Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
151	0.008943	0.2059	b1284	yciT	-9.40	0.179701	94 -- 109	63 -- 77	global regulator of transcription; DeoR family		_____________93_______________110\n_____________\|________________\|\n5'-GCA...CGAAG______U_________AACAA...CCA-3'\n______________GCACCG_GGGAGAUUU\n______________:\|\|\|\|:_\|\|\|\|:\|\|:\|\n______________UGUGGU_CCCUUUAGA\n3'-UUU...GCGGU________________ACCGA...GUG-5'\n_____________\|________________\|\n_____________78_______________62\n	103 -- 109	63 -- 69	-19.5221 kcal/mol	5.38652 kcal/mol	4.72953 kcal/mol	93 110@LB@ \| \|@LB@5'-GCA...CGAAG U AACAA...CCA-3'@LB@ GCACCG GGGAGAUUU@LB@ :\|\|\|\|: \|\|\|\|:\|\|:\|@LB@ UGUGGU CCCUUUAGA@LB@3'-UUU...GCGGU ACCGA...GUG-5'@LB@ \| \|@LB@ 78 62@LB@@LB@@LB@Energy -9.40 kcal/mol@LB@Hybridization Energy -19.5221 kcal/mol@LB@Unfolding Energy - mRNA 5.38652 kcal/mol@LB@Unfolding Energy - sRNA 4.72953 kcal/mol@LB@@LB@Position - mRNA 94 -- 109@LB@Position - sRNA 63 -- 77@LB@Position Seed - mRNA 103 -- 109@LB@Position Seed - sRNA 63 -- 69@LB@
152	0.009044	0.2059	b1448	mnaT	-7.00	0.457084	229 -- 266	50 -- 86	methionine N-acyltransferase; L-amino acid N-acyltransferase		_____________228____________________________________267\n_____________\|______________________________________\|\n5'-CGC...AGCCG_________C_____C________AUAACCA_______UUGUA...CGG-3'\n______________ACUGUGCUG_CAUUG_GGAAAUUU_______CGCCGUG\n______________\|\|\|\|:\|\|::_\|\|:::_\|\|\|\|\|\|:\|_______\|\|\|\|\|\|:\n______________UGACGCGGU_GUGGU_CCUUUAGA_______GCGGCAU\n3'-UUU...GCUUA_________U_____C________ACCGAC________UUAAU...GUG-5'\n_____________\|______________________________________\|\n_____________87_____________________________________49\n	260 -- 266	50 -- 56	-33.8437 kcal/mol	9.99136 kcal/mol	16.8518 kcal/mol	228 267@LB@ \| \|@LB@5'-CGC...AGCCG C C AUAACCA UUGUA...CGG-3'@LB@ ACUGUGCUG CAUUG GGAAAUUU CGCCGUG@LB@ \|\|\|\|:\|\|:: \|\|::: \|\|\|\|\|\|:\| \|\|\|\|\|\|:@LB@ UGACGCGGU GUGGU CCUUUAGA GCGGCAU@LB@3'-UUU...GCUUA U C ACCGAC UUAAU...GUG-5'@LB@ \| \|@LB@ 87 49@LB@@LB@@LB@Energy -7.00 kcal/mol@LB@Hybridization Energy -33.8437 kcal/mol@LB@Unfolding Energy - mRNA 9.99136 kcal/mol@LB@Unfolding Energy - sRNA 16.8518 kcal/mol@LB@@LB@Position - mRNA 229 -- 266@LB@Position - sRNA 50 -- 86@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 50 -- 56@LB@
153	0.009069	0.2059	b3529	yhjK	-8.15	0.299018	186 -- 212	47 -- 74	cyclic-di-GMP phosphodiesterase		_____________185__________________________213\n_____________\|____________________________\|\n5'-AGC...GAUUU_________GACAAU_____________CGCUC...AUC-3'\n______________CCGGGGGGA______UUGCG_CGUAAGU\n______________\|\|:\|\|\|::\|______:\|\|\|\|_\|\|\|\|\|:\|\n______________GGUCCCUUU______GACGC_GCAUUUA\n3'-UUU...GUUGU_________AGAACC_____G_______AUAAU...GUG-5'\n_____________\|____________________________\|\n_____________75___________________________46\n	