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
85	0.002796	0.1082	b4536	yobH	-12.68	0.045962	237 -- 287	1 -- 38	uncharacterized protein	_____________236__________________________________________________288\n_____________\|____________________________________________________\|\n5'-CAA...UAGCA_________AUAGGAUUAUUA__C____GA______C___U__A__GGA___AAAGA...CCG-3'\n______________CUGGUAUGG____________CU_AGCG___UAUGG_GUU_UG_UU___AGC\n______________\|\|\|\|\|\|::\|____________\|\|_\|\|\|:___\|\|\|\|\|_\|\|\|_\|\|_\|\|___\|\|\|\n______________GACCAUGUC____________GA_UCGU___AUACC_CAA_AC_AA___UCG\n3'-UUU...CCAAG____________________________AAA_________U__A__AAG___-5'\n_____________\|___________________________________________________\|\n_____________39__________________________________________________1\n	239 -- 245	30 -- 36	-25.5821 kcal/mol	8.3664 kcal/mol	4.54019 kcal/mol	236 288@LB@ \| \|@LB@5'-CAA...UAGCA AUAGGAUUAUUA C GA C U A GGA AAAGA...CCG-3'@LB@ CUGGUAUGG CU AGCG UAUGG GUU UG UU AGC@LB@ \|\|\|\|\|\|::\| \|\| \|\|\|: \|\|\|\|\| \|\|\| \|\| \|\| \|\|\|@LB@ GACCAUGUC GA UCGU AUACC CAA AC AA UCG@LB@3'-UUU...CCAAG AAA U A AAG -5'@LB@ \| \|@LB@ 39 1@LB@@LB@@LB@Energy -12.68 kcal/mol@LB@Hybridization Energy -25.5821 kcal/mol@LB@Unfolding Energy - mRNA 8.3664 kcal/mol@LB@Unfolding Energy - sRNA 4.54019 kcal/mol@LB@@LB@Position - mRNA 237 -- 287@LB@Position - sRNA 1 -- 38@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 30 -- 36@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@
79	0.002261	0.09621	b2556	glrK	-15.72	0.006745	240 -- 258	20 -- 38	sensor protein kinase regulating glmY sRNA in two-component system with response regulator GlrR	_____________239_________________259\n_____________\|___________________\|\n5'-CUA...GACAA______AU___________UGCUG...CCU-3'\n______________CUGGUA__GCUGGCAUUUU\n______________\|\|\|\|\|\|__\|\|\|:\|\|\|\|\|\|\|\n______________GACCAU__CGAUCGUAAAA\n3'-UUU...CCAAG______GU___________UACCC...UCG-5'\n_____________\|___________________\|\n_____________39__________________19\n	252 -- 258	20 -- 26	-25.6316 kcal/mol	5.4283 kcal/mol	4.48821 kcal/mol	239 259@LB@ \| \|@LB@5'-CUA...GACAA AU UGCUG...CCU-3'@LB@ CUGGUA GCUGGCAUUUU@LB@ \|\|\|\|\|\| \|\|\|:\|\|\|\|\|\|\|@LB@ GACCAU CGAUCGUAAAA@LB@3'-UUU...CCAAG GU UACCC...UCG-5'@LB@ \| \|@LB@ 39 19@LB@@LB@@LB@Energy -15.72 kcal/mol@LB@Hybridization Energy -25.6316 kcal/mol@LB@Unfolding Energy - mRNA 5.4283 kcal/mol@LB@Unfolding Energy - sRNA 4.48821 kcal/mol@LB@@LB@Position - mRNA 240 -- 258@LB@Position - sRNA 20 -- 38@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 20 -- 26@LB@
