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
137	0.01486	0.3575	b3967	murI	-16.98	0.010727	107 -- 167	42 -- 96	glutamate racemase	_____________106__________________________168\n_____________\|____________________________\|\n5'-GUU...GACUG________ACU_____________G___UCGCU...GGU-3'\n______________GGGU_AUU___UAUCAGUAUUUAG_CAC\n______________\|\|\|\|_\|\|\|___:\|:\|\|:\|\|:\|:\|\|_\|\|\|\n______________CCCA_UAA___GUGGUUAUGAGUC_GUG\n3'-UUU...GACCG____C___AAU_____________A___UGUAC...UAG-5'\n_____________\|____________________________\|\n_____________97___________________________41\n	35 -- 41	174 -- 180	-22.1424 kcal/mol	5.45848 kcal/mol	5.03792 kcal/mol	106 168@LB@ \| \|@LB@5'-GUU...GACUG ACU G UCGCU...GGU-3'@LB@ GGGU AUU UAUCAGUAUUUAG CAC@LB@ \|\|\|\| \|\|\| :\|:\|\|:\|\|:\|:\|\| \|\|\|@LB@ CCCA UAA GUGGUUAUGAGUC GUG@LB@3'-UUU...GACCG C AAU A UGUAC...UAG-5'@LB@ \| \|@LB@ 97 41@LB@@LB@@LB@Energy -16.98 kcal/mol@LB@Hybridization Energy -22.1424 kcal/mol@LB@Unfolding Energy - mRNA 5.45848 kcal/mol@LB@Unfolding Energy - sRNA 5.03792 kcal/mol@LB@@LB@Position - mRNA 107 -- 167@LB@Position - sRNA 42 -- 96@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 174 -- 180@LB@
121	0.01323	0.3575	b3429	glgA	-14.56	0.033318	190 -- 240	123 -- 176	glycogen synthase	_____________189__________________241\n_____________\|____________________\|\n5'-GUA...AUGCA__________GU________AGAUG...ACG-3'\n______________GGUUUUACAU__AUGUUCAG\n______________\|:\|\|\|\|\|\|\|:__\|\|::\|\|\|\|\n______________CUAAAAUGUG__UAUGAGUC\n3'-UUU...GCCCA__________GU________AGUGU...UAG-5'\n_____________\|____________________\|\n_____________177__________________122\n	219 -- 225	174 -- 180	-15.9439 kcal/mol	3.46677 kcal/mol	4.94566 kcal/mol	189 241@LB@ \| \|@LB@5'-GUA...AUGCA GU AGAUG...ACG-3'@LB@ GGUUUUACAU AUGUUCAG@LB@ \|:\|\|\|\|\|\|\|: \|\|::\|\|\|\|@LB@ CUAAAAUGUG UAUGAGUC@LB@3'-UUU...GCCCA GU AGUGU...UAG-5'@LB@ \| \|@LB@ 177 122@LB@@LB@@LB@Energy -14.56 kcal/mol@LB@Hybridization Energy -15.9439 kcal/mol@LB@Unfolding Energy - mRNA 3.46677 kcal/mol@LB@Unfolding Energy - sRNA 4.94566 kcal/mol@LB@@LB@Position - mRNA 190 -- 240@LB@Position - sRNA 123 -- 176@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 174 -- 180@LB@
150	0.01679	0.3749	b3550	yiaC	-14.78	0.030008	125 -- 180	123 -- 174	GNAT family putative N-acetyltransferase	_____________124_______________________________________________181\n_____________\|_________________________________________________\|\n5'-AAU...UCUGU_____CU_______G_C________U___G___GA______________GGCUG...GGC-3'\n______________UACUC__UUAUGCA_G_AUGUGGGC_GGU_AAU__UCA____UGUGGUU\n______________\|\|\|\|\|__\|:\|::\|\|_\|_\|\|\|::\|\|\|_:\|\|_\|\|:__\|\|\|____\|\|:\|\|\|:\n______________AUGAG__AGUGUGU_C_UACGUCCG_UCA_UUG__AGU____ACGCCAG\n3'-UUU...UGGUU_____UC_______A__________U___G___AA___CUUA_______UAGGG...UAG-5'\n_____________\|_________________________________________________\|\n_____________175_______________________________________________122\n	