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
41	0.00828	0.5385	b2246	rhmT	-13.65	0.023999	257 -- 273	69 -- 86	putative L-rhamnonate transporter	_____________256________________274\n_____________\|__________________\|\n5'-ACG...AUUCC____________GCU___AUGUG...CGA-3'\n______________GUUUAUGUUGGC____GU\n______________\|\|\|:\|:\|\|\|\|\|\|____\|\|\n______________CAAGUGCAACCG____CA\n3'-CGC...GUUUU____________AAAU__AUAAG...AAG-5'\n_____________\|__________________\|\n_____________87_________________68\n	262 -- 268	75 -- 81	-18.6828 kcal/mol	4.45929 kcal/mol	0.568509 kcal/mol	256 274@LB@ \| \|@LB@5'-ACG...AUUCC GCU AUGUG...CGA-3'@LB@ GUUUAUGUUGGC GU@LB@ \|\|\|:\|:\|\|\|\|\|\| \|\|@LB@ CAAGUGCAACCG CA@LB@3'-CGC...GUUUU AAAU AUAAG...AAG-5'@LB@ \| \|@LB@ 87 68@LB@@LB@@LB@Energy -13.65 kcal/mol@LB@Hybridization Energy -18.6828 kcal/mol@LB@Unfolding Energy - mRNA 4.45929 kcal/mol@LB@Unfolding Energy - sRNA 0.568509 kcal/mol@LB@@LB@Position - mRNA 257 -- 273@LB@Position - sRNA 69 -- 86@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 75 -- 81@LB@
68	0.013	0.5385	b2823	ppdC	-12.74	0.034901	243 -- 262	69 -- 89	putative prepilin peptidase-dependent protein	_____________242___________________263\n_____________\|_____________________\|\n5'-ACG...UGCCG_____A_________GA____GUUGA...UCC-3'\n______________GAGGU__AUGUUGGC__UGGU\n______________:\|:\|\|__\|:\|\|\|\|\|\|__\|:\|\|\n______________UUUCA__UGCAACCG__AUCA\n3'-CGC...GGCGU_____AG________AA____AUAAG...AAG-5'\n_____________\|_____________________\|\n_____________90____________________68\n	250 -- 256	75 -- 81	-18.5568 kcal/mol	5.24273 kcal/mol	0.572143 kcal/mol	242 263@LB@ \| \|@LB@5'-ACG...UGCCG A GA GUUGA...UCC-3'@LB@ GAGGU AUGUUGGC UGGU@LB@ :\|:\|\| \|:\|\|\|\|\|\| \|:\|\|@LB@ UUUCA UGCAACCG AUCA@LB@3'-CGC...GGCGU AG AA AUAAG...AAG-5'@LB@ \| \|@LB@ 90 68@LB@@LB@@LB@Energy -12.74 kcal/mol@LB@Hybridization Energy -18.5568 kcal/mol@LB@Unfolding Energy - mRNA 5.24273 kcal/mol@LB@Unfolding Energy - sRNA 0.572143 kcal/mol@LB@@LB@Position - mRNA 243 -- 262@LB@Position - sRNA 69 -- 89@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 75 -- 81@LB@
75	0.01364	0.5385	b0107	hofB	-15.68	0.010425	272 -- 289	69 -- 87	T2SE secretion family protein; P-loop ATPase superfamily protein	_____________271_________________290\n_____________\|___________________\|\n5'-CCA...GAGGU_____________GG____CGAUG...CUU-3'\n______________GGUUCAUGUUG_C__UAGU\n______________:\|\|\|\|\|:\|\|\|\|_\|__\|\|\|\|\n______________UCAAGUGCAAC_G__AUCA\n3'-CGC...CGUUU___________C_AA____AUAAG...AAG-5'\n_____________\|___________________\|\n_____________88__________________68\n	276 -- 282	77 -- 83	-18.3354 kcal/mol	2.08484 kcal/mol	