Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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	Additional homologs
22	0.001812	0.2633	b2566	era	-10.12	0.260747	283 -- 292	16 -- 26	membrane-associated 16S rRNA-binding GTPase		_____________282________________293\n_____________\|__________________\|\n5'-UUG...AAUGA_________AA_______UGCGG...UCU-3'\n______________GCAUCGAUA___AGUUAC\n______________:\|\|:\|:\|\|\|___\|\|\|:\|\|\n______________UGUGGUUAU___UCAGUG\n3'-UUU...UAAAA_________GAG______UGUAC...UAG-5'\n_____________\|__________________\|\n_____________27_________________15\n	205 -- 211	181 -- 187	-15.5423 kcal/mol	3.87874 kcal/mol	4.86686 kcal/mol	282 293@LB@ \| \|@LB@5'-UUG...AAUGA AA UGCGG...UCU-3'@LB@ GCAUCGAUA AGUUAC@LB@ :\|\|:\|:\|\|\| \|\|\|:\|\|@LB@ UGUGGUUAU UCAGUG@LB@3'-UUU...UAAAA GAG UGUAC...UAG-5'@LB@ \| \|@LB@ 27 15@LB@@LB@@LB@Energy -10.12 kcal/mol@LB@Hybridization Energy -15.5423 kcal/mol@LB@Unfolding Energy - mRNA 3.87874 kcal/mol@LB@Unfolding Energy - sRNA 4.86686 kcal/mol@LB@@LB@Position - mRNA 283 -- 292@LB@Position - sRNA 16 -- 26@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 181 -- 187@LB@
49	0.004667	0.3205	b1277	ribA	-9.86	0.291903	241 -- 249	16 -- 24	GTP cyclohydrolase II		_____________240________250\n_____________\|__________\|\n5'-CCA...AAUAC__________UUAUC...UCG-3'\n______________AGAACCAGCA\n______________\|:\|\|\|\|\|\|\|\|\n______________UUUUGGUCGU\n_______3'-UUUU__________CCAUA...UAG-5'\n_____________\|__________\|\n_____________25_________15\n	178 -- 184	214 -- 220	-13.9783 kcal/mol	2.87719 kcal/mol	5.75438 kcal/mol	240 250@LB@ \| \|@LB@5'-CCA...AAUAC UUAUC...UCG-3'@LB@ AGAACCAGCA@LB@ \|:\|\|\|\|\|\|\|\|@LB@ UUUUGGUCGU@LB@ 3'-UUUU CCAUA...UAG-5'@LB@ \| \|@LB@ 25 15@LB@@LB@@LB@Energy -9.86 kcal/mol@LB@Hybridization Energy -13.9783 kcal/mol@LB@Unfolding Energy - mRNA 2.87719 kcal/mol@LB@Unfolding Energy - sRNA 5.75438 kcal/mol@LB@@LB@Position - mRNA 241 -- 249@LB@Position - sRNA 16 -- 24@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 214 -- 220@LB@
92	0.01029	0.3575	b3360	pabA	-10.28	0.244097	93 -- 100	16 -- 23	aminodeoxychorismate synthase subunit II		_____________92__________101\n_____________\|___________\|\n5'-GCG...ACCUC___________UUGUG...CGU-3'\n______________UACCAGUACUU\n______________:\|\|\|\|:\|\|\|\|:\n______________GUGGUUAUGAG\n3'-UUU...AAAAU___________UCAGU...UAG-5'\n_____________\|___________\|\n_____________24__________15\n	250 -- 256	176 -- 182	-13.2399 kcal/mol	3.06354 kcal/mol	3.38772 kcal/mol	92 101@LB@ \| \|@LB@5'-GCG...ACCUC UUGUG...CGU-3'@LB@ UACCAGUACUU@LB@ :\|\|\|\|:\|\|\|\|:@LB@ GUGGUUAUGAG@LB@3'-UUU...AAAAU UCAGU...UAG-5'@LB@ \| \|@LB@ 24 15@LB@@LB@@LB@Energy -10.28 kcal/mol@LB@Hybridization Energy -13.2399 kcal/mol@LB@Unfolding Energy - mRNA 3.06354 kcal/mol@LB@Unfolding Energy - sRNA 3.38772 kcal/mol@LB@@LB@Position - mRNA 93 -- 100@LB@Position - sRNA 16 -- 23@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 176 -- 182@LB@
