 168 -- 204@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 2 -- 8@LB@
24	0.001922	0.2633	b3017	ftsP	-19.79	0.002953	203 -- 291	63 -- 135	septal ring component that protects the divisome from stress; multicopy suppressor of ftsI(Ts)	_____________202__________________________________________________________________________________________292\n_____________\|____________________________________________________________________________________________\|\n5'-GAC...AAUAU_________GUCG__________A_________C__G______CACU_____CA______GUUCCCCUGAAG____________________AGCAA...CGC-3'\n______________GUCA_CUCA____GCGUCAGUUC_UUCAGGCAU_GG__GAUUG____UUGUG__GGCGCU____________GCCAGCGCAGCCGG_GCAAC\n______________\|\|\|\|_\|:\|\|____\|\|:\|\|\|\|\|:\|_\|\|\|\|:\|\|\|\|_\|\|__:\|\|:\|____\|\|\|\|\|__\|:\|\|\|\|____________:\|\|\|:\|\|\|\|:\|\|:\|_:\|\|\|\|\n______________CAGU_GGGU____CGUAGUCAGG_AAGUUCGUA_CC__UUAGC____AACAC__CUGCGA____________UGGUUGCGUUGGUC_UGUUG\n3'-UUU...AACGC____A____GA_________________________AA______________C_______AU________________________G_____AAGCG...UAG-5'\n_____________\|____________________________________________________________________________________________\|\n_____________136__________________________________________________________________________________________62\n	278 -- 284	71 -- 77	-82.7619 kcal/mol	32.3928 kcal/mol	37.2191 kcal/mol	202 292@LB@ \| \|@LB@5'-GAC...AAUAU GUCG A C G CACU CA GUUCCCCUGAAG AGCAA...CGC-3'@LB@ GUCA CUCA GCGUCAGUUC UUCAGGCAU GG GAUUG UUGUG GGCGCU GCCAGCGCAGCCGG GCAAC@LB@ \|\|\|\| \|:\|\| \|\|:\|\|\|\|\|:\| \|\|\|\|:\|\|\|\| \|\| :\|\|:\| \|\|\|\|\| \|:\|\|\|\| :\|\|\|:\|\|\|\|:\|\|:\| :\|\|\|\|@LB@ CAGU GGGU CGUAGUCAGG AAGUUCGUA CC UUAGC AACAC CUGCGA UGGUUGCGUUGGUC UGUUG@LB@3'-UUU...AACGC A GA AA C AU G AAGCG...UAG-5'@LB@ \| \|@LB@ 136 62@LB@@LB@@LB@Energy -19.79 kcal/mol@LB@Hybridization Energy -82.7619 kcal/mol@LB@Unfolding Energy - mRNA 32.3928 kcal/mol@LB@Unfolding Energy - sRNA 37.2191 kcal/mol@LB@@LB@Position - mRNA 203 -- 291@LB@Position - sRNA 63 -- 135@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 71 -- 77@LB@
20	0.001715	0.2633	b3453	ugpB	-12.22	0.100645	241 -- 257	18 -- 32	sn-glycerol-3-phosphate ABC transporter periplasmic binding protein	_____________240______________258\n_____________\|________________\|\n5'-UUC...AAUUC_____U__________AAGAG...UGG-3'\n______________GCGCA_UCGGUACAAC\n______________:\|\|\|\|_:\|:\|:\|\|\|\|\|\n______________UGCGU_GGUCGUGUUG\n3'-UUU...UUGGU_____U__________AAGCG...UAG-5'\n_____________\|________________\|\n_____________33_______________17\n	180 -- 186	63 -- 69	-22.0099 kcal/mol	5.49331 kcal/mol	9.84719 kcal/mol	240 258@LB@ \| \|@LB@5'-UUC...AAUUC U AAGAG...UGG-3'@LB@ GCGCA UCGGUACAAC@LB@ :\|\|\|\| :\|:\|:\|\|\|\|\|@LB@ UGCGU GGUCGUGUUG@LB@3'-UUU...UUGGU U AAGCG...UAG-5'@LB@ \| \|@LB@ 33 17@LB@@LB@@LB@Energy -12.22 kcal/mol@LB@Hybridization Energy -22.0099 kcal/mol@LB@Unfolding Energy - mRNA 5.49331 kcal/mol@LB@Unfolding Energy - sRNA 9.84719 kcal/mol@LB@@LB@Position - mRNA 241 -- 257@LB@Position - sRNA 18 -- 32@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 63 -- 69@LB@
