Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
41	0.002142	0.1727	b2153	folE	-10.82	0.097170	217 -- 276	53 -- 121	GTP cyclohydrolase I	_____________216________________________________________________________________________277\n_____________\|__________________________________________________________________________\|\n5'-CUG...CAGUA______C__________CAU__AG__UUA_U________G____GA____________________________CGCCC...ACG-3'\n______________AAGAAG_GGCCCUGGUU___GA__CG___G_UGCGCGAG_ACUG____AACACC____________GCUGCGCC\n______________\|\|:\|\|:_\|:\|\|\|:\|\|:\|___\|\|__\|\|___\|_\|\|\|\|\|\|\|:_\|\|\|\|____\|\|\|\|\|\|____________\|\|\|\|\|\|\|\|\n______________UUUUUU_CUGGGGCCGA___CU__GC___C_ACGCGCUU_UGAC____UUGUGG____________CGACGCGG\n___________3'-______A__________U____G___C___C________A____GCGG______UCCCUUUAGAAC________CAUUU...GUG-5'\n______________\|_________________________________________________________________________\|\n______________121_______________________________________________________________________52\n	270 -- 276	53 -- 59	-62.0592 kcal/mol	19.5041 kcal/mol	31.7353 kcal/mol	216 277@LB@ \| \|@LB@5'-CUG...CAGUA C CAU AG UUA U G GA CGCCC...ACG-3'@LB@ AAGAAG GGCCCUGGUU GA CG G UGCGCGAG ACUG AACACC GCUGCGCC@LB@ \|\|:\|\|: \|:\|\|\|:\|\|:\| \|\| \|\| \| \|\|\|\|\|\|\|: \|\|\|\| \|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UUUUUU CUGGGGCCGA CU GC C ACGCGCUU UGAC UUGUGG CGACGCGG@LB@ 3'- A U G C C A GCGG UCCCUUUAGAAC CAUUU...GUG-5'@LB@ \| \|@LB@ 121 52@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -62.0592 kcal/mol@LB@Unfolding Energy - mRNA 19.5041 kcal/mol@LB@Unfolding Energy - sRNA 31.7353 kcal/mol@LB@@LB@Position - mRNA 217 -- 276@LB@Position - sRNA 53 -- 121@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 53 -- 59@LB@
42	0.002147	0.1727	b0082	rsmH	-13.18	0.033634	23 -- 49	70 -- 94	16S rRNA m(4)C1402 methyltransferase SAM-dependent	_____________22__________________________50\n_____________\|___________________________\|\n5'-UGG...UAAUC____C_________G____AU______CUGAC...GUC-3'\n______________GCGC_AGUACUGCG_CAAC__GCCGGG\n______________\|\|\|\|_\|:\|\|\|\|\|\|\|_\|\|\|\|__:\|\|:\|\|\n______________CGCG_UUAUGACGC_GUUG__UGGUCC\n3'-UUU...CCCCA____C_________G____________CUUUA...GUG-5'\n_____________\|___________________________\|\n_____________95__________________________69\n	30 -- 36	81 -- 87	-36.7334 kcal/mol	10.4772 kcal/mol	13.036 kcal/mol	22 50@LB@ \| \|@LB@5'-UGG...UAAUC C G AU CUGAC...GUC-3'@LB@ GCGC AGUACUGCG CAAC GCCGGG@LB@ \|\|\|\| \|:\|\|\|\|\|\|\| \|\|\|\| :\|\|:\|\|@LB@ CGCG UUAUGACGC GUUG UGGUCC@LB@3'-UUU...CCCCA C G CUUUA...GUG-5'@LB@ \| \|@LB@ 95 69@LB@@LB@@LB@Energy -13.18 kcal/mol@LB@Hybridization Energy -36.7334 kcal/mol@LB@Unfolding Energy - mRNA 10.4772 kcal/mol@LB@Unfolding Energy - sRNA 13.036 kcal/mol@LB@@LB@Position - mRNA 23 -- 49@LB@Position - sRNA 70 -- 94@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 81 -- 87@LB@
