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
120	0.01317	0.3575	b1158	pinE	-11.56	0.136715	30 -- 59	115 -- 145	e14 prophage; site-specific DNA recombinase	_____________29_____________________60\n_____________\|______________________\|\n5'-AGC...CCGGG______________GUA_____GAGCC...ACA-3'\n______________ACACCAA____CAG___AUGCA\n______________\|\|\|\|\|\|\|____\|\|\|___\|::\|\|\n______________UGUGGUU____GUC___UGUGU\n3'-UUU...UAAAA_______AUGA___AG______ACUAC...UAG-5'\n_____________\|______________________\|\n_____________146____________________114\n	98 -- 104	181 -- 187	-13.8739 kcal/mol	4.34554 kcal/mol	5.05492 kcal/mol	29 60@LB@ \| \|@LB@5'-AGC...CCGGG GUA GAGCC...ACA-3'@LB@ ACACCAA CAG AUGCA@LB@ \|\|\|\|\|\|\| \|\|\| \|::\|\|@LB@ UGUGGUU GUC UGUGU@LB@3'-UUU...UAAAA AUGA AG ACUAC...UAG-5'@LB@ \| \|@LB@ 146 114@LB@@LB@@LB@Energy -11.56 kcal/mol@LB@Hybridization Energy -13.8739 kcal/mol@LB@Unfolding Energy - mRNA 4.34554 kcal/mol@LB@Unfolding Energy - sRNA 5.05492 kcal/mol@LB@@LB@Position - mRNA 30 -- 59@LB@Position - sRNA 115 -- 145@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 181 -- 187@LB@
131	0.01426	0.3575	b0048	folA	-12.08	0.107221	135 -- 211	115 -- 187	dihydrofolate reductase	_____________134_________212\n_____________\|___________\|\n5'-UCA...UUGUU___________GUAAU...GCA-3'\n______________UUUGUUUCAUU\n______________:\|\|\|:\|\|\|\|\|:\n______________GAACGAAGUAG\n3'-UUU...UGGGG___________-5'\n_____________\|__________\|\n_____________188________115\n	56 -- 62	1 -- 7	-10.5455 kcal/mol	1.7602 kcal/mol	1.03329 kcal/mol	134 212@LB@ \| \|@LB@5'-UCA...UUGUU GUAAU...GCA-3'@LB@ UUUGUUUCAUU@LB@ :\|\|\|:\|\|\|\|\|:@LB@ GAACGAAGUAG@LB@3'-UUU...UGGGG -5'@LB@ \| \|@LB@ 188 115@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -10.5455 kcal/mol@LB@Unfolding Energy - mRNA 1.7602 kcal/mol@LB@Unfolding Energy - sRNA 1.03329 kcal/mol@LB@@LB@Position - mRNA 135 -- 211@LB@Position - sRNA 115 -- 187@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 1 -- 7@LB@
144	0.01541	0.3575	b4555	yicS	-14.57	0.033136	213 -- 290	115 -- 187	putative periplasmic protein	_____________212_________________________________________________________________291\n_____________\|___________________________________________________________________\|\n5'-AUU...CAACG______C______UUU____UUUUUUC__U_____C______UCGUAUACGCCG_____C_______CUCAC...AGA-3'\n______________ACACUA_UGCUUA___UCAC_______GC___AUG_CAGGCA____________AGUCG_CUUUUAG\n______________\|\|\|\|:\|_\|:\|\|:\|___\|\|\|\|_______:\|___\|\|\|_\|\|\|\|\|\|____________\|\|\|\|:_\|\|\|\|:\|\|\n______________UGUGGU_AUGAGU___AGUG_______UG___UAC_GUCCGU____________UCAGU_GAAAGUC\n3'-UUU...UAAAA______U______C_______________UAC___________________________U_______UUAAC...UAG-5'\n_____________\|___________________________________________________________________\|\n_____________188_________________________________________________________________114\n	