187 -- 193	67 -- 73	-27.1977 kcal/mol	10.2409 kcal/mol	8.80319 kcal/mol	185 213@LB@ \| \|@LB@5'-AGC...GAUUU GACAAU CGCUC...AUC-3'@LB@ CCGGGGGGA UUGCG CGUAAGU@LB@ \|\|:\|\|\|::\| :\|\|\|\| \|\|\|\|\|:\|@LB@ GGUCCCUUU GACGC GCAUUUA@LB@3'-UUU...GUUGU AGAACC G AUAAU...GUG-5'@LB@ \| \|@LB@ 75 46@LB@@LB@@LB@Energy -8.15 kcal/mol@LB@Hybridization Energy -27.1977 kcal/mol@LB@Unfolding Energy - mRNA 10.2409 kcal/mol@LB@Unfolding Energy - sRNA 8.80319 kcal/mol@LB@@LB@Position - mRNA 186 -- 212@LB@Position - sRNA 47 -- 74@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 67 -- 73@LB@
154	0.009082	0.2059	b2676	nrdF	-13.94	0.023769	159 -- 176	53 -- 69	ribonucleoside-diphosphate reductase 2 beta subunit ferritin-like protein		_____________158________________177\n_____________\|__________________\|\n5'-AAG...GCACU______GAA_________UCCUG...CAG-3'\n______________GAAAUU___GGCUGCGUC\n______________\|\|\|\|\|:___\|\|\|\|\|\|\|:\|\n______________CUUUAG___CCGACGCGG\n3'-UUU...GGUCC______AA__________CAUUU...GUG-5'\n_____________\|__________________\|\n_____________70_________________52\n	170 -- 176	53 -- 59	-23.1658 kcal/mol	2.38862 kcal/mol	6.83371 kcal/mol	158 177@LB@ \| \|@LB@5'-AAG...GCACU GAA UCCUG...CAG-3'@LB@ GAAAUU GGCUGCGUC@LB@ \|\|\|\|\|: \|\|\|\|\|\|\|:\|@LB@ CUUUAG CCGACGCGG@LB@3'-UUU...GGUCC AA CAUUU...GUG-5'@LB@ \| \|@LB@ 70 52@LB@@LB@@LB@Energy -13.94 kcal/mol@LB@Hybridization Energy -23.1658 kcal/mol@LB@Unfolding Energy - mRNA 2.38862 kcal/mol@LB@Unfolding Energy - sRNA 6.83371 kcal/mol@LB@@LB@Position - mRNA 159 -- 176@LB@Position - sRNA 53 -- 69@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 53 -- 59@LB@
155	0.009115	0.2059	b1531	marA	-9.94	0.142609	213 -- 231	72 -- 89	multiple antibiotic resistance transcriptional regulator		_____________212_________________232\n_____________\|___________________\|\n5'-AAG...GACGC_______A_____U_____UUCAU...AGC-3'\n______________AAUACUG_CGCUA_UACCA\n______________\|\|\|\|\|\|\|_\|\|\|:\|_:\|\|\|\|\n______________UUAUGAC_GCGGU_GUGGU\n3'-UUU...CGCGC_____________U_____CCCUU...GUG-5'\n_____________\|___________________\|\n_____________90__________________71\n	213 -- 219	83 -- 89	-21.2611 kcal/mol	3.54366 kcal/mol	7.77515 kcal/mol	212 232@LB@ \| \|@LB@5'-AAG...GACGC A U UUCAU...AGC-3'@LB@ AAUACUG CGCUA UACCA@LB@ \|\|\|\|\|\|\| \|\|\|:\| :\|\|\|\|@LB@ UUAUGAC GCGGU GUGGU@LB@3'-UUU...CGCGC U CCCUU...GUG-5'@LB@ \| \|@LB@ 90 71@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -21.2611 kcal/mol@LB@Unfolding Energy - mRNA 3.54366 kcal/mol@LB@Unfolding Energy - sRNA 7.77515 kcal/mol@LB@@LB@Position - mRNA 213 -- 231@LB@Position - sRNA 72 -- 89@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 83 -- 89@LB@
