Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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
77	0.00734	0.3134	b1793	yoaF	-12.59	0.071143	233 -- 250	68 -- 86	DUF333 family outer membrane lipoprotein	_____________232_________________251\n_____________\|___________________\|\n5'-GAU...UGCUU___________________UUCAA...UGG-3'\n______________GCUGGU_CCUGGCUGGUUG\n______________\|\|::\|:_\|\|:\|\|\|\|\|\|:\|:\n______________CGGUCG_GGGCCGACCGAU\n_______3'-UUUU______U____________UCAUU...GCG-5'\n_____________\|___________________\|\n_____________87__________________67\n	243 -- 249	69 -- 75	-29.581 kcal/mol	5.32768 kcal/mol	11.6617 kcal/mol	232 251@LB@ \| \|@LB@5'-GAU...UGCUU UUCAA...UGG-3'@LB@ GCUGGU CCUGGCUGGUUG@LB@ \|\|::\|: \|\|:\|\|\|\|\|\|:\|:@LB@ CGGUCG GGGCCGACCGAU@LB@ 3'-UUUU U UCAUU...GCG-5'@LB@ \| \|@LB@ 87 67@LB@@LB@@LB@Energy -12.59 kcal/mol@LB@Hybridization Energy -29.581 kcal/mol@LB@Unfolding Energy - mRNA 5.32768 kcal/mol@LB@Unfolding Energy - sRNA 11.6617 kcal/mol@LB@@LB@Position - mRNA 233 -- 250@LB@Position - sRNA 68 -- 86@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 69 -- 75@LB@
15	0.001024	0.2294	b2822	recC	-16.38	0.016046	234 -- 264	37 -- 63	exonuclease V (RecBCD complex) gamma chain	_____________233______________________________265\n_____________\|________________________________\|\n5'-AGU...UGGAC___________GUU_________UUAU_____AACGC...AGA-3'\n______________GUGCUGGAAGC___GAUG_GAGU____UGUCG\n______________:\|:\|\|\|\|\|\|\|\|___:\|\|\|_\|\|\|:____\|\|\|\|\|\n______________UAUGACCUUCG___UUAC_CUCG____ACAGC\n3'-UUU...UUCAU__________________A____UU_______ACGAA...GCG-5'\n_____________\|________________________________\|\n_____________64_______________________________36\n	238 -- 244	53 -- 59	-30.8262 kcal/mol	11.1454 kcal/mol	3.30267 kcal/mol	233 265@LB@ \| \|@LB@5'-AGU...UGGAC GUU UUAU AACGC...AGA-3'@LB@ GUGCUGGAAGC GAUG GAGU UGUCG@LB@ :\|:\|\|\|\|\|\|\|\| :\|\|\| \|\|\|: \|\|\|\|\|@LB@ UAUGACCUUCG UUAC CUCG ACAGC@LB@3'-UUU...UUCAU A UU ACGAA...GCG-5'@LB@ \| \|@LB@ 64 36@LB@@LB@@LB@Energy -16.38 kcal/mol@LB@Hybridization Energy -30.8262 kcal/mol@LB@Unfolding Energy - mRNA 11.1454 kcal/mol@LB@Unfolding Energy - sRNA 3.30267 kcal/mol@LB@@LB@Position - mRNA 234 -- 264@LB@Position - sRNA 37 -- 63@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 53 -- 59@LB@
31	0.002952	0.2776	b3052	hldE	-18.29	0.007494	235 -- 261	44 -- 68	heptose 7-phosphate kinase and heptose 1-phosphate adenyltransferase	_____________234_________________________262\n_____________\|___________________________\|\n5'-GCG...UGCAG________G___UU__________U__UGGAU...CGC-3'\n______________GAGUGAUG_UGG__GGUGAUGUGA_GC\n______________:\|\|\|:\|\|:_\|\|\|__:\|::\|\|\|\|\|\|_\|\|\n______________UUCAUUAU_ACC__UCGUUACACU_CG\n3'-UUU...ACCGA________G___U______________UUACA...GCG-5'\n_____________\|___________________________\|\n_____________69__________________________43\n	252 -- 258	46 -- 52	-27.5603 kcal/mol	5.96824 kcal/mol	3.30414 kcal/mol	234 262@LB@ \| \|@LB@5'-GCG...UGCAG G UU U UGGAU...CGC-3'@LB@ GAGUGAUG UGG GGUGAUGUGA GC@LB@ :\|\|\|:\|\|: \|\|\| :\|::\|\|\|\|\|\| \|\|@LB@ UUCAUUAU ACC UCGUUACACU CG@LB@3'-UUU...ACCGA G U UUACA...GCG-5'@LB@ \| \|@LB@ 69 43@LB@@LB@@LB@Energy -18.29 kcal/mol@LB@Hybridization Energy -27.5603 kcal/mol@LB@Unfolding Energy - mRNA 5.96824 kcal/mol@LB@Unfolding Energy - sRNA 3.30414 kcal/mol@LB@@LB@Position - mRNA 235 -- 261@LB@Position - sRNA 44 -- 68@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 46 -- 52@LB@
