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
14	0.00083	0.1886	b2721	hycE	-15.91	0.017607	169 -- 185	190 -- 205	hydrogenase 3 large subunit	_____________168_______________186\n_____________\|_________________\|\n5'-UUC...UCUCC__________C______AAAGA...UGA-3'\n______________UUGCUGGCGG_GUGAUU\n______________:\|\|\|\|\|\|\|\|\|_\|\|\|\|\|\|\n______________GACGACCGCC_CACUAA\n3'-UUU...UAUUA_________________AAUGU...UAG-5'\n_____________\|_________________\|\n_____________206_______________189\n	172 -- 178	196 -- 202	-26.9802 kcal/mol	6.4269 kcal/mol	9.06848 kcal/mol	168 186@LB@ \| \|@LB@5'-UUC...UCUCC C AAAGA...UGA-3'@LB@ UUGCUGGCGG GUGAUU@LB@ :\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GACGACCGCC CACUAA@LB@3'-UUU...UAUUA AAUGU...UAG-5'@LB@ \| \|@LB@ 206 189@LB@@LB@@LB@Energy -15.91 kcal/mol@LB@Hybridization Energy -26.9802 kcal/mol@LB@Unfolding Energy - mRNA 6.4269 kcal/mol@LB@Unfolding Energy - sRNA 9.06848 kcal/mol@LB@@LB@Position - mRNA 169 -- 185@LB@Position - sRNA 190 -- 205@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 196 -- 202@LB@
83	0.008941	0.3575	b3343	tusB	-13.46	0.055944	1 -- 14	190 -- 203	mnm(5)-s(2)U34-tRNA synthesis 2-thiolation protein	______________1_____________15\n______________\|_____________\|\n___________5'-_______C______ACAUU...GCG-3'\n______________GCUGGCG_GUGAUU\n______________\|\|\|\|\|\|\|_\|\|\|\|\|\|\n______________CGACCGC_CACUAA\n3'-UUU...UUAGA_______C______AAUGU...UAG-5'\n_____________\|______________\|\n_____________204____________189\n	1 -- 7	197 -- 203	-22.3351 kcal/mol	4.22102 kcal/mol	9.06745 kcal/mol	1 15@LB@ \| \|@LB@ 5'- C ACAUU...GCG-3'@LB@ GCUGGCG GUGAUU@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ CGACCGC CACUAA@LB@3'-UUU...UUAGA C AAUGU...UAG-5'@LB@ \| \|@LB@ 204 189@LB@@LB@@LB@Energy -13.46 kcal/mol@LB@Hybridization Energy -22.3351 kcal/mol@LB@Unfolding Energy - mRNA 4.22102 kcal/mol@LB@Unfolding Energy - sRNA 9.06745 kcal/mol@LB@@LB@Position - mRNA 1 -- 14@LB@Position - sRNA 190 -- 203@LB@Position Seed - mRNA 1 -- 7@LB@Position Seed - sRNA 197 -- 203@LB@
35	0.002845	0.2736	b3887	dtd	-14.98	0.027287	55 -- 74	191 -- 211	D-tyr-tRNA(Tyr) deacylase	_____________54____________________75\n_____________\|_____________________\|\n5'-GGA...UCAUU______G______________CCCCA...UCG-3'\n______________UAUGGU_UGCUGGCGG_UGAU\n______________\|\|\|::\|_\|\|\|\|\|\|\|\|\|_\|\|\|\|\n______________AUAUUA_ACGACCGCC_ACUA\n3'-UUU...CGUCC______G_________C____AAAUG...UAG-5'\n_____________\|_____________________\|\n_____________212___________________190\n	64 -- 70	196 -- 202	-27.702 kcal/mol	6.2401 kcal/mol	11.5765 kcal/mol	54 75@LB@ \| \|@LB@5'-GGA...UCAUU G CCCCA...UCG-3'@LB@ UAUGGU UGCUGGCGG UGAU@LB@ \|\|\|::\| \|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ AUAUUA ACGACCGCC ACUA@LB@3'-UUU...CGUCC G C AAAUG...UAG-5'@LB@ \| \|@LB@ 212 190@LB@@LB@@LB@Energy -14.98 kcal/mol@LB@Hybridization Energy -27.702 kcal/mol@LB@Unfolding Energy - mRNA 6.2401 kcal/mol@LB@Unfolding Energy - sRNA 11.5765 kcal/mol@LB@@LB@Position - mRNA 55 -- 74@LB@Position - sRNA 191 -- 211@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 196 -- 202@LB@