43	0.002187	0.1727	b2222	atoA	-7.38	0.400797	260 -- 273	68 -- 82	acetyl-CoA:acetoacetyl-CoA transferase beta subunit	_____________259_____________274\n_____________\|_______________\|\n5'-CGC...GACAU_______________UCGGU...AUU-3'\n______________CGUUAAC_UUAGGGA\n______________\|\|::\|\|\|_::\|\|\|\|\|\n______________GCGGUUG_GGUCCCU\n3'-UUU...AUGAC_______U_______UUAGA...GUG-5'\n_____________\|_______________\|\n_____________83______________67\n	267 -- 273	68 -- 74	-16.5153 kcal/mol	2.15948 kcal/mol	6.98098 kcal/mol	259 274@LB@ \| \|@LB@5'-CGC...GACAU UCGGU...AUU-3'@LB@ CGUUAAC UUAGGGA@LB@ \|\|::\|\|\| ::\|\|\|\|\|@LB@ GCGGUUG GGUCCCU@LB@3'-UUU...AUGAC U UUAGA...GUG-5'@LB@ \| \|@LB@ 83 67@LB@@LB@@LB@Energy -7.38 kcal/mol@LB@Hybridization Energy -16.5153 kcal/mol@LB@Unfolding Energy - mRNA 2.15948 kcal/mol@LB@Unfolding Energy - sRNA 6.98098 kcal/mol@LB@@LB@Position - mRNA 260 -- 273@LB@Position - sRNA 68 -- 82@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 68 -- 74@LB@
44	0.002208	0.1727	b1859	znuB	-7.63	0.365449	19 -- 38	72 -- 88	zinc ABC transporter permease	_____________18___________________39\n_____________\|____________________\|\n5'-AUG...AUGAA__________UGAAU_____CAUUU...AUU-3'\n______________GUGCUGUGCC_____CACCA\n______________:\|:\|\|\|:\|\|\|_____\|\|\|\|\|\n______________UAUGACGCGG_____GUGGU\n3'-UUU...GCGCU__________UU________CCCUU...GUG-5'\n_____________\|____________________\|\n_____________89___________________71\n	22 -- 28	79 -- 85	-22.3137 kcal/mol	7.44481 kcal/mol	7.24148 kcal/mol	18 39@LB@ \| \|@LB@5'-AUG...AUGAA UGAAU CAUUU...AUU-3'@LB@ GUGCUGUGCC CACCA@LB@ :\|:\|\|\|:\|\|\| \|\|\|\|\|@LB@ UAUGACGCGG GUGGU@LB@3'-UUU...GCGCU UU CCCUU...GUG-5'@LB@ \| \|@LB@ 89 71@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -22.3137 kcal/mol@LB@Unfolding Energy - mRNA 7.44481 kcal/mol@LB@Unfolding Energy - sRNA 7.24148 kcal/mol@LB@@LB@Position - mRNA 19 -- 38@LB@Position - sRNA 72 -- 88@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 79 -- 85@LB@
45	0.002234	0.1727	b0055	djlA	-13.22	0.033048	207 -- 250	35 -- 76	membrane-anchored DnaK co-chaperone DNA-binding protein	_____________206___________________________________________251\n_____________\|_____________________________________________\|\n5'-GAC...UGCAG_________AA____A_____GUG_______CCUUAC________CGGCG...UUG-3'\n______________UAUUGGGGA__AAUC_UUGGC___GCCGUGG_______UGAUGGG\n______________:\|:::\|\|\|\|__\|\|\|\|_\|\|\|\|\|___\|\|\|\|\|::_______\|\|\|\|\|:\|\n______________GUGGUCCCU__UUAG_AACCG___CGGCAUU_______ACUACUC\n3'-UUU...CGGUU_____________________ACG_______UAAUAAU_______AAUGU...GUG-5'\n_____________\|_____________________________________________\|\n_____________77____________________________________________34\n	244 -- 250	35 -- 41	-37.823 kcal/mol	15.2445 kcal/mol	9.3594 kcal/mol	206 251@LB@ \| \|@LB@5'-GAC...UGCAG AA A GUG CCUUAC CGGCG...UUG-3'@LB@ UAUUGGGGA AAUC UUGGC GCCGUGG UGAUGGG@LB@ :\|:::\|\|\|\| \|\|\|\| \|\|\|\|\| \|\|\|\|\|:: \|\|\|\|\|:\|@LB@ GUGGUCCCU UUAG AACCG CGGCAUU ACUACUC@LB@3'-UUU...CGGUU ACG UAAUAAU AAUGU...GUG-5'@LB@ \| \|@LB@ 77 34@LB@@LB@@LB@Energy -13.22 kcal/mol@LB@Hybridization Energy -37.823 kcal/mol@LB@Unfolding Energy - mRNA 15.2445 kcal/mol@LB@Unfolding Energy - sRNA 9.3594 kcal/mol@LB@@LB@Position - mRNA 207 -- 250@LB@Position - sRNA 35 -- 76@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 35 -- 41@LB@
