Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
90	0.002477	0.09689	b4020	yjbB	-17.01	0.000941	168 -- 222	1 -- 56	putative Na+/Pi-cotransporter	_____________167________________________________________________________223\n_____________\|__________________________________________________________\|\n5'-UCC...GCUUC_____CA__UA______A____AACC___AA______GUUA___C_____________UUUCU...UGC-3'\n______________AGGAA__UA__ACGAUA_GGAG_____UG__C_UCGU____ACG_UGC_UUCACCUGC\n______________\|\|\|\|\|__\|\|__\|\|:\|\|\|_\|\|\|\|_____:\|__\|_\|\|\|:____\|\|\|_\|\|\|_\|\|\|\|\|\|\|\|\|\n______________UCCUU__AU__UGUUAU_CCUC_____GC__G_AGCG____UGC_ACG_AAGUGGACG\n3'-UUU...UUUUU_____C___UC______A____GCGUU__GG_U____AAC____A___U_________-5'\n_____________\|_________________________________________________________\|\n_____________57________________________________________________________1\n	216 -- 222	1 -- 7	-44.3986 kcal/mol	10.5518 kcal/mol	16.8439 kcal/mol	167 223@LB@ \| \|@LB@5'-UCC...GCUUC CA UA A AACC AA GUUA C UUUCU...UGC-3'@LB@ AGGAA UA ACGAUA GGAG UG C UCGU ACG UGC UUCACCUGC@LB@ \|\|\|\|\| \|\| \|\|:\|\|\| \|\|\|\| :\| \| \|\|\|: \|\|\| \|\|\| \|\|\|\|\|\|\|\|\|@LB@ UCCUU AU UGUUAU CCUC GC G AGCG UGC ACG AAGUGGACG@LB@3'-UUU...UUUUU C UC A GCGUU GG U AAC A U -5'@LB@ \| \|@LB@ 57 1@LB@@LB@@LB@Energy -17.01 kcal/mol@LB@Hybridization Energy -44.3986 kcal/mol@LB@Unfolding Energy - mRNA 10.5518 kcal/mol@LB@Unfolding Energy - sRNA 16.8439 kcal/mol@LB@@LB@Position - mRNA 168 -- 222@LB@Position - sRNA 1 -- 56@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 1 -- 7@LB@
83	0.001966	0.08273	b1584	speG	-9.79	0.123144	169 -- 214	25 -- 77	spermidine N(1)-acetyltransferase	_____________168_____________________________________________________215\n_____________\|_______________________________________________________\|\n5'-UCU...UAACC__________________________U____G____CGUUAU___CA________CAGUG...GGU-3'\n______________UGUUAU____UGAUUUA____AGGAA_GUAA_GACA_______GC__AGCGCCCA\n______________\|\|:\|\|\|____\|:\|\|\|:\|____\|\|\|\|\|_\|\|\|\|_\|\|\|\|_______\|\|__\|:\|\|\|\|\|\|\n______________ACGAUA____AUUAAGU____UCCUU_CAUU_CUGU_______CG__UUGCGGGU\n3'-UUU...UUAAC______CGUC_______UUUU_______________UAUACCU__CG________AGCGA...ACG-5'\n_____________\|_______________________________________________________\|\n_____________78______________________________________________________24\n	208 -- 214	25 -- 31	-32.6914 kcal/mol	9.23779 kcal/mol	13.6641 kcal/mol	168 215@LB@ \| \|@LB@5'-UCU...UAACC U G CGUUAU CA CAGUG...GGU-3'@LB@ UGUUAU UGAUUUA AGGAA GUAA GACA GC AGCGCCCA@LB@ \|\|:\|\|\| \|:\|\|\|:\| \|\|\|\|\| \|\|\|\| \|\|\|\| \|\| \|:\|\|\|\|\|\|@LB@ ACGAUA AUUAAGU UCCUU CAUU CUGU CG UUGCGGGU@LB@3'-UUU...UUAAC CGUC UUUU UAUACCU CG AGCGA...ACG-5'@LB@ \| \|@LB@ 78 24@LB@@LB@@LB@Energy -9.79 kcal/mol@LB@Hybridization Energy -32.6914 kcal/mol@LB@Unfolding Energy - mRNA 9.23779 kcal/mol@LB@Unfolding Energy - sRNA 13.6641 kcal/mol@LB@@LB@Position - mRNA 169 -- 214@LB@Position - sRNA 25 -- 77@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 25 -- 31@LB@
