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
188	0.0218	0.3833	b3357	crp	-15.41	0.022266	196 -- 257	123 -- 172	cAMP-activated global transcription factor mediator of catabolite repression	_____________195_________________258\n_____________\|___________________\|\n5'-GAC...AUAAC____________UU_____ACCGC...AGG-3'\n______________CGCGCAUGGUGC__GGCAA\n______________\|:\|:\|\|\|\|:\|\|\|__\|\|\|\|\|\n______________GUGUGUACUACG__CCGUU\n3'-UUU...AGUCA____________U______CAGUU...UAG-5'\n_____________\|___________________\|\n_____________173_________________122\n	201 -- 207	161 -- 167	-26.7729 kcal/mol	8.17538 kcal/mol	7.52835 kcal/mol	195 258@LB@ \| \|@LB@5'-GAC...AUAAC UU ACCGC...AGG-3'@LB@ CGCGCAUGGUGC GGCAA@LB@ \|:\|:\|\|\|\|:\|\|\| \|\|\|\|\|@LB@ GUGUGUACUACG CCGUU@LB@3'-UUU...AGUCA U CAGUU...UAG-5'@LB@ \| \|@LB@ 173 122@LB@@LB@@LB@Energy -15.41 kcal/mol@LB@Hybridization Energy -26.7729 kcal/mol@LB@Unfolding Energy - mRNA 8.17538 kcal/mol@LB@Unfolding Energy - sRNA 7.52835 kcal/mol@LB@@LB@Position - mRNA 196 -- 257@LB@Position - sRNA 123 -- 172@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 161 -- 167@LB@
92	0.01029	0.3575	b3360	pabA	-10.28	0.244097	93 -- 100	16 -- 23	aminodeoxychorismate synthase subunit II	_____________92__________101\n_____________\|___________\|\n5'-GCG...ACCUC___________UUGUG...CGU-3'\n______________UACCAGUACUU\n______________:\|\|\|\|:\|\|\|\|:\n______________GUGGUUAUGAG\n3'-UUU...AAAAU___________UCAGU...UAG-5'\n_____________\|___________\|\n_____________24__________15\n	250 -- 256	176 -- 182	-13.2399 kcal/mol	3.06354 kcal/mol	3.38772 kcal/mol	92 101@LB@ \| \|@LB@5'-GCG...ACCUC UUGUG...CGU-3'@LB@ UACCAGUACUU@LB@ :\|\|\|\|:\|\|\|\|:@LB@ GUGGUUAUGAG@LB@3'-UUU...AAAAU UCAGU...UAG-5'@LB@ \| \|@LB@ 24 15@LB@@LB@@LB@Energy -10.28 kcal/mol@LB@Hybridization Energy -13.2399 kcal/mol@LB@Unfolding Energy - mRNA 3.06354 kcal/mol@LB@Unfolding Energy - sRNA 3.38772 kcal/mol@LB@@LB@Position - mRNA 93 -- 100@LB@Position - sRNA 16 -- 23@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 176 -- 182@LB@
121	0.01323	0.3575	b3429	glgA	-14.56	0.033318	190 -- 240	123 -- 176	glycogen synthase	_____________189__________________241\n_____________\|____________________\|\n5'-GUA...AUGCA__________GU________AGAUG...ACG-3'\n______________GGUUUUACAU__AUGUUCAG\n______________\|:\|\|\|\|\|\|\|:__\|\|::\|\|\|\|\n______________CUAAAAUGUG__UAUGAGUC\n3'-UUU...GCCCA__________GU________AGUGU...UAG-5'\n_____________\|____________________\|\n_____________177__________________122\n	219 -- 225	174 -- 180	-15.9439 kcal/mol	3.46677 kcal/mol	4.94566 kcal/mol	189 241@LB@ \| \|@LB@5'-GUA...AUGCA GU AGAUG...ACG-3'@LB@ GGUUUUACAU AUGUUCAG@LB@ \|:\|\|\|\|\|\|\|: \|\|::\|\|\|\|@LB@ CUAAAAUGUG UAUGAGUC@LB@3'-UUU...GCCCA GU AGUGU...UAG-5'@LB@ \| \|@LB@ 177 122@LB@@LB@@LB@Energy -14.56 kcal/mol@LB@Hybridization Energy -15.9439 kcal/mol@LB@Unfolding Energy - mRNA 3.46677 kcal/mol@LB@Unfolding Energy - sRNA 4.94566 kcal/mol@LB@@LB@Position - mRNA 190 -- 240@LB@Position - sRNA 123 -- 176@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 174 -- 180@LB@
178	0.02044	0.3833	b3433	asd	-8.72	0.462346	170 -- 185	58 -- 71	aspartate-semialdehyde dehydrogenase NAD(P)-binding	_____________169__________________186\n_____________\|____________________\|\n5'-UCA...UUAUA___________CUU______AAAAA...UCU-3'\n______________CAG_CACACAU___UGCAGG\n______________\|\|\|_\|\|\|\|\|\|\|___\|\|\|\|\|\|\n______________GUC_GUGUGUA___ACGUCC\n3'-UUU...UAUGA___A_______CU_______GUUCA...UAG-5'\n_____________\|____________________\|\n_____________72___________________57\n	173 -- 179	166 -- 172	-22.5694 kcal/mol	4.04779 kcal/mol	7.34152 kcal/mol	169 186@LB@ \| \|@LB@5'-UCA...UUAUA CUU AAAAA...UCU-3'@LB@ CAG CACACAU UGCAGG@LB@ \|\|\| \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GUC GUGUGUA ACGUCC@LB@3'-UUU...UAUGA A CU GUUCA...UAG-5'@LB@ \| \|@LB@ 72 57@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -22.5694 kcal/mol@LB@Unfolding Energy - mRNA 4.04779 kcal/mol@LB@Unfolding Energy - sRNA 7.34152 kcal/mol@LB@@LB@Position - mRNA 170 -- 185@LB@Position - sRNA 58 -- 71@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 166 -- 172@LB@
115	0.01273	0.3575	b3440	yhhX	-9.67	0.316530	203 -- 215	123 -- 136	putative oxidoreductase	_____________202______________________________216\n_____________\|________________________________\|\n5'-GAC...CGUAU_______AC____AG____A__U____U____CGCAUA-3'\n______________GUACUUA__CGCA___GAU_GC_GGCA_GUCG\n______________:\|\|\|\|:\|__\|:\|\|___\|\|\|_\|\|_\|\|\|\|_\|\|\|:\n______________UAUGAGU__GUGU___CUA_CG_CCGU_CAGU\n3'-UUU...GUGGU_______CA____GUA______U____U____UGAAA...UAG-5'\n_____________\|________________________________\|\n_____________137______________________________122\n	264 -- 270	175 -- 181	-25.3028 kcal/mol	7.53441 kcal/mol	8.15082 kcal/mol	202 216@LB@ \| \|@LB@5'-GAC...CGUAU AC AG A U U CGCAUA-3'@LB@ GUACUUA CGCA GAU GC GGCA GUCG@LB@ :\|\|\|\|:\| \|:\|\| \|\|\| \|\| \|\|\|\| \|\|\|:@LB@ UAUGAGU GUGU CUA CG CCGU CAGU@LB@3'-UUU...GUGGU CA GUA U U UGAAA...UAG-5'@LB@ \| \|@LB@ 137 122@LB@@LB@@LB@Energy -9.67 kcal/mol@LB@Hybridization Energy -25.3028 kcal/mol@LB@Unfolding Energy - mRNA 7.53441 kcal/mol@LB@Unfolding Energy - sRNA 8.15082 kcal/mol@LB@@LB@Position - mRNA 203 -- 215@LB@Position - sRNA 123 -- 136@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 175 -- 181@LB@
