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
97	0.002994	0.1087	b1452	yncE	-13.85	0.010262	151 -- 196	50 -- 89	ATP-binding protein periplasmic function unknown	_____________150_______________________________________________197\n_____________\|_________________________________________________\|\n5'-AUG...GCUUA_____GC_______AA______CAAAAAUAUC______UC_________CGUCA...AAA-3'\n______________GCGAA___AUUGUG____GCAG__________GGUUCA__AAAGGGAGU\n______________:\|\|\|\|___\|\|\|\|\|\|____\|\|\|\|__________::\|\|\|\|__\|\|\|\|\|:\|\|\|\n______________UGCUU___UAACAC____CGUC__________UUAAGU__UUUCCUUCA\n3'-UUU...CAGCA_____AGU______GAUA____A_______________UU_________UUCUG...ACG-5'\n_____________\|_________________________________________________\|\n_____________90________________________________________________49\n	190 -- 196	50 -- 56	-28.7036 kcal/mol	10.1778 kcal/mol	4.68197 kcal/mol	150 197@LB@ \| \|@LB@5'-AUG...GCUUA GC AA CAAAAAUAUC UC CGUCA...AAA-3'@LB@ GCGAA AUUGUG GCAG GGUUCA AAAGGGAGU@LB@ :\|\|\|\| \|\|\|\|\|\| \|\|\|\| ::\|\|\|\| \|\|\|\|\|:\|\|\|@LB@ UGCUU UAACAC CGUC UUAAGU UUUCCUUCA@LB@3'-UUU...CAGCA AGU GAUA A UU UUCUG...ACG-5'@LB@ \| \|@LB@ 90 49@LB@@LB@@LB@Energy -13.85 kcal/mol@LB@Hybridization Energy -28.7036 kcal/mol@LB@Unfolding Energy - mRNA 10.1778 kcal/mol@LB@Unfolding Energy - sRNA 4.68197 kcal/mol@LB@@LB@Position - mRNA 151 -- 196@LB@Position - sRNA 50 -- 89@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 50 -- 56@LB@
112	0.003634	0.1131	b1473	yddG	-8.08	0.286569	177 -- 226	24 -- 55	aromatic amino acid exporter	_____________176________________________________________________227\n_____________\|__________________________________________________\|\n5'-GCG...UUAAC__C___A_______AACA_C____AUGACACGACAAAAA___________AGGGC...CGG-3'\n______________GG_AAG_GAGACAA____G_GAGC_______________GCAACGCUCAU\n______________\|\|_\|\|\|_:\|\|\|\|\|\|____\|_\|\|\|\|_______________\|\|\|\|\|\|\|:\|\|\|\n______________CC_UUC_UUCUGUU____C_CUCG_______________CGUUGCGGGUA\n3'-UUU...UUUUU______A_______AUA_________________________________GCGAA...ACG-5'\n_____________\|__________________________________________________\|\n_____________56_________________________________________________23\n	216 -- 222	28 -- 34	-30.4707 kcal/mol	9.38627 kcal/mol	13.0079 kcal/mol	176 227@LB@ \| \|@LB@5'-GCG...UUAAC C A AACA C AUGACACGACAAAAA AGGGC...CGG-3'@LB@ GG AAG GAGACAA G GAGC GCAACGCUCAU@LB@ \|\| \|\|\| :\|\|\|\|\|\| \| \|\|\|\| \|\|\|\|\|\|\|:\|\|\|@LB@ CC UUC UUCUGUU C CUCG CGUUGCGGGUA@LB@3'-UUU...UUUUU A AUA GCGAA...ACG-5'@LB@ \| \|@LB@ 56 23@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -30.4707 kcal/mol@LB@Unfolding Energy - mRNA 9.38627 kcal/mol@LB@Unfolding Energy - sRNA 13.0079 kcal/mol@LB@@LB@Position - mRNA 177 -- 226@LB@Position - sRNA 24 -- 55@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 28 -- 34@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@