114	0.004808	0.1404	b2372	yfdV	-9.14	0.236047	240 -- 266	1 -- 35	putative transporter	_____________239____________________________________267\n_____________\|______________________________________\|\n5'-UUC...UUAUC___AU__U______________________________GGCAG...CUC-3'\n______________GUA__CA_GCU_GU______UGGGUUAU____UUUAGC\n______________\|\|\|__\|\|_\|\|\|_\|:______\|\|\|\|\|\|\|\|____\|\|:\|\|\|\n______________CAU__GU_CGA_CG______ACCCAAUA____AAGUCG\n3'-UUU...AGGAC___________U__UAAAAU________CAAA______-5'\n_____________\|_____________________________________\|\n_____________36____________________________________1\n	254 -- 260	11 -- 17	-17.7969 kcal/mol	7.16419 kcal/mol	1.49508 kcal/mol	239 267@LB@ \| \|@LB@5'-UUC...UUAUC AU U GGCAG...CUC-3'@LB@ GUA CA GCU GU UGGGUUAU UUUAGC@LB@ \|\|\| \|\| \|\|\| \|: \|\|\|\|\|\|\|\| \|\|:\|\|\|@LB@ CAU GU CGA CG ACCCAAUA AAGUCG@LB@3'-UUU...AGGAC U UAAAAU CAAA -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -17.7969 kcal/mol@LB@Unfolding Energy - mRNA 7.16419 kcal/mol@LB@Unfolding Energy - sRNA 1.49508 kcal/mol@LB@@LB@Position - mRNA 240 -- 266@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 11 -- 17@LB@
128	0.005434	0.142	b1628	rsxB	-10.87	0.114026	241 -- 273	10 -- 44	SoxR iron-sulfur cluster reduction factor component; putative iron-sulfur protein	_____________240___________________________________274\n_____________\|_____________________________________\|\n5'-CAC...CCUGC___G______CGUU____GC_____C___________CCUCC...ACG-3'\n______________UGG__CCUGG____UGGC___CAUU___UGGGUUAUG\n______________\|\|\|__\|\|\|\|\|____::\|\|___\|\|\|\|___\|\|\|\|\|\|\|\|\|\n______________ACC__GGACC____GUCG___GUAA___ACCCAAUAC\n3'-UUU...CCUCC___AA_____AU______AUC____AAU_________AAAAA...UCG-5'\n_____________\|_____________________________________\|\n_____________45____________________________________9\n	267 -- 273	10 -- 16	-28.3112 kcal/mol	12.8396 kcal/mol	4.60525 kcal/mol	240 274@LB@ \| \|@LB@5'-CAC...CCUGC G CGUU GC C CCUCC...ACG-3'@LB@ UGG CCUGG UGGC CAUU UGGGUUAUG@LB@ \|\|\| \|\|\|\|\| ::\|\| \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ ACC GGACC GUCG GUAA ACCCAAUAC@LB@3'-UUU...CCUCC AA AU AUC AAU AAAAA...UCG-5'@LB@ \| \|@LB@ 45 9@LB@@LB@@LB@Energy -10.87 kcal/mol@LB@Hybridization Energy -28.3112 kcal/mol@LB@Unfolding Energy - mRNA 12.8396 kcal/mol@LB@Unfolding Energy - sRNA 4.60525 kcal/mol@LB@@LB@Position - mRNA 241 -- 273@LB@Position - sRNA 10 -- 44@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 10 -- 16@LB@
14	9.306e-05	0.02121	b1205	ychH	-11.92	0.068307	242 -- 277	15 -- 49	DUF2583 family putative inner membrane protein	_____________241____________________________________278\n_____________\|______________________________________\|\n5'-CAA...CUCAU____U___G________GUAAU_G____CGGC______GUAUU...UAC-3'\n______________GGGG_UGG__UCUGGUG_____G_UGGU_____GUGGG\n______________\|\|:\|_\|\|\|__:\|\|\|\|\|:_____\|_\|:\|:_____:\|\|\|\|\n______________CCUC_ACC__GGACCAU_____C_AUCG_____UACCC\n3'-UUU...CGAUU____C___AA_______GU____G____UAAAA_____AAUAC...UCG-5'\n_____________\|______________________________________\|\n_____________50_____________________________________14\n	