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
184	0.02128	0.3833	b2831	mutH	-12.07	0.107608	142 -- 230	114 -- 189	methyl-directed mismatch repair protein	_____________141______________231\n_____________\|________________\|\n5'-UUC...CUGCG________________AUUGC...CGG-3'\n______________AAUAUUCGG_CACAUA\n______________\|\|\|\|:\|\|:\|_\|\|\|\|:\|\n______________UUAUGAGUC_GUGUGU\n3'-UUU...UGUGG_________A______ACUAC...UAG-5'\n_____________\|________________\|\n_____________190______________113\n	154 -- 160	174 -- 180	-15.1193 kcal/mol	2.199 kcal/mol	0.596263 kcal/mol	141 231@LB@ \| \|@LB@5'-UUC...CUGCG AUUGC...CGG-3'@LB@ AAUAUUCGG CACAUA@LB@ \|\|\|\|:\|\|:\| \|\|\|\|:\|@LB@ UUAUGAGUC GUGUGU@LB@3'-UUU...UGUGG A ACUAC...UAG-5'@LB@ \| \|@LB@ 190 113@LB@@LB@@LB@Energy -12.07 kcal/mol@LB@Hybridization Energy -15.1193 kcal/mol@LB@Unfolding Energy - mRNA 2.199 kcal/mol@LB@Unfolding Energy - sRNA 0.596263 kcal/mol@LB@@LB@Position - mRNA 142 -- 230@LB@Position - sRNA 114 -- 189@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 174 -- 180@LB@
100	0.01091	0.3575	b0123	cueO	-12.06	0.108476	211 -- 256	146 -- 195	multicopper oxidase (laccase)	_____________210________________________________________________257\n_____________\|__________________________________________________\|\n5'-CUG...ACGUC_______CUUAA________C_______UG_________U__________GCCGC...CGU-3'\n______________GUGAUUU______AAUAUUC_GUCGCGC__GGUGU_GGC___UCGGCUUU\n______________\|\|\|\|\|\|\|______\|\|\|\|:\|\|_\|\|\|:\|:\|__\|:\|\|:_\|\|\|___\|\|::\|\|\|\|\n______________CACUAAA______UUAUGAG_CAGUGUG__CUACG_CCG___AGUUGAAA\n3'-UUU...CCGCC_______AUGUGG_______U_______UA_____U___UUC________GUCUU...UAG-5'\n_____________\|__________________________________________________\|\n_____________196________________________________________________145\n	250 -- 256	146 -- 152	-42.9672 kcal/mol	13.2361 kcal/mol	12.9468 kcal/mol	210 257@LB@ \| \|@LB@5'-CUG...ACGUC CUUAA C UG U GCCGC...CGU-3'@LB@ GUGAUUU AAUAUUC GUCGCGC GGUGU GGC UCGGCUUU@LB@ \|\|\|\|\|\|\| \|\|\|\|:\|\| \|\|\|:\|:\| \|:\|\|: \|\|\| \|\|::\|\|\|\|@LB@ CACUAAA UUAUGAG CAGUGUG CUACG CCG AGUUGAAA@LB@3'-UUU...CCGCC AUGUGG U UA U UUC GUCUU...UAG-5'@LB@ \| \|@LB@ 196 145@LB@@LB@@LB@Energy -12.06 kcal/mol@LB@Hybridization Energy -42.9672 kcal/mol@LB@Unfolding Energy - mRNA 13.2361 kcal/mol@LB@Unfolding Energy - sRNA 12.9468 kcal/mol@LB@@LB@Position - mRNA 211 -- 256@LB@Position - sRNA 146 -- 195@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 146 -- 152@LB@
139	0.01488	0.3575	b2167	fruA	-12.05	0.108648	223 -- 242	167 -- 187	fused fructose-specific PTS enzymes: IIBcomponent/IIC components	_____________222___________________243\n_____________\|_____________________\|\n5'-CGC...UAUUG_________________G___CGCGC...AAA-3'\n______________ACGCUAAU_CUCGGUCA_GCA\n______________\|\|:\|:\|\|\|_\|\|\|:\|\|\|\|_:\|\|\n______________UGUGGUUA_GAGUCAGU_UGU\n3'-UUU...UAAAA________U________G___ACUAC...UAG-5'\n_____________\|_____________________\|\n_____________188___________________166\n	232 -- 238	171 -- 177	-25.758 kcal/mol	6.7352 kcal/mol	5.05492 kcal/mol	222 243@LB@ \| \|@LB@5'-CGC...UAUUG G CGCGC...AAA-3'@LB@ ACGCUAAU CUCGGUCA GCA@LB@ \|\|:\|:\|\|\| \|\|\|:\|\|\|\| :\|\|@LB@ UGUGGUUA GAGUCAGU UGU@LB@3'-UUU...UAAAA U G ACUAC...UAG-5'@LB@ \| \|@LB@ 188 166@LB@@LB@@LB@Energy -12.05 kcal/mol@LB@Hybridization Energy -25.758 kcal/mol@LB@Unfolding Energy - mRNA 6.7352 kcal/mol@LB@Unfolding Energy - sRNA 5.05492 kcal/mol@LB@@LB@Position - mRNA 223 -- 242@LB@Position - sRNA 167 -- 187@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 171 -- 177@LB@