79	0.008119	0.3458	b0945	pyrD	-11.48	0.141710	30 -- 41	191 -- 202	dihydro-orotate oxidase FMN-linked	_____________29______________________42\n_____________\|_______________________\|\n5'-UGU...AGCAA_____________A___GA____CGU-3'\n______________UUACGCCG_UAUU_CAG__ACGC\n______________\|\|\|\|:\|\|:_\|\|:\|_\|\|\|__\|\|:\|\n______________AAUGUGGU_AUGA_GUC__UGUG\n3'-UUU...ACUAA________U________AG____UACUA...UAG-5'\n_____________\|_______________________\|\n_____________203_____________________190\n	277 -- 283	182 -- 188	-20.4941 kcal/mol	3.55802 kcal/mol	4.91485 kcal/mol	29 42@LB@ \| \|@LB@5'-UGU...AGCAA A GA CGU-3'@LB@ UUACGCCG UAUU CAG ACGC@LB@ \|\|\|\|:\|\|: \|\|:\| \|\|\| \|\|:\|@LB@ AAUGUGGU AUGA GUC UGUG@LB@3'-UUU...ACUAA U AG UACUA...UAG-5'@LB@ \| \|@LB@ 203 190@LB@@LB@@LB@Energy -11.48 kcal/mol@LB@Hybridization Energy -20.4941 kcal/mol@LB@Unfolding Energy - mRNA 3.55802 kcal/mol@LB@Unfolding Energy - sRNA 4.91485 kcal/mol@LB@@LB@Position - mRNA 30 -- 41@LB@Position - sRNA 191 -- 202@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 182 -- 188@LB@
187	0.02173	0.3833	b3679	yidK	-10.16	0.256396	240 -- 256	191 -- 205	putative transporter	_____________239________________________________________257\n_____________\|__________________________________________\|\n5'-UUU...UUACG_________GC______________U____GAA_________AAACA...AAG-3'\n______________CUGCUGGUG__GGUGAU____CACC_GGUG___GGUC_CGCA\n______________\|\|\|\|\|\|\|:\|__\|\|\|\|\|\|____\|\|\|\|_::\|:___:\|\|\|_\|:\|\|\n______________GACGACCGC__CCACUA____GUGG_UUAU___UCAG_GUGU\n3'-UUU...UAUUA_________________AAAU_________GAG____U____ACUAC...UAG-5'\n_____________\|__________________________________________\|\n_____________206________________________________________190\n	242 -- 248	197 -- 203	-39.2862 kcal/mol	16.885 kcal/mol	15.3993 kcal/mol	239 257@LB@ \| \|@LB@5'-UUU...UUACG GC U GAA AAACA...AAG-3'@LB@ CUGCUGGUG GGUGAU CACC GGUG GGUC CGCA@LB@ \|\|\|\|\|\|\|:\| \|\|\|\|\|\| \|\|\|\| ::\|: :\|\|\| \|:\|\|@LB@ GACGACCGC CCACUA GUGG UUAU UCAG GUGU@LB@3'-UUU...UAUUA AAAU GAG U ACUAC...UAG-5'@LB@ \| \|@LB@ 206 190@LB@@LB@@LB@Energy -10.16 kcal/mol@LB@Hybridization Energy -39.2862 kcal/mol@LB@Unfolding Energy - mRNA 16.885 kcal/mol@LB@Unfolding Energy - sRNA 15.3993 kcal/mol@LB@@LB@Position - mRNA 240 -- 256@LB@Position - sRNA 191 -- 205@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 197 -- 203@LB@
48	0.004626	0.3205	b3462	ftsX	-13.20	0.063258	14 -- 27	192 -- 205	putative ABC transporter permease	_____________13_____________28\n_____________\|______________\|\n5'-CAA...CGGUA__________AC__ACCGA...ACG-3'\n______________CUGCUGGCGG__GA\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\n______________GACGACCGCC__CU\n3'-UUU...UAUUA__________CA__AAAAU...UAG-5'\n_____________\|______________\|\n_____________206____________191\n	17 -- 23	196 -- 202	-23.0043 kcal/mol	4.65554 kcal/mol	9.06563 kcal/mol	13 28@LB@ \| \|@LB@5'-CAA...CGGUA AC ACCGA...ACG-3'@LB@ CUGCUGGCGG GA@LB@ \|\|\|\|\|\|\|\|\|\| \|\|@LB@ GACGACCGCC CU@LB@3'-UUU...UAUUA CA AAAAU...UAG-5'@LB@ \| \|@LB@ 206 191@LB@@LB@@LB@Energy -13.20 kcal/mol@LB@Hybridization Energy -23.0043 kcal/mol@LB@Unfolding Energy - mRNA 4.65554 kcal/mol@LB@Unfolding Energy - sRNA 9.06563 kcal/mol@LB@@LB@Position - mRNA 14 -- 27@LB@Position - sRNA 192 -- 205@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 196 -- 202@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@