125	0.01377	0.3575	b2827	thyA	-14.98	0.027366	100 -- 109	16 -- 25	thymidylate synthetase		_____________99_____________________110\n_____________\|______________________\|\n5'-CAG...AAACA________A_____________AAAAG...AGA-3'\n______________GUAUUUAG__AC___UGAUGCA\n______________:\|\|:\|:\|\|__\|\|___\|\|\|\|\|\|\|\n______________UAUGAGUC__UG___ACUACGU\n3'-UUU...GUGGU________AG__UGU_______CCGUU...UAG-5'\n_____________\|______________________\|\n_____________26_____________________15\n	220 -- 226	160 -- 166	-15.3976 kcal/mol	3.04146 kcal/mol	4.80633 kcal/mol	99 110@LB@ \| \|@LB@5'-CAG...AAACA A AAAAG...AGA-3'@LB@ GUAUUUAG AC UGAUGCA@LB@ :\|\|:\|:\|\| \|\| \|\|\|\|\|\|\|@LB@ UAUGAGUC UG ACUACGU@LB@3'-UUU...GUGGU AG UGU CCGUU...UAG-5'@LB@ \| \|@LB@ 26 15@LB@@LB@@LB@Energy -14.98 kcal/mol@LB@Hybridization Energy -15.3976 kcal/mol@LB@Unfolding Energy - mRNA 3.04146 kcal/mol@LB@Unfolding Energy - sRNA 4.80633 kcal/mol@LB@@LB@Position - mRNA 100 -- 109@LB@Position - sRNA 16 -- 25@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 160 -- 166@LB@
132	0.0143	0.3575	b0147	ligT	-9.89	0.288456	69 -- 117	16 -- 69	2'-5' RNA ligase		_____________68__________________________________118\n_____________\|___________________________________\|\n5'-CCA...AAGUA______GUA_G___GCAGCAA_______C_A____ACAAA...CGG-3'\n______________AUUCAG___A_ACG_______CGGGCAA_G_CGAC\n______________\|:\|\|\|\|___\|_\|\|:_______\|:\|\|\|\|\|_\|_\|:\|\|\n______________UGAGUC___U_UGU_______GUCCGUU_C_GUUG\n3'-UUU...GGUUA______AG__G___ACUAC___________A____AAAGU...UAG-5'\n_____________\|___________________________________\|\n_____________70__________________________________15\n	112 -- 118	155 -- 161	-21.4956 kcal/mol	4.52534 kcal/mol	8.18567 kcal/mol	68 118@LB@ \| \|@LB@5'-CCA...AAGUA GUA G GCAGCAA C A ACAAA...CGG-3'@LB@ AUUCAG A ACG CGGGCAA G CGAC@LB@ \|:\|\|\|\| \| \|\|: \|:\|\|\|\|\| \| \|:\|\|@LB@ UGAGUC U UGU GUCCGUU C GUUG@LB@3'-UUU...GGUUA AG G ACUAC A AAAGU...UAG-5'@LB@ \| \|@LB@ 70 15@LB@@LB@@LB@Energy -9.89 kcal/mol@LB@Hybridization Energy -21.4956 kcal/mol@LB@Unfolding Energy - mRNA 4.52534 kcal/mol@LB@Unfolding Energy - sRNA 8.18567 kcal/mol@LB@@LB@Position - mRNA 69 -- 117@LB@Position - sRNA 16 -- 69@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 155 -- 161@LB@
113	0.01268	0.3575	b2066	udk	-9.33	0.364673	240 -- 253	17 -- 31	uridine/cytidine kinase		_____________239________________254\n_____________\|__________________\|\n5'-CGC...UUCGU_________C__AA____CAGGU...GUG-3'\n______________CGCCCCCUU_CU__CAUC\n______________\|:\|\|\|\|\|\|\|_\|\|__\|\|\|\|\n______________GUGGGGGAA_GA__GUAG\n3'-UUU...ACCCC_________C__A_____-5'\n_____________\|_________________\|\n_____________32________________17\n	161 -- 167	9 -- 15	-20.5437 kcal/mol	3.26859 kcal/mol	7.16879 kcal/mol	239 254@LB@ \| \|@LB@5'-CGC...UUCGU C AA CAGGU...GUG-3'@LB@ CGCCCCCUU CU CAUC@LB@ \|:\|\|\|\|\|\|\| \|\| \|\|\|\|@LB@ GUGGGGGAA GA GUAG@LB@3'-UUU...ACCCC C A -5'@LB@ \| \|@LB@ 32 17@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -20.5437 kcal/mol@LB@Unfolding Energy - mRNA 3.26859 kcal/mol@LB@Unfolding Energy - sRNA 7.16879 kcal/mol@LB@@LB@Position - mRNA 240 -- 253@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 9 -- 15@LB@
151	0.01691	0.3749	b2442	intZ	-12.49	0.088679	278 -- 291	17 -- 31	CPZ-55 prophage; putative phage integrase	b2349	_____________277_________________292\n_____________\|___________________\|\n5'-ACA...AAACU____________C_G____CGGGG...UGC-3'\n______________CACCGAU__UCA_U_ACGC\n______________\|\|\|\|:\|\|__\|\|\|_\|_\|\|:\|\n______________GUGGUUA__AGU_A_UGUG\n3'-UUU...AAAAU_______UG___C_G____UACUA...UAG-5'\n_____________\|___________________\|\n_____________32__________________16\n	269 -- 275	180 -- 186	-14.1411 kcal/mol	1.5591 kcal/mol	4.88042 kcal/mol	277 292@LB@ \| \|@LB@5'-ACA...AAACU C G CGGGG...UGC-3'@LB@ CACCGAU UCA U ACGC@LB@ \|\|\|\|:\|\| \|\|\| \| \|\|:\|@LB@ GUGGUUA AGU A UGUG@LB@3'-UUU...AAAAU UG C G UACUA...UAG-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -12.49 kcal/mol@LB@Hybridization Energy -14.1411 kcal/mol@LB@Unfolding Energy - mRNA 1.5591 kcal/mol@LB@Unfolding Energy - sRNA 4.88042 kcal/mol@LB@@LB@Position - mRNA 278 -- 291@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 180 -- 186@LB@