15	2.607e-05	0.006123	b2552	hmp	-15.14	0.004063	170 -- 224	20 -- 85	fused nitric oxide dioxygenase/dihydropteridine reductase 2	_____________169___________________________________________________________________225\n_____________\|_____________________________________________________________________\|\n5'-AUU...GAUAC_______AAG_______________________________C_____CUU______UCAAA________ACAGU...UUA-3'\n______________AUCAAUU_____AUGCA_______AAAAAAGGA____AGAC_AUAUG___GA_CGC_____CCAUCGCU\n______________\|\|\|\|\|\|\|_____\|\|\|\|\|_______\|\|\|\|\|\|\|\|\|____\|\|\|\|_\|\|\|\|\|___\|\|_\|\|\|_____\|\|\|\|\|\|\|\|\n______________UAGUUAA_____UACGU_______UUUUUUCCU____UCUG_UAUAC___CU_GCG_____GGUAGCGA\n3'-UUU...AUGCU_______CACGA_____CAUUAAG_________UCAU____U__________C___UUGCG________ACUGC...ACG-5'\n_____________\|_____________________________________________________________________\|\n_____________86____________________________________________________________________19\n	218 -- 224	20 -- 26	-42.0201 kcal/mol	9.32625 kcal/mol	17.5545 kcal/mol	169 225@LB@ \| \|@LB@5'-AUU...GAUAC AAG C CUU UCAAA ACAGU...UUA-3'@LB@ AUCAAUU AUGCA AAAAAAGGA AGAC AUAUG GA CGC CCAUCGCU@LB@ \|\|\|\|\|\|\| \|\|\|\|\| \|\|\|\|\|\|\|\|\| \|\|\|\| \|\|\|\|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ UAGUUAA UACGU UUUUUUCCU UCUG UAUAC CU GCG GGUAGCGA@LB@3'-UUU...AUGCU CACGA CAUUAAG UCAU U C UUGCG ACUGC...ACG-5'@LB@ \| \|@LB@ 86 19@LB@@LB@@LB@Energy -15.14 kcal/mol@LB@Hybridization Energy -42.0201 kcal/mol@LB@Unfolding Energy - mRNA 9.32625 kcal/mol@LB@Unfolding Energy - sRNA 17.5545 kcal/mol@LB@@LB@Position - mRNA 170 -- 224@LB@Position - sRNA 20 -- 85@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 20 -- 26@LB@
23	8.752e-05	0.01341	b1476	fdnI	-10.32	0.092280	170 -- 193	36 -- 57	formate dehydrogenase-N cytochrome B556 (gamma) subunit nitrate-inducible	_____________169_______________________194\n_____________\|_________________________\|\n5'-CGU...CGAAU_________________ACGA____GAUCA...UUU-3'\n______________AAGGAAGU_GGACGAUG____GGAG\n______________\|\|\|\|\|\|\|\|_:\|\|\|:\|\|:____\|\|\|\|\n______________UUCCUUCA_UCUGUUAU____CCUC\n3'-UUU...GUUUU________U________A_______GCGUU...ACG-5'\n_____________\|_________________________\|\n_____________58________________________35\n	179 -- 185	41 -- 47	-22.1274 kcal/mol	8.02585 kcal/mol	3.74338 kcal/mol	169 194@LB@ \| \|@LB@5'-CGU...CGAAU ACGA GAUCA...UUU-3'@LB@ AAGGAAGU GGACGAUG GGAG@LB@ \|\|\|\|\|\|\|\| :\|\|\|:\|\|: \|\|\|\|@LB@ UUCCUUCA UCUGUUAU CCUC@LB@3'-UUU...GUUUU U A GCGUU...ACG-5'@LB@ \| \|@LB@ 58 35@LB@@LB@@LB@Energy -10.32 kcal/mol@LB@Hybridization Energy -22.1274 kcal/mol@LB@Unfolding Energy - mRNA 8.02585 kcal/mol@LB@Unfolding Energy - sRNA 3.74338 kcal/mol@LB@@LB@Position - mRNA 170 -- 193@LB@Position - sRNA 36 -- 57@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 41 -- 47@LB@