271 -- 277	143 -- 149	-34.4495 kcal/mol	11.6435 kcal/mol	13.2932 kcal/mol	212 291@LB@ \| \|@LB@5'-AUU...CAACG C UUU UUUUUUC U C UCGUAUACGCCG C CUCAC...AGA-3'@LB@ ACACUA UGCUUA UCAC GC AUG CAGGCA AGUCG CUUUUAG@LB@ \|\|\|\|:\| \|:\|\|:\| \|\|\|\| :\| \|\|\| \|\|\|\|\|\| \|\|\|\|: \|\|\|\|:\|\|@LB@ UGUGGU AUGAGU AGUG UG UAC GUCCGU UCAGU GAAAGUC@LB@3'-UUU...UAAAA U C UAC U UUAAC...UAG-5'@LB@ \| \|@LB@ 188 114@LB@@LB@@LB@Energy -14.57 kcal/mol@LB@Hybridization Energy -34.4495 kcal/mol@LB@Unfolding Energy - mRNA 11.6435 kcal/mol@LB@Unfolding Energy - sRNA 13.2932 kcal/mol@LB@@LB@Position - mRNA 213 -- 290@LB@Position - sRNA 115 -- 187@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 143 -- 149@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@
29	0.002294	0.2633	b0624	flc	-16.49	0.013425	233 -- 293	118 -- 176	fluoride efflux channel dual topology membrane protein	_____________232_____________________294\n_____________\|_______________________\|\n5'-AAA...CGGCG_______UA______C_______AAUCA...UUC-3'\n______________UUACACU_____UCA_UCAUACA\n______________\|\|\|\|\|\|:_____\|\|\|_\|\|\|:\|\|\|\n______________AAUGUGG_____AGU_AGUGUGU\n3'-UUU...ACUAA_______UUAUG___C_______ACUAC...UAG-5'\n_____________\|_______________________\|\n_____________177_____________________117\n	172 -- 178	167 -- 173	-16.8792 kcal/mol	2.93634 kcal/mol	5.08824 kcal/mol	232 294@LB@ \| \|@LB@5'-AAA...CGGCG UA C AAUCA...UUC-3'@LB@ UUACACU UCA UCAUACA@LB@ \|\|\|\|\|\|: \|\|\| \|\|\|:\|\|\|@LB@ AAUGUGG AGU AGUGUGU@LB@3'-UUU...ACUAA UUAUG C ACUAC...UAG-5'@LB@ \| \|@LB@ 177 117@LB@@LB@@LB@Energy -16.49 kcal/mol@LB@Hybridization Energy -16.8792 kcal/mol@LB@Unfolding Energy - mRNA 2.93634 kcal/mol@LB@Unfolding Energy - sRNA 5.08824 kcal/mol@LB@@LB@Position - mRNA 233 -- 293@LB@Position - sRNA 118 -- 176@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 167 -- 173@LB@
55	0.005617	0.3247	b2829	ptsP	-11.41	0.146041	68 -- 133	122 -- 174	PEP-protein phosphotransferase enzyme I; GAF domain containing protein	______________68____________________________________________________________134\n______________\|_____________________________________________________________\|\n___________5'-_______UACACCAGA__U_____G_______AUG___AAGU_________C______G___GGUGG...UGG-3'\n______________CCAGCAG_________GU_UGA_C_GCUGGCG___GGU____UACUGGUAU_CGGUCA_ACA\n______________\|\|\|\|\|\|\|_________\|\|_\|:\|_\|_\|\|\|\|\|\|\|___\|:\|____:\|\|:::\|\|:_\|:\|\|\|\|_\|\|\|\n______________GGUCGUC_________CA_AUU_G_CGACCGC___CUA____GUGGUUAUG_GUCAGU_UGU\n___3'-UUUUUUUU__________________U___A_A_______CCA___AAAU_________A______G___ACUAC...UAG-5'\n_____________\|______________________________________________________________\|\n_____________175____________________________________________________________121\n	25 -- 31	197 -- 203	-46.8098 kcal/mol	17.4414 kcal/mol	18.4949 kcal/mol	68 134@LB@ \| \|@LB@ 5'- UACACCAGA U G AUG AAGU C G GGUGG...UGG-3'@LB@ CCAGCAG GU UGA C GCUGGCG GGU UACUGGUAU CGGUCA ACA@LB@ \|\|\|\|\|\|\| \|\| \|:\| \| \|\|\|\|\|\|\| \|:\| :\|\|:::\|\|: \|:\|\|\|\| \|\|\|@LB@ GGUCGUC CA AUU G CGACCGC CUA GUGGUUAUG GUCAGU UGU@LB@ 3'-UUUUUUUU U A A CCA AAAU A G ACUAC...UAG-5'@LB@ \| \|@LB@ 175 121@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -46.8098 kcal/mol@LB@Unfolding Energy - mRNA 17.4414 kcal/mol@LB@Unfolding Energy - sRNA 18.4949 kcal/mol@LB@@LB@Position - mRNA 68 -- 133@LB@Position - sRNA 122 -- 174@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 197 -- 203@LB@
26	0.002141	0.2633	b0183	rnhB	-16.17	0.015603	251 -- 292	123 -- 175	ribonuclease HII degrades RNA of DNA-RNA hybrids	______________251_______________________________________________________293\n______________\|_________________________________________________________\|\n___________5'-____________________________AG_G_______AAGAAUUAU__________AGUGU...UCC-3'\n______________AAUCUGCUGGCGGG___________CAG__A_UUAGUCA_________UGCAGG_AAG\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|\|___________\|\|:__\|_\|:\|\|\|\|\|_________\|\|\|\|\|\|_\|\|\|\n______________UUAGACGACCGCCC___________GUU__U_AGUCAGU_________ACGUCC_UUC\n3'-UUU...CCAUA______________ACUAAAAUGUG___A__G_______GUGUACU________G___AGUUG...UAG-5'\n_____________\|__________________________________________________________\|\n_____________176________________________________________________________122\n	22 -- 28	171 -- 177	-46.3072 kcal/mol	12.4456 kcal/mol	20.994 kcal/mol	251 293@LB@ \| \|@LB@ 5'- AG G AAGAAUUAU AGUGU...UCC-3'@LB@ AAUCUGCUGGCGGG CAG A UUAGUCA UGCAGG AAG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\|\| \|\|: \| \|:\|\|\|\|\| \|\|\|\|\|\| \|\|\|@LB@ UUAGACGACCGCCC GUU U AGUCAGU ACGUCC UUC@LB@3'-UUU...CCAUA ACUAAAAUGUG A G GUGUACU G AGUUG...UAG-5'@LB@ \| \|@LB@ 176 122@LB@@LB@@LB@Energy -16.17 kcal/mol@LB@Hybridization Energy -46.3072 kcal/mol@LB@Unfolding Energy - mRNA 12.4456 kcal/mol@LB@Unfolding Energy - sRNA 20.994 kcal/mol@LB@@LB@Position - mRNA 251 -- 292@LB@Position - sRNA 123 -- 175@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 171 -- 177@LB@
36	0.002935	0.2744	b3152	yraR	-13.11	0.066158	241 -- 255	123 -- 138	putative nucleoside-diphosphate-sugar epimerase	_____________240______________256\n_____________\|________________\|\n5'-ACU...GGUGG________________GGAUG...CGA-3'\n______________GCGGUCA_CCUGCUGC\n______________\|\|\|\|\|\|\|_\|\|::\|\|\|\|\n______________CGCCAGU_GGGUGACG\n3'-UUU...CUUAA_______A________UAGUC...UAG-5'\n_____________\|________________\|\n_____________139______________122\n	241 -- 247	132 -- 138	-26.7154 kcal/mol	6.55898 kcal/mol	13.7588 kcal/mol	240 256@LB@ \| \|@LB@5'-ACU...GGUGG GGAUG...CGA-3'@LB@ GCGGUCA CCUGCUGC@LB@ \|\|\|\|\|\|\| \|\|::\|\|\|\|@LB@ CGCCAGU GGGUGACG@LB@3'-UUU...CUUAA A UAGUC...UAG-5'@LB@ \| \|@LB@ 139 122@LB@@LB@@LB@Energy -13.11 kcal/mol@LB@Hybridization Energy -26.7154 kcal/mol@LB@Unfolding Energy - mRNA 6.55898 kcal/mol@LB@Unfolding Energy - sRNA 13.7588 kcal/mol@LB@@LB@Position - mRNA 241 -- 255@LB@Position - sRNA 123 -- 138@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 132 -- 138@LB@
85	0.009065	0.3575	b3155	yhbQ	-10.34	0.236900	54 -- 88	123 -- 160	GIY-YIG nuclease superfamily protein	_____________53______________________89\n_____________\|_______________________\|\n5'-UUU...GAUCC_____G__GACAAUAA_______ACCGG...GCG-3'\n______________GUACC_CC________GCUUUAU\n______________\|:\|\|\|_\|\|________\|\|\|\|:\|\|\n______________CGUGG_GG________CGAAGUA\n3'-UUU...UACCC_____G__AA_____________G-5'\n_____________\|_______________________\|\n_____________161_____________________122\n	245 -- 251	2 -- 8	-16.2438 kcal/mol	1.2562 kcal/mol	7.2187 kcal/mol	53 89@LB@ \| \|@LB@5'-UUU...GAUCC G GACAAUAA ACCGG...GCG-3'@LB@ GUACC CC GCUUUAU@LB@ \|:\|\|\| \|\| \|\|\|\|:\|\|@LB@ CGUGG GG CGAAGUA@LB@3'-UUU...UACCC G AA G-5'@LB@ \| \|@LB@ 161 122@LB@@LB@@LB@Energy -10.34 kcal/mol@LB@Hybridization Energy -16.2438 kcal/mol@LB@Unfolding Energy - mRNA 1.2562 kcal/mol@LB@Unfolding Energy - sRNA 7.2187 kcal/mol@LB@@LB@Position - mRNA 54 -- 88@LB@Position - sRNA 123 -- 160@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 2 -- 8@LB@
89	0.009985	0.3575	b0477	gsk	-9.51	0.338446	88 -- 115	123 -- 150	inosine/guanosine kinase	_____________87_____________116\n_____________\|______________\|\n5'-UUU...UCGCC_________AC___CCGUA...CUG-3'\n______________GCUCAGUUA__CAC\n______________:\|\|\|\|\|\|:\|__\|\|\|\n______________UGAGUCAGU__GUG\n3'-UUU...GGUUA______________UACUA...UAG-5'\n_____________\|______________\|\n_____________151____________122\n	175 -- 181	171 -- 177	-13.3754 kcal/mol	2.68541 kcal/mol	0.283892 kcal/mol	87 116@LB@ \| \|@LB@5'-UUU...UCGCC AC CCGUA...CUG-3'@LB@ GCUCAGUUA CAC@LB@ :\|\|\|\|\|\|:\| \|\|\|@LB@ UGAGUCAGU GUG@LB@3'-UUU...GGUUA UACUA...UAG-5'@LB@ \| \|@LB@ 151 122@LB@@LB@@LB@Energy -9.51 kcal/mol@LB@Hybridization Energy -13.3754 kcal/mol@LB@Unfolding Energy - mRNA 2.68541 kcal/mol@LB@Unfolding Energy - sRNA 0.283892 kcal/mol@LB@@LB@Position - mRNA 88 -- 115@LB@Position - sRNA 123 -- 150@LB@Position Seed - mRNA 175 -- 181@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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