Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
134	0.01498	0.3759	b3388	damX	-9.22	0.174550	186 -- 204	42 -- 59	cell division protein that binds to the septal ring	_____________185__________________205\n_____________\|____________________\|\n5'-GGG...ACCUU_____________UA_____AUGAA...AAC-3'\n______________UUAGUGG_GGUGU__AAUGG\n______________\|:\|\|\|\|\|_::\|\|:__\|\|\|\|\|\n______________AGUCACC_UUACG__UUACC\n3'-UUU...CUUUU_______G____________GGGUU...UUG-5'\n_____________\|____________________\|\n_____________60___________________41\n	186 -- 192	53 -- 59	-16.4488 kcal/mol	3.53707 kcal/mol	3.69565 kcal/mol	185 205@LB@ \| \|@LB@5'-GGG...ACCUU UA AUGAA...AAC-3'@LB@ UUAGUGG GGUGU AAUGG@LB@ \|:\|\|\|\|\| ::\|\|: \|\|\|\|\|@LB@ AGUCACC UUACG UUACC@LB@3'-UUU...CUUUU G GGGUU...UUG-5'@LB@ \| \|@LB@ 60 41@LB@@LB@@LB@Energy -9.22 kcal/mol@LB@Hybridization Energy -16.4488 kcal/mol@LB@Unfolding Energy - mRNA 3.53707 kcal/mol@LB@Unfolding Energy - sRNA 3.69565 kcal/mol@LB@@LB@Position - mRNA 186 -- 204@LB@Position - sRNA 42 -- 59@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 53 -- 59@LB@
98	0.009218	0.3118	b3391	hofQ	-10.83	0.081241	8 -- 57	7 -- 65	DNA catabolic putative fimbrial transporter	_____________7_____________________________________________________________58\n_____________\|_____________________________________________________________\|\n____5'-CUAUCAG____UGG_________G____GC__A___U___UGU_________________________AAAGA...UAG-3'\n______________GGGA___UAG_GGCGA_GCGA__GC_UCA_CGG___AAUAAAA_____GAC_____GGGCA\n______________\|\|:\|___:\|\|_\|\|\|:\|_\|\|:\|__\|\|_:\|\|_\|:\|___\|\|\|\|\|\|\|_____\|\|\|_____:\|\|\|\|\n______________CCUU___GUC_CCGUU_CGUU__CG_GGU_GUC___UUAUUUU_____CUG_____UCCGU\n3'-UUU...UACAA____UUA___A_____A____AC______U___UU________AGACA___UUAUU_____AUAUUG-5'\n_____________\|_____________________________________________________________\|\n_____________66____________________________________________________________6\n	43 -- 49	25 -- 31	-34.6984 kcal/mol	11.715 kcal/mol	12.1538 kcal/mol	7 58@LB@ \| \|@LB@ 5'-CUAUCAG UGG G GC A U UGU AAAGA...UAG-3'@LB@ GGGA UAG GGCGA GCGA GC UCA CGG AAUAAAA GAC GGGCA@LB@ \|\|:\| :\|\| \|\|\|:\| \|\|:\| \|\| :\|\| \|:\| \|\|\|\|\|\|\| \|\|\| :\|\|\|\|@LB@ CCUU GUC CCGUU CGUU CG GGU GUC UUAUUUU CUG UCCGU@LB@3'-UUU...UACAA UUA A A AC U UU AGACA UUAUU AUAUUG-5'@LB@ \| \|@LB@ 66 6@LB@@LB@@LB@Energy -10.83 kcal/mol@LB@Hybridization Energy -34.6984 kcal/mol@LB@Unfolding Energy - mRNA 11.715 kcal/mol@LB@Unfolding Energy - sRNA 12.1538 kcal/mol@LB@@LB@Position - mRNA 8 -- 57@LB@Position - sRNA 7 -- 65@LB@Position Seed - mRNA 43 -- 49@LB@Position Seed - sRNA 25 -- 31@LB@
