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	Additional homologs
102	0.009578	0.3118	b1247	oppF	-10.09	0.116865	264 -- 290	39 -- 63	oligopeptide ABC transporter ATPase		_____________263__________________________291\n_____________\|____________________________\|\n5'-GCG...ACUUU______AA__A______A__________UGGCA...CGC-3'\n______________GAAAUC__AG_UGGCAA__CAGUGGUUC\n______________:\|\|\|\|\|__\|\|_\|\|\|\|\|\|__\|\|:\|\|\|::\|\n______________UUUUAG__UC_ACCGUU__GUUACCGGG\n3'-UUU...CAACC_________________AC_________UUGUC...UUG-5'\n_____________\|____________________________\|\n_____________64___________________________38\n	284 -- 290	39 -- 45	-23.4236 kcal/mol	6.69228 kcal/mol	6.64584 kcal/mol	263 291@LB@ \| \|@LB@5'-GCG...ACUUU AA A A UGGCA...CGC-3'@LB@ GAAAUC AG UGGCAA CAGUGGUUC@LB@ :\|\|\|\|\| \|\| \|\|\|\|\|\| \|\|:\|\|\|::\|@LB@ UUUUAG UC ACCGUU GUUACCGGG@LB@3'-UUU...CAACC AC UUGUC...UUG-5'@LB@ \| \|@LB@ 64 38@LB@@LB@@LB@Energy -10.09 kcal/mol@LB@Hybridization Energy -23.4236 kcal/mol@LB@Unfolding Energy - mRNA 6.69228 kcal/mol@LB@Unfolding Energy - sRNA 6.64584 kcal/mol@LB@@LB@Position - mRNA 264 -- 290@LB@Position - sRNA 39 -- 63@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 39 -- 45@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@
24	0.001299	0.182	b1267	yciO	-12.11	0.041783	4 -- 24	36 -- 58	putative RNA binding protein		_____________3_______________________25\n_____________\|_______________________\|\n________5'-GCG_____C_________C_______GAACG...CAA-3'\n______________CAGUG_CA__GCAAU_GCCCAAU\n______________\|\|\|\|\|_\|\|__\|\|\|\|\|_\|\|\|\|\|\|:\n______________GUCAC_GU__CGUUA_CGGGUUG\n3'-UUU...UUUUA_____C__UA_____C_______UCUUU...UUG-5'\n_____________\|_______________________\|\n_____________59______________________35\n	18 -- 24	36 -- 42	-24.2706 kcal/mol	1.86377 kcal/mol	10.2972 kcal/mol	3 25@LB@ \| \|@LB@ 5'-GCG C C GAACG...CAA-3'@LB@ CAGUG CA GCAAU GCCCAAU@LB@ \|\|\|\|\| \|\| \|\|\|\|\| \|\|\|\|\|\|:@LB@ GUCAC GU CGUUA CGGGUUG@LB@3'-UUU...UUUUA C UA C UCUUU...UUG-5'@LB@ \| \|@LB@ 59 35@LB@@LB@@LB@Energy -12.11 kcal/mol@LB@Hybridization Energy -24.2706 kcal/mol@LB@Unfolding Energy - mRNA 1.86377 kcal/mol@LB@Unfolding Energy - sRNA 10.2972 kcal/mol@LB@@LB@Position - mRNA 4 -- 24@LB@Position - sRNA 36 -- 58@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 36 -- 42@LB@
128	0.01375	0.3614	b1271	yciK	-9.18	0.177475	2 -- 35	4 -- 52	putative EmrKY-TolC system oxoacyl-(acyl carrier protein) reductase		_____________1_________________________________________________36\n_____________\|_________________________________________________\|\n__________5'-A___C__UU___________UUU________________C__________UAAGC...CAC-3'\n______________CAA_GC__UGGCUC_ACAG_______________ACAA___AGGCAUGU\n______________\|\|\|_\|\|__\|\|\|\|:\|_\|\|\|\|_______________\|\|\|\|___\|\|\|\|\|\|:\|\n______________GUU_CG__ACCGGG_UGUC_______________UGUU___UCCGUAUA\n3'-UUU...UCACC___A__UU______U____UUUUAUUUUAGACAC____AUU________UUG-5'\n_____________\|_________________________________________________\|\n_____________53________________________________________________3\n	