Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
132	0.004965	0.1313	b0876	ybjD	-10.35	0.091015	20 -- 74	49 -- 93	putative OLD family ATP-dependent endonuclease; DUF2813 family protein		_____________19______________________________________________________75\n_____________\|_______________________________________________________\|\n5'-CGU...AUUUA__A___U_____U___AUUU_____UUUU_____ACUUA____C___________UAACG...GGG-3'\n______________UC_UGC_AAUUA_UUG____UGUUG____UGCAG_____UCAG_AAGAGGGAGUA\n______________\|\|_\|:\|_\|\|\|:\|_\|\|\|____\|\|:\|:____\|\|\|\|\|_____\|\|\|:_\|\|:\|\|\|:\|\|\|\|\n______________AG_AUG_UUAGU_AAC____ACGAU____ACGUC_____AGUU_UUUUCCUUCAU\n3'-UUU...GCCGC__C___C_____U_____________________AUUA_________________UCUGU...ACG-5'\n_____________\|_______________________________________________________\|\n_____________94______________________________________________________48\n	68 -- 74	49 -- 55	-28.5607 kcal/mol	13.348 kcal/mol	4.86987 kcal/mol	19 75@LB@ \| \|@LB@5'-CGU...AUUUA A U U AUUU UUUU ACUUA C UAACG...GGG-3'@LB@ UC UGC AAUUA UUG UGUUG UGCAG UCAG AAGAGGGAGUA@LB@ \|\| \|:\| \|\|\|:\| \|\|\| \|\|:\|: \|\|\|\|\| \|\|\|: \|\|:\|\|\|:\|\|\|\|@LB@ AG AUG UUAGU AAC ACGAU ACGUC AGUU UUUUCCUUCAU@LB@3'-UUU...GCCGC C C U AUUA UCUGU...ACG-5'@LB@ \| \|@LB@ 94 48@LB@@LB@@LB@Energy -10.35 kcal/mol@LB@Hybridization Energy -28.5607 kcal/mol@LB@Unfolding Energy - mRNA 13.348 kcal/mol@LB@Unfolding Energy - sRNA 4.86987 kcal/mol@LB@@LB@Position - mRNA 20 -- 74@LB@Position - sRNA 49 -- 93@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 49 -- 55@LB@
175	0.007208	0.145	b1444	patD	-10.32	0.092173	197 -- 205	69 -- 77	gamma-aminobutyraldehyde dehydrogenase		_____________196_______206\n_____________\|_________\|\n5'-UCG...GAAUA_________ACAUA...UUG-3'\n______________UGCUAUGCA\n______________\|\|\|\|\|\|\|\|\|\n______________ACGAUACGU\n3'-UUU...UUAAC_________CAUUA...ACG-5'\n_____________\|_________\|\n_____________78________68\n	199 -- 205	69 -- 75	-13.9965 kcal/mol	1.91367 kcal/mol	1.75858 kcal/mol	196 206@LB@ \| \|@LB@5'-UCG...GAAUA ACAUA...UUG-3'@LB@ UGCUAUGCA@LB@ \|\|\|\|\|\|\|\|\|@LB@ ACGAUACGU@LB@3'-UUU...UUAAC CAUUA...ACG-5'@LB@ \| \|@LB@ 78 68@LB@@LB@@LB@Energy -10.32 kcal/mol@LB@Hybridization Energy -13.9965 kcal/mol@LB@Unfolding Energy - mRNA 1.91367 kcal/mol@LB@Unfolding Energy - sRNA 1.75858 kcal/mol@LB@@LB@Position - mRNA 197 -- 205@LB@Position - sRNA 69 -- 77@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 69 -- 75@LB@
23	8.752e-05	0.01341	b1476	fdnI	-10.32	0.092280	170 -- 193	36 -- 57	formate dehydrogenase-N cytochrome B556 (gamma) subunit nitrate-inducible		_____________169_______________________194\n_____________\|_________________________\|\n5'-CGU...CGAAU_________________ACGA____GAUCA...UUU-3'\n______________AAGGAAGU_GGACGAUG____GGAG\n______________\|\|\|\|\|\|\|\|_:\|\|\|:\|\|:____\|\|\|\|\n______________UUCCUUCA_UCUGUUAU____CCUC\n3'-UUU...GUUUU________U________A_______GCGUU...ACG-5'\n_____________\|_________________________\|\n_____________58________________________35\n	