81	0.008086	0.3318	b3114	tdcE	-10.99	0.130865	237 -- 290	38 -- 86	pyruvate formate-lyase 4/2-ketobutyrate formate-lyase	_____________236_____________________________________________________291\n_____________\|_______________________________________________________\|\n5'-AGA...UGUAC____A___A____U_____UUAA_____CGG_______AAACGAAAU________CGCGA...UUA-3'\n______________GCCG_CGC_UGGC_UGGCU____AGGUA___ACUGGAA__________UAAUGUC\n______________\|\|\|:_\|:\|_:\|\|\|_\|\|\|\|\|____\|:\|\|\|___\|\|\|\|\|\|\|__________:\|\|\|\|\|\|\n______________CGGU_GUG_GCCG_ACCGA____UUCAU___UGACCUU__________GUUACAG\n_______3'-UUUU____C___G___________________UA________CGUUACACUC_______CACGA...GCG-5'\n_____________\|_______________________________________________________\|\n_____________87______________________________________________________37\n	284 -- 290	38 -- 44	-39.8415 kcal/mol	13.9412 kcal/mol	14.9106 kcal/mol	236 291@LB@ \| \|@LB@5'-AGA...UGUAC A A U UUAA CGG AAACGAAAU CGCGA...UUA-3'@LB@ GCCG CGC UGGC UGGCU AGGUA ACUGGAA UAAUGUC@LB@ \|\|\|: \|:\| :\|\|\| \|\|\|\|\| \|:\|\|\| \|\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ CGGU GUG GCCG ACCGA UUCAU UGACCUU GUUACAG@LB@ 3'-UUUU C G UA CGUUACACUC CACGA...GCG-5'@LB@ \| \|@LB@ 87 37@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -39.8415 kcal/mol@LB@Unfolding Energy - mRNA 13.9412 kcal/mol@LB@Unfolding Energy - sRNA 14.9106 kcal/mol@LB@@LB@Position - mRNA 237 -- 290@LB@Position - sRNA 38 -- 86@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 38 -- 44@LB@
37	0.003144	0.2776	b3743	asnC	-18.99	0.005660	240 -- 261	40 -- 60	transcriptional activator of asnA; autorepressor	_____________239____________________262\n_____________\|______________________\|\n5'-AUU...GCAUC_________UUAA_________CGCGC...GCG-3'\n______________CUGGAAGCA____UGGGCAAUG\n______________\|\|\|\|\|\|\|\|\|____\|\|:\|\|\|\|\|\|\n______________GACCUUCGU____ACUCGUUAC\n3'-UUU...AUUAU_________UAC__________AGCAC...GCG-5'\n_____________\|______________________\|\n_____________61_____________________39\n	255 -- 261	40 -- 46	-27.3577 kcal/mol	5.06736 kcal/mol	3.29985 kcal/mol	239 262@LB@ \| \|@LB@5'-AUU...GCAUC UUAA CGCGC...GCG-3'@LB@ CUGGAAGCA UGGGCAAUG@LB@ \|\|\|\|\|\|\|\|\| \|\|:\|\|\|\|\|\|@LB@ GACCUUCGU ACUCGUUAC@LB@3'-UUU...AUUAU UAC AGCAC...GCG-5'@LB@ \| \|@LB@ 61 39@LB@@LB@@LB@Energy -18.99 kcal/mol@LB@Hybridization Energy -27.3577 kcal/mol@LB@Unfolding Energy - mRNA 5.06736 kcal/mol@LB@Unfolding Energy - sRNA 3.29985 kcal/mol@LB@@LB@Position - mRNA 240 -- 261@LB@Position - sRNA 40 -- 60@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 40 -- 46@LB@
