Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
64	0.01278	0.5385	b1718	infC	-10.82	0.076139	1 -- 9	71 -- 79	translation initiation factor IF-3	______________1________10\n______________\|________\|\n___________5'-_________AAAUC...AGC-3'\n______________UUGGCUUUA\n______________\|\|\|\|\|\|\|\|\|\n______________AACCGAAAU\n3'-CGC...AGUGC_________CAAUA...AAG-5'\n_____________\|_________\|\n_____________80________70\n	3 -- 9	71 -- 77	-11.2516 kcal/mol	0.206511 kcal/mol	0.222833 kcal/mol	1 10@LB@ \| \|@LB@ 5'- AAAUC...AGC-3'@LB@ UUGGCUUUA@LB@ \|\|\|\|\|\|\|\|\|@LB@ AACCGAAAU@LB@3'-CGC...AGUGC CAAUA...AAG-5'@LB@ \| \|@LB@ 80 70@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -11.2516 kcal/mol@LB@Unfolding Energy - mRNA 0.206511 kcal/mol@LB@Unfolding Energy - sRNA 0.222833 kcal/mol@LB@@LB@Position - mRNA 1 -- 9@LB@Position - sRNA 71 -- 79@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 71 -- 77@LB@
158	0.02721	0.5559	b1724	ydiZ	-8.58	0.183444	272 -- 279	57 -- 64	uncharacterized protein	_____________271______280\n_____________\|________\|\n5'-UUU...AUUAA________AUAAU...ACG-3'\n______________CGAGUUGA\n______________\|\|\|\|\|\|\|\|\n______________GCUCAACU\n3'-CGC...AAUAA________CUUUG...AAG-5'\n_____________\|________\|\n_____________65_______56\n	273 -- 279	57 -- 63	-11.4752 kcal/mol	1.7639 kcal/mol	1.12823 kcal/mol	271 280@LB@ \| \|@LB@5'-UUU...AUUAA AUAAU...ACG-3'@LB@ CGAGUUGA@LB@ \|\|\|\|\|\|\|\|@LB@ GCUCAACU@LB@3'-CGC...AAUAA CUUUG...AAG-5'@LB@ \| \|@LB@ 65 56@LB@@LB@@LB@Energy -8.58 kcal/mol@LB@Hybridization Energy -11.4752 kcal/mol@LB@Unfolding Energy - mRNA 1.7639 kcal/mol@LB@Unfolding Energy - sRNA 1.12823 kcal/mol@LB@@LB@Position - mRNA 272 -- 279@LB@Position - sRNA 57 -- 64@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 57 -- 63@LB@
54	0.01077	0.5385	b1820	yobD	-10.70	0.079862	85 -- 97	73 -- 84	UPF0266 family inner membrane protein	_____________84____________98\n_____________\|_____________\|\n5'-ACC...GUGGA___U_________CUUCG...CCC-3'\n______________UCA_CGUUGGCUU\n______________\|\|\|_\|\|\|\|\|\|\|\|\|\n______________AGU_GCAACCGAA\n3'-CGC...UUUCA_____________AUCAA...AAG-5'\n_____________\|_____________\|\n_____________85____________72\n	91 -- 97	73 -- 79	-16.3135 kcal/mol	5.10116 kcal/mol	0.508835 kcal/mol	84 98@LB@ \| \|@LB@5'-ACC...GUGGA U CUUCG...CCC-3'@LB@ UCA CGUUGGCUU@LB@ \|\|\| \|\|\|\|\|\|\|\|\|@LB@ AGU GCAACCGAA@LB@3'-CGC...UUUCA AUCAA...AAG-5'@LB@ \| \|@LB@ 85 72@LB@@LB@@LB@Energy -10.70 kcal/mol@LB@Hybridization Energy -16.3135 kcal/mol@LB@Unfolding Energy - mRNA 5.10116 kcal/mol@LB@Unfolding Energy - sRNA 0.508835 kcal/mol@LB@@LB@Position - mRNA 85 -- 97@LB@Position - sRNA 73 -- 84@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 73 -- 79@LB@
12	0.002293	0.5385	b1823	cspC	-13.69	0.023618	13 -- 32	14 -- 35	stress protein member of the CspA-family	_____________12_____________________33\n_____________\|______________________\|\n5'-UAU...UAACA________________C_____ACAGU...UCU-3'\n______________GAUUUC__GGGUUAAA_GAGGU\n______________\|\|:\|\|\|__\|\|\|\|\|\|\|\|_\|\|\|\|\|\n______________CUGAAG__CCCAAUUU_CUCCA\n3'-CGC...CGUCA______UU________U_____CGGCG...AAG-5'\n_____________\|______________________\|\n_____________36_____________________13\n	20 -- 26	20 -- 26	-23.8593 kcal/mol	6.83349 kcal/mol	3.33183 kcal/mol	12 33@LB@ \| \|@LB@5'-UAU...UAACA C ACAGU...UCU-3'@LB@ GAUUUC GGGUUAAA GAGGU@LB@ \|\|:\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ CUGAAG CCCAAUUU CUCCA@LB@3'-CGC...CGUCA UU U CGGCG...AAG-5'@LB@ \| \|@LB@ 36 13@LB@@LB@@LB@Energy -13.69 kcal/mol@LB@Hybridization Energy -23.8593 kcal/mol@LB@Unfolding Energy - mRNA 6.83349 kcal/mol@LB@Unfolding Energy - sRNA 3.33183 kcal/mol@LB@@LB@Position - mRNA 13 -- 32@LB@Position - sRNA 14 -- 35@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 20 -- 26@LB@