134 -- 140	167 -- 173	-39.4647 kcal/mol	14.8163 kcal/mol	12.8033 kcal/mol	124 181@LB@ \| \|@LB@5'-AAU...UCUGU CU G C U G GA GGCUG...GGC-3'@LB@ UACUC UUAUGCA G AUGUGGGC GGU AAU UCA UGUGGUU@LB@ \|\|\|\|\| \|:\|::\|\| \| \|\|\|::\|\|\| :\|\| \|\|: \|\|\| \|\|:\|\|\|:@LB@ AUGAG AGUGUGU C UACGUCCG UCA UUG AGU ACGCCAG@LB@3'-UUU...UGGUU UC A U G AA CUUA UAGGG...UAG-5'@LB@ \| \|@LB@ 175 122@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -39.4647 kcal/mol@LB@Unfolding Energy - mRNA 14.8163 kcal/mol@LB@Unfolding Energy - sRNA 12.8033 kcal/mol@LB@@LB@Position - mRNA 125 -- 180@LB@Position - sRNA 123 -- 174@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 167 -- 173@LB@
49	0.004667	0.3205	b1277	ribA	-9.86	0.291903	241 -- 249	16 -- 24	GTP cyclohydrolase II	_____________240________250\n_____________\|__________\|\n5'-CCA...AAUAC__________UUAUC...UCG-3'\n______________AGAACCAGCA\n______________\|:\|\|\|\|\|\|\|\|\n______________UUUUGGUCGU\n_______3'-UUUU__________CCAUA...UAG-5'\n_____________\|__________\|\n_____________25_________15\n	178 -- 184	214 -- 220	-13.9783 kcal/mol	2.87719 kcal/mol	5.75438 kcal/mol	240 250@LB@ \| \|@LB@5'-CCA...AAUAC UUAUC...UCG-3'@LB@ AGAACCAGCA@LB@ \|:\|\|\|\|\|\|\|\|@LB@ UUUUGGUCGU@LB@ 3'-UUUU CCAUA...UAG-5'@LB@ \| \|@LB@ 25 15@LB@@LB@@LB@Energy -9.86 kcal/mol@LB@Hybridization Energy -13.9783 kcal/mol@LB@Unfolding Energy - mRNA 2.87719 kcal/mol@LB@Unfolding Energy - sRNA 5.75438 kcal/mol@LB@@LB@Position - mRNA 241 -- 249@LB@Position - sRNA 16 -- 24@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 214 -- 220@LB@
99	0.01084	0.3575	b0872	hcr	-12.58	0.084706	106 -- 121	192 -- 205	HCP oxidoreductase NADH-dependent	_____________105______________122\n_____________\|________________\|\n5'-UCC...CAGAC__________U_C___ACGAG...AUU-3'\n______________CUGCUGGCGG_G_UGA\n______________\|\|\|\|\|\|\|\|\|\|_\|_\|\|\|\n______________GACGACCGCC_C_ACU\n3'-UUU...UAUUA________________AAAAU...UAG-5'\n_____________\|________________\|\n_____________206______________191\n	109 -- 115	196 -- 202	-24.2797 kcal/mol	6.55023 kcal/mol	9.06563 kcal/mol	105 122@LB@ \| \|@LB@5'-UCC...CAGAC U C ACGAG...AUU-3'@LB@ CUGCUGGCGG G UGA@LB@ \|\|\|\|\|\|\|\|\|\| \| \|\|\|@LB@ GACGACCGCC C ACU@LB@3'-UUU...UAUUA AAAAU...UAG-5'@LB@ \| \|@LB@ 206 191@LB@@LB@@LB@Energy -12.58 kcal/mol@LB@Hybridization Energy -24.2797 kcal/mol@LB@Unfolding Energy - mRNA 6.55023 kcal/mol@LB@Unfolding Energy - sRNA 9.06563 kcal/mol@LB@@LB@Position - mRNA 106 -- 121@LB@Position - sRNA 192 -- 205@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 196 -- 202@LB@
