Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
19	0.0004926	0.08107	b0820	ybiT	-10.62	0.010514	37 -- 84	2 -- 44	ABC-F family putative regulatory ATPase	_____________36________________________________________________85\n_____________\|_________________________________________________\|\n5'-CCU...GUAUU________A___U_______A__CCA__U_A___U______A_______ACGAA...UUG-3'\n______________GGAAGCGC_UUA__AAGUUC_UU___GC_C_CAG_GAAAUC_GAUGUGU\n______________:\|\|\|\|\|:\|_\|\|\|__\|\|:\|\|\|_\|\|___:\|_\|_\|\|\|_\|\|\|\|\|\|_\|\|\|\|\|\|\|\n______________UCUUCGUG_AAU__UUUAAG_AA___UG_G_GUC_CUUUAG_CUACACA\n3'-UUU...UUCGU____________UU______C_______U____________A_______A-5'\n_____________\|_________________________________________________\|\n_____________45________________________________________________1\n	38 -- 44	37 -- 43	-34.6599 kcal/mol	11.843 kcal/mol	12.1934 kcal/mol	36 85@LB@ \| \|@LB@5'-CCU...GUAUU A U A CCA U A U A ACGAA...UUG-3'@LB@ GGAAGCGC UUA AAGUUC UU GC C CAG GAAAUC GAUGUGU@LB@ :\|\|\|\|\|:\| \|\|\| \|\|:\|\|\| \|\| :\| \| \|\|\| \|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UCUUCGUG AAU UUUAAG AA UG G GUC CUUUAG CUACACA@LB@3'-UUU...UUCGU UU C U A A-5'@LB@ \| \|@LB@ 45 1@LB@@LB@@LB@Energy -10.62 kcal/mol@LB@Hybridization Energy -34.6599 kcal/mol@LB@Unfolding Energy - mRNA 11.843 kcal/mol@LB@Unfolding Energy - sRNA 12.1934 kcal/mol@LB@@LB@Position - mRNA 37 -- 84@LB@Position - sRNA 2 -- 44@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 37 -- 43@LB@
48	0.002202	0.1465	b3209	elbB	-11.61	0.005163	95 -- 137	2 -- 41	isoprenoid biosynthesis protein with amidotransferase-like domain	_____________94__________________________________________138\n_____________\|___________________________________________\|\n5'-GCG...AAGAU___AAA_______U____________G_AUC____AA______GAUGC...GUG-3'\n______________AGC___ACUUAAA_GAUUUGUUACAU_A___AGUU__AUGUGU\n______________\|\|\|___\|\|\|\|\|\|\|_:\|\|\|:\|\|\|\|\|\|:_\|___\|:\|:__\|\|\|\|\|\|\n______________UCG___UGAAUUU_UUAAGCAAUGUG_U___UUAG__UACACA\n3'-UUU...GUUCU_____________U____________G_CCU____AC______A-5'\n_____________\|___________________________________________\|\n_____________42__________________________________________1\n	101 -- 107	32 -- 38	-29.0989 kcal/mol	8.27062 kcal/mol	9.22136 kcal/mol	94 138@LB@ \| \|@LB@5'-GCG...AAGAU AAA U G AUC AA GAUGC...GUG-3'@LB@ AGC ACUUAAA GAUUUGUUACAU A AGUU AUGUGU@LB@ \|\|\| \|\|\|\|\|\|\| :\|\|\|:\|\|\|\|\|\|: \| \|:\|: \|\|\|\|\|\|@LB@ UCG UGAAUUU UUAAGCAAUGUG U UUAG UACACA@LB@3'-UUU...GUUCU U G CCU AC A-5'@LB@ \| \|@LB@ 42 1@LB@@LB@@LB@Energy -11.61 kcal/mol@LB@Hybridization Energy -29.0989 kcal/mol@LB@Unfolding Energy - mRNA 8.27062 kcal/mol@LB@Unfolding Energy - sRNA 9.22136 kcal/mol@LB@@LB@Position - mRNA 95 -- 137@LB@Position - sRNA 2 -- 41@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 32 -- 38@LB@