179 -- 185	41 -- 47	-22.1274 kcal/mol	8.02585 kcal/mol	3.74338 kcal/mol	169 194@LB@ \| \|@LB@5'-CGU...CGAAU ACGA GAUCA...UUU-3'@LB@ AAGGAAGU GGACGAUG GGAG@LB@ \|\|\|\|\|\|\|\| :\|\|\|:\|\|: \|\|\|\|@LB@ UUCCUUCA UCUGUUAU CCUC@LB@3'-UUU...GUUUU U A GCGUU...ACG-5'@LB@ \| \|@LB@ 58 35@LB@@LB@@LB@Energy -10.32 kcal/mol@LB@Hybridization Energy -22.1274 kcal/mol@LB@Unfolding Energy - mRNA 8.02585 kcal/mol@LB@Unfolding Energy - sRNA 3.74338 kcal/mol@LB@@LB@Position - mRNA 170 -- 193@LB@Position - sRNA 36 -- 57@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 41 -- 47@LB@
37	0.0003128	0.02889	b1107	nagZ	-10.24	0.096497	189 -- 204	38 -- 57	beta N-acetyl-glucosaminidase		_____________188__________________205\n_____________\|____________________\|\n5'-AUU...ACAAU____________________GUCCA...CGC-3'\n______________AAGGA___GAG_CAGUGUGG\n______________\|\|\|\|\|___:\|\|_\|\|:\|:\|\|\|\n______________UUCCU___UUC_GUUAUACC\n3'-UUU...GUUUU_____UCA___U________UCGCG...ACG-5'\n_____________\|____________________\|\n_____________58___________________37\n	198 -- 204	38 -- 44	-15.5747 kcal/mol	1.78066 kcal/mol	3.52446 kcal/mol	188 205@LB@ \| \|@LB@5'-AUU...ACAAU GUCCA...CGC-3'@LB@ AAGGA GAG CAGUGUGG@LB@ \|\|\|\|\| :\|\| \|\|:\|:\|\|\|@LB@ UUCCU UUC GUUAUACC@LB@3'-UUU...GUUUU UCA U UCGCG...ACG-5'@LB@ \| \|@LB@ 58 37@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -15.5747 kcal/mol@LB@Unfolding Energy - mRNA 1.78066 kcal/mol@LB@Unfolding Energy - sRNA 3.52446 kcal/mol@LB@@LB@Position - mRNA 189 -- 204@LB@Position - sRNA 38 -- 57@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 38 -- 44@LB@
50	0.0005726	0.04013	b2215	ompC	-10.22	0.097386	138 -- 180	44 -- 87	outer membrane porin protein C	b0929 b0241 b1377	_____________137___________________________________________181\n_____________\|_____________________________________________\|\n5'-AUC...AAUGA________CAG____________CA________CAAAUA______UAUAA...AUC-3'\n______________GGGUUAAU_____UAUGCAGUGG__UAAAAAAG______AAGGCA\n______________\|::\|:\|\|\|_____\|\|\|\|\|\|\|\|::__:\|\|\|\|\|\|\|______\|\|\|:\|\|\n______________CUUAGUUA_____AUACGUCAUU__GUUUUUUC______UUCUGU\n3'-UUU...GCAUG________ACACG__________AA________CUUCA_______UAUAC...ACG-5'\n_____________\|_____________________________________________\|\n_____________88____________________________________________43\n	162 -- 168	55 -- 61	-25.937 kcal/mol	10.0096 kcal/mol	5.70573 kcal/mol	137 181@LB@ \| \|@LB@5'-AUC...AAUGA CAG CA CAAAUA UAUAA...AUC-3'@LB@ GGGUUAAU UAUGCAGUGG UAAAAAAG AAGGCA@LB@ \|::\|:\|\|\| \|\|\|\|\|\|\|\|:: :\|\|\|\|\|\|\| \|\|\|:\|\|@LB@ CUUAGUUA AUACGUCAUU GUUUUUUC UUCUGU@LB@3'-UUU...GCAUG ACACG AA CUUCA UAUAC...ACG-5'@LB@ \| \|@LB@ 88 43@LB@@LB@@LB@Energy -10.22 kcal/mol@LB@Hybridization Energy -25.937 kcal/mol@LB@Unfolding Energy - mRNA 10.0096 kcal/mol@LB@Unfolding Energy - sRNA 5.70573 kcal/mol@LB@@LB@Position - mRNA 138 -- 180@LB@Position - sRNA 44 -- 87@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 55 -- 61@LB@