18	0.003137	0.5385	b1824	yobF	-13.30	0.027752	169 -- 188	14 -- 35	DUF2527 family heat-induced protein	_____________168____________________189\n_____________\|______________________\|\n5'-GCC...UAACA________________C_____ACAGU...UGU-3'\n______________GAUUUC__GGGUUAAA_GAGGU\n______________\|\|:\|\|\|__\|\|\|\|\|\|\|\|_\|\|\|\|\|\n______________CUGAAG__CCCAAUUU_CUCCA\n3'-CGC...CGUCA______UU________U_____CGGCG...AAG-5'\n_____________\|______________________\|\n_____________36_____________________13\n	176 -- 182	20 -- 26	-23.4961 kcal/mol	6.86312 kcal/mol	3.33183 kcal/mol	168 189@LB@ \| \|@LB@5'-GCC...UAACA C ACAGU...UGU-3'@LB@ GAUUUC GGGUUAAA GAGGU@LB@ \|\|:\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ CUGAAG CCCAAUUU CUCCA@LB@3'-CGC...CGUCA UU U CGGCG...AAG-5'@LB@ \| \|@LB@ 36 13@LB@@LB@@LB@Energy -13.30 kcal/mol@LB@Hybridization Energy -23.4961 kcal/mol@LB@Unfolding Energy - mRNA 6.86312 kcal/mol@LB@Unfolding Energy - sRNA 3.33183 kcal/mol@LB@@LB@Position - mRNA 169 -- 188@LB@Position - sRNA 14 -- 35@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 20 -- 26@LB@
138	0.02324	0.5385	b1826	mgrB	-8.64	0.179438	205 -- 238	60 -- 90	regulatory peptide for PhoPQ feedback inhibition	_____________204__________________________________239\n_____________\|____________________________________\|\n5'-UAC...AGUGA___________A___G_CGUUC__________U___GUUGG...AAU-3'\n______________AAAAGUUU_CG_UGG_U_____UGGUUGU_CG_GGU\n______________\|\|\|\|\|\|\|:_\|\|_\|\|\|_\|_____\|:\|\|\|:\|_\|\|_:\|\|\n______________UUUUCAAG_GC_ACC_A_____AUCAAUA_GC_UCA\n3'-CGC...AGGCG________U__A___G_A___________A______ACUCU...AAG-5'\n_____________\|____________________________________\|\n_____________91___________________________________59\n	226 -- 232	66 -- 72	-16.3224 kcal/mol	5.97183 kcal/mol	1.70935 kcal/mol	204 239@LB@ \| \|@LB@5'-UAC...AGUGA A G CGUUC U GUUGG...AAU-3'@LB@ AAAAGUUU CG UGG U UGGUUGU CG GGU@LB@ \|\|\|\|\|\|\|: \|\| \|\|\| \| \|:\|\|\|:\| \|\| :\|\|@LB@ UUUUCAAG GC ACC A AUCAAUA GC UCA@LB@3'-CGC...AGGCG U A G A A ACUCU...AAG-5'@LB@ \| \|@LB@ 91 59@LB@@LB@@LB@Energy -8.64 kcal/mol@LB@Hybridization Energy -16.3224 kcal/mol@LB@Unfolding Energy - mRNA 5.97183 kcal/mol@LB@Unfolding Energy - sRNA 1.70935 kcal/mol@LB@@LB@Position - mRNA 205 -- 238@LB@Position - sRNA 60 -- 90@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 66 -- 72@LB@
194	0.03409	0.5559	b1836	yebV	-7.98	0.229830	12 -- 23	77 -- 87	uncharacterized protein	_____________11___________24\n_____________\|____________\|\n5'-CCA...GGAUU________A___AAAAA...CUG-3'\n______________GGUUCGCG_UUG\n______________:\|\|\|\|:\|\|_\|\|\|\n______________UCAAGUGC_AAC\n3'-CGC...CGUUU____________CGAAA...AAG-5'\n_____________\|____________\|\n_____________88___________76\n	13 -- 19	80 -- 86	-12.5297 kcal/mol	4.04369 kcal/mol	0.505155 kcal/mol	11 24@LB@ \| \|@LB@5'-CCA...GGAUU A AAAAA...CUG-3'@LB@ GGUUCGCG UUG@LB@ :\|\|\|\|:\|\| \|\|\|@LB@ UCAAGUGC AAC@LB@3'-CGC...CGUUU CGAAA...AAG-5'@LB@ \| \|@LB@ 88 76@LB@@LB@@LB@Energy -7.98 kcal/mol@LB@Hybridization Energy -12.5297 kcal/mol@LB@Unfolding Energy - mRNA 4.04369 kcal/mol@LB@Unfolding Energy - sRNA 0.505155 kcal/mol@LB@@LB@Position - mRNA 12 -- 23@LB@Position - sRNA 77 -- 87@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 80 -- 86@LB@