20	0.001715	0.2633	b3453	ugpB	-12.22	0.100645	241 -- 257	18 -- 32	sn-glycerol-3-phosphate ABC transporter periplasmic binding protein	_____________240______________258\n_____________\|________________\|\n5'-UUC...AAUUC_____U__________AAGAG...UGG-3'\n______________GCGCA_UCGGUACAAC\n______________:\|\|\|\|_:\|:\|:\|\|\|\|\|\n______________UGCGU_GGUCGUGUUG\n3'-UUU...UUGGU_____U__________AAGCG...UAG-5'\n_____________\|________________\|\n_____________33_______________17\n	180 -- 186	63 -- 69	-22.0099 kcal/mol	5.49331 kcal/mol	9.84719 kcal/mol	240 258@LB@ \| \|@LB@5'-UUC...AAUUC U AAGAG...UGG-3'@LB@ GCGCA UCGGUACAAC@LB@ :\|\|\|\| :\|:\|:\|\|\|\|\|@LB@ UGCGU GGUCGUGUUG@LB@3'-UUU...UUGGU U AAGCG...UAG-5'@LB@ \| \|@LB@ 33 17@LB@@LB@@LB@Energy -12.22 kcal/mol@LB@Hybridization Energy -22.0099 kcal/mol@LB@Unfolding Energy - mRNA 5.49331 kcal/mol@LB@Unfolding Energy - sRNA 9.84719 kcal/mol@LB@@LB@Position - mRNA 241 -- 257@LB@Position - sRNA 18 -- 32@LB@Position Seed - mRNA 180 -- 186@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@
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@
18	0.001156	0.216	b3474	yhhT	-13.05	0.067927	149 -- 189	169 -- 204	UPF0118 family putative transporter	_____________148__________________________________________________________________190\n_____________\|____________________________________________________________________\|\n5'-GAC...GACGU____________UAAG____AGAAUAU________U_ACUCCCGC_____U______AAAA_______AGGAA...UCA-3'\n______________GAAAAUCAGCAG____AAUC_______UGCUGGCG_G________UACAC_UAAUAC____AGUCACA\n______________:\|\|\|\|:\|\|\|\|\|\|____\|\|\|\|_______\|\|\|\|\|\|\|\|_\|________\|\|\|\|\|_:\|\|\|\|\|____\|\|\|\|\|\|\|\n______________UUUUUGGUCGUC____UUAG_______ACGACCGC_C________AUGUG_GUUAUG____UCAGUGU\n________3'-UUU____________CAUA_____________________CACUAAA_____________AG_________GUACU...UAG-5'\n_____________\|____________________________________________________________________\|\n_____________205__________________________________________________________________168\n	183 -- 189	169 -- 175	-48.4478 kcal/mol	16.2259 kcal/mol	18.3074 kcal/mol	148 190@LB@ \| \|@LB@5'-GAC...GACGU UAAG AGAAUAU U ACUCCCGC U AAAA AGGAA...UCA-3'@LB@ GAAAAUCAGCAG AAUC UGCUGGCG G UACAC UAAUAC AGUCACA@LB@ :\|\|\|\|:\|\|\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\| \| \|\|\|\|\| :\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UUUUUGGUCGUC UUAG ACGACCGC C AUGUG GUUAUG UCAGUGU@LB@ 3'-UUU CAUA CACUAAA AG GUACU...UAG-5'@LB@ \| \|@LB@ 205 168@LB@@LB@@LB@Energy -13.05 kcal/mol@LB@Hybridization Energy -48.4478 kcal/mol@LB@Unfolding Energy - mRNA 16.2259 kcal/mol@LB@Unfolding Energy - sRNA 18.3074 kcal/mol@LB@@LB@Position - mRNA 149 -- 189@LB@Position - sRNA 169 -- 204@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 169 -- 175@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@

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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