251 -- 257	33 -- 39	-28.7764 kcal/mol	12.2787 kcal/mol	4.57366 kcal/mol	241 278@LB@ \| \|@LB@5'-CAA...CUCAU U G GUAAU G CGGC GUAUU...UAC-3'@LB@ GGGG UGG UCUGGUG G UGGU GUGGG@LB@ \|\|:\| \|\|\| :\|\|\|\|\|: \| \|:\|: :\|\|\|\|@LB@ CCUC ACC GGACCAU C AUCG UACCC@LB@3'-UUU...CGAUU C AA GU G UAAAA AAUAC...UCG-5'@LB@ \| \|@LB@ 50 14@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -28.7764 kcal/mol@LB@Unfolding Energy - mRNA 12.2787 kcal/mol@LB@Unfolding Energy - sRNA 4.57366 kcal/mol@LB@@LB@Position - mRNA 242 -- 277@LB@Position - sRNA 15 -- 49@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 33 -- 39@LB@
68	0.001845	0.09081	b2957	ansB	-14.03	0.020893	243 -- 268	22 -- 43	periplasmic L-asparaginase 2	_____________242________________________269\n_____________\|__________________________\|\n5'-AGC...UUAUG______AG_________AU_______ACCCA...GGA-3'\n______________GGUUUU__UGGUGCAGC__UGGCAUU\n______________\|\|\|\|::__\|\|\|\|:\|\|\|\|__\|:\|\|\|\|\|\n______________CCAAGG__ACCAUGUCG__AUCGUAA\n3'-UUU...CUCCA__________________________AAUAC...UCG-5'\n_____________\|__________________________\|\n_____________44_________________________21\n	262 -- 268	22 -- 28	-26.4763 kcal/mol	7.8858 kcal/mol	4.55803 kcal/mol	242 269@LB@ \| \|@LB@5'-AGC...UUAUG AG AU ACCCA...GGA-3'@LB@ GGUUUU UGGUGCAGC UGGCAUU@LB@ \|\|\|\|:: \|\|\|\|:\|\|\|\| \|:\|\|\|\|\|@LB@ CCAAGG ACCAUGUCG AUCGUAA@LB@3'-UUU...CUCCA AAUAC...UCG-5'@LB@ \| \|@LB@ 44 21@LB@@LB@@LB@Energy -14.03 kcal/mol@LB@Hybridization Energy -26.4763 kcal/mol@LB@Unfolding Energy - mRNA 7.8858 kcal/mol@LB@Unfolding Energy - sRNA 4.55803 kcal/mol@LB@@LB@Position - mRNA 243 -- 268@LB@Position - sRNA 22 -- 43@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 22 -- 28@LB@
40	0.0008246	0.06626	b4019	metH	-11.44	0.086775	244 -- 271	15 -- 42	homocysteine-N5-methyltetrahydrofolate transmethylase B12-dependent	_____________243____________________________272\n_____________\|______________________________\|\n5'-UGA...UGAAC__A_________U__AC____G________CACCA...ACG-3'\n______________GU_UUCUGGUGC_GG__GGCG___UAUGGG\n______________\|\|_\|:\|\|\|\|\|:\|_:\|__:\|\|:___\|\|\|\|\|\|\n______________CA_AGGACCAUG_UC__UCGU___AUACCC\n3'-UUU...UCCAC_______________GA____AAA______AAUAC...UCG-5'\n_____________\|______________________________\|\n_____________43_____________________________14\n	249 -- 255	32 -- 38	-26.1297 kcal/mol	10.116 kcal/mol	4.57031 kcal/mol	243 272@LB@ \| \|@LB@5'-UGA...UGAAC A U AC G CACCA...ACG-3'@LB@ GU UUCUGGUGC GG GGCG UAUGGG@LB@ \|\| \|:\|\|\|\|\|:\| :\| :\|\|: \|\|\|\|\|\|@LB@ CA AGGACCAUG UC UCGU AUACCC@LB@3'-UUU...UCCAC GA AAA AAUAC...UCG-5'@LB@ \| \|@LB@ 43 14@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -26.1297 kcal/mol@LB@Unfolding Energy - mRNA 10.116 kcal/mol@LB@Unfolding Energy - sRNA 4.57031 kcal/mol@LB@@LB@Position - mRNA 244 -- 271@LB@Position - sRNA 15 -- 42@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 32 -- 38@LB@