171	0.01954	0.3812	b3687	ibpA	-6.40	0.875621	11 -- 20	10 -- 18	heat shock chaperone	_____________10____________21\n_____________\|_____________\|\n5'-AAC...GCCCC_______U_____AUAGA...GCU-3'\n______________CUCAGUC_AUGCA\n______________\|\|\|\|\|\|\|_\|::\|\|\n______________GAGUCAG_UGUGU\n3'-UUU...GUUAU_____________ACUAC...UAG-5'\n_____________\|_____________\|\n_____________19____________9\n	19 -- 25	172 -- 178	-14.2159 kcal/mol	5.36362 kcal/mol	0.433674 kcal/mol	10 21@LB@ \| \|@LB@5'-AAC...GCCCC U AUAGA...GCU-3'@LB@ CUCAGUC AUGCA@LB@ \|\|\|\|\|\|\| \|::\|\|@LB@ GAGUCAG UGUGU@LB@3'-UUU...GUUAU ACUAC...UAG-5'@LB@ \| \|@LB@ 19 9@LB@@LB@@LB@Energy -6.40 kcal/mol@LB@Hybridization Energy -14.2159 kcal/mol@LB@Unfolding Energy - mRNA 5.36362 kcal/mol@LB@Unfolding Energy - sRNA 0.433674 kcal/mol@LB@@LB@Position - mRNA 11 -- 20@LB@Position - sRNA 10 -- 18@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 172 -- 178@LB@
13	0.0007116	0.1842	b3052	hldE	-13.53	0.054228	111 -- 134	141 -- 169	heptose 7-phosphate kinase and heptose 1-phosphate adenyltransferase	_____________110______________135\n_____________\|________________\|\n5'-GCG...CGUGA________________CUGGC...CGC-3'\n______________AC_UGGUGCGGGCAAG\n______________\|\|_\|\|:\|\|\|:\|\|\|\|\|\|\n______________UG_ACUACGUCCGUUC\n3'-UUU...CAGUG__U_____________AGUUG...UAG-5'\n_____________\|________________\|\n_____________170______________140\n	119 -- 125	154 -- 160	-22.7709 kcal/mol	5.4675 kcal/mol	7.07904 kcal/mol	110 135@LB@ \| \|@LB@5'-GCG...CGUGA CUGGC...CGC-3'@LB@ AC UGGUGCGGGCAAG@LB@ \|\| \|\|:\|\|\|:\|\|\|\|\|\|@LB@ UG ACUACGUCCGUUC@LB@3'-UUU...CAGUG U AGUUG...UAG-5'@LB@ \| \|@LB@ 170 140@LB@@LB@@LB@Energy -13.53 kcal/mol@LB@Hybridization Energy -22.7709 kcal/mol@LB@Unfolding Energy - mRNA 5.4675 kcal/mol@LB@Unfolding Energy - sRNA 7.07904 kcal/mol@LB@@LB@Position - mRNA 111 -- 134@LB@Position - sRNA 141 -- 169@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 154 -- 160@LB@
53	0.005067	0.3217	b3666	uhpT	-10.07	0.266829	134 -- 177	167 -- 215	hexose phosphate transporter	_____________133_______________________________________________________178\n_____________\|_________________________________________________________\|\n5'-GCC...UGGAC____UCU____CC______________________UA________AUGCC_______GGUAU...UGG-3'\n______________GCUA___CAGG__UGAUUUGCU_GC___UGAUUUU____CAAUGC_____UCACGCA\n______________:\|:\|___\|\|\|\|__\|:\|\|:\|\|\|\|_\|\|___\|\|\|\|\|\|\|____\|\|\|\|:\|_____\|\|\|\|:\|\|\n______________UGGU___GUCC__AUUAGACGA_CG___ACUAAAA____GUUAUG_____AGUGUGU\n____3'-UUUUUUU____C______AU_________C__CCC_______UGUG______AGUC________ACUAC...UAG-5'\n_____________\|_________________________________________________________\|\n_____________216_______________________________________________________166\n	171 -- 177	167 -- 173	-37.7334 kcal/mol	11.6521 kcal/mol	18.4949 kcal/mol	133 178@LB@ \| \|@LB@5'-GCC...UGGAC UCU CC UA AUGCC GGUAU...UGG-3'@LB@ GCUA CAGG UGAUUUGCU GC UGAUUUU CAAUGC UCACGCA@LB@ :\|:\| \|\|\|\| \|:\|\|:\|\|\|\| \|\| \|\|\|\|\|\|\| \|\|\|\|:\| \|\|\|\|:\|\|@LB@ UGGU GUCC AUUAGACGA CG ACUAAAA GUUAUG AGUGUGU@LB@ 3'-UUUUUUU C AU C CCC UGUG AGUC ACUAC...UAG-5'@LB@ \| \|@LB@ 216 166@LB@@LB@@LB@Energy -10.07 kcal/mol@LB@Hybridization Energy -37.7334 kcal/mol@LB@Unfolding Energy - mRNA 11.6521 kcal/mol@LB@Unfolding Energy - sRNA 18.4949 kcal/mol@LB@@LB@Position - mRNA 134 -- 177@LB@Position - sRNA 167 -- 215@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 167 -- 173@LB@