48	0.004482	0.2905	b4045	yjbJ	-14.69	0.031336	242 -- 268	42 -- 68	stress-induced protein UPF0337 family	_____________241___________________________269\n_____________\|_____________________________\|\n5'-CGU...UUUAA________G__AAA_______________ACUGA...AAG-3'\n______________AGGUAA_A_UG___GAGCAAUG_GGGCAA\n______________\|:\|\|\|\|_\|_\|\|___:\|\|\|\|\|\|\|_\|:\|\|\|\|\n______________UUCAUU_U_AC___UUCGUUAC_CUCGUU\n3'-UUU...ACCGA______A_G__C__________A______ACAGC...GCG-5'\n_____________\|_____________________________\|\n_____________69____________________________41\n	256 -- 262	49 -- 55	-22.1594 kcal/mol	4.16538 kcal/mol	3.30492 kcal/mol	241 269@LB@ \| \|@LB@5'-CGU...UUUAA G AAA ACUGA...AAG-3'@LB@ AGGUAA A UG GAGCAAUG GGGCAA@LB@ \|:\|\|\|\| \| \|\| :\|\|\|\|\|\|\| \|:\|\|\|\|@LB@ UUCAUU U AC UUCGUUAC CUCGUU@LB@3'-UUU...ACCGA A G C A ACAGC...GCG-5'@LB@ \| \|@LB@ 69 41@LB@@LB@@LB@Energy -14.69 kcal/mol@LB@Hybridization Energy -22.1594 kcal/mol@LB@Unfolding Energy - mRNA 4.16538 kcal/mol@LB@Unfolding Energy - sRNA 3.30492 kcal/mol@LB@@LB@Position - mRNA 242 -- 268@LB@Position - sRNA 42 -- 68@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 49 -- 55@LB@
154	0.01903	0.4072	b2823	ppdC	-17.47	0.010387	242 -- 260	40 -- 58	putative prepilin peptidase-dependent protein	_____________241_________________261\n_____________\|___________________\|\n5'-ACG...CUGCC___________U_______GUGUU...UCC-3'\n______________GGAGGUAAUGU_GGCGAUG\n______________\|\|\|:\|:\|\|\|\|\|_:\|\|:\|\|\|\n______________CCUUCGUUACA_UCGUUAC\n3'-UUU...UAUGA___________C_______AGCAC...GCG-5'\n_____________\|___________________\|\n_____________59__________________39\n	254 -- 260	40 -- 46	-26.2879 kcal/mol	5.60197 kcal/mol	3.21578 kcal/mol	241 261@LB@ \| \|@LB@5'-ACG...CUGCC U GUGUU...UCC-3'@LB@ GGAGGUAAUGU GGCGAUG@LB@ \|\|\|:\|:\|\|\|\|\| :\|\|:\|\|\|@LB@ CCUUCGUUACA UCGUUAC@LB@3'-UUU...UAUGA C AGCAC...GCG-5'@LB@ \| \|@LB@ 59 39@LB@@LB@@LB@Energy -17.47 kcal/mol@LB@Hybridization Energy -26.2879 kcal/mol@LB@Unfolding Energy - mRNA 5.60197 kcal/mol@LB@Unfolding Energy - sRNA 3.21578 kcal/mol@LB@@LB@Position - mRNA 242 -- 260@LB@Position - sRNA 40 -- 58@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 40 -- 46@LB@
95	0.009964	0.3393	b3902	rhaD	-16.21	0.017174	243 -- 283	43 -- 89	rhamnulose-1-phosphate aldolase	_____________242_______________________________________________284\n_____________\|_________________________________________________\|\n5'-AGA...UGAUC_______C____GA__C________AAG_____________________CAACG...UGA-3'\n______________AAAGCCA_CACC__CG_CUGGCUGA_____GCUGGGA______UGAGCG\n______________\|\|\|\|\|\|\|_\|\|\|\|__\|\|_\|\|\|\|\|\|:\|_____:\|\|\|\|:\|______\|\|\|\|\|:\n______________UUUCGGU_GUGG__GC_GACCGAUU_____UGACCUU______ACUCGU\n__________3'-U_______C________C________CAUUA_______CGUUAC______UACAG...GCG-5'\n_____________\|_________________________________________________\|\n_____________90________________________________________________42\n	271 -- 277	55 -- 61	-44.1539 kcal/mol	13.0365 kcal/mol	14.9102 kcal/mol	242 284@LB@ \| \|@LB@5'-AGA...UGAUC C GA C AAG