141	0.005411	0.1351	b3260	dusB	-10.20	0.098848	236 -- 254	20 -- 38	tRNA-dihydrouridine synthase B		_____________235_________________255\n_____________\|___________________\|\n5'-ACU...CGCCU__U____________G___GGCAU...GAG-3'\n______________GA_CGCAGCGCCCAU_GCU\n______________\|\|_\|\|\|\|:\|\|\|\|\|\|\|_\|\|\|\n______________CU_GCGUUGCGGGUA_CGA\n3'-UUU...UAUAC__C____________G___ACUGC...ACG-5'\n_____________\|___________________\|\n_____________39__________________19\n	244 -- 250	24 -- 30	-30.8965 kcal/mol	8.5282 kcal/mol	12.1733 kcal/mol	235 255@LB@ \| \|@LB@5'-ACU...CGCCU U G GGCAU...GAG-3'@LB@ GA CGCAGCGCCCAU GCU@LB@ \|\| \|\|\|\|:\|\|\|\|\|\|\| \|\|\|@LB@ CU GCGUUGCGGGUA CGA@LB@3'-UUU...UAUAC C G ACUGC...ACG-5'@LB@ \| \|@LB@ 39 19@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -30.8965 kcal/mol@LB@Unfolding Energy - mRNA 8.5282 kcal/mol@LB@Unfolding Energy - sRNA 12.1733 kcal/mol@LB@@LB@Position - mRNA 236 -- 254@LB@Position - sRNA 20 -- 38@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 24 -- 30@LB@
106	0.003401	0.1114	b1848	yebG	-10.18	0.099613	222 -- 299	16 -- 71	DNA damage-inducible protein regulated by LexA		_____________221_______________________________________________________________________________300\n_____________\|_________________________________________________________________________________\|\n5'-GUU...AAUAC_____C_____U_____C_________A_____CGUUUACCAGCAAAAA__A______________GACAAAA________A-3'\n______________GUAGU_AUUCG_GAGGG_GAAG__AGA_AAUGU________________GG_AGC_CGAUGCUUAU_______UGCUUGAU\n______________\|:\|\|\|_\|\|\|\|:_:\|::\|_\|\|\|\|__\|\|\|_\|\|\|:\|________________\|\|_\|\|\|_\|:\|:\|\|::\|\|_______:\|\|\|\|\|\|:\n______________CGUCA_UAAGU_UUUUC_CUUC__UCU_UUAUA________________CC_UCG_GUUGCGGGUA_______GCGAACUG\n3'-UUU...CGAUA_____U_____U__________AU___G___________________________C_________________________CAACG...ACG-5'\n_____________\|_________________________________________________________________________________\|\n_____________72________________________________________________________________________________15\n	293 -- 299	16 -- 22	-43.4853 kcal/mol	15.7801 kcal/mol	17.5254 kcal/mol	221 300@LB@ \| \|@LB@5'-GUU...AAUAC C U C A CGUUUACCAGCAAAAA A GACAAAA A-3'@LB@ GUAGU AUUCG GAGGG GAAG AGA AAUGU GG AGC CGAUGCUUAU UGCUUGAU@LB@ \|:\|\|\| \|\|\|\|: :\|::\| \|\|\|\| \|\|\| \|\|\|:\| \|\| \|\|\| \|:\|:\|\|::\|\| :\|\|\|\|\|\|:@LB@ CGUCA UAAGU UUUUC CUUC UCU UUAUA CC UCG GUUGCGGGUA GCGAACUG@LB@3'-UUU...CGAUA U U AU G C CAACG...ACG-5'@LB@ \| \|@LB@ 72 15@LB@@LB@@LB@Energy -10.18 kcal/mol@LB@Hybridization Energy -43.4853 kcal/mol@LB@Unfolding Energy - mRNA 15.7801 kcal/mol@LB@Unfolding Energy - sRNA 17.5254 kcal/mol@LB@@LB@Position - mRNA 222 -- 299@LB@Position - sRNA 16 -- 71@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 16 -- 22@LB@
