Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
28	0.000409	0.0491	b1688	ydiK	-9.69	0.189548	195 -- 219	1 -- 33	UPF0118 family inner membrane protein	_____________194_______________________________220\n_____________\|_________________________________\|\n5'-AUG...GAAAA__________________UAA_____CG_____CCAGG...CCU-3'\n______________GUAGUUA________UGG___AUGUU__UCAGC\n______________::\|\|:\|\|________\|\|\|___\|\|\|\|\|__\|\|\|\|\|\n______________UGUCGAU________ACC___UACAA__AGUCG\n3'-UUU...GACCA_______CGUAAAAU___CAA_____AA_____-5'\n_____________\|________________________________\|\n_____________34_______________________________1\n	195 -- 201	27 -- 33	-14.5165 kcal/mol	3.32905 kcal/mol	1.49313 kcal/mol	194 220@LB@ \| \|@LB@5'-AUG...GAAAA UAA CG CCAGG...CCU-3'@LB@ GUAGUUA UGG AUGUU UCAGC@LB@ ::\|\|:\|\| \|\|\| \|\|\|\|\| \|\|\|\|\|@LB@ UGUCGAU ACC UACAA AGUCG@LB@3'-UUU...GACCA CGUAAAAU CAA AA -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -9.69 kcal/mol@LB@Hybridization Energy -14.5165 kcal/mol@LB@Unfolding Energy - mRNA 3.32905 kcal/mol@LB@Unfolding Energy - sRNA 1.49313 kcal/mol@LB@@LB@Position - mRNA 195 -- 219@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 27 -- 33@LB@
31	0.0004941	0.05357	b1272	sohB	-11.06	0.104388	188 -- 235	1 -- 51	inner membrane protein S49 peptidase family protein	_____________187__________________________________________________236\n_____________\|____________________________________________________\|\n5'-UGU...UAACC____U_____AC__G___A__U____U_UGAA_____UU_____________GAAAA...AAC-3'\n______________AAGG_GG_GG__UC_UGG_AU_GUUG_C____UAUGG____UGUUUUU_GGC\n______________\|\|\|\|_\|\|_\|\|__\|\|_\|\|\|_\|:_\|:\|:_\|____\|\|\|\|\|____\|\|\|\|\|\|\|_:\|\|\n______________UUCC_CC_CC__AG_ACC_UG_CGAU_G____AUACC____ACAAAAA_UCG\n3'-UUU...UCCGA____U__A__A___G___A__U____C_UAAA_____CAAU_______G___-5'\n_____________\|___________________________________________________\|\n_____________52__________________________________________________1\n	226 -- 232	5 -- 11	-30.2617 kcal/mol	14.5124 kcal/mol	4.69283 kcal/mol	187 236@LB@ \| \|@LB@5'-UGU...UAACC U AC G A U U UGAA UU GAAAA...AAC-3'@LB@ AAGG GG GG UC UGG AU GUUG C UAUGG UGUUUUU GGC@LB@ \|\|\|\| \|\| \|\| \|\| \|\|\| \|: \|:\|: \| \|\|\|\|\| \|\|\|\|\|\|\| :\|\|@LB@ UUCC CC CC AG ACC UG CGAU G AUACC ACAAAAA UCG@LB@3'-UUU...UCCGA U A A G A U C UAAA CAAU G -5'@LB@ \| \|@LB@ 52 1@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -30.2617 kcal/mol@LB@Unfolding Energy - mRNA 14.5124 kcal/mol@LB@Unfolding Energy - sRNA 4.69283 kcal/mol@LB@@LB@Position - mRNA 188 -- 235@LB@Position - sRNA 1 -- 51@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 5 -- 11@LB@