17	0.001014	0.2007	b4032	malG	-14.09	0.041561	127 -- 139	193 -- 205	maltose transporter subunit	_____________126___________140\n_____________\|_____________\|\n5'-CGU...UCUUC_____________CGCUG...UGG-3'\n______________CUGCUGGUGGGUG\n______________\|\|\|\|\|\|\|:\|\|\|\|\|\n______________GACGACCGCCCAC\n3'-UUU...UAUUA_____________UAAAA...UAG-5'\n_____________\|_____________\|\n_____________206___________192\n	132 -- 138	194 -- 200	-26.9183 kcal/mol	7.69341 kcal/mol	9.06058 kcal/mol	126 140@LB@ \| \|@LB@5'-CGU...UCUUC CGCUG...UGG-3'@LB@ CUGCUGGUGGGUG@LB@ \|\|\|\|\|\|\|:\|\|\|\|\|@LB@ GACGACCGCCCAC@LB@3'-UUU...UAUUA UAAAA...UAG-5'@LB@ \| \|@LB@ 206 192@LB@@LB@@LB@Energy -14.09 kcal/mol@LB@Hybridization Energy -26.9183 kcal/mol@LB@Unfolding Energy - mRNA 7.69341 kcal/mol@LB@Unfolding Energy - sRNA 9.06058 kcal/mol@LB@@LB@Position - mRNA 127 -- 139@LB@Position - sRNA 193 -- 205@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 194 -- 200@LB@
127	0.01385	0.3575	b3832	rmuC	-11.83	0.120260	236 -- 246	193 -- 203	DNA recombination protein	_____________235____________________________________________________________247\n_____________\|______________________________________________________________\|\n5'-AAA...UUGUA________AUUC___UUU_____________GUU__G______AGGC_______AUU_____AUCAU...AGC-3'\n______________CAG_CACA____UAU___GUGCGGGUAAGUU___GC__UCAGG____GUUGUGG___UCUCA\n______________\|\|\|_\|\|\|\|____:\|\|___:\|\|\|:\|\|:\|\|\|\|:___:\|__\|\|\|\|:____:\|\|\|:\|\|___\|\|:\|\|\n______________GUC_GUGU____GUA___UACGUCCGUUCAG___UG__AGUCU____UAACGCC___AGGGU\n3'-UUU...UAUGA___A___________C_______________U____AA________________AGU_____GACGU...UAG-5'\n_____________\|______________________________________________________________\|\n_____________204____________________________________________________________192\n	198 -- 204	135 -- 141	-42.9883 kcal/mol	19.1075 kcal/mol	15.6146 kcal/mol	235 247@LB@ \| \|@LB@5'-AAA...UUGUA AUUC UUU GUU G AGGC AUU AUCAU...AGC-3'@LB@ CAG CACA UAU GUGCGGGUAAGUU GC UCAGG GUUGUGG UCUCA@LB@ \|\|\| \|\|\|\| :\|\| :\|\|\|:\|\|:\|\|\|\|: :\| \|\|\|\|: :\|\|\|:\|\| \|\|:\|\|@LB@ GUC GUGU GUA UACGUCCGUUCAG UG AGUCU UAACGCC AGGGU@LB@3'-UUU...UAUGA A C U AA AGU GACGU...UAG-5'@LB@ \| \|@LB@ 204 192@LB@@LB@@LB@Energy -11.83 kcal/mol@LB@Hybridization Energy -42.9883 kcal/mol@LB@Unfolding Energy - mRNA 19.1075 kcal/mol@LB@Unfolding Energy - sRNA 15.6146 kcal/mol@LB@@LB@Position - mRNA 236 -- 246@LB@Position - sRNA 193 -- 203@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 135 -- 141@LB@
165	0.01884	0.3812	b3291	mscL	-11.12	0.167422	252 -- 267	193 -- 208	mechanosensitive channel protein high conductance	_____________251_____268\n_____________\|_______\|\n5'-UGU...UGUCG_______AGGGA...UCU-3'\n______________GCUUCAU\n______________\|\|\|\|\|\|\|\n______________CGAAGUA\n3'-UUU...GGGAA_______G-5'\n_____________\|_______\|\n_____________209_____192\n	182 -- 188	2 -- 8	-9.41561 kcal/mol	2.23742 kcal/mol	0.70263 kcal/mol	251 268@LB@ \| \|@LB@5'-UGU...UGUCG AGGGA...UCU-3'@LB@ GCUUCAU@LB@ \|\|\|\|\|\|\|@LB@ CGAAGUA@LB@3'-UUU...GGGAA G-5'@LB@ \| \|@LB@ 209 192@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -9.41561 kcal/mol@LB@Unfolding Energy - mRNA 2.23742 kcal/mol@LB@Unfolding Energy - sRNA 0.70263 kcal/mol@LB@@LB@Position - mRNA 252 -- 267@LB@Position - sRNA 193 -- 208@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 2 -- 8@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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