53	0.0006788	0.04512	b3949	frwC	-10.17	0.100438	200 -- 218	68 -- 90	putative enzyme IIC component of PTS		_____________199_____________________219\n_____________\|_______________________\|\n5'-UUG...CAGCU_______G_______________AUCCU...UGG-3'\n______________UAUGAAU_AGUUG____GUGCAG\n______________\|\|:\|\|\|\|_\|:\|\|\|____:\|\|\|\|\|\n______________AUGCUUA_UUAAC____UACGUC\n3'-UUU...GCAGC_______G_____ACGA______AUUAA...ACG-5'\n_____________\|_______________________\|\n_____________91______________________67\n	200 -- 206	84 -- 90	-18.2816 kcal/mol	3.60123 kcal/mol	4.51505 kcal/mol	199 219@LB@ \| \|@LB@5'-UUG...CAGCU G AUCCU...UGG-3'@LB@ UAUGAAU AGUUG GUGCAG@LB@ \|\|:\|\|\|\| \|:\|\|\| :\|\|\|\|\|@LB@ AUGCUUA UUAAC UACGUC@LB@3'-UUU...GCAGC G ACGA AUUAA...ACG-5'@LB@ \| \|@LB@ 91 67@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -18.2816 kcal/mol@LB@Unfolding Energy - mRNA 3.60123 kcal/mol@LB@Unfolding Energy - sRNA 4.51505 kcal/mol@LB@@LB@Position - mRNA 200 -- 218@LB@Position - sRNA 68 -- 90@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 84 -- 90@LB@
82	0.001946	0.08273	b2661	gabD	-10.13	0.102437	19 -- 25	1 -- 7	succinate-semialdehyde dehydrogenase I NADP-dependent		_____________18______26\n_____________\|_______\|\n5'-CAC...AUCCA_______AAUGC...CGG-3'\n______________CACCUGC\n______________\|\|\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	19 -- 25	1 -- 7	-13.7555 kcal/mol	1.28845 kcal/mol	2.34039 kcal/mol	18 26@LB@ \| \|@LB@5'-CAC...AUCCA AAUGC...CGG-3'@LB@ CACCUGC@LB@ \|\|\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -10.13 kcal/mol@LB@Hybridization Energy -13.7555 kcal/mol@LB@Unfolding Energy - mRNA 1.28845 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 19 -- 25@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 1 -- 7@LB@
122	0.004264	0.1231	b2914	rpiA	-10.11	0.103884	190 -- 234	45 -- 89	ribose 5-phosphate isomerase constitutive		_____________189______________________________________________235\n_____________\|________________________________________________\|\n5'-GAA...CACAG_____A____CA__AC______GAUGA___G_______C_________GGGCG...CAC-3'\n______________GCGAA_CGAU__UG____GCAG_____AUU_AAAAAAG__AGUAGGAU\n______________:\|\|\|\|_\|:\|\|__\|\|____\|\|\|\|_____\|\|\|_\|\|\|\|\|\|\|__\|\|\|\|:\|\|:\n______________UGCUU_GUUA__AC____CGUC_____UAA_UUUUUUC__UCAUUCUG\n3'-UUU...CAGCA_____A____AC__GAUA____AU______G_______CU________UUAUA...ACG-5'\n_____________\|________________________________________________\|\n_____________90_______________________________________________44\n	228 -- 234	45 -- 51	-27.3521 kcal/mol	11.527 kcal/mol	5.72096 kcal/mol	189 235@LB@ \| \|@LB@5'-GAA...CACAG A CA AC GAUGA G C GGGCG...CAC-3'@LB@ GCGAA CGAU UG GCAG AUU AAAAAAG AGUAGGAU@LB@ :\|\|\|\| \|:\|\| \|\| \|\|\|\| \|\|\| \|\|\|\|\|\|\| \|\|\|\|:\|\|:@LB@ UGCUU GUUA AC CGUC UAA UUUUUUC UCAUUCUG@LB@3'-UUU...CAGCA A AC GAUA AU G CU UUAUA...ACG-5'@LB@ \| \|@LB@ 90 44@LB@@LB@@LB@Energy -10.11 kcal/mol@LB@Hybridization Energy -27.3521 kcal/mol@LB@Unfolding Energy - mRNA 11.527 kcal/mol@LB@Unfolding Energy - sRNA 5.72096 kcal/mol@LB@@LB@Position - mRNA 190 -- 234@LB@Position - sRNA 45 -- 89@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 45 -- 51@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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