Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
123	0.01951	0.5155	b0032	carA	-10.10	0.092857	258 -- 264	55 -- 61	carbamoyl phosphate synthetase small subunit glutamine amidotransferase	_____________257_____265\n_____________\|_______\|\n5'-UUG...GGGCC_______CAACA...AUA-3'\n______________AUAGGGG\n______________\|\|\|\|\|\|\|\n______________UAUCCCC\n3'-UUU...AACUU_______AUUUG...UCG-5'\n_____________\|_______\|\n_____________62______54\n	258 -- 264	55 -- 61	-10.8319 kcal/mol	0.710423 kcal/mol	0.0258473 kcal/mol	257 265@LB@ \| \|@LB@5'-UUG...GGGCC CAACA...AUA-3'@LB@ AUAGGGG@LB@ \|\|\|\|\|\|\|@LB@ UAUCCCC@LB@3'-UUU...AACUU AUUUG...UCG-5'@LB@ \| \|@LB@ 62 54@LB@@LB@@LB@Energy -10.10 kcal/mol@LB@Hybridization Energy -10.8319 kcal/mol@LB@Unfolding Energy - mRNA 0.710423 kcal/mol@LB@Unfolding Energy - sRNA 0.0258473 kcal/mol@LB@@LB@Position - mRNA 258 -- 264@LB@Position - sRNA 55 -- 61@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 55 -- 61@LB@
145	0.02447	0.526	b4518	ymdF	-10.96	0.061577	258 -- 296	23 -- 64	KGG family protein	_____________257________________________________________________297\n_____________\|__________________________________________________\|\n5'-UUU...CAUCA____C___UAAAAAA_________C___GC_____________G______UUCA-3'\n______________GAAG_AGG_______GGUGGACAG_ACA_____________GG_GGUAAU\n______________\|\|\|:_\|\|\|_______\|\|\|::\|\|\|\|_\|\|\|_____________\|:_\|\|\|\|\|\|\n______________CUUU_UCC_______CCAUUUGUC_UGU_____________CU_CCAUUA\n3'-UUU...GCCAA____A_______________________AAGUCUUUACUUA__G______UUUAU...UCG-5'\n_____________\|__________________________________________________\|\n_____________65_________________________________________________22\n	275 -- 281	48 -- 54	-22.543 kcal/mol	5.2615 kcal/mol	6.31898 kcal/mol	257 297@LB@ \| \|@LB@5'-UUU...CAUCA C UAAAAAA C GC G UUCA-3'@LB@ GAAG AGG GGUGGACAG ACA GG GGUAAU@LB@ \|\|\|: \|\|\| \|\|\|::\|\|\|\| \|\|\| \|: \|\|\|\|\|\|@LB@ CUUU UCC CCAUUUGUC UGU CU CCAUUA@LB@3'-UUU...GCCAA A AAGUCUUUACUUA G UUUAU...UCG-5'@LB@ \| \|@LB@ 65 22@LB@@LB@@LB@Energy -10.96 kcal/mol@LB@Hybridization Energy -22.543 kcal/mol@LB@Unfolding Energy - mRNA 5.2615 kcal/mol@LB@Unfolding Energy - sRNA 6.31898 kcal/mol@LB@@LB@Position - mRNA 258 -- 296@LB@Position - sRNA 23 -- 64@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 48 -- 54@LB@
21	0.001002	0.1516	b4045	yjbJ	-13.25	0.018991	259 -- 290	28 -- 62	stress-induced protein UPF0337 family	_____________258__________________________________291\n_____________\|____________________________________\|\n5'-CGU...AGAGC_______C_____U___CGAU________U______AUCAU...AAG-3'\n______________AAUGGGG__AAAC_GAC_______GAUGA_AUGACG\n______________\|\|\|:\|\|\|__\|\|\|\|_\|\|\|_______:\|\|\|\|_\|\|\|\|\|\|\n______________UUAUCCC__UUUG_CUG_______UUACU_UACUGC\n3'-UUU...CAACU_______CA____U___UAAGUCU____________CAUUA...UCG-5'\n_____________\|____________________________________\|\n_____________63___________________________________27\n	