179	0.02059	0.3833	b2535	csiE	-10.55	0.216292	103 -- 142	58 -- 90	stationary phase inducible protein	_____________102___________143\n_____________\|_____________\|\n5'-GCA...GAUUA__________C__CAUUU...UGG-3'\n______________GCAUUCCCUU_GC\n______________\|\|\|::\|\|\|\|\|_\|\|\n______________CGUGGGGGAA_CG\n3'-UUU...UACCC_____________AAGUAG-5'\n_____________\|_____________\|\n_____________91____________57\n	133 -- 139	9 -- 15	-16.9052 kcal/mol	2.85301 kcal/mol	6.64496 kcal/mol	102 143@LB@ \| \|@LB@5'-GCA...GAUUA C CAUUU...UGG-3'@LB@ GCAUUCCCUU GC@LB@ \|\|\|::\|\|\|\|\| \|\|@LB@ CGUGGGGGAA CG@LB@3'-UUU...UACCC AAGUAG-5'@LB@ \| \|@LB@ 91 57@LB@@LB@@LB@Energy -10.55 kcal/mol@LB@Hybridization Energy -16.9052 kcal/mol@LB@Unfolding Energy - mRNA 2.85301 kcal/mol@LB@Unfolding Energy - sRNA 6.64496 kcal/mol@LB@@LB@Position - mRNA 103 -- 142@LB@Position - sRNA 58 -- 90@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 9 -- 15@LB@
147	0.01564	0.358	b3153	yhbO	-15.63	0.020103	154 -- 186	72 -- 98	stress-resistance protein	_____________153_______________________________187\n_____________\|_________________________________\|\n5'-GUU...AUCCC__A________AAUU___CUCAU__________AACGC...UUA-3'\n______________CG_UUGUGGGA____CGC_____CCAAUGCAAC\n______________\|\|_\|\|\|\|\|\|\|\|____\|\|\|_____\|\|\|\|:\|\|\|\|\|\n______________GC_AACACCCU____GCG_____GGUUGCGUUG\n3'-UUU...AAUUA__________________AAUU___________GUCGU...UAG-5'\n_____________\|_________________________________\|\n_____________99________________________________71\n	180 -- 186	72 -- 78	-31.4938 kcal/mol	8.17407 kcal/mol	13.9341 kcal/mol	153 187@LB@ \| \|@LB@5'-GUU...AUCCC A AAUU CUCAU AACGC...UUA-3'@LB@ CG UUGUGGGA CGC CCAAUGCAAC@LB@ \|\| \|\|\|\|\|\|\|\| \|\|\| \|\|\|\|:\|\|\|\|\|@LB@ GC AACACCCU GCG GGUUGCGUUG@LB@3'-UUU...AAUUA AAUU GUCGU...UAG-5'@LB@ \| \|@LB@ 99 71@LB@@LB@@LB@Energy -15.63 kcal/mol@LB@Hybridization Energy -31.4938 kcal/mol@LB@Unfolding Energy - mRNA 8.17407 kcal/mol@LB@Unfolding Energy - sRNA 13.9341 kcal/mol@LB@@LB@Position - mRNA 154 -- 186@LB@Position - sRNA 72 -- 98@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 72 -- 78@LB@