41	0.0003478	0.02948	b1478	adhP	-14.79	0.005262	167 -- 196	51 -- 77	ethanol-active dehydrogenase/acetaldehyde-active reductase	_____________166____________________________197\n_____________\|______________________________\|\n5'-GCA...UCACC__________AACA___UCC__________AACUA...GUU-3'\n______________UGCUAUGCAG____UCA___GAAAAGGAGG\n______________\|\|\|\|\|\|\|\|\|\|____\|\|\|___:\|\|\|\|\|\|\|:\|\n______________ACGAUACGUC____AGU___UUUUUCCUUC\n3'-UUU...UUAAC__________AUUA________________AUUCU...ACG-5'\n_____________\|______________________________\|\n_____________78_____________________________50\n	190 -- 196	51 -- 57	-28.1635 kcal/mol	8.82843 kcal/mol	4.54711 kcal/mol	166 197@LB@ \| \|@LB@5'-GCA...UCACC AACA UCC AACUA...GUU-3'@LB@ UGCUAUGCAG UCA GAAAAGGAGG@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\| :\|\|\|\|\|\|\|:\|@LB@ ACGAUACGUC AGU UUUUUCCUUC@LB@3'-UUU...UUAAC AUUA AUUCU...ACG-5'@LB@ \| \|@LB@ 78 50@LB@@LB@@LB@Energy -14.79 kcal/mol@LB@Hybridization Energy -28.1635 kcal/mol@LB@Unfolding Energy - mRNA 8.82843 kcal/mol@LB@Unfolding Energy - sRNA 4.54711 kcal/mol@LB@@LB@Position - mRNA 167 -- 196@LB@Position - sRNA 51 -- 77@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 51 -- 57@LB@
65	0.001098	0.05953	b1479	maeA	-10.62	0.077885	180 -- 205	37 -- 65	malate dehydrogenase decarboxylating NAD-requiring; malic enzyme	_____________179___________________________206\n_____________\|_____________________________\|\n5'-UAG...UGGAU_______________________C_____ACCAA...GCA-3'\n______________AUUCAAAAAAG__AGUGAG_UGA_AUGGA\n______________\|\|\|\|\|\|\|\|\|\|\|__\|\|\|:\|\|_::\|_\|\|\|\|\|\n______________UAAGUUUUUUC__UCAUUC_GUU_UACCU\n3'-UUU...GUCAU___________CU______U___A_____CGCGU...ACG-5'\n_____________\|_____________________________\|\n_____________66____________________________36\n	184 -- 190	55 -- 61	-21.4117 kcal/mol	4.89609 kcal/mol	5.88101 kcal/mol	179 206@LB@ \| \|@LB@5'-UAG...UGGAU C ACCAA...GCA-3'@LB@ AUUCAAAAAAG AGUGAG UGA AUGGA@LB@ \|\|\|\|\|\|\|\|\|\|\| \|\|\|:\|\| ::\| \|\|\|\|\|@LB@ UAAGUUUUUUC UCAUUC GUU UACCU@LB@3'-UUU...GUCAU CU U A CGCGU...ACG-5'@LB@ \| \|@LB@ 66 36@LB@@LB@@LB@Energy -10.62 kcal/mol@LB@Hybridization Energy -21.4117 kcal/mol@LB@Unfolding Energy - mRNA 4.89609 kcal/mol@LB@Unfolding Energy - sRNA 5.88101 kcal/mol@LB@@LB@Position - mRNA 180 -- 205@LB@Position - sRNA 37 -- 65@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 55 -- 61@LB@