20	0.001715	0.2633	b3453	ugpB	-12.22	0.100645	241 -- 257	18 -- 32	sn-glycerol-3-phosphate ABC transporter periplasmic binding protein		_____________240______________258\n_____________\|________________\|\n5'-UUC...AAUUC_____U__________AAGAG...UGG-3'\n______________GCGCA_UCGGUACAAC\n______________:\|\|\|\|_:\|:\|:\|\|\|\|\|\n______________UGCGU_GGUCGUGUUG\n3'-UUU...UUGGU_____U__________AAGCG...UAG-5'\n_____________\|________________\|\n_____________33_______________17\n	180 -- 186	63 -- 69	-22.0099 kcal/mol	5.49331 kcal/mol	9.84719 kcal/mol	240 258@LB@ \| \|@LB@5'-UUC...AAUUC U AAGAG...UGG-3'@LB@ GCGCA UCGGUACAAC@LB@ :\|\|\|\| :\|:\|:\|\|\|\|\|@LB@ UGCGU GGUCGUGUUG@LB@3'-UUU...UUGGU U AAGCG...UAG-5'@LB@ \| \|@LB@ 33 17@LB@@LB@@LB@Energy -12.22 kcal/mol@LB@Hybridization Energy -22.0099 kcal/mol@LB@Unfolding Energy - mRNA 5.49331 kcal/mol@LB@Unfolding Energy - sRNA 9.84719 kcal/mol@LB@@LB@Position - mRNA 241 -- 257@LB@Position - sRNA 18 -- 32@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 63 -- 69@LB@
60	0.005924	0.3261	b4201	priB	-15.35	0.022961	159 -- 180	18 -- 40	primosomal protein N		_____________158_____________181\n_____________\|_______________\|\n5'-AGG...GAAAC_______C_______ACGAU...AUC-3'\n______________UACCUUC__GCUUCA\n______________:\|\|\|::\|__\|\|\|\|\|\|\n______________GUGGGGG__CGAAGU\n3'-UUU...ACCCC_______AA______AG-5'\n_____________\|_______________\|\n_____________41______________17\n	26 -- 32	11 -- 17	-15.0598 kcal/mol	3.0465 kcal/mol	7.09151 kcal/mol	158 181@LB@ \| \|@LB@5'-AGG...GAAAC C ACGAU...AUC-3'@LB@ UACCUUC GCUUCA@LB@ :\|\|\|::\| \|\|\|\|\|\|@LB@ GUGGGGG CGAAGU@LB@3'-UUU...ACCCC AA AG-5'@LB@ \| \|@LB@ 41 17@LB@@LB@@LB@Energy -15.35 kcal/mol@LB@Hybridization Energy -15.0598 kcal/mol@LB@Unfolding Energy - mRNA 3.0465 kcal/mol@LB@Unfolding Energy - sRNA 7.09151 kcal/mol@LB@@LB@Position - mRNA 159 -- 180@LB@Position - sRNA 18 -- 40@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 11 -- 17@LB@
157	0.01768	0.3749	b1216	chaA	-11.60	0.134178	242 -- 292	18 -- 65	calcium/sodium:proton antiporter		_____________241_______________293\n_____________\|_________________\|\n5'-AUU...AAUGU_________C___A___UUUCU...GCC-3'\n______________UACCGAUAU_CAG_CAC\n______________:\|\|\|:\|\|\|:_\|\|\|_\|\|\|\n______________GUGGUUAUG_GUC_GUG\n3'-UUU...AAAAU_________A___A___UGUAC...UAG-5'\n_____________\|_________________\|\n_____________66________________17\n	120 -- 126	178 -- 184	-16.2011 kcal/mol	3.68451 kcal/mol	4.86651 kcal/mol	241 293@LB@ \| \|@LB@5'-AUU...AAUGU C A UUUCU...GCC-3'@LB@ UACCGAUAU CAG CAC@LB@ :\|\|\|:\|\|\|: \|\|\| \|\|\|@LB@ GUGGUUAUG GUC GUG@LB@3'-UUU...AAAAU A A UGUAC...UAG-5'@LB@ \| \|@LB@ 66 17@LB@@LB@@LB@Energy -11.60 kcal/mol@LB@Hybridization Energy -16.2011 kcal/mol@LB@Unfolding Energy - mRNA 3.68451 kcal/mol@LB@Unfolding Energy - sRNA 4.86651 kcal/mol@LB@@LB@Position - mRNA 242 -- 292@LB@Position - sRNA 18 -- 65@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 178 -- 184@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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service.

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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