156	0.009123	0.2059	b2683	ygaH	-13.79	0.025463	164 -- 213	27 -- 86	putative L-valine exporter norvaline resistance protein		_____________163______________________________________________________________214\n_____________\|________________________________________________________________\|\n5'-AUU...GCCUC_________________CAU________AAGGA_____C_________________C_______UUCUG...CAA-3'\n______________ACUGCGUUAAU_CCAGG____UC_UGGC_____GCGCC____________GAUGAG_UAUGAGG\n______________\|\|\|\|\|\|::\|\|:_\|\|\|\|\|____\|\|_\|\|\|\|_____\|\|\|\|\|____________\|\|\|\|\|\|_\|\|::\|\|\|\n______________UGACGCGGUUG_GGUCC____AG_ACCG_____CGCGG____________CUACUC_AUGUUCC\n3'-UUU...GCUUA___________U_____CUUU__A____A_________CAUUUAAUAAUA______A_______CGUGU...GUG-5'\n_____________\|________________________________________________________________\|\n_____________87_______________________________________________________________26\n	207 -- 213	27 -- 33	-50.2075 kcal/mol	19.3484 kcal/mol	17.0667 kcal/mol	163 214@LB@ \| \|@LB@5'-AUU...GCCUC CAU AAGGA C C UUCUG...CAA-3'@LB@ ACUGCGUUAAU CCAGG UC UGGC GCGCC GAUGAG UAUGAGG@LB@ \|\|\|\|\|\|::\|\|: \|\|\|\|\| \|\| \|\|\|\| \|\|\|\|\| \|\|\|\|\|\| \|\|::\|\|\|@LB@ UGACGCGGUUG GGUCC AG ACCG CGCGG CUACUC AUGUUCC@LB@3'-UUU...GCUUA U CUUU A A CAUUUAAUAAUA A CGUGU...GUG-5'@LB@ \| \|@LB@ 87 26@LB@@LB@@LB@Energy -13.79 kcal/mol@LB@Hybridization Energy -50.2075 kcal/mol@LB@Unfolding Energy - mRNA 19.3484 kcal/mol@LB@Unfolding Energy - sRNA 17.0667 kcal/mol@LB@@LB@Position - mRNA 164 -- 213@LB@Position - sRNA 27 -- 86@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 27 -- 33@LB@
157	0.009216	0.2062	b3361	fic	-9.77	0.153316	103 -- 112	5 -- 14	stationary phase-induced protein putative toxin		_____________102________113\n_____________\|__________\|\n5'-CGC...CGUAA__________AGUCG...AAC-3'\n______________UUUUCAGGCC\n______________\|\|\|\|\|\|\|\|\|\|\n______________AAAAGUCCGG\n3'-UUU...UGACA__________CGUG-5'\n_____________\|__________\|\n_____________15_________4\n	106 -- 112	5 -- 11	-15.6889 kcal/mol	1.64573 kcal/mol	4.24834 kcal/mol	102 113@LB@ \| \|@LB@5'-CGC...CGUAA AGUCG...AAC-3'@LB@ UUUUCAGGCC@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ AAAAGUCCGG@LB@3'-UUU...UGACA CGUG-5'@LB@ \| \|@LB@ 15 4@LB@@LB@@LB@Energy -9.77 kcal/mol@LB@Hybridization Energy -15.6889 kcal/mol@LB@Unfolding Energy - mRNA 1.64573 kcal/mol@LB@Unfolding Energy - sRNA 4.24834 kcal/mol@LB@@LB@Position - mRNA 103 -- 112@LB@Position - sRNA 5 -- 14@LB@Position Seed - mRNA 106 -- 112@LB@Position Seed - sRNA 5 -- 11@LB@