34	0.00612	0.5385	b1837	yebW	-12.39	0.040382	203 -- 226	63 -- 86	uncharacterized protein	_____________202______________________227\n_____________\|________________________\|\n5'-ACC...GAAAU_______C____ACUUU_______CUACC...UGA-3'\n______________GUUCGCG_UGGU_____UUGUUUG\n______________\|\|\|\|:\|\|_\|\|\|:_____\|\|:\|\|:\|\n______________CAAGUGC_ACCG_____AAUAAGC\n3'-CGC...GUUUU_______A____AAAUC_______UCAAC...AAG-5'\n_____________\|________________________\|\n_____________87_______________________62\n	220 -- 226	63 -- 69	-18.9836 kcal/mol	4.90011 kcal/mol	1.69827 kcal/mol	202 227@LB@ \| \|@LB@5'-ACC...GAAAU C ACUUU CUACC...UGA-3'@LB@ GUUCGCG UGGU UUGUUUG@LB@ \|\|\|\|:\|\| \|\|\|: \|\|:\|\|:\|@LB@ CAAGUGC ACCG AAUAAGC@LB@3'-CGC...GUUUU A AAAUC UCAAC...AAG-5'@LB@ \| \|@LB@ 87 62@LB@@LB@@LB@Energy -12.39 kcal/mol@LB@Hybridization Energy -18.9836 kcal/mol@LB@Unfolding Energy - mRNA 4.90011 kcal/mol@LB@Unfolding Energy - sRNA 1.69827 kcal/mol@LB@@LB@Position - mRNA 203 -- 226@LB@Position - sRNA 63 -- 86@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 63 -- 69@LB@
141	0.02331	0.5385	b1844	exoX	-7.22	0.302733	200 -- 217	62 -- 83	exodeoxyribonuclease 10; DNA exonuclease X	_____________199_____________________218\n_____________\|_______________________\|\n5'-UUA...CAUGC_______C__A____________UACAG...UGA-3'\n______________CAUGUUG_GC_UUA_____UCGA\n______________\|\|:\|\|\|\|_\|\|_\|\|\|_____\|\|\|\|\n______________GUGCAAC_CG_AAU_____AGCU\n3'-CGC...UUCAA__________A___CAAUA____CAACU...AAG-5'\n_____________\|_______________________\|\n_____________84______________________61\n	200 -- 206	77 -- 83	-13.618 kcal/mol	4.77882 kcal/mol	1.62352 kcal/mol	199 218@LB@ \| \|@LB@5'-UUA...CAUGC C A UACAG...UGA-3'@LB@ CAUGUUG GC UUA UCGA@LB@ \|\|:\|\|\|\| \|\| \|\|\| \|\|\|\|@LB@ GUGCAAC CG AAU AGCU@LB@3'-CGC...UUCAA A CAAUA CAACU...AAG-5'@LB@ \| \|@LB@ 84 61@LB@@LB@@LB@Energy -7.22 kcal/mol@LB@Hybridization Energy -13.618 kcal/mol@LB@Unfolding Energy - mRNA 4.77882 kcal/mol@LB@Unfolding Energy - sRNA 1.62352 kcal/mol@LB@@LB@Position - mRNA 200 -- 217@LB@Position - sRNA 62 -- 83@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 77 -- 83@LB@
84	0.01516	0.5385	b1871	cmoB	-9.91	0.109770	166 -- 183	71 -- 87	tRNA (cmo5U34)-carboxymethyltransferase carboxy-SAM-dependent	_____________165________________184\n_____________\|__________________\|\n5'-CAC...ACUUU_______U_G____A___AAAGC...AGC-3'\n______________GGUUCAC_G_UGGC_UUA\n______________:\|\|\|\|\|\|_\|_\|\|\|\|_\|\|\|\n______________UCAAGUG_C_ACCG_AAU\n3'-CGC...CGUUU_________A____A___CAAUA...AAG-5'\n_____________\|__________________\|\n_____________88_________________70\n	166 -- 172	81 -- 87	-14.4863 kcal/mol	4.01825 kcal/mol	0.562376 kcal/mol	165 184@LB@ \| \|@LB@5'-CAC...ACUUU U G A AAAGC...AGC-3'@LB@ GGUUCAC G UGGC UUA@LB@ :\|\|\|\|\|\| \| \|\|\|\| \|\|\|@LB@ UCAAGUG C ACCG AAU@LB@3'-CGC...CGUUU A A CAAUA...AAG-5'@LB@ \| \|@LB@ 88 70@LB@@LB@@LB@Energy -9.91 kcal/mol@LB@Hybridization Energy -14.4863 kcal/mol@LB@Unfolding Energy - mRNA 4.01825 kcal/mol@LB@Unfolding Energy - sRNA 0.562376 kcal/mol@LB@@LB@Position - mRNA 166 -- 183@LB@Position - sRNA 71 -- 87@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 81 -- 87@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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