0.569189 kcal/mol	271 290@LB@ \| \|@LB@5'-CCA...GAGGU GG CGAUG...CUU-3'@LB@ GGUUCAUGUUG C UAGU@LB@ :\|\|\|\|\|:\|\|\|\| \| \|\|\|\|@LB@ UCAAGUGCAAC G AUCA@LB@3'-CGC...CGUUU C AA AUAAG...AAG-5'@LB@ \| \|@LB@ 88 68@LB@@LB@@LB@Energy -15.68 kcal/mol@LB@Hybridization Energy -18.3354 kcal/mol@LB@Unfolding Energy - mRNA 2.08484 kcal/mol@LB@Unfolding Energy - sRNA 0.569189 kcal/mol@LB@@LB@Position - mRNA 272 -- 289@LB@Position - sRNA 69 -- 87@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 77 -- 83@LB@
85	0.01519	0.5385	b0094	ftsA	-12.00	0.047343	234 -- 271	69 -- 107	ATP-binding cell division FtsK recruitment protein	_____________233__________________________________________272\n_____________\|____________________________________________\|\n5'-AAU...UAGUA_____________UGGUA___________GC_____________AGGGG...UCA-3'\n______________GGA__CUGGAGAU_____CCGCGAAGGUU__C____GCUUUAGU\n______________\|\|\|__\|\|\|\|\|\|\|\|_____\|\|\|\|:\|\|:\|\|\|__\|____\|\|\|\|\|\|\|\|\n______________CCU__GACCUCUA_____GGCGUUUUCAA__G____CGAAAUCA\n_________3'-CG___AG________________________GU_CAAC________AUAAG...AAG-5'\n_____________\|____________________________________________\|\n_____________108__________________________________________68\n	265 -- 271	69 -- 75	-38.6824 kcal/mol	14.7528 kcal/mol	11.9342 kcal/mol	233 272@LB@ \| \|@LB@5'-AAU...UAGUA UGGUA GC AGGGG...UCA-3'@LB@ GGA CUGGAGAU CCGCGAAGGUU C GCUUUAGU@LB@ \|\|\| \|\|\|\|\|\|\|\| \|\|\|\|:\|\|:\|\|\| \| \|\|\|\|\|\|\|\|@LB@ CCU GACCUCUA GGCGUUUUCAA G CGAAAUCA@LB@ 3'-CG AG GU CAAC AUAAG...AAG-5'@LB@ \| \|@LB@ 108 68@LB@@LB@@LB@Energy -12.00 kcal/mol@LB@Hybridization Energy -38.6824 kcal/mol@LB@Unfolding Energy - mRNA 14.7528 kcal/mol@LB@Unfolding Energy - sRNA 11.9342 kcal/mol@LB@@LB@Position - mRNA 234 -- 271@LB@Position - sRNA 69 -- 107@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 69 -- 75@LB@
90	0.01553	0.5385	b1043	csgC	-15.92	0.009464	100 -- 115	69 -- 84	curli assembly protein	_____________99_______________116\n_____________\|________________\|\n5'-GUG...GUGAC___G____________AACAA...UUA-3'\n______________UCA_GUUGGCUUUGGU\n______________\|\|\|_\|\|\|\|\|\|\|\|\|:\|\|\n______________AGU_CAACCGAAAUCA\n3'-CGC...UUUCA___G____________AUAAG...AAG-5'\n_____________\|________________\|\n_____________85_______________68\n	109 -- 115	69 -- 75	-23.6243 kcal/mol	7.14442 kcal/mol	0.563592 kcal/mol	99 116@LB@ \| \|@LB@5'-GUG...GUGAC G AACAA...UUA-3'@LB@ UCA GUUGGCUUUGGU@LB@ \|\|\| \|\|\|\|\|\|\|\|\|:\|\|@LB@ AGU CAACCGAAAUCA@LB@3'-CGC...UUUCA G AUAAG...AAG-5'@LB@ \| \|@LB@ 85 68@LB@@LB@@LB@Energy -15.92 kcal/mol@LB@Hybridization Energy -23.6243 kcal/mol@LB@Unfolding Energy - mRNA 7.14442 kcal/mol@LB@Unfolding Energy - sRNA 0.563592 kcal/mol@LB@@LB@Position - mRNA 100 -- 115@LB@Position - sRNA 69 -- 84@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 69 -- 75@LB@