134	0.004994	0.1313	b1518	lsrG	-14.53	0.006358	14 -- 66	30 -- 79	autoinducer-2 (AI-2) degrading protein LsrG	_____________13_______________________________________________________67\n_____________\|________________________________________________________\|\n5'-GAG...GGAAA____________GCUA____UC____CGCUUCU____UG_________________AUUUU...AAG-3'\n______________UGUGCUG_GCAG____UCGA__AGGG_______GGUG____GAUAUGGGGCGUAAU\n______________\|\|\|\|\|\|:_\|\|\|\|____\|\|:\|__\|:\|\|_______:\|\|:____:\|\|\|\|\|\|:\|\|\|:\|\|:\n______________ACACGAU_CGUC____AGUU__UUCC_______UCAU____UUAUACCUCGCGUUG\n3'-UUU...AGUUA_______A____AUUA____UU____U__________UCUG_______________CGGGU...ACG-5'\n_____________\|________________________________________________________\|\n_____________80_______________________________________________________29\n	58 -- 64	32 -- 38	-43.6874 kcal/mol	15.7058 kcal/mol	13.4555 kcal/mol	13 67@LB@ \| \|@LB@5'-GAG...GGAAA GCUA UC CGCUUCU UG AUUUU...AAG-3'@LB@ UGUGCUG GCAG UCGA AGGG GGUG GAUAUGGGGCGUAAU@LB@ \|\|\|\|\|\|: \|\|\|\| \|\|:\| \|:\|\| :\|\|: :\|\|\|\|\|\|:\|\|\|:\|\|:@LB@ ACACGAU CGUC AGUU UUCC UCAU UUAUACCUCGCGUUG@LB@3'-UUU...AGUUA A AUUA UU U UCUG CGGGU...ACG-5'@LB@ \| \|@LB@ 80 29@LB@@LB@@LB@Energy -14.53 kcal/mol@LB@Hybridization Energy -43.6874 kcal/mol@LB@Unfolding Energy - mRNA 15.7058 kcal/mol@LB@Unfolding Energy - sRNA 13.4555 kcal/mol@LB@@LB@Position - mRNA 14 -- 66@LB@Position - sRNA 30 -- 79@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 32 -- 38@LB@
7	8.167e-06	0.003921	b1531	marA	-12.70	0.022098	183 -- 204	40 -- 62	multiple antibiotic resistance transcriptional regulator	_____________182_____________________205\n_____________\|_______________________\|\n5'-AAG...GUAAA______________U________CCAGA...AGC-3'\n______________CAAAAAA_GAGGUA_GACGAUGU\n______________\|\|\|\|\|\|\|_\|\|:\|\|\|_\|\|\|:\|\|:\|\n______________GUUUUUU_CUUCAU_CUGUUAUA\n3'-UUU...AUUAA_______C______U________CCUCG...ACG-5'\n_____________\|_______________________\|\n_____________63______________________39\n	198 -- 204	40 -- 46	-19.9636 kcal/mol	3.18051 kcal/mol	4.08673 kcal/mol	182 205@LB@ \| \|@LB@5'-AAG...GUAAA U CCAGA...AGC-3'@LB@ CAAAAAA GAGGUA GACGAUGU@LB@ \|\|\|\|\|\|\| \|\|:\|\|\| \|\|\|:\|\|:\|@LB@ GUUUUUU CUUCAU CUGUUAUA@LB@3'-UUU...AUUAA C U CCUCG...ACG-5'@LB@ \| \|@LB@ 63 39@LB@@LB@@LB@Energy -12.70 kcal/mol@LB@Hybridization Energy -19.9636 kcal/mol@LB@Unfolding Energy - mRNA 3.18051 kcal/mol@LB@Unfolding Energy - sRNA 4.08673 kcal/mol@LB@@LB@Position - mRNA 183 -- 204@LB@Position - sRNA 40 -- 62@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 40 -- 46@LB@