146	0.01469	0.3231	b0026	ileS	-7.82	0.067581	147 -- 206	2 -- 59	isoleucyl-tRNA synthetase	_____________146_____________________________________________________________207\n_____________\|_______________________________________________________________\|\n5'-AUG...UAACA____CG________CU_UUAU___AUCAAACC_____A__GA______A___________A__GACUA...CUG-3'\n______________AAAC__GCUUAAGC__G____GUA________GAAAU_CG____ACCG__GAAUCUGAUG_GU\n______________\|\|\|\|__\|\|\|\|\|\|\|\|__\|____\|:\|________:\|\|\|\|_\|\|____\|\|\|:__:\|\|\|\|\|\|\|\|\|_\|\|\n______________UUUG__CGAAUUCG__C____CGU________UUUUA_GC____UGGU__UUUAGACUAC_CA\n3'-UUU...CCUAC____AA________UU_UU_____GAAUU________A__AAUG____CC__________A__A-5'\n_____________\|_______________________________________________________________\|\n_____________60______________________________________________________________1\n	197 -- 203	5 -- 11	-33.6314 kcal/mol	11.9684 kcal/mol	13.8468 kcal/mol	146 207@LB@ \| \|@LB@5'-AUG...UAACA CG CU UUAU AUCAAACC A GA A A GACUA...CUG-3'@LB@ AAAC GCUUAAGC G GUA GAAAU CG ACCG GAAUCUGAUG GU@LB@ \|\|\|\| \|\|\|\|\|\|\|\| \| \|:\| :\|\|\|\| \|\| \|\|\|: :\|\|\|\|\|\|\|\|\| \|\|@LB@ UUUG CGAAUUCG C CGU UUUUA GC UGGU UUUAGACUAC CA@LB@3'-UUU...CCUAC AA UU UU GAAUU A AAUG CC A A-5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -7.82 kcal/mol@LB@Hybridization Energy -33.6314 kcal/mol@LB@Unfolding Energy - mRNA 11.9684 kcal/mol@LB@Unfolding Energy - sRNA 13.8468 kcal/mol@LB@@LB@Position - mRNA 147 -- 206@LB@Position - sRNA 2 -- 59@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 5 -- 11@LB@
185	0.02171	0.3768	b0059	rapA	-7.86	0.065955	35 -- 74	2 -- 42	RNA polymerase remodeling/recycling factor ATPase; RNA polymerase-associated ATP-dependent RNA translocase	_____________34___________________________________________75\n_____________\|____________________________________________\|\n5'-GCU...AUUUU_____AAAA__________CCAG______U___________C__GACGA...UUU-3'\n______________GAGCA____AAAGAGUUCG____AUACCA_____UUUGAUG_GU\n______________:\|\|\|\|____\|\|\|:\|:\|\|\|\|____\|:\|\|\|\|_____\|:\|\|\|\|\|_\|\|\n______________UUCGU____UUUUUUAAGC____UGUGGU_____AGACUAC_CA\n3'-UUU...CGUUC_____GAA___________AA________CCUUU_______A__A-5'\n_____________\|____________________________________________\|\n_____________43___________________________________________1\n	47 -- 53	25 -- 31	-26.2778 kcal/mol	9.20057 kcal/mol	9.22149 kcal/mol	34 75@LB@ \| \|@LB@5'-GCU...AUUUU AAAA CCAG U C GACGA...UUU-3'@LB@ GAGCA AAAGAGUUCG AUACCA UUUGAUG GU@LB@ :\|\|\|\| \|\|\|:\|:\|\|\|\| \|:\|\|\|\| \|:\|\|\|\|\| \|\|@LB@ UUCGU UUUUUUAAGC UGUGGU AGACUAC CA@LB@3'-UUU...CGUUC GAA AA CCUUU A A-5'@LB@ \| \|@LB@ 43 1@LB@@LB@@LB@Energy -7.86 kcal/mol@LB@Hybridization Energy -26.2778 kcal/mol@LB@Unfolding Energy - mRNA 9.20057 kcal/mol@LB@Unfolding Energy - sRNA 9.22149 kcal/mol@LB@@LB@Position - mRNA 35 -- 74@LB@Position - sRNA 2 -- 42@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 25 -- 31@LB@