92	0.01569	0.5385	b1246	oppD	-11.32	0.062179	266 -- 290	69 -- 90	oligopeptide ABC transporter ATPase	_____________265_______________________291\n_____________\|_________________________\|\n5'-AGC...AACGU_____A_______GUCAC_______ACCCC...ACG-3'\n______________GAAAG_UUUGCGU_____CUUUAGU\n______________:\|\|\|\|_\|\|::\|\|\|_____\|\|\|\|\|\|\|\n______________UUUUC_AAGUGCA_____GAAAUCA\n3'-CGC...AGGCG_____________ACC_________AUAAG...AAG-5'\n_____________\|_________________________\|\n_____________91________________________68\n	284 -- 290	69 -- 75	-14.6652 kcal/mol	2.76867 kcal/mol	0.572281 kcal/mol	265 291@LB@ \| \|@LB@5'-AGC...AACGU A GUCAC ACCCC...ACG-3'@LB@ GAAAG UUUGCGU CUUUAGU@LB@ :\|\|\|\| \|\|::\|\|\| \|\|\|\|\|\|\|@LB@ UUUUC AAGUGCA GAAAUCA@LB@3'-CGC...AGGCG ACC AUAAG...AAG-5'@LB@ \| \|@LB@ 91 68@LB@@LB@@LB@Energy -11.32 kcal/mol@LB@Hybridization Energy -14.6652 kcal/mol@LB@Unfolding Energy - mRNA 2.76867 kcal/mol@LB@Unfolding Energy - sRNA 0.572281 kcal/mol@LB@@LB@Position - mRNA 266 -- 290@LB@Position - sRNA 69 -- 90@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 69 -- 75@LB@
146	0.0246	0.5467	b2813	mltA	-8.67	0.177423	203 -- 222	69 -- 90	membrane-bound lytic murein transglycosylase A	_____________202____________________223\n_____________\|______________________\|\n5'-UGC...ACAAU_____G_________G_AA___ACCUU...AAG-3'\n______________GAAAG___ACGUUGG_U__AGU\n______________:\|\|\|\|___\|\|\|\|\|\|\|_\|__\|\|\|\n______________UUUUC___UGCAACC_A__UCA\n3'-CGC...AGGCG_____AAG_______G_AA___AUAAG...AAG-5'\n_____________\|______________________\|\n_____________91_____________________68\n	209 -- 215	76 -- 82	-14.1188 kcal/mol	4.87564 kcal/mol	0.572281 kcal/mol	202 223@LB@ \| \|@LB@5'-UGC...ACAAU G G AA ACCUU...AAG-3'@LB@ GAAAG ACGUUGG U AGU@LB@ :\|\|\|\| \|\|\|\|\|\|\| \| \|\|\|@LB@ UUUUC UGCAACC A UCA@LB@3'-CGC...AGGCG AAG G AA AUAAG...AAG-5'@LB@ \| \|@LB@ 91 68@LB@@LB@@LB@Energy -8.67 kcal/mol@LB@Hybridization Energy -14.1188 kcal/mol@LB@Unfolding Energy - mRNA 4.87564 kcal/mol@LB@Unfolding Energy - sRNA 0.572281 kcal/mol@LB@@LB@Position - mRNA 203 -- 222@LB@Position - sRNA 69 -- 90@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 76 -- 82@LB@