259 -- 265	56 -- 62	-23.7721 kcal/mol	4.22826 kcal/mol	6.29418 kcal/mol	258 291@LB@ \| \|@LB@5'-CGU...AGAGC C U CGAU U AUCAU...AAG-3'@LB@ AAUGGGG AAAC GAC GAUGA AUGACG@LB@ \|\|\|:\|\|\| \|\|\|\| \|\|\| :\|\|\|\| \|\|\|\|\|\|@LB@ UUAUCCC UUUG CUG UUACU UACUGC@LB@3'-UUU...CAACU CA U UAAGUCU CAUUA...UCG-5'@LB@ \| \|@LB@ 63 27@LB@@LB@@LB@Energy -13.25 kcal/mol@LB@Hybridization Energy -23.7721 kcal/mol@LB@Unfolding Energy - mRNA 4.22826 kcal/mol@LB@Unfolding Energy - sRNA 6.29418 kcal/mol@LB@@LB@Position - mRNA 259 -- 290@LB@Position - sRNA 28 -- 62@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 56 -- 62@LB@
129	0.02061	0.5217	b0633	rlpA	-9.57	0.117965	261 -- 273	1 -- 12	septal ring protein suppressor of prc minor lipoprotein	_____________260___________274\n_____________\|_____________\|\n5'-CGG...CAAGC_________C___AACAG...CUG-3'\n______________GAUGAUGGU_AGC\n______________:\|\|\|\|\|\|:\|_\|\|\|\n______________UUACUACUA_UCG\n3'-UUU...UUCAA_____________-5'\n_____________\|____________\|\n_____________13___________1\n	263 -- 269	4 -- 10	-13.3317 kcal/mol	3.7231 kcal/mol	0.0394463 kcal/mol	260 274@LB@ \| \|@LB@5'-CGG...CAAGC C AACAG...CUG-3'@LB@ GAUGAUGGU AGC@LB@ :\|\|\|\|\|\|:\| \|\|\|@LB@ UUACUACUA UCG@LB@3'-UUU...UUCAA -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -9.57 kcal/mol@LB@Hybridization Energy -13.3317 kcal/mol@LB@Unfolding Energy - mRNA 3.7231 kcal/mol@LB@Unfolding Energy - sRNA 0.0394463 kcal/mol@LB@@LB@Position - mRNA 261 -- 273@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 4 -- 10@LB@
148	0.02477	0.526	b2262	menB	-9.56	0.118602	261 -- 300	25 -- 56	dihydroxynaphthoic acid synthetase	_____________260______________________________________300\n_____________\|________________________________________\|\n5'-CGU...CCGAA___UUCGA__________UU_____AAAUCCACC_______-3'\n______________GGU_____GGACAUUC_G__AUGAA_________GACGGUA\n______________\|\|\|_____:\|\|\|\|\|\|\|_\|__\|\|\|\|\|_________\|\|\|\|\|\|\|\n______________CCA_____UCUGUAAG_C__UACUU_________CUGCCAU\n3'-UUU...UAUCC___UUUG_________U_UU_____A_______________UAUUU...UCG-5'\n_____________\|_________________________________________\|\n_____________57________________________________________24\n	294 -- 300	25 -- 31	-24.8577 kcal/mol	9.0019 kcal/mol	6.29869 kcal/mol	260 300@LB@ \| \|@LB@5'-CGU...CCGAA UUCGA UU AAAUCCACC -3'@LB@ GGU GGACAUUC G AUGAA GACGGUA@LB@ \|\|\| :\|\|\|\|\|\|\| \| \|\|\|\|\| \|\|\|\|\|\|\|@LB@ CCA UCUGUAAG C UACUU CUGCCAU@LB@3'-UUU...UAUCC UUUG U UU A UAUUU...UCG-5'@LB@ \| \|@LB@ 57 24@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -24.8577 kcal/mol@LB@Unfolding Energy - mRNA 9.0019 kcal/mol@LB@Unfolding Energy - sRNA 6.29869 kcal/mol@LB@@LB@Position - mRNA 261 -- 300@LB@Position - sRNA 25 -- 56@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 25 -- 31@LB@
