Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
146	0.02871	0.6177	b1120	cobB	-8.56	0.080407	32 -- 40	43 -- 51	deacetylase of acs and cheY chemotaxis regulator	_____________31________41\n_____________\|_________\|\n5'-CGC...GAUGC_________GCGUG...AUC-3'\n______________GGGAGGAAU\n______________::\|\|\|\|\|\|\|\n______________UUCUCCUUA\n3'-UUU...GCAGU_________AAGUA...ACA-5'\n_____________\|_________\|\n_____________52________42\n	34 -- 40	43 -- 49	-11.3695 kcal/mol	1.94725 kcal/mol	0.859837 kcal/mol	31 41@LB@ \| \|@LB@5'-CGC...GAUGC GCGUG...AUC-3'@LB@ GGGAGGAAU@LB@ ::\|\|\|\|\|\|\|@LB@ UUCUCCUUA@LB@3'-UUU...GCAGU AAGUA...ACA-5'@LB@ \| \|@LB@ 52 42@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -11.3695 kcal/mol@LB@Unfolding Energy - mRNA 1.94725 kcal/mol@LB@Unfolding Energy - sRNA 0.859837 kcal/mol@LB@@LB@Position - mRNA 32 -- 40@LB@Position - sRNA 43 -- 51@LB@Position Seed - mRNA 34 -- 40@LB@Position Seed - sRNA 43 -- 49@LB@
147	0.02922	0.6177	b3836	tatA	-6.91	0.169904	186 -- 195	44 -- 53	TatABCE protein translocation system subunit	_____________185________196\n_____________\|__________\|\n5'-CUA...UCUAC__C_______CAUGU...GUG-3'\n______________CA_AGAGGAA\n______________\|\|_\|\|\|\|\|\|\|\n______________GU_UCUCCUU\n3'-UUU...GGGCA__U_______AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	189 -- 195	44 -- 50	-10.6779 kcal/mol	2.84312 kcal/mol	0.927997 kcal/mol	185 196@LB@ \| \|@LB@5'-CUA...UCUAC C CAUGU...GUG-3'@LB@ CA AGAGGAA@LB@ \|\| \|\|\|\|\|\|\|@LB@ GU UCUCCUU@LB@3'-UUU...GGGCA U AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -6.91 kcal/mol@LB@Hybridization Energy -10.6779 kcal/mol@LB@Unfolding Energy - mRNA 2.84312 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 186 -- 195@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
148	0.02945	0.6177	b0692	potE	-8.42	0.085901	187 -- 195	44 -- 52	putrescine/proton symporter: putrescine/ornithine antiporter	_____________186_______196\n_____________\|_________\|\n5'-UGU...UGUUG_________AAAUU...AGC-3'\n______________AAAGGGGAA\n______________\|\|\|\|:\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	189 -- 195	44 -- 50	-10.6161 kcal/mol	1.33649 kcal/mol	0.860683 kcal/mol	186 196@LB@ \| \|@LB@5'-UGU...UGUUG AAAUU...AGC-3'@LB@ AAAGGGGAA@LB@ \|\|\|\|:\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.42 kcal/mol@LB@Hybridization Energy -10.6161 kcal/mol@LB@Unfolding Energy - mRNA 1.33649 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 187 -- 195@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
149	0.03014	0.6177	b4470	yhaM	-8.71	0.074988	251 -- 260	44 -- 54	putative L-serine dehydratase alpha chain	_____________250_________261\n_____________\|___________\|\n5'-UGU...GCCGU___________GUAAA...UGG-3'\n______________UC_AGGAGGAA\n______________\|\|_\|:\|\|\|\|\|\|\n______________AG_UUCUCCUU\n3'-UUU...CGGGC__U________AAAGU...ACA-5'\n_____________\|___________\|\n_____________55__________43\n	254 -- 260	44 -- 50	-10.8529 kcal/mol	1.19981 kcal/mol	0.939671 kcal/mol	250 261@LB@ \| \|@LB@5'-UGU...GCCGU GUAAA...UGG-3'@LB@ UC AGGAGGAA@LB@ \|\| \|:\|\|\|\|\|\|@LB@ AG UUCUCCUU@LB@3'-UUU...CGGGC U AAAGU...ACA-5'@LB@ \| \|@LB@ 55 43@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -10.8529 kcal/mol@LB@Unfolding Energy - mRNA 1.19981 kcal/mol@LB@Unfolding Energy - sRNA 0.939671 kcal/mol@LB@@LB@Position - mRNA 251 -- 260@LB@Position - sRNA 44 -- 54@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 44 -- 50@LB@