38	0.0007298	0.06455	b3196	yrbG	-13.22	0.033821	90 -- 115	1 -- 31	putative calcium/sodium:proton antiporter	_____________89______________________________116\n_____________\|_______________________________\|\n5'-UUC...GCGAA___________________UUAC________CGCAU...UUG-3'\n______________AGCUGGCAUUU_____GUU____UUUUUAGC\n______________\|\|\|\|:\|\|\|\|\|\|_____\|\|\|____\|\|\|\|:\|\|\|\n______________UCGAUCGUAAA_____CAA____AAAAGUCG\n3'-UUU...CCAUG___________AUACC___UACA________-5'\n_____________\|______________________________\|\n_____________32_____________________________1\n	109 -- 115	1 -- 7	-21.7779 kcal/mol	7.06678 kcal/mol	1.48722 kcal/mol	89 116@LB@ \| \|@LB@5'-UUC...GCGAA UUAC CGCAU...UUG-3'@LB@ AGCUGGCAUUU GUU UUUUUAGC@LB@ \|\|\|\|:\|\|\|\|\|\| \|\|\| \|\|\|\|:\|\|\|@LB@ UCGAUCGUAAA CAA AAAAGUCG@LB@3'-UUU...CCAUG AUACC UACA -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -13.22 kcal/mol@LB@Hybridization Energy -21.7779 kcal/mol@LB@Unfolding Energy - mRNA 7.06678 kcal/mol@LB@Unfolding Energy - sRNA 1.48722 kcal/mol@LB@@LB@Position - mRNA 90 -- 115@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 1 -- 7@LB@
43	0.0008959	0.07003	b3068	mug	-12.52	0.050096	232 -- 248	1 -- 17	G/U mismatch-specific DNA glycosylase; xanthine DNA glycosylase	_____________231_______________249\n_____________\|_________________\|\n5'-UGG...GUUAC____C_______G____AUCAA...CGG-3'\n______________GGGU_GUGUUUU_CGGU\n______________\|\|\|\|_:\|\|\|\|\|\|_\|:\|:\n______________CCCA_UACAAAA_GUCG\n3'-UUU...AAAUA____A_______A____-5'\n_____________\|________________\|\n_____________18_______________1\n	237 -- 243	6 -- 12	-17.5569 kcal/mol	4.10869 kcal/mol	0.931609 kcal/mol	231 249@LB@ \| \|@LB@5'-UGG...GUUAC C G AUCAA...CGG-3'@LB@ GGGU GUGUUUU CGGU@LB@ \|\|\|\| :\|\|\|\|\|\| \|:\|:@LB@ CCCA UACAAAA GUCG@LB@3'-UUU...AAAUA A A -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -12.52 kcal/mol@LB@Hybridization Energy -17.5569 kcal/mol@LB@Unfolding Energy - mRNA 4.10869 kcal/mol@LB@Unfolding Energy - sRNA 0.931609 kcal/mol@LB@@LB@Position - mRNA 232 -- 248@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 6 -- 12@LB@
44	0.0009392	0.07174	b3453	ugpB	-12.21	0.059079	239 -- 268	1 -- 32	sn-glycerol-3-phosphate ABC transporter periplasmic binding protein	_____________238_______________________________269\n_____________\|_________________________________\|\n5'-UUC...GCGCU___A________A______GA___CACA_____AGUGA...UGG-3'\n______________CGG_CUGGCGUU__AUGGG__AUG______GGC\n______________\|:\|_\|\|:\|\|:\|\|__\|\|\|\|\|__\|\|\|______:\|\|\n______________GUC_GAUCGUAA__UACCC__UAC______UCG\n3'-UUU...ACCAU____________AA_____AA___AAAAAG___-5'\n_____________\|________________________________\|\n_____________33_______________________________1\n	244 -- 250	22 -- 28	-24.6308 kcal/mol	10.9347 kcal/mol	1.49075 kcal/mol	238 269@LB@ \| \|@LB@5'-UUC...GCGCU A A GA CACA AGUGA...UGG-3'@LB@ CGG CUGGCGUU AUGGG AUG GGC@LB@ \|:\| \|\|:\|\|:\|\| \|\|\|\|\| \|\|\| :\|\|@LB@ GUC GAUCGUAA UACCC UAC UCG@LB@3'-UUU...ACCAU AA AA AAAAAG -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -12.21 kcal/mol@LB@Hybridization Energy -24.6308 kcal/mol@LB@Unfolding Energy - mRNA 10.9347 kcal/mol@LB@Unfolding Energy - sRNA 1.49075 kcal/mol@LB@@LB@Position - mRNA 239 -- 268@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 22 -- 28@LB@
46	0.00106	0.07744	b3234	degQ	-13.26	0.033170	226 -- 262	1 -- 35	serine endoprotease periplasmic	_____________225____________________________________263\n_____________\|______________________________________\|\n5'-CUG...GUUGA______________AAG___C______ACUCUC_____GUCAU...UUG-3'\n______________GUGCA_UUAGCGUU___UGU_GGGUUA______UCGGC\n______________\|\|:\|\|_:\|\|\|\|:\|\|___\|:\|_\|\|\|\|\|\|______\|\|:\|\|\n______________CAUGU_GAUCGUAA___AUA_CCCAAU______AGUCG\n3'-UUU...AGGAC_____C________A____________ACAAAA_____-5'\n_____________\|_____________________________________\|\n_____________36____________________________________1\n	232 -- 238	22 -- 28	-28.0432 kcal/mol	13.2904 kcal/mol	1.49508 kcal/mol	225 263@LB@ \| \|@LB@5'-CUG...GUUGA AAG C ACUCUC GUCAU...UUG-3'@LB@ GUGCA UUAGCGUU UGU GGGUUA UCGGC@LB@ \|\|:\|\| :\|\|\|\|:\|\| \|:\| \|\|\|\|\|\| \|\|:\|\|@LB@ CAUGU GAUCGUAA AUA CCCAAU AGUCG@LB@3'-UUU...AGGAC C A ACAAAA -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -13.26 kcal/mol@LB@Hybridization Energy -28.0432 kcal/mol@LB@Unfolding Energy - mRNA 13.2904 kcal/mol@LB@Unfolding Energy - sRNA 1.49508 kcal/mol@LB@@LB@Position - mRNA 226 -- 262@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 22 -- 28@LB@
50	0.001175	0.07744	b3543	dppB	-14.13	0.019609	196 -- 210	1 -- 17	dipeptide/heme ABC transporter permease	_____________195_______________211\n_____________\|_________________\|\n5'-CGG...AAUCC__________G______UUAUU...AUC-3'\n______________GGGUUAUGUU___CAGU\n______________\|\|\|\|\|\|\|\|\|\|___\|\|\|:\n______________CCCAAUACAA___GUCG\n3'-UUU...AAAUA__________AAA____-5'\n_____________\|________________\|\n_____________18_______________1\n	199 -- 205	8 -- 14	-17.9134 kcal/mol	2.84721 kcal/mol	0.931609 kcal/mol	195 211@LB@ \| \|@LB@5'-CGG...AAUCC G UUAUU...AUC-3'@LB@ GGGUUAUGUU CAGU@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|:@LB@ CCCAAUACAA GUCG@LB@3'-UUU...AAAUA AAA -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -14.13 kcal/mol@LB@Hybridization Energy -17.9134 kcal/mol@LB@Unfolding Energy - mRNA 2.84721 kcal/mol@LB@Unfolding Energy - sRNA 0.931609 kcal/mol@LB@@LB@Position - mRNA 196 -- 210@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 8 -- 14@LB@
59	0.00143	0.08147	b0848	ybjM	-6.77	0.507403	86 -- 118	1 -- 33	inner membrane protein	_____________85_________________________________119\n_____________\|__________________________________\|\n5'-GAA...UAUCA___________GAAU__C____GCCUAUA_____AUGGA...GGG-3'\n______________ACGGCUA_UAU____UG_GUUG_______UUAGC\n______________\|\|:\|\|\|\|_:\|\|____\|\|_\|\|\|:_______\|:\|\|\|\n______________UGUCGAU_GUA____AC_CAAU_______AGUCG\n3'-UUU...GACCA_______C___AAAU__C____ACAAAA______-5'\n_____________\|_________________________________\|\n_____________34________________________________1\n	