29 -- 35	4 -- 10	-28.8633 kcal/mol	7.6461 kcal/mol	12.0385 kcal/mol	1 36@LB@ \| \|@LB@ 5'-A C UU UUU C UAAGC...CAC-3'@LB@ CAA GC UGGCUC ACAG ACAA AGGCAUGU@LB@ \|\|\| \|\| \|\|\|\|:\| \|\|\|\| \|\|\|\| \|\|\|\|\|\|:\|@LB@ GUU CG ACCGGG UGUC UGUU UCCGUAUA@LB@3'-UUU...UCACC A UU U UUUUAUUUUAGACAC AUU UUG-5'@LB@ \| \|@LB@ 53 3@LB@@LB@@LB@Energy -9.18 kcal/mol@LB@Hybridization Energy -28.8633 kcal/mol@LB@Unfolding Energy - mRNA 7.6461 kcal/mol@LB@Unfolding Energy - sRNA 12.0385 kcal/mol@LB@@LB@Position - mRNA 2 -- 35@LB@Position - sRNA 4 -- 52@LB@Position Seed - mRNA 29 -- 35@LB@Position Seed - sRNA 4 -- 10@LB@
33	0.002101	0.2088	b1300	puuC	-8.92	0.198515	81 -- 101	2 -- 20	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase; succinate semialdehyde dehydrogenase	b0312	_____________80____________________102\n_____________\|_____________________\|\n5'-GGC...CGGCU___AG_______U________AGAAU...AAA-3'\n______________UGA__GAUGAAG_GUAUAUAA\n______________\|\|\|__:\|\|:\|\|\|_\|:\|\|\|\|\|\|\n______________ACU__UUAUUUC_CGUAUAUU\n3'-UUU...UAGAC___G_________________G-5'\n_____________\|_____________________\|\n_____________21____________________1\n	94 -- 100	3 -- 9	-14.4968 kcal/mol	1.34672 kcal/mol	4.22649 kcal/mol	80 102@LB@ \| \|@LB@5'-GGC...CGGCU AG U AGAAU...AAA-3'@LB@ UGA GAUGAAG GUAUAUAA@LB@ \|\|\| :\|\|:\|\|\| \|:\|\|\|\|\|\|@LB@ ACU UUAUUUC CGUAUAUU@LB@3'-UUU...UAGAC G G-5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -8.92 kcal/mol@LB@Hybridization Energy -14.4968 kcal/mol@LB@Unfolding Energy - mRNA 1.34672 kcal/mol@LB@Unfolding Energy - sRNA 4.22649 kcal/mol@LB@@LB@Position - mRNA 81 -- 101@LB@Position - sRNA 2 -- 20@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 3 -- 9@LB@
63	0.004757	0.2539	b1342	ydaN	-13.10	0.024145	140 -- 198	7 -- 70	putative Zn(II) transporter		_____________139_______________________________________________________________199\n_____________\|_________________________________________________________________\|\n5'-CGU...AUGAG______CGU__________CA_____A____A___UAC_______UGCGU_______________CUGUG...AUG-3'\n______________AUGUUG___AA_CAG_GGC_____GA_GGCU_GAC___AAAAUAA______UGAUGAUGGAGGCA\n______________\|\|\|\|\|\|___\|\|_\|\|\|_\|\|\|_____:\|_\|\|\|:_:\|\|___\|\|\|\|\|\|\|______\|\|\|::\|\|::\|\|\|\|\|\n______________UACAAC___UU_GUC_CCG_____UU_CCGG_UUG___UUUUAUU______ACUGUUAUUUCCGU\n3'-UUU...AAAUA______CUU__A___A___UUACG__A____G___UC________UUAGAC______________AUAUUG-5'\n_____________\|_________________________________________________________________\|\n_____________71________________________________________________________________6\n	192 -- 198	7 -- 13	-39.9747 kcal/mol	14.7113 kcal/mol	12.1606 kcal/mol	139 199@LB@ \| \|@LB@5'-CGU...AUGAG CGU CA A A UAC UGCGU CUGUG...AUG-3'@LB@ AUGUUG AA CAG GGC GA GGCU GAC AAAAUAA UGAUGAUGGAGGCA@LB@ \|\|\|\|\|\| \|\| \|\|\| \|\|\| :\| \|\|\|: :\|\| \|\|\|\|\|\|\| \|\|\|::\|\|::\|\|\|\|\|@LB@ UACAAC UU GUC CCG UU CCGG UUG UUUUAUU ACUGUUAUUUCCGU@LB@3'-UUU...AAAUA CUU A A UUACG A G UC UUAGAC AUAUUG-5'@LB@ \| \|@LB@ 71 6@LB@@LB@@LB@Energy -13.10 kcal/mol@LB@Hybridization Energy -39.9747 kcal/mol@LB@Unfolding Energy - mRNA 14.7113 kcal/mol@LB@Unfolding Energy - sRNA 12.1606 kcal/mol@LB@@LB@Position - mRNA 140 -- 198@LB@Position - sRNA 7 -- 70@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 7 -- 13@LB@
42	0.002679	0.2088	b1427	rimL	-12.89	0.027177	178 -- 217	11 -- 49	ribosomal-protein-L7/L12-serine acetyltransferase		_____________177_______________________________________218\n_____________\|_________________________________________\|\n5'-GAU...ACAAC________AU____U___________GA___AA________AGUAA...CCU-3'\n______________UGC_AUGG__UGAC_GGAGAUAAGAU__CUG__ACGAUAAA\n______________\|\|\|_\|\|\|\|__::\|\|_\|:\|:\|\|\|\|:\|\|__\|\|\|__\|\|:\|\|\|\|\|\n______________ACG_UACC__GUUG_CUUUUAUUUUA__GAC__UGUUAUUU\n3'-UUU...CCGUU___U____GG____U________________AC________CCGUA...UUG-5'\n_____________\|_________________________________________\|\n_____________50________________________________________10\n	211 -- 217	11 -- 17	-27.9575 kcal/mol	3.9779 kcal/mol	11.0867 kcal/mol	177 218@LB@ \| \|@LB@5'-GAU...ACAAC AU U GA AA AGUAA...CCU-3'@LB@ UGC AUGG UGAC GGAGAUAAGAU CUG ACGAUAAA@LB@ \|\|\| \|\|\|\| ::\|\| \|:\|:\|\|\|\|:\|\| \|\|\| \|\|:\|\|\|\|\|@LB@ ACG UACC GUUG CUUUUAUUUUA GAC UGUUAUUU@LB@3'-UUU...CCGUU U GG U AC CCGUA...UUG-5'@LB@ \| \|@LB@ 50 10@LB@@LB@@LB@Energy -12.89 kcal/mol@LB@Hybridization Energy -27.9575 kcal/mol@LB@Unfolding Energy - mRNA 3.9779 kcal/mol@LB@Unfolding Energy - sRNA 11.0867 kcal/mol@LB@@LB@Position - mRNA 178 -- 217@LB@Position - sRNA 11 -- 49@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 11 -- 17@LB@
155	0.01799	0.3828	b1446	ydcY	-7.41	0.363872	123 -- 175	11 -- 59	DUF2526 family protein		_____________122______________________________________________________176\n_____________\|________________________________________________________\|\n5'-UAU...CUUAC___C____U___AC_____A___C_____CUU___UC_____GA___AU_______UUUCA...ACG-3'\n______________UCA_UGGC__UG____GGC_CCA_GCAGA___AUA__AUUUG__UGA__CGAUAAA\n______________\|\|\|_\|\|\|\|__\|\|____\|\|\|_\|\|\|_:\|\|\|\|___\|\|\|__\|\|:\|\|__\|\|\|__\|:\|\|\|\|\|\n______________AGU_ACCG__AC____CCG_GGU_UGUCU___UAU__UAGAC__ACU__GUUAUUU\n3'-UUU...CUUUU___C____UU__GUUA_____________UU____UU___________________CCGUA...UUG-5'\n_____________\|________________________________________________________\|\n_____________60_______________________________________________________10\n	169 -- 175	11 -- 17	-29.7235 kcal/mol	11.188 kcal/mol	11.1233 kcal/mol	122 176@LB@ \| \|@LB@5'-UAU...CUUAC C U AC A C CUU UC GA AU UUUCA...ACG-3'@LB@ UCA UGGC UG GGC CCA GCAGA AUA AUUUG UGA CGAUAAA@LB@ \|\|\| \|\|\|\| \|\| \|\|\| \|\|\| :\|\|\|\| \|\|\| \|\|:\|\| \|\|\| \|:\|\|\|\|\|@LB@ AGU ACCG AC CCG GGU UGUCU UAU UAGAC ACU GUUAUUU@LB@3'-UUU...CUUUU C UU GUUA UU UU CCGUA...UUG-5'@LB@ \| \|@LB@ 60 10@LB@@LB@@LB@Energy -7.41 kcal/mol@LB@Hybridization Energy -29.7235 kcal/mol@LB@Unfolding Energy - mRNA 11.188 kcal/mol@LB@Unfolding Energy - sRNA 11.1233 kcal/mol@LB@@LB@Position - mRNA 123 -- 175@LB@Position - sRNA 11 -- 59@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 11 -- 17@LB@