150	0.03022	0.6177	b1285	gmr	-9.04	0.064446	208 -- 218	47 -- 57	cyclic-di-GMP phosphodiesterase; csgD regulator; modulator of RNase II stability	_____________207_________219\n_____________\|___________\|\n5'-UUU...GAAAA___________UCCAC...CUA-3'\n______________CCGUUAGGGAG\n______________\|\|\|\|:\|::\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	212 -- 218	47 -- 53	-14.7452 kcal/mol	2.96952 kcal/mol	2.73556 kcal/mol	207 219@LB@ \| \|@LB@5'-UUU...GAAAA UCCAC...CUA-3'@LB@ CCGUUAGGGAG@LB@ \|\|\|\|:\|::\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -9.04 kcal/mol@LB@Hybridization Energy -14.7452 kcal/mol@LB@Unfolding Energy - mRNA 2.96952 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 208 -- 218@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 47 -- 53@LB@
151	0.03043	0.6177	b3081	fadH	-8.56	0.080347	290 -- 297	43 -- 50	2 4-dienoyl-CoA reductase NADH and FMN-linked	_____________289______298\n_____________\|________\|\n5'-UGG...GGGCU________ACC-3'\n______________GGAGGAAU\n______________:\|\|\|\|\|\|\|\n______________UCUCCUUA\n3'-UUU...CAGUU________AAGUA...ACA-5'\n_____________\|________\|\n_____________51_______42\n	291 -- 297	43 -- 49	-10.5858 kcal/mol	1.17616 kcal/mol	0.845564 kcal/mol	289 298@LB@ \| \|@LB@5'-UGG...GGGCU ACC-3'@LB@ GGAGGAAU@LB@ :\|\|\|\|\|\|\|@LB@ UCUCCUUA@LB@3'-UUU...CAGUU AAGUA...ACA-5'@LB@ \| \|@LB@ 51 42@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -10.5858 kcal/mol@LB@Unfolding Energy - mRNA 1.17616 kcal/mol@LB@Unfolding Energy - sRNA 0.845564 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 43 -- 50@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 43 -- 49@LB@
152	0.03059	0.6177	b2609	rpsP	-6.70	0.186060	187 -- 203	23 -- 53	30S ribosomal subunit protein S16	_____________186______________________________204\n_____________\|________________________________\|\n5'-UCA...AUUCA__C_____________________________GUAAC...UCG-3'\n______________CA_AAGAGGA_______________UGUUAUG\n______________\|\|_\|\|\|\|\|\|\|_______________\|:\|\|\|\|\|\n______________GU_UUCUCCU_______________AUAAUAC\n3'-UUU...GGGCA__________UAAAGUAAAAAAAUA_______GGCAG...ACA-5'\n_____________\|________________________________\|\n_____________54_______________________________22\n	197 -- 203	23 -- 29	-10.7305 kcal/mol	2.84664 kcal/mol	1.18482 kcal/mol	186 204@LB@ \| \|@LB@5'-UCA...AUUCA C GUAAC...UCG-3'@LB@ CA AAGAGGA UGUUAUG@LB@ \|\| \|\|\|\|\|\|\| \|:\|\|\|\|\|@LB@ GU UUCUCCU AUAAUAC@LB@3'-UUU...GGGCA UAAAGUAAAAAAAUA GGCAG...ACA-5'@LB@ \| \|@LB@ 54 22@LB@@LB@@LB@Energy -6.70 kcal/mol@LB@Hybridization Energy -10.7305 kcal/mol@LB@Unfolding Energy - mRNA 2.84664 kcal/mol@LB@Unfolding Energy - sRNA 1.18482 kcal/mol@LB@@LB@Position - mRNA 187 -- 203@LB@Position - sRNA 23 -- 53@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 23 -- 29@LB@