96	0.002937	0.1078	b1539	ydfG	-11.63	0.043083	159 -- 205	42 -- 78	NADP-dependent 3-hydroxy acid dehydrogenase; malonic semialdehyde reductase	_____________158_____________________________________________206\n_____________\|_______________________________________________\|\n5'-GAU...AUCCC_________UAUUGACACA_____GCGUU_____AC___________CGUUU...GCC-3'\n______________GUGCUAUGU__________CAAAA_____GAGGA__AGUGAGAUGAU\n______________\|\|\|\|\|\|\|\|:__________\|\|\|\|\|_____:\|\|\|\|__\|\|\|:\|\|\|::\|\|\n______________CACGAUACG__________GUUUU_____UUCCU__UCAUUCUGUUA\n3'-UUU...GUUAA_________UCAUUAA_______________________________UACCU...ACG-5'\n_____________\|_______________________________________________\|\n_____________79______________________________________________41\n	199 -- 205	42 -- 48	-28.6775 kcal/mol	11.4217 kcal/mol	5.62659 kcal/mol	158 206@LB@ \| \|@LB@5'-GAU...AUCCC UAUUGACACA GCGUU AC CGUUU...GCC-3'@LB@ GUGCUAUGU CAAAA GAGGA AGUGAGAUGAU@LB@ \|\|\|\|\|\|\|\|: \|\|\|\|\| :\|\|\|\| \|\|\|:\|\|\|::\|\|@LB@ CACGAUACG GUUUU UUCCU UCAUUCUGUUA@LB@3'-UUU...GUUAA UCAUUAA UACCU...ACG-5'@LB@ \| \|@LB@ 79 41@LB@@LB@@LB@Energy -11.63 kcal/mol@LB@Hybridization Energy -28.6775 kcal/mol@LB@Unfolding Energy - mRNA 11.4217 kcal/mol@LB@Unfolding Energy - sRNA 5.62659 kcal/mol@LB@@LB@Position - mRNA 159 -- 205@LB@Position - sRNA 42 -- 78@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 42 -- 48@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@
147	0.005701	0.1366	b1622	malY	-7.52	0.364460	44 -- 91	35 -- 85	PLP-dependent beta-cystathionase and maltose regulon regulator	_____________43____________________________________________________92\n_____________\|_____________________________________________________\|\n5'-UCG...GAUAU____C____UAA_______GCACU__________CAAUC___________C__AGUAC...UCA-3'\n______________GUCG_UUGU___UGUGCAG_________GAAGGA_____GGGCAAU_UGG_GU\n______________:\|\|:_\|\|\|\|___\|:\|\|\|\|\|_________:\|\|\|\|\|_____:\|:\|\|\|\|_\|\|\|_\|:\n______________UAGU_AACA___AUACGUC_________UUUCCU_____UCUGUUA_ACC_CG\n3'-UUU...AUGCU____U____CG________AUUAAGUUU______UCAU________U___U__CGUUG...ACG-5'\n_____________\|_____________________________________________________\|\n_____________86____________________________________________________34\n	79 -- 85	42 -- 48	-29.3049 kcal/mol	13.5755 kcal/mol	8.20283 kcal/mol	43 92@LB@ \| \|@LB@5'-UCG...GAUAU C UAA GCACU CAAUC C AGUAC...UCA-3'@LB@ GUCG UUGU UGUGCAG GAAGGA GGGCAAU UGG GU@LB@ :\|\|: \|\|\|\| \|:\|\|\|\|\| :\|\|\|\|\| :\|:\|\|\|\| \|\|\| \|:@LB@ UAGU AACA AUACGUC UUUCCU UCUGUUA ACC CG@LB@3'-UUU...AUGCU U CG AUUAAGUUU UCAU U U CGUUG...ACG-5'@LB@ \| \|@LB@ 86 34@LB@@LB@@LB@Energy -7.52 kcal/mol@LB@Hybridization Energy -29.3049 kcal/mol@LB@Unfolding Energy - mRNA 13.5755 kcal/mol@LB@Unfolding Energy - sRNA 8.20283 kcal/mol@LB@@LB@Position - mRNA 44 -- 91@LB@Position - sRNA 35 -- 85@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 42 -- 48@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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