172	0.03064	0.5559	b1542	ydfI	-13.08	0.030437	273 -- 290	69 -- 86	putative NAD-dependent D-mannonate oxidoreductase	_____________272________________291\n_____________\|__________________\|\n5'-CUC...GAAUU______UUA_________GCAUU...ACC-3'\n______________GUUCAU___GGCUUUGGU\n______________\|\|\|\|\|:___\|\|\|\|\|\|:\|\|\n______________CAAGUG___CCGAAAUCA\n3'-CGC...GUUUU______CAA_________AUAAG...AAG-5'\n_____________\|__________________\|\n_____________87_________________68\n	284 -- 290	69 -- 75	-19.6529 kcal/mol	6.00837 kcal/mol	0.568509 kcal/mol	272 291@LB@ \| \|@LB@5'-CUC...GAAUU UUA GCAUU...ACC-3'@LB@ GUUCAU GGCUUUGGU@LB@ \|\|\|\|\|: \|\|\|\|\|\|:\|\|@LB@ CAAGUG CCGAAAUCA@LB@3'-CGC...GUUUU CAA AUAAG...AAG-5'@LB@ \| \|@LB@ 87 68@LB@@LB@@LB@Energy -13.08 kcal/mol@LB@Hybridization Energy -19.6529 kcal/mol@LB@Unfolding Energy - mRNA 6.00837 kcal/mol@LB@Unfolding Energy - sRNA 0.568509 kcal/mol@LB@@LB@Position - mRNA 273 -- 290@LB@Position - sRNA 69 -- 86@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 69 -- 75@LB@
191	0.03353	0.5559	b2129	yehX	-7.36	0.287226	59 -- 67	69 -- 77	putative ABC transporter ATPase	_____________58________68\n_____________\|_________\|\n5'-GGU...CAGGC_________GCGCU...UUG-3'\n______________GGUUUUGGU\n______________\|\|:\|\|\|:\|\|\n______________CCGAAAUCA\n3'-CGC...UGCAA_________AUAAG...AAG-5'\n_____________\|_________\|\n_____________78________68\n	61 -- 67	69 -- 75	-10.3561 kcal/mol	2.74802 kcal/mol	0.243235 kcal/mol	58 68@LB@ \| \|@LB@5'-GGU...CAGGC GCGCU...UUG-3'@LB@ GGUUUUGGU@LB@ \|\|:\|\|\|:\|\|@LB@ CCGAAAUCA@LB@3'-CGC...UGCAA AUAAG...AAG-5'@LB@ \| \|@LB@ 78 68@LB@@LB@@LB@Energy -7.36 kcal/mol@LB@Hybridization Energy -10.3561 kcal/mol@LB@Unfolding Energy - mRNA 2.74802 kcal/mol@LB@Unfolding Energy - sRNA 0.243235 kcal/mol@LB@@LB@Position - mRNA 59 -- 67@LB@Position - sRNA 69 -- 77@LB@Position Seed - mRNA 61 -- 67@LB@Position Seed - sRNA 69 -- 75@LB@
70	0.01301	0.5385	b1424	opgD	-12.13	0.044753	222 -- 240	70 -- 90	OPG biosynthetic periplasmic protein	_____________221___________________241\n_____________\|_____________________\|\n5'-AAU...UUAUU_________A_______A___CCGCC...CAG-3'\n______________AAAGGUUCA___UGGCU_UGG\n______________\|\|\|:\|\|\|\|\|___\|\|\|\|\|_\|:\|\n______________UUUUCAAGU___ACCGA_AUC\n3'-CGC...AGGCG_________GCA_____A___AAUAA...AAG-5'\n_____________\|_____________________\|\n_____________91____________________69\n	224 -- 230	82 -- 88	-16.4191 kcal/mol	3.71348 kcal/mol	0.572228 kcal/mol	221 241@LB@ \| \|@LB@5'-AAU...UUAUU A A CCGCC...CAG-3'@LB@ AAAGGUUCA UGGCU UGG@LB@ \|\|\|:\|\|\|\|\| \|\|\|\|\| \|:\|@LB@ UUUUCAAGU ACCGA AUC@LB@3'-CGC...AGGCG GCA A AAUAA...AAG-5'@LB@ \| \|@LB@ 91 69@LB@@LB@@LB@Energy -12.13 kcal/mol@LB@Hybridization Energy -16.4191 kcal/mol@LB@Unfolding Energy - mRNA 3.71348 kcal/mol@LB@Unfolding Energy - sRNA 0.572228 kcal/mol@LB@@LB@Position - mRNA 222 -- 240@LB@Position - sRNA 70 -- 90@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 82 -- 88@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching