Input and runtime details for job 7743500 (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 7743500 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:35:00 CET 2018
	CopraRNA Started		@ Fri Feb 16 21:27:12 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 06:56:30 CET 2018
	Post-Processing Finished		@ Sat Feb 17 06:56:38 CET 2018
	Job Completed		@ Sat Feb 17 06:57:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7743500&toolName=CopraRNA ( 30 days expiry )

Description of the job

PrrF1

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_002516 Pseudomonas aeruginosa PAO1

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
92	0.001266	0.06327	pa1307	N/A	-13.15	0.033214	250 -- 278	41 -- 65	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________249___________________________279\n_____________\|_____________________________\|\n5'-UGC...CGUCU_______C_____A_____GCAG______GGCGG...GCG-3'\n______________UCAGCUU_ACCGG_CUGAU____CGCGGC\n______________\|\|\|\|\|\|\|_\|\|\|\|\|_\|\|\|\|\|____\|\|\|\|:\|\n______________AGUCGAA_UGGCC_GACUA____GCGCUG\n3'-UUU...CAGAG___________________GA________GUCAA...GUU-5'\n_____________\|_____________________________\|\n_____________66____________________________40\n	250 -- 256	59 -- 65	-34.6223 kcal/mol	8.37343 kcal/mol	13.1048 kcal/mol	249 279@LB@ \| \|@LB@5'-UGC...CGUCU C A GCAG GGCGG...GCG-3'@LB@ UCAGCUU ACCGG CUGAU CGCGGC@LB@ \|\|\|\|\|\|\| \|\|\|\|\| \|\|\|\|\| \|\|\|\|:\|@LB@ AGUCGAA UGGCC GACUA GCGCUG@LB@3'-UUU...CAGAG GA GUCAA...GUU-5'@LB@ \| \|@LB@ 66 40@LB@@LB@@LB@Energy -13.15 kcal/mol@LB@Hybridization Energy -34.6223 kcal/mol@LB@Unfolding Energy - mRNA 8.37343 kcal/mol@LB@Unfolding Energy - sRNA 13.1048 kcal/mol@LB@@LB@Position - mRNA 250 -- 278@LB@Position - sRNA 41 -- 65@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 59 -- 65@LB@
130	0.002619	0.0912	pa1320	cyoD	-12.20	0.057664	172 -- 192	99 -- 119	cytochrome o ubiquinol oxidase subunit IV		_____________171____________________193\n_____________\|______________________\|\n5'-UUC...UCUUC_____C_UC_____________GCCCU...CGU-3'\n______________ACCGU_G__UA_CCUGAUGGGG\n______________\|\|\|\|\|_\|__\|\|_\|\|\|\|\|\|\|:\|\|\n______________UGGCA_C__AU_GGACUACUCC\n3'-UUU...GUUUU_______UA__C__________UCUAU...GUU-5'\n_____________\|______________________\|\n_____________120____________________98\n	186 -- 192	99 -- 105	-23.5184 kcal/mol	9.07359 kcal/mol	2.24961 kcal/mol	171 193@LB@ \| \|@LB@5'-UUC...UCUUC C UC GCCCU...CGU-3'@LB@ ACCGU G UA CCUGAUGGGG@LB@ \|\|\|\|\| \| \|\| \|\|\|\|\|\|\|:\|\|@LB@ UGGCA C AU GGACUACUCC@LB@3'-UUU...GUUUU UA C UCUAU...GUU-5'@LB@ \| \|@LB@ 120 98@LB@@LB@@LB@Energy -12.20 kcal/mol@LB@Hybridization Energy -23.5184 kcal/mol@LB@Unfolding Energy - mRNA 9.07359 kcal/mol@LB@Unfolding Energy - sRNA 2.24961 kcal/mol@LB@@LB@Position - mRNA 172 -- 192@LB@Position - sRNA 99 -- 119@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 99 -- 105@LB@
6	4.972e-06	0.003808	pa1336	N/A	-12.31	0.054230	242 -- 253	107 -- 120	two-component sensor		_____________241____________254\n_____________\|______________\|\n5'-GUC...UCACU______________CCGCC...UGA-3'\n______________GACCGUGA__AGCC\n______________:\|\|\|\|\|\|\|__\|\|\|\|\n______________UUGGCACU__UCGG\n3'-UUU...AGUUU________AA____ACUAC...GUU-5'\n_____________\|______________\|\n_____________121____________106\n	243 -- 249	113 -- 119	-17.7907 kcal/mol	3.25304 kcal/mol	2.2351 kcal/mol	241 254@LB@ \| \|@LB@5'-GUC...UCACU CCGCC...UGA-3'@LB@ GACCGUGA AGCC@LB@ :\|\|\|\|\|\|\| \|\|\|\|@LB@ UUGGCACU UCGG@LB@3'-UUU...AGUUU AA ACUAC...GUU-5'@LB@ \| \|@LB@ 121 106@LB@@LB@@LB@Energy -12.31 kcal/mol@LB@Hybridization Energy -17.7907 kcal/mol@LB@Unfolding Energy - mRNA 3.25304 kcal/mol@LB@Unfolding Energy - sRNA 2.2351 kcal/mol@LB@@LB@Position - mRNA 242 -- 253@LB@Position - sRNA 107 -- 120@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 113 -- 119@LB@
44	0.0002709	0.02829	pa1340	N/A	-13.31	0.030188	17 -- 34	101 -- 117	amino acid ABC transporter permease		_____________16_________________35\n_____________\|__________________\|\n5'-AAC...GGCGU__C____C__________AGCUG...UCG-3'\n______________CG_UGAU_GGCCUGAUGG\n______________\|\|_\|\|\|\|_:\|\|\|\|\|\|\|\|:\n______________GC_ACUA_UCGGACUACU\n3'-UUU...UUUUG_______A__________CCUCU...GUU-5'\n_____________\|__________________\|\n_____________118________________100\n	28 -- 34	101 -- 107	-22.4618 kcal/mol	6.92464 kcal/mol	2.23144 kcal/mol	16 35@LB@ \| \|@LB@5'-AAC...GGCGU C C AGCUG...UCG-3'@LB@ CG UGAU GGCCUGAUGG@LB@ \|\| \|\|\|\| :\|\|\|\|\|\|\|\|:@LB@ GC ACUA UCGGACUACU@LB@3'-UUU...UUUUG A CCUCU...GUU-5'@LB@ \| \|@LB@ 118 100@LB@@LB@@LB@Energy -13.31 kcal/mol@LB@Hybridization Energy -22.4618 kcal/mol@LB@Unfolding Energy - mRNA 6.92464 kcal/mol@LB@Unfolding Energy - sRNA 2.23144 kcal/mol@LB@@LB@Position - mRNA 17 -- 34@LB@Position - sRNA 101 -- 117@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 101 -- 107@LB@
87	0.001101	0.05816	pa1343	N/A	-16.83	0.002748	192 -- 238	44 -- 87	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________191______________________________________________239\n_____________\|________________________________________________\|\n5'-UCG...CGCCU_______CCA____CUA_____AUCC_____C_______C_UG_____CGCAC...CCC-3'\n______________GGAGUCC___UGCG____UCUC____UCAGC_UGCUGGC_G__CUCGC\n______________:\|\|\|\|\|\|___\|\|\|\|____\|\|\|\|____\|\|\|\|\|_\|:\|:\|\|\|_\|__\|\|\|\|\|\n______________UCUCAGG___ACGC____AGAG____AGUCG_AUGGCCG_C__GAGCG\n3'-UUU...AGACU_______CUG____ACCC_____________A_______A_UA_____CUGGU...GUU-5'\n_____________\|________________________________________________\|\n_____________88_______________________________________________43\n	192 -- 198	81 -- 87	-49.5275 kcal/mol	13.8321 kcal/mol	18.8647 kcal/mol	191 239@LB@ \| \|@LB@5'-UCG...CGCCU