46	0.002359	0.1727	b4139	aspA	-15.43	0.012067	239 -- 273	37 -- 76	aspartate ammonia-lyase	_____________238_______________________________________274\n_____________\|_________________________________________\|\n5'-GAU...UUGGG_____________CCA____A____________C_______UUCAC...ACU-3'\n______________UACCAGGGAAGUU___GCUG_UGCC______UA_UAUGGUG\n______________:\|\|\|\|\|\|\|\|\|:\|:___\|\|\|\|_:\|\|\|______\|\|_\|\|\|\|:\|\|\n______________GUGGUCCCUUUAG___CGAC_GCGG______AU_AUACUAC\n3'-UUU...CGGUU_____________AAC_________CAUUUA__A_______UCAAU...GUG-5'\n_____________\|_________________________________________\|\n_____________77________________________________________36\n	267 -- 273	37 -- 43	-35.8845 kcal/mol	11.095 kcal/mol	9.35931 kcal/mol	238 274@LB@ \| \|@LB@5'-GAU...UUGGG CCA A C UUCAC...ACU-3'@LB@ UACCAGGGAAGUU GCUG UGCC UA UAUGGUG@LB@ :\|\|\|\|\|\|\|\|\|:\|: \|\|\|\| :\|\|\| \|\| \|\|\|\|:\|\|@LB@ GUGGUCCCUUUAG CGAC GCGG AU AUACUAC@LB@3'-UUU...CGGUU AAC CAUUUA A UCAAU...GUG-5'@LB@ \| \|@LB@ 77 36@LB@@LB@@LB@Energy -15.43 kcal/mol@LB@Hybridization Energy -35.8845 kcal/mol@LB@Unfolding Energy - mRNA 11.095 kcal/mol@LB@Unfolding Energy - sRNA 9.35931 kcal/mol@LB@@LB@Position - mRNA 239 -- 273@LB@Position - sRNA 37 -- 76@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 37 -- 43@LB@
47	0.002359	0.1727	b1520	yneE	-16.33	0.007995	225 -- 237	50 -- 62	bestrophin family putative inner membrane protein	_____________224___________238\n_____________\|_____________\|\n5'-CGU...AACAC_____________UUUUU...UCU-3'\n______________UGGCUGCGCCGUA\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________ACCGACGCGGCAU\n3'-UUU...UUAGA_____________UUAAU...GUG-5'\n_____________\|_____________\|\n_____________63____________49\n	231 -- 237	50 -- 56	-27.5123 kcal/mol	5.30923 kcal/mol	5.87004 kcal/mol	224 238@LB@ \| \|@LB@5'-CGU...AACAC UUUUU...UCU-3'@LB@ UGGCUGCGCCGUA@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ ACCGACGCGGCAU@LB@3'-UUU...UUAGA UUAAU...GUG-5'@LB@ \| \|@LB@ 63 49@LB@@LB@@LB@Energy -16.33 kcal/mol@LB@Hybridization Energy -27.5123 kcal/mol@LB@Unfolding Energy - mRNA 5.30923 kcal/mol@LB@Unfolding Energy - sRNA 5.87004 kcal/mol@LB@@LB@Position - mRNA 225 -- 237@LB@Position - sRNA 50 -- 62@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 50 -- 56@LB@
48	0.002388	0.1727	b2198	ccmD	-12.59	0.043972	250 -- 282	36 -- 77	cytochrome c biogenesis protein; heme export ABC transporter holo-CcmE release factor	_____________249________________________________________283\n_____________\|__________________________________________\|\n5'-UGG...CGGUU_____UUUUUU_____________G_________________CCGUU...UGG-3'\n______________ACGCC______GUC_UGGCUG_GC_GUG_______GUGAUGA\n______________\|\|:\|\|______:\|\|_\|\|\|\|\|\|_\|\|_\|\|:_______:\|\|\|\|\|\|\n______________UGUGG______UAG_ACCGAC_CG_CAU_______UACUACU\n3'-UUU...GCGGU_____UCCCUU___A______G__G___UUAAUAA_______CAAUG...GUG-5'\n_____________\|__________________________________________\|\n_____________78_________________________________________35\n	