121	0.004137	0.1205	b0353	mhpT	-11.58	0.044392	170 -- 179	1 -- 10	3-hydroxyphenylpropionic transporter	_____________169________180\n_____________\|__________\|\n5'-CGG...UCGCG__________ACUCG...CGG-3'\n______________AUUCACCUGC\n______________\|\|\|\|\|\|\|\|\|\|\n______________UAAGUGGACG\n3'-UUU...CAACG__________-5'\n_____________\|_________\|\n_____________11________1\n	173 -- 179	1 -- 7	-16.6324 kcal/mol	2.26547 kcal/mol	2.7891 kcal/mol	169 180@LB@ \| \|@LB@5'-CGG...UCGCG ACUCG...CGG-3'@LB@ AUUCACCUGC@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UAAGUGGACG@LB@3'-UUU...CAACG -5'@LB@ \| \|@LB@ 11 1@LB@@LB@@LB@Energy -11.58 kcal/mol@LB@Hybridization Energy -16.6324 kcal/mol@LB@Unfolding Energy - mRNA 2.26547 kcal/mol@LB@Unfolding Energy - sRNA 2.7891 kcal/mol@LB@@LB@Position - mRNA 170 -- 179@LB@Position - sRNA 1 -- 10@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 1 -- 7@LB@
131	0.004841	0.1302	b3242	aaeX	-9.57	0.138370	170 -- 176	1 -- 7	DUF1656 family putative inner membrane efflux pump associated protein	_____________169_____177\n_____________\|_______\|\n5'-GCG...AAUAA_______UCUCU...GGG-3'\n______________CGCCUGC\n______________\|:\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	170 -- 176	1 -- 7	-12.9142 kcal/mol	1.00865 kcal/mol	2.34039 kcal/mol	169 177@LB@ \| \|@LB@5'-GCG...AAUAA UCUCU...GGG-3'@LB@ CGCCUGC@LB@ \|:\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.57 kcal/mol@LB@Hybridization Energy -12.9142 kcal/mol@LB@Unfolding Energy - mRNA 1.00865 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 170 -- 176@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 1 -- 7@LB@
157	0.006139	0.1377	b2347	yfdC	-9.29	0.160067	171 -- 205	37 -- 76	putative inner membrane protein	_____________170________________________________________206\n_____________\|__________________________________________\|\n5'-GCA...CUUUA_____AC___C_______________________C_______CAACG...UCC-3'\n______________GCUAU__GUG_UAAUUCAAGA___GAAG__AGAC___AUGGA\n______________\|\|\|\|\|__\|::_\|\|\|\|\|\|\|\|:\|___\|\|\|\|__\|\|\|\|___\|\|\|\|\|\n______________CGAUA__CGU_AUUAAGUUUU___CUUC__UCUG___UACCU\n3'-UUU...UAACA__________C__________UUC____AU____UUA_____CGCGU...ACG-5'\n_____________\|__________________________________________\|\n_____________77_________________________________________36\n	185 -- 191	58 -- 64	-24.5838 kcal/mol	7.63937 kcal/mol	7.64142 kcal/mol	170 206@LB@ \| \|@LB@5'-GCA...CUUUA AC C C CAACG...UCC-3'@LB@ GCUAU GUG UAAUUCAAGA GAAG AGAC AUGGA@LB@ \|\|\|\|\| \|:: \|\|\|\|\|\|\|\|:\| \|\|\|\| \|\|\|\| \|\|\|\|\|@LB@ CGAUA CGU AUUAAGUUUU CUUC UCUG UACCU@LB@3'-UUU...UAACA C UUC AU UUA CGCGU...ACG-5'@LB@ \| \|@LB@ 77 36@LB@@LB@@LB@Energy -9.29 kcal/mol@LB@Hybridization Energy -24.5838 kcal/mol@LB@Unfolding Energy - mRNA 7.63937 kcal/mol@LB@Unfolding Energy - sRNA 7.64142 kcal/mol@LB@@LB@Position - mRNA 171 -- 205@LB@Position - sRNA 37 -- 76@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 58 -- 64@LB@