185	0.03096	0.5492	b1686	menI	-12.09	0.035132	263 -- 300	22 -- 58	1 4-dihydroxy-2-naphthoyl-CoA hydrolase	_____________262____________________________________300\n_____________\|______________________________________\|\n5'-GGC...AUGGU_____UCCU_________CUU_____CAUAU________-3'\n______________GGGGU____GGAUAUUCG____UGAA_____UGGUGAUG\n______________\|\|\|\|\|____:\|\|:\|\|\|\|:____\|\|\|\|_____:\|\|\|:\|\|:\n______________CCCCA____UCUGUAAGU____ACUU_____GCCAUUAU\n3'-UUU...UUUAU_____UUUG_________CUUU____ACU__________UUAUU...UCG-5'\n_____________\|_______________________________________\|\n_____________59______________________________________21\n	294 -- 300	22 -- 28	-26.9755 kcal/mol	8.57608 kcal/mol	6.31389 kcal/mol	262 300@LB@ \| \|@LB@5'-GGC...AUGGU UCCU CUU CAUAU -3'@LB@ GGGGU GGAUAUUCG UGAA UGGUGAUG@LB@ \|\|\|\|\| :\|\|:\|\|\|\|: \|\|\|\| :\|\|\|:\|\|:@LB@ CCCCA UCUGUAAGU ACUU GCCAUUAU@LB@3'-UUU...UUUAU UUUG CUUU ACU UUAUU...UCG-5'@LB@ \| \|@LB@ 59 21@LB@@LB@@LB@Energy -12.09 kcal/mol@LB@Hybridization Energy -26.9755 kcal/mol@LB@Unfolding Energy - mRNA 8.57608 kcal/mol@LB@Unfolding Energy - sRNA 6.31389 kcal/mol@LB@@LB@Position - mRNA 263 -- 300@LB@Position - sRNA 22 -- 58@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 22 -- 28@LB@
20	0.0009027	0.1482	b2696	csrA	-13.42	0.017327	268 -- 280	48 -- 60	pleiotropic regulatory protein for carbon source metabolism	_____________267___________281\n_____________\|_____________\|\n5'-CGG...AGUUU__________G__CAACC...GCG-3'\n______________UAGGGGUAAA_GG\n______________\|\|\|\|\|\|\|\|\|\|_:\|\n______________AUCCCCAUUU_UC\n3'-UUU...ACUUU__________G__UGUAA...UCG-5'\n_____________\|_____________\|\n_____________61____________47\n	271 -- 277	51 -- 57	-17.9026 kcal/mol	2.43021 kcal/mol	2.05446 kcal/mol	267 281@LB@ \| \|@LB@5'-CGG...AGUUU G CAACC...GCG-3'@LB@ UAGGGGUAAA GG@LB@ \|\|\|\|\|\|\|\|\|\| :\|@LB@ AUCCCCAUUU UC@LB@3'-UUU...ACUUU G UGUAA...UCG-5'@LB@ \| \|@LB@ 61 47@LB@@LB@@LB@Energy -13.42 kcal/mol@LB@Hybridization Energy -17.9026 kcal/mol@LB@Unfolding Energy - mRNA 2.43021 kcal/mol@LB@Unfolding Energy - sRNA 2.05446 kcal/mol@LB@@LB@Position - mRNA 268 -- 280@LB@Position - sRNA 48 -- 60@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 51 -- 57@LB@