CCA CUA AUCC C C UG CGCAC...CCC-3'@LB@ GGAGUCC UGCG UCUC UCAGC UGCUGGC G CUCGC@LB@ :\|\|\|\|\|\| \|\|\|\| \|\|\|\| \|\|\|\|\| \|:\|:\|\|\| \| \|\|\|\|\|@LB@ UCUCAGG ACGC AGAG AGUCG AUGGCCG C GAGCG@LB@3'-UUU...AGACU CUG ACCC A A UA CUGGU...GUU-5'@LB@ \| \|@LB@ 88 43@LB@@LB@@LB@Energy -16.83 kcal/mol@LB@Hybridization Energy -49.5275 kcal/mol@LB@Unfolding Energy - mRNA 13.8321 kcal/mol@LB@Unfolding Energy - sRNA 18.8647 kcal/mol@LB@@LB@Position - mRNA 192 -- 238@LB@Position - sRNA 44 -- 87@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 81 -- 87@LB@
57	0.0004766	0.03843	pa1413	N/A	-13.23	0.031643	209 -- 220	33 -- 44	transcriptional regulator	pa0708 pa4203	_____________208__________221\n_____________\|____________\|\n5'-GGU...GAGUU____________GAUUU...CGA-3'\n______________CGGCCAGUUGAG\n______________\|\|:\|\|\|\|\|\|\|\|\|\n______________GCUGGUCAACUC\n3'-UUU...AGAGC____________ACUGU...GUU-5'\n_____________\|____________\|\n_____________45___________32\n	214 -- 220	33 -- 39	-19.8607 kcal/mol	4.38796 kcal/mol	2.24787 kcal/mol	208 221@LB@ \| \|@LB@5'-GGU...GAGUU GAUUU...CGA-3'@LB@ CGGCCAGUUGAG@LB@ \|\|:\|\|\|\|\|\|\|\|\|@LB@ GCUGGUCAACUC@LB@3'-UUU...AGAGC ACUGU...GUU-5'@LB@ \| \|@LB@ 45 32@LB@@LB@@LB@Energy -13.23 kcal/mol@LB@Hybridization Energy -19.8607 kcal/mol@LB@Unfolding Energy - mRNA 4.38796 kcal/mol@LB@Unfolding Energy - sRNA 2.24787 kcal/mol@LB@@LB@Position - mRNA 209 -- 220@LB@Position - sRNA 33 -- 44@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 33 -- 39@LB@
134	0.002678	0.0912	pa1421	gbuA	-12.45	0.050008	184 -- 195	107 -- 120	guanidinobutyrase		_____________183____________196\n_____________\|______________\|\n5'-UCC...ACAAC______________ACCCC...CCG-3'\n______________GACCGUGA__GGCC\n______________:\|\|\|\|\|\|\|__:\|\|\|\n______________UUGGCACU__UCGG\n3'-UUU...AGUUU________AA____ACUAC...GUU-5'\n_____________\|______________\|\n_____________121____________106\n	185 -- 191	113 -- 119	-18.3112 kcal/mol	3.63401 kcal/mol	2.2351 kcal/mol	183 196@LB@ \| \|@LB@5'-UCC...ACAAC ACCCC...CCG-3'@LB@ GACCGUGA GGCC@LB@ :\|\|\|\|\|\|\| :\|\|\|@LB@ UUGGCACU UCGG@LB@3'-UUU...AGUUU AA ACUAC...GUU-5'@LB@ \| \|@LB@ 121 106@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -18.3112 kcal/mol@LB@Unfolding Energy - mRNA 3.63401 kcal/mol@LB@Unfolding Energy - sRNA 2.2351 kcal/mol@LB@@LB@Position - mRNA 184 -- 195@LB@Position - sRNA 107 -- 120@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 113 -- 119@LB@
60	0.000522	0.0395	pa1477	ccmC	-13.58	0.025601	178 -- 207	98 -- 123	heme exporter protein CcmC		_____________177____________________________208\n_____________\|______________________________\|\n5'-GCG...UUCCA_______C__UAAACAG__________U__AUUGG...UGC-3'\n______________AAGAGCC_UG_______AGCCUGAUGA_GA\n______________\|\|:\|:\|\|_\|\|_______\|\|\|\|\|\|\|\|\|\|_\|\|\n______________UUUUUGG_AC_______UCGGACUACU_CU\n3'-UUU...CCCAG_______C__UAA______________C__CUAUU...GUU-5'\n_____________\|______________________________\|\n_____________124____________________________97\n	