18	4.045e-05	0.007917	b0723	sdhA	-14.73	0.005501	172 -- 195	67 -- 90	succinate dehydrogenase flavoprotein subunit	_____________171______________________196\n_____________\|________________________\|\n5'-GGU...UGAUU________C______G____G___GUGUG...GUG-3'\n______________UAUGGAUU_GUUGUG_UGUG_GGU\n______________\|\|:\|:\|\|:_:\|\|\|\|\|_\|:\|\|_:\|\|\n______________AUGCUUAG_UAACAC_AUAC_UCA\n3'-UUU...GCAGC________U______G____G___UUAAG...ACG-5'\n_____________\|________________________\|\n_____________91_______________________66\n	173 -- 179	83 -- 89	-23.9499 kcal/mol	4.69238 kcal/mol	4.5307 kcal/mol	171 196@LB@ \| \|@LB@5'-GGU...UGAUU C G G GUGUG...GUG-3'@LB@ UAUGGAUU GUUGUG UGUG GGU@LB@ \|\|:\|:\|\|: :\|\|\|\|\| \|:\|\| :\|\|@LB@ AUGCUUAG UAACAC AUAC UCA@LB@3'-UUU...GCAGC U G G UUAAG...ACG-5'@LB@ \| \|@LB@ 91 66@LB@@LB@@LB@Energy -14.73 kcal/mol@LB@Hybridization Energy -23.9499 kcal/mol@LB@Unfolding Energy - mRNA 4.69238 kcal/mol@LB@Unfolding Energy - sRNA 4.5307 kcal/mol@LB@@LB@Position - mRNA 172 -- 195@LB@Position - sRNA 67 -- 90@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 83 -- 89@LB@
177	0.007289	0.1451	b4002	zraP	-14.65	0.005839	172 -- 192	36 -- 54	Zn-dependent periplasmic chaperone	_____________171___________________193\n_____________\|_____________________\|\n5'-AAU...UACCC____________CCAC_____GAUUA...GGC-3'\n______________GAAGUAAGACAA____UGGAG\n______________\|\|\|\|\|\|\|\|\|\|\|\|____\|\|\|\|\|\n______________CUUCAUUCUGUU____ACCUC\n3'-UUU...UUUUC____________AU_______GCGUU...ACG-5'\n_____________\|_____________________\|\n_____________55____________________35\n	177 -- 183	43 -- 49	-21.9873 kcal/mol	3.76916 kcal/mol	3.53499 kcal/mol	171 193@LB@ \| \|@LB@5'-AAU...UACCC CCAC GAUUA...GGC-3'@LB@ GAAGUAAGACAA UGGAG@LB@ \|\|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ CUUCAUUCUGUU ACCUC@LB@3'-UUU...UUUUC AU GCGUU...ACG-5'@LB@ \| \|@LB@ 55 35@LB@@LB@@LB@Energy -14.65 kcal/mol@LB@Hybridization Energy -21.9873 kcal/mol@LB@Unfolding Energy - mRNA 3.76916 kcal/mol@LB@Unfolding Energy - sRNA 3.53499 kcal/mol@LB@@LB@Position - mRNA 172 -- 192@LB@Position - sRNA 36 -- 54@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 43 -- 49@LB@
44	0.0004181	0.03347	b3429	glgA	-12.00	0.034422	173 -- 196	35 -- 55	glycogen synthase	_____________172______________________197\n_____________\|________________________\|\n5'-GUA...GCUAC_____U_______UAAACA_____GAUAA...ACG-3'\n______________GGAAG_UAGGGCA______GGAGC\n______________\|\|\|\|\|_\|\|:\|:\|\|______\|\|\|\|\|\n______________CCUUC_AUUCUGU______CCUCG\n3'-UUU...UUUUU_____________UAUA_______CGUUG...ACG-5'\n_____________\|________________________\|\n_____________56_______________________34\n	179 -- 185	44 -- 50	-21.7083 kcal/mol	5.57994 kcal/mol	4.0932 kcal/mol	172 197@LB@ \| \|@LB@5'-GUA...GCUAC U UAAACA GAUAA...ACG-3'@LB@ GGAAG UAGGGCA GGAGC@LB@ \|\|\|\|\| \|\|:\|:\|\| \|\|\|\|\|@LB@ CCUUC AUUCUGU CCUCG@LB@3'-UUU...UUUUU UAUA CGUUG...ACG-5'@LB@ \| \|@LB@ 56 34@LB@@LB@@LB@Energy -12.00 kcal/mol@LB@Hybridization Energy -21.7083 kcal/mol@LB@Unfolding Energy - mRNA 5.57994 kcal/mol@LB@Unfolding Energy - sRNA 4.0932 kcal/mol@LB@@LB@Position - mRNA 173 -- 196@LB@Position - sRNA 35 -- 55@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 44 -- 50@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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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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