32	0.0005297	0.05563	b3456	livM	-14.95	0.011565	245 -- 274	15 -- 42	branched-chain amino acid ABC transporter permease	_____________244____________________________275\n_____________\|______________________________\|\n5'-GCC...GCGAU______U____U___G_____C________CGUGC...CCA-3'\n______________GUUCUU_GUGC_GGC_GGCGU_UUUAUGGG\n______________\|\|\|\|:\|_\|\|:\|_:\|\|_:\|\|:\|_\|\|\|\|\|\|\|\|\n______________CAAGGA_CAUG_UCG_UCGUA_AAAUACCC\n3'-UUU...UCCAC______C________A______________AAUAC...UCG-5'\n_____________\|______________________________\|\n_____________43_____________________________14\n	268 -- 274	15 -- 21	-29.6256 kcal/mol	10.1077 kcal/mol	4.57031 kcal/mol	244 275@LB@ \| \|@LB@5'-GCC...GCGAU U U G C CGUGC...CCA-3'@LB@ GUUCUU GUGC GGC GGCGU UUUAUGGG@LB@ \|\|\|\|:\| \|\|:\| :\|\| :\|\|:\| \|\|\|\|\|\|\|\|@LB@ CAAGGA CAUG UCG UCGUA AAAUACCC@LB@3'-UUU...UCCAC C A AAUAC...UCG-5'@LB@ \| \|@LB@ 43 14@LB@@LB@@LB@Energy -14.95 kcal/mol@LB@Hybridization Energy -29.6256 kcal/mol@LB@Unfolding Energy - mRNA 10.1077 kcal/mol@LB@Unfolding Energy - sRNA 4.57031 kcal/mol@LB@@LB@Position - mRNA 245 -- 274@LB@Position - sRNA 15 -- 42@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 15 -- 21@LB@
192	0.01101	0.1919	b2478	dapA	-6.78	0.505920	248 -- 269	25 -- 47	dihydrodipicolinate synthase	_____________247_____________________270\n_____________\|_______________________\|\n5'-GGC...GAAAA____AAUG____UCG________UUGAA...CCA-3'\n______________AGGU____UCUG____GGCUAGC\n______________\|\|\|\|____:\|\|\|____:\|\|\|\|\|\|\n______________UCCA____GGAC____UCGAUCG\n3'-UUU...AUUCC____CCAA____CAUG_______UAAAA...UCG-5'\n_____________\|_______________________\|\n_____________48______________________24\n	263 -- 269	25 -- 31	-19.6963 kcal/mol	8.35751 kcal/mol	4.55753 kcal/mol	247 270@LB@ \| \|@LB@5'-GGC...GAAAA AAUG UCG UUGAA...CCA-3'@LB@ AGGU UCUG GGCUAGC@LB@ \|\|\|\| :\|\|\| :\|\|\|\|\|\|@LB@ UCCA GGAC UCGAUCG@LB@3'-UUU...AUUCC CCAA CAUG UAAAA...UCG-5'@LB@ \| \|@LB@ 48 24@LB@@LB@@LB@Energy -6.78 kcal/mol@LB@Hybridization Energy -19.6963 kcal/mol@LB@Unfolding Energy - mRNA 8.35751 kcal/mol@LB@Unfolding Energy - sRNA 4.55753 kcal/mol@LB@@LB@Position - mRNA 248 -- 269@LB@Position - sRNA 25 -- 47@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 25 -- 31@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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