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
86	0.002341	0.09591	b0144	gluQ	-7.21	0.411815	221 -- 264	26 -- 65	glutamyl-Q tRNA(Asp) synthetase	_____________220__________________________________________265\n_____________\|____________________________________________\|\n5'-AGA...UUUUU__________AU__C__ACAC_______AUU__C___UU_____CCUCU...UGA-3'\n______________GUUCAAAGAG__GA_AG____ACAGUAU___GG_CGC__CGCCC\n______________:\|\|\|\|\|\|:\|:__\|\|_\|\|____\|\|\|:\|\|\|___:\|_\|\|\|__\|\|\|\|\|\n______________UAAGUUUUUU__CU_UC____UGUUAUA___UC_GCG__GCGGG\n3'-UUU...GUCAU__________C______AUUC_______CC_______UU_____UAGCG...ACG-5'\n_____________\|____________________________________________\|\n_____________66___________________________________________25\n	242 -- 248	40 -- 46	-28.4973 kcal/mol	7.75098 kcal/mol	13.5387 kcal/mol	220 265@LB@ \| \|@LB@5'-AGA...UUUUU AU C ACAC AUU C UU CCUCU...UGA-3'@LB@ GUUCAAAGAG GA AG ACAGUAU GG CGC CGCCC@LB@ :\|\|\|\|\|\|:\|: \|\| \|\| \|\|\|:\|\|\| :\| \|\|\| \|\|\|\|\|@LB@ UAAGUUUUUU CU UC UGUUAUA UC GCG GCGGG@LB@3'-UUU...GUCAU C AUUC CC UU UAGCG...ACG-5'@LB@ \| \|@LB@ 66 25@LB@@LB@@LB@Energy -7.21 kcal/mol@LB@Hybridization Energy -28.4973 kcal/mol@LB@Unfolding Energy - mRNA 7.75098 kcal/mol@LB@Unfolding Energy - sRNA 13.5387 kcal/mol@LB@@LB@Position - mRNA 221 -- 264@LB@Position - sRNA 26 -- 65@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 40 -- 46@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@
197	0.008895	0.1548	b2844	yqeF	-5.48	0.714940	222 -- 246	20 -- 39	short chain acyltransferase	_____________221_______________________247\n_____________\|_________________________\|\n5'-CCA...UUGUC_______UACG___A_______G__GCUUU...UCG-3'\n______________GGGGCGU____GAC_CCUAUCG_CU\n______________\|\|:\|\|\|:____:\|\|_\|\|:\|\|\|\|_\|\|\n______________CCUCGCG____UUG_GGGUAGC_GA\n3'-UUU...UUAUA______________C__________ACUGC...ACG-5'\n_____________\|_________________________\|\n_____________40________________________19\n	237 -- 243	22 -- 28	-25.7666 kcal/mol	8.11246 kcal/mol	12.1811 kcal/mol	221 247@LB@ \| \|@LB@5'-CCA...UUGUC UACG A G GCUUU...UCG-3'@LB@ GGGGCGU GAC CCUAUCG CU@LB@ \|\|:\|\|\|: :\|\| \|\|:\|\|\|\| \|\|@LB@ CCUCGCG UUG GGGUAGC GA@LB@3'-UUU...UUAUA C ACUGC...ACG-5'@LB@ \| \|@LB@ 40 19@LB@@LB@@LB@Energy -5.48 kcal/mol@LB@Hybridization Energy -25.7666 kcal/mol@LB@Unfolding Energy - mRNA 8.11246 kcal/mol@LB@Unfolding Energy - sRNA 12.1811 kcal/mol@LB@@LB@Position - mRNA 222 -- 246@LB@Position - sRNA 20 -- 39@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 22 -- 28@LB@
200	0.008935	0.1548	b1427	rimL	-11.51	0.046463	223 -- 252	68 -- 89	ribosomal-protein-L7/L12-serine acetyltransferase	_____________222____________________________253\n_____________\|______________________________\|\n5'-GAU...AGUAA________C___AAUUACA_____U_____AAAAU...CCU-3'\n______________GCGAAUCA_UUG_______UGCUG_UGCAG\n______________:\|\|\|\|\|\|\|_\|\|\|_______\|\|\|\|:_\|\|\|\|\|\n______________UGCUUAGU_AAC_______ACGAU_ACGUC\n3'-UUU...CAGCA________U_____________________AUUAA...ACG-5'\n_____________\|______________________________\|\n_____________90_____________________________67\n	224 -- 230	82 -- 88	-23.0393 kcal/mol	7.0303 kcal/mol	4.506 kcal/mol	222 253@LB@ \| \|@LB@5'-GAU...AGUAA C AAUUACA U AAAAU...CCU-3'@LB@ GCGAAUCA UUG UGCUG UGCAG@LB@ :\|\|\|\|\|\|\| \|\|\| \|\|\|\|: \|\|\|\|\|@LB@ UGCUUAGU AAC ACGAU ACGUC@LB@3'-UUU...CAGCA U AUUAA...ACG-5'@LB@ \| \|@LB@ 90 67@LB@@LB@@LB@Energy -11.51 kcal/mol@LB@Hybridization Energy -23.0393 kcal/mol@LB@Unfolding Energy - mRNA 7.0303 kcal/mol@LB@Unfolding Energy - sRNA 4.506 kcal/mol@LB@@LB@Position - mRNA 223 -- 252@LB@Position - sRNA 68 -- 89@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 82 -- 88@LB@