183	0.02111	0.3833	b0461	tomB	-12.41	0.091700	125 -- 158	128 -- 160	Hha toxicity attenuator; conjugation-related protein	_____________124_________________________________________159\n_____________\|___________________________________________\|\n5'-UGC...GGAUG________CCCAAA_G_______AUC____C__C____G____UCUGU...AUC-3'\n______________AAUACUCA______A_ACAUGAU____GCA_AG_UUAA_UUUC\n______________\|\|\|\|\|\|\|\|______\|_\|\|\|\|\|\|\|____\|\|\|_\|\|_\|:\|\|_\|\|\|\|\n______________UUAUGAGU______U_UGUACUA____CGU_UC_AGUU_AAAG\n3'-UUU...UGUGG________CAG____G_______CGUC___________G____UCUUA...UAG-5'\n_____________\|___________________________________________\|\n_____________161_________________________________________127\n	224 -- 230	163 -- 169	-23.2008 kcal/mol	3.84731 kcal/mol	8.26055 kcal/mol	124 159@LB@ \| \|@LB@5'-UGC...GGAUG CCCAAA G AUC C C G UCUGU...AUC-3'@LB@ AAUACUCA A ACAUGAU GCA AG UUAA UUUC@LB@ \|\|\|\|\|\|\|\| \| \|\|\|\|\|\|\| \|\|\| \|\| \|:\|\| \|\|\|\|@LB@ UUAUGAGU U UGUACUA CGU UC AGUU AAAG@LB@3'-UUU...UGUGG CAG G CGUC G UCUUA...UAG-5'@LB@ \| \|@LB@ 161 127@LB@@LB@@LB@Energy -12.41 kcal/mol@LB@Hybridization Energy -23.2008 kcal/mol@LB@Unfolding Energy - mRNA 3.84731 kcal/mol@LB@Unfolding Energy - sRNA 8.26055 kcal/mol@LB@@LB@Position - mRNA 125 -- 158@LB@Position - sRNA 128 -- 160@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 163 -- 169@LB@
62	0.006126	0.3261	b3824	rhtB	-10.68	0.204362	7 -- 23	171 -- 187	homoserine homoserine lactone and S-methyl-methionine efflux pump	_____________6_________________24\n_____________\|_________________\|\n_____5'-ACGCUG_______AAA_______GCGGU...ACC-3'\n______________ACGCCAG___UCAGUCA\n______________\|\|:\|\|\|:___\|\|\|\|\|\|\|\n______________UGUGGUU___AGUCAGU\n3'-UUU...UAAAA_______AUG_______GUGUA...UAG-5'\n_____________\|_________________\|\n_____________188_______________170\n	17 -- 23	171 -- 177	-18.1223 kcal/mol	1.9449 kcal/mol	4.7016 kcal/mol	6 24@LB@ \| \|@LB@ 5'-ACGCUG AAA GCGGU...ACC-3'@LB@ ACGCCAG UCAGUCA@LB@ \|\|:\|\|\|: \|\|\|\|\|\|\|@LB@ UGUGGUU AGUCAGU@LB@3'-UUU...UAAAA AUG GUGUA...UAG-5'@LB@ \| \|@LB@ 188 170@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -18.1223 kcal/mol@LB@Unfolding Energy - mRNA 1.9449 kcal/mol@LB@Unfolding Energy - sRNA 4.7016 kcal/mol@LB@@LB@Position - mRNA 7 -- 23@LB@Position - sRNA 171 -- 187@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 171 -- 177@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)

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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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