178	0.02184	0.4127	b1466	narW	-11.23	0.066200	254 -- 267	42 -- 56	nitrate reductase 2 (NRZ) delta subunit (assembly subunit)		_____________253_____________268\n_____________\|_______________\|\n5'-AUU...CUGUU____G__________AGGAC...CGC-3'\n______________GUGG_AAUGCAA_GG\n______________\|\|\|\|_\|\|\|\|\|\|\|_\|\|\n______________CACC_UUACGUU_CC\n3'-UUU...UUAGU____G_______A__GGGUU...UUG-5'\n_____________\|_______________\|\n_____________57______________41\n	259 -- 265	45 -- 51	-17.8423 kcal/mol	3.07693 kcal/mol	3.53153 kcal/mol	253 268@LB@ \| \|@LB@5'-AUU...CUGUU G AGGAC...CGC-3'@LB@ GUGG AAUGCAA GG@LB@ \|\|\|\| \|\|\|\|\|\|\| \|\|@LB@ CACC UUACGUU CC@LB@3'-UUU...UUAGU G A GGGUU...UUG-5'@LB@ \| \|@LB@ 57 41@LB@@LB@@LB@Energy -11.23 kcal/mol@LB@Hybridization Energy -17.8423 kcal/mol@LB@Unfolding Energy - mRNA 3.07693 kcal/mol@LB@Unfolding Energy - sRNA 3.53153 kcal/mol@LB@@LB@Position - mRNA 254 -- 267@LB@Position - sRNA 42 -- 56@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 45 -- 51@LB@
66	0.005339	0.2645	b1476	fdnI	-10.79	0.082799	156 -- 194	9 -- 48	formate dehydrogenase-N cytochrome B556 (gamma) subunit nitrate-inducible		_____________155________________________________________195\n_____________\|__________________________________________\|\n5'-CGU...CAUCG___U________AUA_____________GA______G_____AUCAU...UUU-3'\n______________GUA_UGGCCCGA___AGGAAGUGGA__C__UGACGA__GAGG\n______________\|:\|_\|\|\|\|\|\|:\|___\|\|:\|\|:\|::\|__\|__\|\|\|\|:\|__:\|\|\|\n______________CGU_ACCGGGUU___UCUUUUAUUU__G__ACUGUU__UUCC\n3'-UUU...CGUUA___U________G____________UA_AC______AU____GUAUAUUG-5'\n_____________\|__________________________________________\|\n_____________49_________________________________________8\n	161 -- 167	37 -- 43	-34.1322 kcal/mol	12.2398 kcal/mol	11.1008 kcal/mol	155 195@LB@ \| \|@LB@5'-CGU...CAUCG U AUA GA G AUCAU...UUU-3'@LB@ GUA UGGCCCGA AGGAAGUGGA C UGACGA GAGG@LB@ \|:\| \|\|\|\|\|\|:\| \|\|:\|\|:\|::\| \| \|\|\|\|:\| :\|\|\|@LB@ CGU ACCGGGUU UCUUUUAUUU G ACUGUU UUCC@LB@3'-UUU...CGUUA U G UA AC AU GUAUAUUG-5'@LB@ \| \|@LB@ 49 8@LB@@LB@@LB@Energy -10.79 kcal/mol@LB@Hybridization Energy -34.1322 kcal/mol@LB@Unfolding Energy - mRNA 12.2398 kcal/mol@LB@Unfolding Energy - sRNA 11.1008 kcal/mol@LB@@LB@Position - mRNA 156 -- 194@LB@Position - sRNA 9 -- 48@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 37 -- 43@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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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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