158	0.009324	0.2062	b3574	yiaJ	-10.56	0.109206	175 -- 190	70 -- 85	transcriptional repressor for the yiaKLMNO-lyxK-sgbHUE operon		_____________174______________191\n_____________\|________________\|\n5'-CCC...ACACU________C_______ACGCG...UUG-3'\n______________UUGCGCUA_CAUCAGG\n______________:\|\|\|\|\|:\|_\|\|:\|\|\|\|\n______________GACGCGGU_GUGGUCC\n3'-UUU...CUUAU________U_______CUUUA...GUG-5'\n_____________\|________________\|\n_____________86_______________69\n	184 -- 190	70 -- 76	-22.9924 kcal/mol	5.16069 kcal/mol	7.27689 kcal/mol	174 191@LB@ \| \|@LB@5'-CCC...ACACU C ACGCG...UUG-3'@LB@ UUGCGCUA CAUCAGG@LB@ :\|\|\|\|\|:\| \|\|:\|\|\|\|@LB@ GACGCGGU GUGGUCC@LB@3'-UUU...CUUAU U CUUUA...GUG-5'@LB@ \| \|@LB@ 86 69@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -22.9924 kcal/mol@LB@Unfolding Energy - mRNA 5.16069 kcal/mol@LB@Unfolding Energy - sRNA 7.27689 kcal/mol@LB@@LB@Position - mRNA 175 -- 190@LB@Position - sRNA 70 -- 85@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 70 -- 76@LB@
159	0.009346	0.2062	b3661	nlpA	-7.63	0.365650	232 -- 240	1 -- 9	cytoplasmic membrane lipoprotein-28		_____________231_______241\n_____________\|_________\|\n5'-UGU...GACAG_________UAUUG...ACA-3'\n______________GGGCCGCAU\n______________:\|\|\|\|\|\|\|:\n______________UCCGGCGUG\n3'-UUU...AAAAG_________-5'\n_____________\|________\|\n_____________10_______1\n	234 -- 240	1 -- 7	-16.6231 kcal/mol	3.46198 kcal/mol	5.10726 kcal/mol	231 241@LB@ \| \|@LB@5'-UGU...GACAG UAUUG...ACA-3'@LB@ GGGCCGCAU@LB@ :\|\|\|\|\|\|\|:@LB@ UCCGGCGUG@LB@3'-UUU...AAAAG -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -16.6231 kcal/mol@LB@Unfolding Energy - mRNA 3.46198 kcal/mol@LB@Unfolding Energy - sRNA 5.10726 kcal/mol@LB@@LB@Position - mRNA 232 -- 240@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 1 -- 7@LB@
160	0.009416	0.2062	b2095	gatZ	-8.10	0.305092	155 -- 170	18 -- 33	D-tagatose 1 6-bisphosphate aldolase 2 subunit	b3132	_____________154______________171\n_____________\|________________\|\n5'-AAU...GUGGC__________G_____AACGC...UUG-3'\n______________UGCGAGGGCA_GGCAU\n______________\|:\|:\|\|\|\|\|\|_:\|\|\|:\n______________AUGUUCCCGU_UCGUG\n3'-UUU...ACUCA__________G_____ACAAA...GUG-5'\n_____________\|________________\|\n_____________34_______________17\n	158 -- 164	24 -- 30	-26.3287 kcal/mol	9.40457 kcal/mol	8.82204 kcal/mol	154 171@LB@ \| \|@LB@5'-AAU...GUGGC G AACGC...UUG-3'@LB@ UGCGAGGGCA GGCAU@LB@ \|:\|:\|\|\|\|\|\| :\|\|\|:@LB@ AUGUUCCCGU UCGUG@LB@3'-UUU...ACUCA G ACAAA...GUG-5'@LB@ \| \|@LB@ 34 17@LB@@LB@@LB@Energy -8.10 kcal/mol@LB@Hybridization Energy -26.3287 kcal/mol@LB@Unfolding Energy - mRNA 9.40457 kcal/mol@LB@Unfolding Energy - sRNA 8.82204 kcal/mol@LB@@LB@Position - mRNA 155 -- 170@LB@Position - sRNA 18 -- 33@LB@Position Seed - mRNA 158 -- 164@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)

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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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