276 -- 282	36 -- 42	-31.2682 kcal/mol	9.31707 kcal/mol	9.36195 kcal/mol	249 283@LB@ \| \|@LB@5'-UGG...CGGUU UUUUUU G CCGUU...UGG-3'@LB@ ACGCC GUC UGGCUG GC GUG GUGAUGA@LB@ \|\|:\|\| :\|\| \|\|\|\|\|\| \|\| \|\|: :\|\|\|\|\|\|@LB@ UGUGG UAG ACCGAC CG CAU UACUACU@LB@3'-UUU...GCGGU UCCCUU A G G UUAAUAA CAAUG...GUG-5'@LB@ \| \|@LB@ 78 35@LB@@LB@@LB@Energy -12.59 kcal/mol@LB@Hybridization Energy -31.2682 kcal/mol@LB@Unfolding Energy - mRNA 9.31707 kcal/mol@LB@Unfolding Energy - sRNA 9.36195 kcal/mol@LB@@LB@Position - mRNA 250 -- 282@LB@Position - sRNA 36 -- 77@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 36 -- 42@LB@
49	0.00252	0.1727	b3452	ugpA	-14.40	0.019328	59 -- 78	52 -- 70	sn-glycerol-3-phosphate ABC transporter permease	_____________58___________________79\n_____________\|____________________\|\n5'-GAG...AGCGU_______AGUU_________CUUUG...CGG-3'\n______________GGAAAUC____GCUGCGCCG\n______________\|\|\|\|\|\|\|____\|\|\|\|\|\|\|\|\|\n______________CCUUUAG____CGACGCGGC\n3'-UUU...UGGUC_______AAC__________AUUUA...GUG-5'\n_____________\|____________________\|\n_____________71___________________51\n	72 -- 78	52 -- 58	-27.9409 kcal/mol	6.69662 kcal/mol	6.84683 kcal/mol	58 79@LB@ \| \|@LB@5'-GAG...AGCGU AGUU CUUUG...CGG-3'@LB@ GGAAAUC GCUGCGCCG@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ CCUUUAG CGACGCGGC@LB@3'-UUU...UGGUC AAC AUUUA...GUG-5'@LB@ \| \|@LB@ 71 51@LB@@LB@@LB@Energy -14.40 kcal/mol@LB@Hybridization Energy -27.9409 kcal/mol@LB@Unfolding Energy - mRNA 6.69662 kcal/mol@LB@Unfolding Energy - sRNA 6.84683 kcal/mol@LB@@LB@Position - mRNA 59 -- 78@LB@Position - sRNA 52 -- 70@LB@Position Seed - mRNA 72 -- 78@LB@Position Seed - sRNA 52 -- 58@LB@
50	0.002535	0.1727	b1879	flhA	-12.13	0.054078	218 -- 247	64 -- 89	putative flagellar export pore protein	_____________217______________________________248\n_____________\|________________________________\|\n5'-GCC...GCCGC___________U__CCGCAA___U________GACAC...CGA-3'\n______________GAUGCUGCGCC_GC______ACC___GAAAUC\n______________:\|\|:\|\|\|\|\|\|\|_:\|______\|\|\|___\|\|\|\|\|\|\n______________UUAUGACGCGG_UG______UGG___CUUUAG\n3'-UUU...CGCGC___________U___________UCC______AACCG...GUG-5'\n_____________\|________________________________\|\n_____________90_______________________________63\n	222 -- 228	79 -- 85	-26.8051 kcal/mol	6.79061 kcal/mol	7.88317 kcal/mol	217 248@LB@ \| \|@LB@5'-GCC...GCCGC U CCGCAA U GACAC...CGA-3'@LB@ GAUGCUGCGCC GC ACC GAAAUC@LB@ :\|\|:\|\|\|\|\|\|\| :\| \|\|\| \|\|\|\|\|\|@LB@ UUAUGACGCGG UG UGG CUUUAG@LB@3'-UUU...CGCGC U UCC AACCG...GUG-5'@LB@ \| \|@LB@ 90 63@LB@@LB@@LB@Energy -12.13 kcal/mol@LB@Hybridization Energy -26.8051 kcal/mol@LB@Unfolding Energy - mRNA 6.79061 kcal/mol@LB@Unfolding Energy - sRNA 7.88317 kcal/mol@LB@@LB@Position - mRNA 218 -- 247@LB@Position - sRNA 64 -- 89@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 79 -- 85@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

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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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