86 -- 92	27 -- 33	-17.6492 kcal/mol	9.38597 kcal/mol	1.49313 kcal/mol	85 119@LB@ \| \|@LB@5'-GAA...UAUCA GAAU C GCCUAUA AUGGA...GGG-3'@LB@ ACGGCUA UAU UG GUUG UUAGC@LB@ \|\|:\|\|\|\| :\|\| \|\| \|\|\|: \|:\|\|\|@LB@ UGUCGAU GUA AC CAAU AGUCG@LB@3'-UUU...GACCA C AAAU C ACAAAA -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -6.77 kcal/mol@LB@Hybridization Energy -17.6492 kcal/mol@LB@Unfolding Energy - mRNA 9.38597 kcal/mol@LB@Unfolding Energy - sRNA 1.49313 kcal/mol@LB@@LB@Position - mRNA 86 -- 118@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 27 -- 33@LB@
66	0.001771	0.09017	b0924	mukB	-12.08	0.063147	4 -- 24	1 -- 22	chromosome condensin MukBEF ATPase and DNA-binding subunit	_____________3______________________25\n_____________\|______________________\|\n________5'-UGG________CCACGACAG_____AAGUU...CUG-3'\n______________UUUAUGGG__________CAGC\n______________\|\|\|\|\|\|\|\|__________\|\|\|\|\n______________AAAUACCC__________GUCG\n3'-UUU...UCGUA________AAUACAAAAA____-5'\n_____________\|_____________________\|\n_____________23____________________1\n	5 -- 11	15 -- 21	-14.8798 kcal/mol	1.84387 kcal/mol	0.958674 kcal/mol	3 25@LB@ \| \|@LB@ 5'-UGG CCACGACAG AAGUU...CUG-3'@LB@ UUUAUGGG CAGC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|@LB@ AAAUACCC GUCG@LB@3'-UUU...UCGUA AAUACAAAAA -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -14.8798 kcal/mol@LB@Unfolding Energy - mRNA 1.84387 kcal/mol@LB@Unfolding Energy - sRNA 0.958674 kcal/mol@LB@@LB@Position - mRNA 4 -- 24@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 15 -- 21@LB@
67	0.00183	0.09081	b1607	ydgC	-12.69	0.045650	228 -- 262	1 -- 36	GlpM family inner membrane protein	_____________227__________________________________263\n_____________\|____________________________________\|\n5'-AUG...CGCUC_____________GUGCUGUUGAUUG__G_______AAAAA...CAC-3'\n______________GGUGC_GCUGGUA_____________GU_UUUUAGC\n______________\|\|\|:\|_\|\|\|:\|:\|_____________\|\|_\|\|\|:\|\|\|\n______________CCAUG_CGAUCGU_____________CA_AAAGUCG\n3'-UUU...AAGGA_____U_______AAAAUACCCAAUA__A_______-5'\n_____________\|___________________________________\|\n_____________37__________________________________1\n	256 -- 262	1 -- 7	-24.769 kcal/mol	10.5859 kcal/mol	1.49509 kcal/mol	227 263@LB@ \| \|@LB@5'-AUG...CGCUC GUGCUGUUGAUUG G AAAAA...CAC-3'@LB@ GGUGC GCUGGUA GU UUUUAGC@LB@ \|\|\|:\| \|\|\|:\|:\| \|\| \|\|\|:\|\|\|@LB@ CCAUG CGAUCGU CA AAAGUCG@LB@3'-UUU...AAGGA U AAAAUACCCAAUA A -5'@LB@ \| \|@LB@ 37 1@LB@@LB@@LB@Energy -12.69 kcal/mol@LB@Hybridization Energy -24.769 kcal/mol@LB@Unfolding Energy - mRNA 10.5859 kcal/mol@LB@Unfolding Energy - sRNA 1.49509 kcal/mol@LB@@LB@Position - mRNA 228 -- 262@LB@Position - sRNA 1 -- 36@LB@Position Seed - mRNA 256 -- 262@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)

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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