121	0.01216	0.338	b3416	malQ	-13.35	0.020947	179 -- 225	13 -- 54	4-alpha-glucanotransferase (amylomaltase)	_____________178______________________________________________226\n_____________\|________________________________________________\|\n5'-GCG...UGGCA_____AAC__U__GGAA_____________C___C_____________CCGCG...CCA-3'\n______________GGCAA___GC_AA____GCUCGAUGGAAAG_AAA_GUCUG_GAUAAUG\n______________\|\|\|\|\|___\|\|_\|\|____\|\|:\|:\|::\|\|\|\|:_\|\|\|_:\|\|\|\|_\|\|:\|\|\|:\n______________CCGUU___CG_UU____CGGGUUGUCUUUU_UUU_UAGAC_CUGUUAU\n3'-UUU...AGUCA_____A_______AC_______________A_________A_______UUCCG...UUG-5'\n_____________\|________________________________________________\|\n_____________55_______________________________________________12\n	219 -- 225	13 -- 19	-33.3316 kcal/mol	8.88616 kcal/mol	11.0933 kcal/mol	178 226@LB@ \| \|@LB@5'-GCG...UGGCA AAC U GGAA C C CCGCG...CCA-3'@LB@ GGCAA GC AA GCUCGAUGGAAAG AAA GUCUG GAUAAUG@LB@ \|\|\|\|\| \|\| \|\| \|\|:\|:\|::\|\|\|\|: \|\|\| :\|\|\|\| \|\|:\|\|\|:@LB@ CCGUU CG UU CGGGUUGUCUUUU UUU UAGAC CUGUUAU@LB@3'-UUU...AGUCA A AC A A UUCCG...UUG-5'@LB@ \| \|@LB@ 55 12@LB@@LB@@LB@Energy -13.35 kcal/mol@LB@Hybridization Energy -33.3316 kcal/mol@LB@Unfolding Energy - mRNA 8.88616 kcal/mol@LB@Unfolding Energy - sRNA 11.0933 kcal/mol@LB@@LB@Position - mRNA 179 -- 225@LB@Position - sRNA 13 -- 54@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 13 -- 19@LB@
113	0.01136	0.3326	b3417	malP	-12.46	0.034450	250 -- 272	38 -- 60	maltodextrin phosphorylase	_____________249_____________________273\n_____________\|_______________________\|\n5'-ACA...UUCAC___________C__U________AAUUC...GCC-3'\n______________GUCAGUGGCAG_GU_AUGGCUUA\n______________:\|\|\|\|\|\|\|\|\|:_\|:_\|\|\|\|\|::\|\n______________UAGUCACCGUU_CG_UACCGGGU\n3'-UUU...CCUUU___________A__U________UGUCU...UUG-5'\n_____________\|_______________________\|\n_____________61______________________37\n	266 -- 272	38 -- 44	-30.8718 kcal/mol	11.793 kcal/mol	6.61394 kcal/mol	249 273@LB@ \| \|@LB@5'-ACA...UUCAC C U AAUUC...GCC-3'@LB@ GUCAGUGGCAG GU AUGGCUUA@LB@ :\|\|\|\|\|\|\|\|\|: \|: \|\|\|\|\|::\|@LB@ UAGUCACCGUU CG UACCGGGU@LB@3'-UUU...CCUUU A U UGUCU...UUG-5'@LB@ \| \|@LB@ 61 37@LB@@LB@@LB@Energy -12.46 kcal/mol@LB@Hybridization Energy -30.8718 kcal/mol@LB@Unfolding Energy - mRNA 11.793 kcal/mol@LB@Unfolding Energy - sRNA 6.61394 kcal/mol@LB@@LB@Position - mRNA 250 -- 272@LB@Position - sRNA 38 -- 60@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 38 -- 44@LB@
89	0.007733	0.2889	b3426	glpD	-8.48	0.239884	186 -- 234	7 -- 64	sn-glycerol-3-phosphate dehydrogenase aerobic FAD/NAD(P)-binding	_____________185__________________________________________________________235\n_____________\|____________________________________________________________\|\n5'-AAC...CGAAA_U____G________________AAA________UCU_______________________GCAUC...AGG-3'\n______________G_GAAU_AG_GGCA__GC_AUGG___CCAA_AGA______GA_UUGUGAUAG__GGGGCG\n______________\|_:\|\|\|_\|\|_\|\|\|\|__\|\|_\|\|\|\|___\|\|\|\|_\|\|\|______:\|_:\|\|\|\|\|:\|:__::\|\|\|:\n______________C_UUUA_UC_CCGU__CG_UACC___GGUU_UCU______UU_GACACUGUU__UUCCGU\n3'-UUU...ACAAC_U____G__A____UA__U____G______G___UUUAUU__A_________AU______AUAUUG-5'\n_____________\|____________________________________________________________\|\n_____________65___________________________________________________________6\n	222 -- 228	15 -- 21	-34.508 kcal/mol	13.8761 kcal/mol	12.1536 kcal/mol	185 235@LB@ \| \|@LB@5'-AAC...CGAAA U G AAA UCU GCAUC...AGG-3'@LB@ G GAAU AG GGCA GC AUGG CCAA AGA GA UUGUGAUAG GGGGCG@LB@ \| :\|\|\| \|\| \|\|\|\| \|\| \|\|\|\| \|\|\|\| \|\|\| :\| :\|\|\|\|\|:\|: ::\|\|\|:@LB@ C UUUA UC CCGU CG UACC GGUU UCU UU GACACUGUU UUCCGU@LB@3'-UUU...ACAAC U G A UA U G G UUUAUU A AU AUAUUG-5'@LB@ \| \|@LB@ 65 6@LB@@LB@@LB@Energy -8.48 kcal/mol@LB@Hybridization Energy -34.508 kcal/mol@LB@Unfolding Energy - mRNA 13.8761 kcal/mol@LB@Unfolding Energy - sRNA 12.1536 kcal/mol@LB@@LB@Position - mRNA 186 -- 234@LB@Position - sRNA 7 -- 64@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 15 -- 21@LB@
10	0.0004066	0.1262	b3429	glgA	-9.74	0.137242	173 -- 185	51 -- 64	glycogen synthase	_____________172____________186\n_____________\|______________\|\n5'-GUA...GCUAC______________UAAAC...ACG-3'\n______________GGAAGUUAG_GGCA\n______________\|:\|\|:\|:\|\|_\|\|\|\|\n______________CUUUUAGUC_CCGU\n3'-UUU...ACAAC_________A____UACGU...UUG-5'\n_____________\|______________\|\n_____________65_____________50\n	175 -- 181	56 -- 62	-15.3924 kcal/mol	2.76007 kcal/mol	2.8882 kcal/mol	172 186@LB@ \| \|@LB@5'-GUA...GCUAC UAAAC...ACG-3'@LB@ GGAAGUUAG GGCA@LB@ \|:\|\|:\|:\|\| \|\|\|\|@LB@ CUUUUAGUC CCGU@LB@3'-UUU...ACAAC A UACGU...UUG-5'@LB@ \| \|@LB@ 65 50@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -15.3924 kcal/mol@LB@Unfolding Energy - mRNA 2.76007 kcal/mol@LB@Unfolding Energy - sRNA 2.8882 kcal/mol@LB@@LB@Position - mRNA 173 -- 185@LB@Position - sRNA 51 -- 64@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 56 -- 62@LB@
44	0.002732	0.2088	b3450	ugpC	-10.48	0.096645	106 -- 116	47 -- 57	sn-glycerol-3-phosphate ABC transporter ATPase	_____________105_________117\n_____________\|___________\|\n5'-GUG...GUGAU___________UGUUA...UCG-3'\n______________GGUGGCGAUGU\n______________:\|\|\|\|\|:\|\|\|:\n______________UCACCGUUACG\n3'-UUU...UUUAG___________UUACC...UUG-5'\n_____________\|___________\|\n_____________58__________46\n	110 -- 116	47 -- 53	-17.083 kcal/mol	3.56469 kcal/mol	3.03952 kcal/mol	105 117@LB@ \| \|@LB@5'-GUG...GUGAU UGUUA...UCG-3'@LB@ GGUGGCGAUGU@LB@ :\|\|\|\|\|:\|\|\|:@LB@ UCACCGUUACG@LB@3'-UUU...UUUAG UUACC...UUG-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -10.48 kcal/mol@LB@Hybridization Energy -17.083 kcal/mol@LB@Unfolding Energy - mRNA 3.56469 kcal/mol@LB@Unfolding Energy - sRNA 3.03952 kcal/mol@LB@@LB@Position - mRNA 106 -- 116@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 110 -- 116@LB@Position Seed - sRNA 47 -- 53@LB@
185	0.02287	0.4143	b3460	livJ	-12.49	0.033972	245 -- 276	28 -- 54	branched-chain amino acid ABC transporter periplasmic binding protein	_____________244______________________________277\n_____________\|________________________________\|\n5'-AAU...GCGCU____UUCA___AU_______U___________UUAAA...CAA-3'\n______________GGCA____GCA__AUGGCUC_GGCAGAAGAUA\n______________\|\|\|\|____\|\|\|__\|\|\|\|\|:\|_::\|\|\|\|\|:\|\|\|\n______________CCGU____CGU__UACCGGG_UUGUCUUUUAU\n3'-UUU...AGUCA____UA__________________________UUUAG...UUG-5'\n_____________\|________________________________\|\n_____________55_______________________________27\n	