CAACG...UGA-3'@LB@ AAAGCCA CACC CG CUGGCUGA GCUGGGA UGAGCG@LB@ \|\|\|\|\|\|\| \|\|\|\| \|\| \|\|\|\|\|\|:\| :\|\|\|\|:\| \|\|\|\|\|:@LB@ UUUCGGU GUGG GC GACCGAUU UGACCUU ACUCGU@LB@ 3'-U C C CAUUA CGUUAC UACAG...GCG-5'@LB@ \| \|@LB@ 90 42@LB@@LB@@LB@Energy -16.21 kcal/mol@LB@Hybridization Energy -44.1539 kcal/mol@LB@Unfolding Energy - mRNA 13.0365 kcal/mol@LB@Unfolding Energy - sRNA 14.9102 kcal/mol@LB@@LB@Position - mRNA 243 -- 283@LB@Position - sRNA 43 -- 89@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 55 -- 61@LB@
98	0.01017	0.3393	b1234	rssA	-9.29	0.241768	243 -- 258	1 -- 20	putative patatin-like family phospholipase	_____________242___________________259\n_____________\|_____________________\|\n5'-GAU...GCGCG_____A_______________AUAUU...AAA-3'\n______________GCGAG_GGU_____UGGUCGC\n______________\|\|\|\|\|_\|\|\|_____\|\|:\|\|\|\|\n______________CGCUC_CCA_____ACUAGCG\n3'-UUU...AGAGG_________GAAGG_______-5'\n_____________\|____________________\|\n_____________21___________________1\n	252 -- 258	1 -- 7	-21.3571 kcal/mol	5.88093 kcal/mol	6.18231 kcal/mol	242 259@LB@ \| \|@LB@5'-GAU...GCGCG A AUAUU...AAA-3'@LB@ GCGAG GGU UGGUCGC@LB@ \|\|\|\|\| \|\|\| \|\|:\|\|\|\|@LB@ CGCUC CCA ACUAGCG@LB@3'-UUU...AGAGG GAAGG -5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -9.29 kcal/mol@LB@Hybridization Energy -21.3571 kcal/mol@LB@Unfolding Energy - mRNA 5.88093 kcal/mol@LB@Unfolding Energy - sRNA 6.18231 kcal/mol@LB@@LB@Position - mRNA 243 -- 258@LB@Position - sRNA 1 -- 20@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 1 -- 7@LB@
76	0.007246	0.3134	b4174	hflK	-10.43	0.160892	249 -- 292	51 -- 90	modulator for HflB protease specific for phage lambda cII repressor	_____________248_____________________________________________293\n_____________\|_______________________________________________\|\n5'-AGA...CGUGG__________AA___________AACUC____GGAAA______A___AGGCGGUC-3'\n______________GGAAG_CAGC__ACCUGGC_GGC_____UGAG______UGGAA_CAA\n______________::\|\|\|_\|\|\|\|__\|\|\|:\|\|\|_\|\|\|_____\|:\|\|______\|\|\|\|\|_\|\|\|\n______________UUUUC_GUCG__UGGGCCG_CCG_____AUUC______ACCUU_GUU\n___________3'-_____G_____________A____________AUUAUG_____C___ACACU...GCG-5'\n______________\|______________________________________________\|\n______________90_____________________________________________50\n	260 -- 266	74 -- 80	-34.0568 kcal/mol	9.12339 kcal/mol	14.5017 kcal/mol	248 293@LB@ \| \|@LB@5'-AGA...CGUGG AA AACUC GGAAA A AGGCGGUC-3'@LB@ GGAAG CAGC ACCUGGC GGC UGAG UGGAA CAA@LB@ ::\|\|\| \|\|\|\| \|\|\|:\|\|\| \|\|\| \|:\|\| \|\|\|\|\| \|\|\|@LB@ UUUUC GUCG UGGGCCG CCG AUUC ACCUU GUU@LB@ 3'- G A AUUAUG C ACACU...GCG-5'@LB@ \| \|@LB@ 90 50@LB@@LB@@LB@Energy -10.43 kcal/mol@LB@Hybridization Energy -34.0568 kcal/mol@LB@Unfolding Energy - mRNA 9.12339 kcal/mol@LB@Unfolding Energy - sRNA 14.5017 kcal/mol@LB@@LB@Position - mRNA 249 -- 292@LB@Position - sRNA 51 -- 90@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 74 -- 80@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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