15	0.0006204	0.1358	b0652	gltL	-11.66	0.043639	269 -- 295	1 -- 25	glutamate/aspartate ABC transporter ATPase	_____________268_________________________296\n_____________\|___________________________\|\n5'-CUC...ACCGA______A____GCGA____________UUGCG-3'\n______________AGUGAA_AAAG____AGUGGUGGUGGU\n______________\|:\|:\|\|_\|\|\|\|____\|:\|\|:\|\|:\|:\|:\n______________UUAUUU_UUUC____UUACUACUAUCG\n3'-UUU...UGCCA______A____AA______________-5'\n_____________\|__________________________\|\n_____________26_________________________1\n	289 -- 295	1 -- 7	-17.2962 kcal/mol	5.52495 kcal/mol	0.112205 kcal/mol	268 296@LB@ \| \|@LB@5'-CUC...ACCGA A GCGA UUGCG-3'@LB@ AGUGAA AAAG AGUGGUGGUGGU@LB@ \|:\|:\|\| \|\|\|\| \|:\|\|:\|\|:\|:\|:@LB@ UUAUUU UUUC UUACUACUAUCG@LB@3'-UUU...UGCCA A AA -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -17.2962 kcal/mol@LB@Unfolding Energy - mRNA 5.52495 kcal/mol@LB@Unfolding Energy - sRNA 0.112205 kcal/mol@LB@@LB@Position - mRNA 269 -- 295@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 1 -- 7@LB@
199	0.03375	0.5555	b3860	dsbA	-9.14	0.142422	273 -- 281	48 -- 56	periplasmic protein disulfide isomerase I	_____________272_______282\n_____________\|_________\|\n5'-UUU...AAGAU_________UACAC...AAC-3'\n______________GGUAAACAG\n______________\|\|\|\|\|\|\|\|\|\n______________CCAUUUGUC\n3'-UUU...UAUCC_________UGUAA...UCG-5'\n_____________\|_________\|\n_____________57________47\n	275 -- 281	48 -- 54	-12.2563 kcal/mol	1.07557 kcal/mol	2.03935 kcal/mol	272 282@LB@ \| \|@LB@5'-UUU...AAGAU UACAC...AAC-3'@LB@ GGUAAACAG@LB@ \|\|\|\|\|\|\|\|\|@LB@ CCAUUUGUC@LB@3'-UUU...UAUCC UGUAA...UCG-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -12.2563 kcal/mol@LB@Unfolding Energy - mRNA 1.07557 kcal/mol@LB@Unfolding Energy - sRNA 2.03935 kcal/mol@LB@@LB@Position - mRNA 273 -- 281@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 48 -- 54@LB@
99	0.01587	0.5059	b2155	cirA	-12.92	0.022646	275 -- 290	1 -- 16	colicin IA outer membrane receptor and translocator; ferric iron-catecholate transporter	_____________274______________291\n_____________\|________________\|\n5'-GGA...UUAGC___C____________GAAAC...UGG-3'\n______________GGU_GAUGAUGAUGGC\n______________:\|\|_:\|\|\|\|\|\|\|\|:\|\|\n______________UCA_UUACUACUAUCG\n3'-UUU...UUAUU___A____________-5'\n_____________\|_______________\|\n_____________17______________1\n	284 -- 290	1 -- 7	-19.8516 kcal/mol	6.87927 kcal/mol	0.0492804 kcal/mol	274 291@LB@ \| \|@LB@5'-GGA...UUAGC C GAAAC...UGG-3'@LB@ GGU GAUGAUGAUGGC@LB@ :\|\| :\|\|\|\|\|\|\|\|:\|\|@LB@ UCA UUACUACUAUCG@LB@3'-UUU...UUAUU A -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -12.92 kcal/mol@LB@Hybridization Energy -19.8516 kcal/mol@LB@Unfolding Energy - mRNA 6.87927 kcal/mol@LB@Unfolding Energy - sRNA 0.0492804 kcal/mol@LB@@LB@Position - mRNA 275 -- 290@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 1 -- 7@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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