258 -- 264	39 -- 45	-29.3573 kcal/mol	7.88401 kcal/mol	8.98285 kcal/mol	244 277@LB@ \| \|@LB@5'-AAU...GCGCU UUCA AU U UUAAA...CAA-3'@LB@ GGCA GCA AUGGCUC GGCAGAAGAUA@LB@ \|\|\|\| \|\|\| \|\|\|\|\|:\| ::\|\|\|\|\|:\|\|\|@LB@ CCGU CGU UACCGGG UUGUCUUUUAU@LB@3'-UUU...AGUCA UA UUUAG...UUG-5'@LB@ \| \|@LB@ 55 27@LB@@LB@@LB@Energy -12.49 kcal/mol@LB@Hybridization Energy -29.3573 kcal/mol@LB@Unfolding Energy - mRNA 7.88401 kcal/mol@LB@Unfolding Energy - sRNA 8.98285 kcal/mol@LB@@LB@Position - mRNA 245 -- 276@LB@Position - sRNA 28 -- 54@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 39 -- 45@LB@
70	0.005852	0.2791	b3524	yhjG	-5.99	0.576071	198 -- 212	7 -- 18	putative inner membrane-anchored periplasmic AsmA family protein	_____________197_____________213\n_____________\|_______________\|\n5'-UUG...AGCGA_______GCA_____GGCAA...GAC-3'\n______________ACGAUGA___AGGCA\n______________\|\|:\|\|:\|___\|\|\|\|\|\n______________UGUUAUU___UCCGU\n3'-UUU...GACAC_______________AUAUUG-5'\n_____________\|_______________\|\n_____________19______________6\n	198 -- 204	12 -- 18	-10.9915 kcal/mol	1.73561 kcal/mol	3.26755 kcal/mol	197 213@LB@ \| \|@LB@5'-UUG...AGCGA GCA GGCAA...GAC-3'@LB@ ACGAUGA AGGCA@LB@ \|\|:\|\|:\| \|\|\|\|\|@LB@ UGUUAUU UCCGU@LB@3'-UUU...GACAC AUAUUG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -5.99 kcal/mol@LB@Hybridization Energy -10.9915 kcal/mol@LB@Unfolding Energy - mRNA 1.73561 kcal/mol@LB@Unfolding Energy - sRNA 3.26755 kcal/mol@LB@@LB@Position - mRNA 198 -- 212@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 12 -- 18@LB@
23	0.001281	0.182	b3541	dppD	-11.06	0.072175	116 -- 139	1 -- 23	dipeptide/heme ABC transporter ATPas	_____________115______________________140\n_____________\|________________________\|\n5'-UUU...CGAUC___C________CU_____U____CUGAU...GCG-3'\n______________CUG_UGACGGUG__GGCAU_UAAC\n______________\|\|\|_\|\|\|\|::\|:__\|\|\|\|\|_\|\|\|\|\n______________GAC_ACUGUUAU__CCGUA_AUUG\n3'-UUU...UUUUA____________UU_____U____-5'\n_____________\|_______________________\|\n_____________24______________________1\n	121 -- 127	13 -- 19	-21.9665 kcal/mol	6.28511 kcal/mol	4.61692 kcal/mol	115 140@LB@ \| \|@LB@5'-UUU...CGAUC C CU U CUGAU...GCG-3'@LB@ CUG UGACGGUG GGCAU UAAC@LB@ \|\|\| \|\|\|\|::\|: \|\|\|\|\| \|\|\|\|@LB@ GAC ACUGUUAU CCGUA AUUG@LB@3'-UUU...UUUUA UU U -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -21.9665 kcal/mol@LB@Unfolding Energy - mRNA 6.28511 kcal/mol@LB@Unfolding Energy - sRNA 4.61692 kcal/mol@LB@@LB@Position - mRNA 116 -- 139@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 13 -- 19@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)

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

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service.

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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