101	0.003313	0.1114	b1193	emtA	-10.98	0.063602	227 -- 257	55 -- 82	lytic murein endotransglycosylase E	_____________226_____________________________258\n_____________\|_______________________________\|\n5'-UUG...UUUUU___________UA____GUU_____UC____CAUGA...UGC-3'\n______________GAUUGUGUUAU__GCGG___GUUCA__AAAG\n______________:\|\|\|\|\|\|:\|\|\|__\|\|:\|___:\|\|\|\|__\|\|\|\|\n______________UUAACACGAUA__CGUC___UAAGU__UUUC\n3'-UUU...CUUAG_________________AU______UU____CUUCA...ACG-5'\n_____________\|_______________________________\|\n_____________83______________________________54\n	231 -- 237	72 -- 78	-21.9468 kcal/mol	7.33111 kcal/mol	3.63929 kcal/mol	226 258@LB@ \| \|@LB@5'-UUG...UUUUU UA GUU UC CAUGA...UGC-3'@LB@ GAUUGUGUUAU GCGG GUUCA AAAG@LB@ :\|\|\|\|\|\|:\|\|\| \|\|:\| :\|\|\|\| \|\|\|\|@LB@ UUAACACGAUA CGUC UAAGU UUUC@LB@3'-UUU...CUUAG AU UU CUUCA...ACG-5'@LB@ \| \|@LB@ 83 54@LB@@LB@@LB@Energy -10.98 kcal/mol@LB@Hybridization Energy -21.9468 kcal/mol@LB@Unfolding Energy - mRNA 7.33111 kcal/mol@LB@Unfolding Energy - sRNA 3.63929 kcal/mol@LB@@LB@Position - mRNA 227 -- 257@LB@Position - sRNA 55 -- 82@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 72 -- 78@LB@
91	0.002503	0.09689	b1062	pyrC	-7.37	0.386343	231 -- 263	1 -- 35	dihydro-orotase	_____________230_______________________________________264\n_____________\|_________________________________________\|\n5'-GCG...AGAUC_____________________ACUG___CC_______CC__GAUGG...CCA-3'\n______________CGC__CGCCCA______GACG____GCA__UUCACCU__GC\n______________\|\|\|__\|\|\|\|\|\|______\|\|\|\|____\|\|\|__\|\|\|\|\|\|\|__\|\|\n______________GCG__GCGGGU______CUGC____CGU__AAGUGGA__CG\n3'-UUU...ACCUC___UU______AGCGAA____AA__________________-5'\n_____________\|________________________________________\|\n_____________36_______________________________________1\n	253 -- 259	3 -- 9	-30.041 kcal/mol	7.38685 kcal/mol	15.286 kcal/mol	230 264@LB@ \| \|@LB@5'-GCG...AGAUC ACUG CC CC GAUGG...CCA-3'@LB@ CGC CGCCCA GACG GCA UUCACCU GC@LB@ \|\|\| \|\|\|\|\|\| \|\|\|\| \|\|\| \|\|\|\|\|\|\| \|\|@LB@ GCG GCGGGU CUGC CGU AAGUGGA CG@LB@3'-UUU...ACCUC UU AGCGAA AA -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -7.37 kcal/mol@LB@Hybridization Energy -30.041 kcal/mol@LB@Unfolding Energy - mRNA 7.38685 kcal/mol@LB@Unfolding Energy - sRNA 15.286 kcal/mol@LB@@LB@Position - mRNA 231 -- 263@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 3 -- 9@LB@
3	7.57e-07	0.0008889	b1763	topB	-11.97	0.035059	233 -- 258	1 -- 37	DNA topoisomerase III	_____________232___________________________________259\n_____________\|_____________________________________\|\n5'-UCU...AGUCU_____________________________________CCAAA...GUA-3'\n______________GGCGC_GCG_CCAUUGCU_GAUGU________CCUGC\n______________:\|\|\|\|_:\|\|_\|\|\|\|:\|\|\|_\|\|:\|\|________\|\|\|\|\|\n______________UCGCG_UGC_GGUAGCGA_CUGCA________GGACG\n3'-UUU...AUACC_____U___G________A_____ACGUAAGU_____-5'\n_____________\|____________________________________\|\n_____________38___________________________________1\n	