198 -- 204	101 -- 107	-23.0207 kcal/mol	7.19156 kcal/mol	2.25245 kcal/mol	177 208@LB@ \| \|@LB@5'-GCG...UUCCA C UAAACAG U AUUGG...UGC-3'@LB@ AAGAGCC UG AGCCUGAUGA GA@LB@ \|\|:\|:\|\| \|\| \|\|\|\|\|\|\|\|\|\| \|\|@LB@ UUUUUGG AC UCGGACUACU CU@LB@3'-UUU...CCCAG C UAA C CUAUU...GUU-5'@LB@ \| \|@LB@ 124 97@LB@@LB@@LB@Energy -13.58 kcal/mol@LB@Hybridization Energy -23.0207 kcal/mol@LB@Unfolding Energy - mRNA 7.19156 kcal/mol@LB@Unfolding Energy - sRNA 2.25245 kcal/mol@LB@@LB@Position - mRNA 178 -- 207@LB@Position - sRNA 98 -- 123@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 101 -- 107@LB@
144	0.003137	0.1001	pa1516	N/A	-10.35	0.151671	51 -- 72	44 -- 62	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________50_____________________73\n_____________\|______________________\|\n5'-GUG...GGCCU__A_____________GG____CCGGC...AGA-3'\n______________GC_UUGCCGGUUGAUC__UCGC\n______________\|\|_\|\|:\|\|\|\|:\|\|\|\|\|__\|\|\|\|\n______________CG_AAUGGCCGACUAG__AGCG\n3'-UUU...AGAGU______________________CUGGU...GUU-5'\n_____________\|______________________\|\n_____________63_____________________43\n	57 -- 63	51 -- 57	-28.648 kcal/mol	8.16614 kcal/mol	10.1396 kcal/mol	50 73@LB@ \| \|@LB@5'-GUG...GGCCU A GG CCGGC...AGA-3'@LB@ GC UUGCCGGUUGAUC UCGC@LB@ \|\| \|\|:\|\|\|\|:\|\|\|\|\| \|\|\|\|@LB@ CG AAUGGCCGACUAG AGCG@LB@3'-UUU...AGAGU CUGGU...GUU-5'@LB@ \| \|@LB@ 63 43@LB@@LB@@LB@Energy -10.35 kcal/mol@LB@Hybridization Energy -28.648 kcal/mol@LB@Unfolding Energy - mRNA 8.16614 kcal/mol@LB@Unfolding Energy - sRNA 10.1396 kcal/mol@LB@@LB@Position - mRNA 51 -- 72@LB@Position - sRNA 44 -- 62@LB@Position Seed - mRNA 57 -- 63@LB@Position Seed - sRNA 51 -- 57@LB@
182	0.004765	0.1199	pa1522	N/A	-10.50	0.140829	28 -- 41	106 -- 119	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________27_____________42\n_____________\|______________\|\n5'-AUC...AGGAC_______CC_____CGCCG...CCG-3'\n______________GCCGUGG__AGCCU\n______________:\|\|\|\|\|:__\|\|\|\|\|\n______________UGGCACU__UCGGA\n3'-UUU...GUUUU_______AA_____CUACU...GUU-5'\n_____________\|______________\|\n_____________120____________105\n	28 -- 34	113 -- 119	-17.7026 kcal/mol	4.96349 kcal/mol	2.24014 kcal/mol	27 42@LB@ \| \|@LB@5'-AUC...AGGAC CC CGCCG...CCG-3'@LB@ GCCGUGG AGCCU@LB@ :\|\|\|\|\|: \|\|\|\|\|@LB@ UGGCACU UCGGA@LB@3'-UUU...GUUUU AA CUACU...GUU-5'@LB@ \| \|@LB@ 120 105@LB@@LB@@LB@Energy -10.50 kcal/mol@LB@Hybridization Energy -17.7026 kcal/mol@LB@Unfolding Energy - mRNA 4.96349 kcal/mol@LB@Unfolding Energy - sRNA 2.24014 kcal/mol@LB@@LB@Position - mRNA 28 -- 41@LB@Position - sRNA 106 -- 119@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 113 -- 119@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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