40	0.003515	0.2912	b0188	tilS	-11.97	0.112782	278 -- 295	116 -- 133	tRNA(Ile)-lysidine synthetase	______________278__________________296\n______________\|____________________\|\n___________5'-_________GG____G_____CCUUG...UGC-3'\n______________CAUCGAUGC__CAGU_GCGCA\n______________\|\|:\|:\|\|:\|__\|\|\|\|_:\|:\|\|\n______________GUGGUUAUG__GUCA_UGUGU\n3'-UUU...AAAAU_________A_____G_____ACUAC...UAG-5'\n_____________\|_____________________\|\n_____________134___________________115\n	3 -- 9	178 -- 184	-23.3684 kcal/mol	8.15392 kcal/mol	5.05466 kcal/mol	278 296@LB@ \| \|@LB@ 5'- GG G CCUUG...UGC-3'@LB@ CAUCGAUGC CAGU GCGCA@LB@ \|\|:\|:\|\|:\| \|\|\|\| :\|:\|\|@LB@ GUGGUUAUG GUCA UGUGU@LB@3'-UUU...AAAAU A G ACUAC...UAG-5'@LB@ \| \|@LB@ 134 115@LB@@LB@@LB@Energy -11.97 kcal/mol@LB@Hybridization Energy -23.3684 kcal/mol@LB@Unfolding Energy - mRNA 8.15392 kcal/mol@LB@Unfolding Energy - sRNA 5.05466 kcal/mol@LB@@LB@Position - mRNA 278 -- 295@LB@Position - sRNA 116 -- 133@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 178 -- 184@LB@
45	0.003942	0.2948	b0686	ybfF	-11.97	0.113030	234 -- 245	63 -- 74	acyl-CoA esterase	_____________233__________246\n_____________\|____________\|\n5'-CUU...CACAA____________AAUUC...GCG-3'\n______________AACCAGCACAAU\n______________\|\|\|\|\|\|\|\|\|\|\|:\n______________UUGGUCGUGUUG\n3'-UUU...UUGCG____________AAGCG...UAG-5'\n_____________\|____________\|\n_____________75___________62\n	239 -- 245	63 -- 69	-18.9732 kcal/mol	1.15073 kcal/mol	9.24135 kcal/mol	233 246@LB@ \| \|@LB@5'-CUU...CACAA AAUUC...GCG-3'@LB@ AACCAGCACAAU@LB@ \|\|\|\|\|\|\|\|\|\|\|:@LB@ UUGGUCGUGUUG@LB@3'-UUU...UUGCG AAGCG...UAG-5'@LB@ \| \|@LB@ 75 62@LB@@LB@@LB@Energy -11.97 kcal/mol@LB@Hybridization Energy -18.9732 kcal/mol@LB@Unfolding Energy - mRNA 1.15073 kcal/mol@LB@Unfolding Energy - sRNA 9.24135 kcal/mol@LB@@LB@Position - mRNA 234 -- 245@LB@Position - sRNA 63 -- 74@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 63 -- 69@LB@
32	0.002513	0.2642	b3456	livM	-11.89	0.117100	251 -- 271	186 -- 206	branched-chain amino acid ABC transporter permease	_____________250___________________________272\n_____________\|_____________________________\|\n5'-GCC...CUGCU______GCCG___________UG______CCGGA...CCA-3'\n______________GGUGAU_____ACCGGUAUUC__GGUCGC\n______________\|\|\|\|\|\|_____\|\|\|::\|\|:\|\|__:\|\|\|:\|\n______________CCACUA_____UGGUUAUGAG__UCAGUG\n3'-UUU...ACCGC______AAAUG__________________UGUAC...UAG-5'\n_____________\|_____________________________\|\n_____________207___________________________185\n	169 -- 175	176 -- 182	-27.5836 kcal/mol	14.0763 kcal/mol	5.03772 kcal/mol	250 272@LB@ \| \|@LB@5'-GCC...CUGCU GCCG UG CCGGA...CCA-3'@LB@ GGUGAU ACCGGUAUUC GGUCGC@LB@ \|\|\|\|\|\| \|\|\|::\|\|:\|\| :\|\|\|:\|@LB@ CCACUA UGGUUAUGAG UCAGUG@LB@3'-UUU...ACCGC AAAUG UGUAC...UAG-5'@LB@ \| \|@LB@ 207 185@LB@@LB@@LB@Energy -11.89 kcal/mol@LB@Hybridization Energy -27.5836 kcal/mol@LB@Unfolding Energy - mRNA 14.0763 kcal/mol@LB@Unfolding Energy - sRNA 5.03772 kcal/mol@LB@@LB@Position - mRNA 251 -- 271@LB@Position - sRNA 186 -- 206@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 176 -- 182@LB@