108	0.01175	0.3575	b0723	sdhA	-10.39	0.232370	178 -- 209	28 -- 62	succinate dehydrogenase flavoprotein subunit	_____________177_______________________210\n_____________\|_________________________\|\n5'-GGU...GAAAU__________G_G_AUU________UUGUG...GUG-3'\n______________UGC_CAGUCA_A_A___UGAUGCAG\n______________\|:\|_\|\|\|\|\|\|_\|_\|___\|\|\|\|\|\|\|\|\n______________AUG_GUCAGU_U_U___ACUACGUC\n3'-UUU...UGGUU___A______G_G____________CGUUC...UAG-5'\n_____________\|_________________________\|\n_____________63________________________27\n	225 -- 231	159 -- 165	-22.5908 kcal/mol	8.24888 kcal/mol	4.81331 kcal/mol	177 210@LB@ \| \|@LB@5'-GGU...GAAAU G G AUU UUGUG...GUG-3'@LB@ UGC CAGUCA A A UGAUGCAG@LB@ \|:\| \|\|\|\|\|\| \| \| \|\|\|\|\|\|\|\|@LB@ AUG GUCAGU U U ACUACGUC@LB@3'-UUU...UGGUU A G G CGUUC...UAG-5'@LB@ \| \|@LB@ 63 27@LB@@LB@@LB@Energy -10.39 kcal/mol@LB@Hybridization Energy -22.5908 kcal/mol@LB@Unfolding Energy - mRNA 8.24888 kcal/mol@LB@Unfolding Energy - sRNA 4.81331 kcal/mol@LB@@LB@Position - mRNA 178 -- 209@LB@Position - sRNA 28 -- 62@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 159 -- 165@LB@
197	0.02355	0.3833	b2764	cysJ	-10.17	0.255883	3 -- 30	98 -- 123	sulfite reductase alpha subunit flavoprotein	_____________2________31\n_____________\|________\|\n5'-UUC...AACAG________ACUGG...UUG-3'\n______________CUUUGCUU\n______________\|:\|\|\|\|\|\|\n______________GGAACGAA\n3'-UUU...GUGGG________GUAG-5'\n_____________\|________\|\n_____________124______97\n	176 -- 182	5 -- 11	-8.59037 kcal/mol	0.881795 kcal/mol	1.04254 kcal/mol	2 31@LB@ \| \|@LB@5'-UUC...AACAG ACUGG...UUG-3'@LB@ CUUUGCUU@LB@ \|:\|\|\|\|\|\|@LB@ GGAACGAA@LB@3'-UUU...GUGGG GUAG-5'@LB@ \| \|@LB@ 124 97@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -8.59037 kcal/mol@LB@Unfolding Energy - mRNA 0.881795 kcal/mol@LB@Unfolding Energy - sRNA 1.04254 kcal/mol@LB@@LB@Position - mRNA 3 -- 30@LB@Position - sRNA 98 -- 123@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 5 -- 11@LB@
80	0.008443	0.3551	b3791	wecE	-14.19	0.039608	22 -- 66	14 -- 64	TDP-4-oxo-6-deoxy-D-glucose transaminase	_____________21______________67\n_____________\|_______________\|\n5'-GAC...ACCGC_______________GGUGA...CCC-3'\n______________GUACU_GGUUAUACA\n______________:\|\|\|\|_:\|\|:\|:\|\|\|\n______________UAUGA_UCAGUGUGU\n3'-UUU...GUGGU_____G_________ACUAC...UAG-5'\n_____________\|_______________\|\n_____________65______________13\n	185 -- 191	167 -- 173	-12.5686 kcal/mol	2.73267 kcal/mol	0.435744 kcal/mol	21 67@LB@ \| \|@LB@5'-GAC...ACCGC GGUGA...CCC-3'@LB@ GUACU GGUUAUACA@LB@ :\|\|\|\| :\|\|:\|:\|\|\|@LB@ UAUGA UCAGUGUGU@LB@3'-UUU...GUGGU G ACUAC...UAG-5'@LB@ \| \|@LB@ 65 13@LB@@LB@@LB@Energy -14.19 kcal/mol@LB@Hybridization Energy -12.5686 kcal/mol@LB@Unfolding Energy - mRNA 2.73267 kcal/mol@LB@Unfolding Energy - sRNA 0.435744 kcal/mol@LB@@LB@Position - mRNA 22 -- 66@LB@Position - sRNA 14 -- 64@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 167 -- 173@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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