242 -- 248	20 -- 26	-35.9728 kcal/mol	8.72127 kcal/mol	15.288 kcal/mol	232 259@LB@ \| \|@LB@5'-UCU...AGUCU CCAAA...GUA-3'@LB@ GGCGC GCG CCAUUGCU GAUGU CCUGC@LB@ :\|\|\|\| :\|\| \|\|\|\|:\|\|\| \|\|:\|\| \|\|\|\|\|@LB@ UCGCG UGC GGUAGCGA CUGCA GGACG@LB@3'-UUU...AUACC U G A ACGUAAGU -5'@LB@ \| \|@LB@ 38 1@LB@@LB@@LB@Energy -11.97 kcal/mol@LB@Hybridization Energy -35.9728 kcal/mol@LB@Unfolding Energy - mRNA 8.72127 kcal/mol@LB@Unfolding Energy - sRNA 15.288 kcal/mol@LB@@LB@Position - mRNA 233 -- 258@LB@Position - sRNA 1 -- 37@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 20 -- 26@LB@
74	0.001758	0.08273	b4012	yjaB	-8.69	0.215298	234 -- 243	51 -- 60	GNAT-family putative N-acetyltransferase; acetyl coenzyme A-binding protein	_____________233________244\n_____________\|__________\|\n5'-AAG...AUGAG__________AACUC...CAG-3'\n______________GAAGGGGAGG\n______________:\|\|::\|\|\|:\|\n______________UUUUUCCUUC\n3'-UUU...UAAGU__________AUUCU...ACG-5'\n_____________\|__________\|\n_____________61_________50\n	237 -- 243	51 -- 57	-10.2171 kcal/mol	0.810771 kcal/mol	0.715621 kcal/mol	233 244@LB@ \| \|@LB@5'-AAG...AUGAG AACUC...CAG-3'@LB@ GAAGGGGAGG@LB@ :\|\|::\|\|\|:\|@LB@ UUUUUCCUUC@LB@3'-UUU...UAAGU AUUCU...ACG-5'@LB@ \| \|@LB@ 61 50@LB@@LB@@LB@Energy -8.69 kcal/mol@LB@Hybridization Energy -10.2171 kcal/mol@LB@Unfolding Energy - mRNA 0.810771 kcal/mol@LB@Unfolding Energy - sRNA 0.715621 kcal/mol@LB@@LB@Position - mRNA 234 -- 243@LB@Position - sRNA 51 -- 60@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 51 -- 57@LB@
81	0.001932	0.08273	b2763	cysI	-12.36	0.027367	234 -- 285	1 -- 58	sulfite reductase beta subunit NAD(P)-binding heme-binding	_____________233_________________________________________________________286\n_____________\|___________________________________________________________\|\n5'-GAA...UGGUC_______AACU_____ACGCC__________AA______A___AA_____AC_______GCGGC...CGG-3'\n______________GAAGGAA____GACAG_____GAGCGC_AUG______GC_UGA____GCA__UACCUGC\n______________:\|\|\|\|\|\|____\|\|\|\|:_____\|\|\|\|\|\|_\|:\|______\|\|_\|\|\|____\|\|\|__:\|\|\|\|\|\|\n______________UUUCCUU____CUGUU_____CUCGCG_UGC______CG_ACU____CGU__GUGGACG\n3'-UUU...AGUUU_______CAUU_____AUAC_______U___GGGUAG__A___GCAA___AA_______-5'\n_____________\|__________________________________________________________\|\n_____________59_________________________________________________________1\n	279 -- 285	1 -- 7	-40.3147 kcal/mol	11.0832 kcal/mol	16.8724 kcal/mol	233 286@LB@ \| \|@LB@5'-GAA...UGGUC AACU ACGCC AA A AA AC GCGGC...CGG-3'@LB@ GAAGGAA GACAG GAGCGC AUG GC UGA GCA UACCUGC@LB@ :\|\|\|\|\|\| \|\|\|\|: \|\|\|\|\|\| \|:\| \|\| \|\|\| \|\|\| :\|\|\|\|\|\|@LB@ UUUCCUU CUGUU CUCGCG UGC CG ACU CGU GUGGACG@LB@3'-UUU...AGUUU CAUU AUAC U GGGUAG A GCAA AA -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -12.36 kcal/mol@LB@Hybridization Energy -40.3147 kcal/mol@LB@Unfolding Energy - mRNA 11.0832 kcal/mol@LB@Unfolding Energy - sRNA 16.8724 kcal/mol@LB@@LB@Position - mRNA 234 -- 285@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 1 -- 7@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@

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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