106	0.01145	0.3575	b2350	gtrA	-11.86	0.119007	4 -- 25	148 -- 167	CPS-53 (KpLE1) prophage; bactoprenol-linked glucose translocase/flippase	_____________3_____________26\n_____________\|_____________\|\n5'-GAA...UGUAU__AU_________ACAAACC-3'\n______________CU__GUCGCGCAU\n______________\|\|__\|\|\|:\|:\|\|\|\n______________GA__CAGUGUGUA\n3'-UUU...GUUAU__GU_________CUACG...UAG-5'\n_____________\|_____________\|\n_____________168___________147\n	287 -- 293	166 -- 172	-13.6011 kcal/mol	2.0532 kcal/mol	0.604639 kcal/mol	3 26@LB@ \| \|@LB@5'-GAA...UGUAU AU ACAAACC-3'@LB@ CU GUCGCGCAU@LB@ \|\| \|\|\|:\|:\|\|\|@LB@ GA CAGUGUGUA@LB@3'-UUU...GUUAU GU CUACG...UAG-5'@LB@ \| \|@LB@ 168 147@LB@@LB@@LB@Energy -11.86 kcal/mol@LB@Hybridization Energy -13.6011 kcal/mol@LB@Unfolding Energy - mRNA 2.0532 kcal/mol@LB@Unfolding Energy - sRNA 0.604639 kcal/mol@LB@@LB@Position - mRNA 4 -- 25@LB@Position - sRNA 148 -- 167@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 166 -- 172@LB@
23	0.00185	0.2633	b3492	yhiN	-11.85	0.119629	108 -- 154	124 -- 161	putative oxidoreductase	_____________107_______________________________________155\n_____________\|_________________________________________\|\n5'-CGG...GGAAA_____G______U____AUAG____________________AUGUU...AUA-3'\n______________GGUUU_AUGCCA_UAUU_____GCGC_UGGUGC_GGCGGGU\n______________\|:\|\|\|_\|::\|\|\|_\|\|:\|_____:\|:\|_\|\|:\|\|\|_\|\|\|::\|\|\n______________CUAAA_UGUGGU_AUGA_____UGUG_ACUACG_CCGUUCA\n3'-UUU...GCCCA_____A______U____GUCAG____U______U_______GUUGA...UAG-5'\n_____________\|_________________________________________\|\n_____________162_______________________________________123\n	239 -- 245	153 -- 159	-35.0652 kcal/mol	11.4478 kcal/mol	11.9045 kcal/mol	107 155@LB@ \| \|@LB@5'-CGG...GGAAA G U AUAG AUGUU...AUA-3'@LB@ GGUUU AUGCCA UAUU GCGC UGGUGC GGCGGGU@LB@ \|:\|\|\| \|::\|\|\| \|\|:\| :\|:\| \|\|:\|\|\| \|\|\|::\|\|@LB@ CUAAA UGUGGU AUGA UGUG ACUACG CCGUUCA@LB@3'-UUU...GCCCA A U GUCAG U U GUUGA...UAG-5'@LB@ \| \|@LB@ 162 123@LB@@LB@@LB@Energy -11.85 kcal/mol@LB@Hybridization Energy -35.0652 kcal/mol@LB@Unfolding Energy - mRNA 11.4478 kcal/mol@LB@Unfolding Energy - sRNA 11.9045 kcal/mol@LB@@LB@Position - mRNA 108 -- 154@LB@Position - sRNA 124 -- 161@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 153 -- 159@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@
176	0.01994	0.3812	b2170	setB	-11.80	0.122017	181 -- 237	58 -- 116	lactose/glucose efflux system	_____________180____________238\n_____________\|______________\|\n5'-GCU...GAUCG______________AACUC...UGC-3'\n______________AC_CAG_CAUGCAU\n______________\|\|_\|\|\|_\|\|::\|\|\|\n______________UG_GUC_GUGUGUA\n3'-UUU...GGUUA__A___A_______CUACG...UAG-5'\n_____________\|______________\|\n_____________117____________57\n	200 -- 206	166 -- 172	-10.2756 kcal/mol	1.89616 kcal/mol	0.604817 kcal/mol	180 238@LB@ \| \|@LB@5'-GCU...GAUCG AACUC...UGC-3'@LB@ AC CAG CAUGCAU@LB@ \|\| \|\|\| \|\|::\|\|\|@LB@ UG GUC GUGUGUA@LB@3'-UUU...GGUUA A A CUACG...UAG-5'@LB@ \| \|@LB@ 117 57@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -10.2756 kcal/mol@LB@Unfolding Energy - mRNA 1.89616 kcal/mol@LB@Unfolding Energy - sRNA 0.604817 kcal/mol@LB@@LB@Position - mRNA 181 -- 237@LB@Position - sRNA 58 -- 116@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 166 -- 172@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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