153	0.03061	0.6177	b4060	yjcB	-6.94	0.167417	88 -- 108	29 -- 50	putative inner membrane protein	_____________87_____________________109\n_____________\|______________________\|\n5'-AUA...CAAAC____U____________G____CUGCA...GGU-3'\n______________AGAG__GUUUCAUUUUU_UGUU\n______________\|\|\|\|__:\|\|\|\|\|\|\|\|\|\|_\|:\|\|\n______________UCUC__UAAAGUAAAAA_AUAA\n3'-UUU...CAGUU____CU___________A____UAAUA...ACA-5'\n_____________\|______________________\|\n_____________51_____________________28\n	97 -- 103	34 -- 40	-13.8913 kcal/mol	5.87088 kcal/mol	1.08007 kcal/mol	87 109@LB@ \| \|@LB@5'-AUA...CAAAC U G CUGCA...GGU-3'@LB@ AGAG GUUUCAUUUUU UGUU@LB@ \|\|\|\| :\|\|\|\|\|\|\|\|\|\| \|:\|\|@LB@ UCUC UAAAGUAAAAA AUAA@LB@3'-UUU...CAGUU CU A UAAUA...ACA-5'@LB@ \| \|@LB@ 51 28@LB@@LB@@LB@Energy -6.94 kcal/mol@LB@Hybridization Energy -13.8913 kcal/mol@LB@Unfolding Energy - mRNA 5.87088 kcal/mol@LB@Unfolding Energy - sRNA 1.08007 kcal/mol@LB@@LB@Position - mRNA 88 -- 108@LB@Position - sRNA 29 -- 50@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 34 -- 40@LB@
154	0.03071	0.6177	b0368	tauD	-7.18	0.150437	69 -- 85	40 -- 55	taurine dioxygenase 2-oxoglutarate-dependent	_____________68________________86\n_____________\|_________________\|\n5'-GUG...GUUCA_____C___U_______UCGCA...AAC-3'\n______________GUCAG_GGG_GAAUUUC\n______________\|\|\|\|:_\|:\|_\|\|\|\|\|\|\|\n______________CAGUU_CUC_CUUAAAG\n3'-UUU...CCGGG_____U___________UAAAA...ACA-5'\n_____________\|_________________\|\n_____________56________________39\n	79 -- 85	40 -- 46	-16.0696 kcal/mol	7.86965 kcal/mol	1.01784 kcal/mol	68 86@LB@ \| \|@LB@5'-GUG...GUUCA C U UCGCA...AAC-3'@LB@ GUCAG GGG GAAUUUC@LB@ \|\|\|\|: \|:\| \|\|\|\|\|\|\|@LB@ CAGUU CUC CUUAAAG@LB@3'-UUU...CCGGG U UAAAA...ACA-5'@LB@ \| \|@LB@ 56 39@LB@@LB@@LB@Energy -7.18 kcal/mol@LB@Hybridization Energy -16.0696 kcal/mol@LB@Unfolding Energy - mRNA 7.86965 kcal/mol@LB@Unfolding Energy - sRNA 1.01784 kcal/mol@LB@@LB@Position - mRNA 69 -- 85@LB@Position - sRNA 40 -- 55@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 40 -- 46@LB@
155	0.03087	0.6177	b1003	yccJ	-9.03	0.064630	130 -- 145	43 -- 56	uncharacterized protein	_____________129______________146\n_____________\|________________\|\n5'-CCU...UUGCU_____UC_________AUGUC...GGU-3'\n______________CGUUA__AAGGGGAAU\n______________\|\|\|:\|__\|\|\|:\|\|\|\|\|\n______________GCAGU__UUCUCCUUA\n3'-UUU...ACCGG________________AAGUA...ACA-5'\n_____________\|________________\|\n_____________57_______________42\n	139 -- 145	43 -- 49	-13.8314 kcal/mol	3.84343 kcal/mol	0.953958 kcal/mol	129 146@LB@ \| \|@LB@5'-CCU...UUGCU UC AUGUC...GGU-3'@LB@ CGUUA AAGGGGAAU@LB@ \|\|\|:\| \|\|\|:\|\|\|\|\|@LB@ GCAGU UUCUCCUUA@LB@3'-UUU...ACCGG AAGUA...ACA-5'@LB@ \| \|@LB@ 57 42@LB@@LB@@LB@Energy -9.03 kcal/mol@LB@Hybridization Energy -13.8314 kcal/mol@LB@Unfolding Energy - mRNA 3.84343 kcal/mol@LB@Unfolding Energy - sRNA 0.953958 kcal/mol@LB@@LB@Position - mRNA 130 -- 145@LB@Position - sRNA 43 -- 56@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 43 -- 49@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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