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
12	0.0007005	0.1842	b1101	ptsG	-16.86	0.011310	173 -- 192	168 -- 187	fused glucose-specific PTS enzymes: IIB component/IIC component	_____________172__________________193\n_____________\|____________________\|\n5'-CAU...AAAAA_____C________GA____UCUCA...GUU-3'\n______________GCACC_AUACUCAG__GCAC\n______________:\|\|\|\|_\|\|\|\|\|\|\|\|__:\|\|\|\n______________UGUGG_UAUGAGUC__UGUG\n3'-UUU...UAAAA_____U________AG____UACUA...UAG-5'\n_____________\|____________________\|\n_____________188__________________167\n	180 -- 186	174 -- 180	-27.3381 kcal/mol	3.90127 kcal/mol	4.88067 kcal/mol	172 193@LB@ \| \|@LB@5'-CAU...AAAAA C GA UCUCA...GUU-3'@LB@ GCACC AUACUCAG GCAC@LB@ :\|\|\|\| \|\|\|\|\|\|\|\| :\|\|\|@LB@ UGUGG UAUGAGUC UGUG@LB@3'-UUU...UAAAA U AG UACUA...UAG-5'@LB@ \| \|@LB@ 188 167@LB@@LB@@LB@Energy -16.86 kcal/mol@LB@Hybridization Energy -27.3381 kcal/mol@LB@Unfolding Energy - mRNA 3.90127 kcal/mol@LB@Unfolding Energy - sRNA 4.88067 kcal/mol@LB@@LB@Position - mRNA 173 -- 192@LB@Position - sRNA 168 -- 187@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 174 -- 180@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@
74	0.007724	0.3458	b1261	trpB	-16.40	0.014006	36 -- 47	195 -- 206	tryptophan synthase beta subunit	_____________35___________48\n_____________\|____________\|\n5'-UGG...AACGU____________GGGCU...UCA-3'\n______________UCUGCUGGCGGG\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________AGACGACCGCCC\n3'-UUU...AUAUU____________ACUAA...UAG-5'\n_____________\|____________\|\n_____________207__________194\n	41 -- 47	195 -- 201	-26.9412 kcal/mol	6.0368 kcal/mol	9.05854 kcal/mol	35 48@LB@ \| \|@LB@5'-UGG...AACGU GGGCU...UCA-3'@LB@ UCUGCUGGCGGG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ AGACGACCGCCC@LB@3'-UUU...AUAUU ACUAA...UAG-5'@LB@ \| \|@LB@ 207 194@LB@@LB@@LB@Energy -16.40 kcal/mol@LB@Hybridization Energy -26.9412 kcal/mol@LB@Unfolding Energy - mRNA 6.0368 kcal/mol@LB@Unfolding Energy - sRNA 9.05854 kcal/mol@LB@@LB@Position - mRNA 36 -- 47@LB@Position - sRNA 195 -- 206@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 195 -- 201@LB@
16	0.0008966	0.1886	b0807	rlmF	-16.29	0.014793	117 -- 160	51 -- 97	23S rRNA m(6)A1618 methyltransferase SAM-dependent	_____________116_____________________________________________161\n_____________\|_______________________________________________\|\n5'-AUU...UUAAG___U_____AA______A_______________U__A_C________UUAUG...UCC-3'\n______________GUU_UGGGG____UGAU_AACGCAGCCAG_AUA_UU_C_CUGUCGCG\n______________\|\|\|_\|\|\|\|:____\|:\|:_\|\|\|\|\|\|:\|\|\|\|_\|:\|_:\|_\|_\|\|\|\|\|\|\|\|\n______________CAA_ACCCU____AUUG_UUGCGUUGGUC_UGU_GA_G_GACAGCGC\n3'-UUU...AUUAG___C_____GCGA____G___________G___U__A_C________CAUUU...UAG-5'\n_____________\|_______________________________________________\|\n_____________98______________________________________________50\n	154 -- 160	51 -- 57	-44.7843 kcal/mol	10.0752 kcal/mol	25.3667 kcal/mol	116 161@LB@ \| \|@LB@5'-AUU...UUAAG U AA A U A C UUAUG...UCC-3'@LB@ GUU UGGGG UGAU AACGCAGCCAG AUA UU C CUGUCGCG@LB@ \|\|\| \|\|\|\|: \|:\|: \|\|\|\|\|\|:\|\|\|\| \|:\| :\| \| \|\|\|\|\|\|\|\|@LB@ CAA ACCCU AUUG UUGCGUUGGUC UGU GA G GACAGCGC@LB@3'-UUU...AUUAG C GCGA G G U A C CAUUU...UAG-5'@LB@ \| \|@LB@ 98 50@LB@@LB@@LB@Energy -16.29 kcal/mol@LB@Hybridization Energy -44.7843 kcal/mol@LB@Unfolding Energy - mRNA 10.0752 kcal/mol@LB@Unfolding Energy - sRNA 25.3667 kcal/mol@LB@@LB@Position - mRNA 117 -- 160@LB@Position - sRNA 51 -- 97@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 51 -- 57@LB@
119	0.013	0.3575	b0801	ybiC	-16.26	0.015008	158 -- 253	108 -- 187	putative dehydrogenase	_____________157____________________________________________________________________________________________254\n_____________\|______________________________________________________________________________________________\|\n5'-GCU...AUAAA_____AA__AA______ACAUAAA_____________CAU_____A__________G_UUUGAUGCUCAGAC_____________UA_______UGUAU...UUG-3'\n______________AAUAC__CA__CACAUA_______CAGG__AGUUAAC____GGAA__GUGGUCAUC_C______________GCUGCA_CAGUUU__UUCAGGC\n______________\|\|\|\|\|__\|\|__\|\|\|\|:\|_______\|\|\|\|__\|\|\|:\|\|\|____:\|\|\|__\|:\|\|\|\|\|\|\|_\|______________:\|\|\|\|\|_\|\|\|\|::__\|\|\|\|:\|\|\n______________UUAUG__GU__GUGUGU_______GUCC__UCAGUUG____UCUU__CGCCAGUAG_G______________UGACGU_GUCAGG__AAGUUCG\n3'-UUU...UGUGG_____A___CA______ACUAC______GU_______AAAG____AA_________G_____________________A_______________UACCA...UAG-5'\n_____________\|______________________________________________________________________________________________\|\n_____________188____________________________________________________________________________________________107\n	247 -- 253	108 -- 114	-56.5044 kcal/mol	18.8914 kcal/mol	26.5178 kcal/mol	157 254@LB@ \| \|@LB@5'-GCU...AUAAA AA AA ACAUAAA CAU A G UUUGAUGCUCAGAC UA UGUAU...UUG-3'@LB@ AAUAC CA CACAUA CAGG AGUUAAC GGAA GUGGUCAUC C GCUGCA CAGUUU UUCAGGC@LB@ \|\|\|\|\| \|\| \|\|\|\|:\| \|\|\|\| \|\|\|:\|\|\| :\|\|\| \|:\|\|\|\|\|\|\| \| :\|\|\|\|\| \|\|\|\|:: \|\|\|\|:\|\|@LB@ UUAUG GU GUGUGU GUCC UCAGUUG UCUU CGCCAGUAG G UGACGU GUCAGG AAGUUCG@LB@3'-UUU...UGUGG A CA ACUAC GU AAAG AA G A UACCA...UAG-5'@LB@ \| \|@LB@ 188 107@LB@@LB@@LB@Energy -16.26 kcal/mol@LB@Hybridization Energy -56.5044 kcal/mol@LB@Unfolding Energy - mRNA 18.8914 kcal/mol@LB@Unfolding Energy - sRNA 26.5178 kcal/mol@LB@@LB@Position - mRNA 158 -- 253@LB@Position - sRNA 108 -- 187@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 108 -- 114@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@
91	0.01018	0.3575	b1660	ydhC	-16.12	0.016020	223 -- 255	172 -- 209	putative arabinose efflux transporter	_____________222_____________________________________256\n_____________\|_______________________________________\|\n5'-GAA...AUUUU______G_________________A______________UUCUG...AGG-3'\n______________UAGUCU_GCUGGCGGGU____UUG_GC__GUACUCGGUU\n______________\|\|:\|\|\|_\|\|\|\|\|\|\|\|\|\|____\|\|:_:\|__:\|\|\|\|\|:\|\|:\n______________AUUAGA_CGACCGCCCA____AAU_UG__UAUGAGUCAG\n3'-UUU...UCCAU_________________CUAA___G__GU__________UGUGU...UAG-5'\n_____________\|_______________________________________\|\n_____________210_____________________________________171\n	249 -- 255	172 -- 178	-38.0361 kcal/mol	10.2504 kcal/mol	15.0669 kcal/mol	222 256@LB@ \| \|@LB@5'-GAA...AUUUU G A UUCUG...AGG-3'@LB@ UAGUCU GCUGGCGGGU UUG GC GUACUCGGUU@LB@ \|\|:\|\|\| \|\|\|\|\|\|\|\|\|\| \|\|: :\| :\|\|\|\|\|:\|\|:@LB@ AUUAGA CGACCGCCCA AAU UG UAUGAGUCAG@LB@3'-UUU...UCCAU CUAA G GU UGUGU...UAG-5'@LB@ \| \|@LB@ 210 171@LB@@LB@@LB@Energy -16.12 kcal/mol@LB@Hybridization Energy -38.0361 kcal/mol@LB@Unfolding Energy - mRNA 10.2504 kcal/mol@LB@Unfolding Energy - sRNA 15.0669 kcal/mol@LB@@LB@Position - mRNA 223 -- 255@LB@Position - sRNA 172 -- 209@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 172 -- 178@LB@
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@
135	0.01453	0.3575	b2934	cmtB	-15.85	0.018111	229 -- 275	145 -- 186	putative mannitol-specific enzyme IIA component of PTS	_____________228___________________276\n_____________\|_____________________\|\n5'-AUA...AGAAU_____________________UCAGC...UGG-3'\n______________CAUCAAU_CUCAGUUAUACAU\n______________\|\|:\|\|\|\|_\|\|\|\|\|\|:\|:\|\|\|\|\n______________GUGGUUA_GAGUCAGUGUGUA\n3'-UUU...AAAAU_______U_____________CUACG...UAG-5'\n_____________\|_____________________\|\n_____________187___________________144\n	242 -- 248	166 -- 172	-24.8158 kcal/mol	1.5387 kcal/mol	5.06797 kcal/mol	228 276@LB@ \| \|@LB@5'-AUA...AGAAU UCAGC...UGG-3'@LB@ CAUCAAU CUCAGUUAUACAU@LB@ \|\|:\|\|\|\| \|\|\|\|\|\|:\|:\|\|\|\|@LB@ GUGGUUA GAGUCAGUGUGUA@LB@3'-UUU...AAAAU U CUACG...UAG-5'@LB@ \| \|@LB@ 187 144@LB@@LB@@LB@Energy -15.85 kcal/mol@LB@Hybridization Energy -24.8158 kcal/mol@LB@Unfolding Energy - mRNA 1.5387 kcal/mol@LB@Unfolding Energy - sRNA 5.06797 kcal/mol@LB@@LB@Position - mRNA 229 -- 275@LB@Position - sRNA 145 -- 186@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 166 -- 172@LB@
47	0.004619	0.3205	b4142	groS	-15.85	0.018169	259 -- 271	196 -- 208	Cpn10 chaperonin GroES small subunit of GroESL	_____________258_______________________________272\n_____________\|_________________________________\|\n5'-UGA...AACUA_____________CAUCGUUCUG__________UGCAG...CUA-3'\n______________AAUCUGCUGGCGG__________ACCG__GCUC\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|__________\|\|\|:__:\|\|\|\n______________UUAGACGACCGCC__________UGGU__UGAG\n3'-UUU...CCAUA_____________CACUAAAAUG____UA____UCAGU...UAG-5'\n_____________\|_________________________________\|\n_____________209_______________________________195\n	265 -- 271	196 -- 202	-33.1058 kcal/mol	10.148 kcal/mol	14.8106 kcal/mol	258 272@LB@ \| \|@LB@5'-UGA...AACUA CAUCGUUCUG UGCAG...CUA-3'@LB@ AAUCUGCUGGCGG ACCG GCUC@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|: :\|\|\|@LB@ UUAGACGACCGCC UGGU UGAG@LB@3'-UUU...CCAUA CACUAAAAUG UA UCAGU...UAG-5'@LB@ \| \|@LB@ 209 195@LB@@LB@@LB@Energy -15.85 kcal/mol@LB@Hybridization Energy -33.1058 kcal/mol@LB@Unfolding Energy - mRNA 10.148 kcal/mol@LB@Unfolding Energy - sRNA 14.8106 kcal/mol@LB@@LB@Position - mRNA 259 -- 271@LB@Position - sRNA 196 -- 208@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 196 -- 202@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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