91	0.006547	0.2317	b1323	tyrR	-8.26	0.051378	202 -- 222	3 -- 23	aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase	_____________201___________________223\n_____________\|_____________________\|\n5'-UCG...UCCCA______U________UU____AAGAC...UUG-3'\n______________UGCGUC_GGAAGUCU__UGUG\n______________\|:\|::\|_\|\|\|\|:\|\|\|__\|\|\|\|\n______________AUGUGG_CCUUUAGA__ACAC\n3'-UUU...AAGCA______U________CU____AA-5'\n_____________\|_____________________\|\n_____________24____________________2\n	209 -- 215	10 -- 16	-19.6247 kcal/mol	3.79223 kcal/mol	7.5769 kcal/mol	201 223@LB@ \| \|@LB@5'-UCG...UCCCA U UU AAGAC...UUG-3'@LB@ UGCGUC GGAAGUCU UGUG@LB@ \|:\|::\| \|\|\|\|:\|\|\| \|\|\|\|@LB@ AUGUGG CCUUUAGA ACAC@LB@3'-UUU...AAGCA U CU AA-5'@LB@ \| \|@LB@ 24 2@LB@@LB@@LB@Energy -8.26 kcal/mol@LB@Hybridization Energy -19.6247 kcal/mol@LB@Unfolding Energy - mRNA 3.79223 kcal/mol@LB@Unfolding Energy - sRNA 7.5769 kcal/mol@LB@@LB@Position - mRNA 202 -- 222@LB@Position - sRNA 3 -- 23@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 10 -- 16@LB@
173	0.01972	0.3669	b3426	glpD	-5.91	0.203159	207 -- 224	3 -- 20	sn-glycerol-3-phosphate dehydrogenase aerobic FAD/NAD(P)-binding	_____________206_________________225\n_____________\|___________________\|\n5'-AAC...UGGAA____A_________U____AUAGG...AGG-3'\n______________ACCA__AGAUCUGA_UGUG\n______________\|\|\|\|__\|:\|\|\|\|\|\|_\|\|\|\|\n______________UGGU__UUUAGACU_ACAC\n3'-UUU...CAAUG____CC_____________AA-5'\n_____________\|___________________\|\n_____________21__________________2\n	213 -- 219	7 -- 13	-16.1802 kcal/mol	2.74973 kcal/mol	7.52321 kcal/mol	206 225@LB@ \| \|@LB@5'-AAC...UGGAA A U AUAGG...AGG-3'@LB@ ACCA AGAUCUGA UGUG@LB@ \|\|\|\| \|:\|\|\|\|\|\| \|\|\|\|@LB@ UGGU UUUAGACU ACAC@LB@3'-UUU...CAAUG CC AA-5'@LB@ \| \|@LB@ 21 2@LB@@LB@@LB@Energy -5.91 kcal/mol@LB@Hybridization Energy -16.1802 kcal/mol@LB@Unfolding Energy - mRNA 2.74973 kcal/mol@LB@Unfolding Energy - sRNA 7.52321 kcal/mol@LB@@LB@Position - mRNA 207 -- 224@LB@Position - sRNA 3 -- 20@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 7 -- 13@LB@
10	0.0001005	0.03239	b1260	trpA	-10.26	0.013526	184 -- 203	5 -- 22	tryptophan synthase alpha subunit	_____________183__________________204\n_____________\|____________________\|\n5'-GCC...UGAAA____GAG_____________GAACG...CAU-3'\n______________GCAC___GGGAAAUCUGAUG\n______________:\|\|\|___:\|\|\|\|\|\|\|\|\|\|\|\|\n______________UGUG___UCCUUUAGACUAC\n3'-UUU...AGCAA____G_______________ACAA-5'\n_____________\|____________________\|\n_____________23___________________4\n	192 -- 198	10 -- 16	-23.1901 kcal/mol	5.35202 kcal/mol	7.57357 kcal/mol	183 204@LB@ \| \|@LB@5'-GCC...UGAAA GAG GAACG...CAU-3'@LB@ GCAC GGGAAAUCUGAUG@LB@ :\|\|\| :\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UGUG UCCUUUAGACUAC@LB@3'-UUU...AGCAA G ACAA-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -10.26 kcal/mol@LB@Hybridization Energy -23.1901 kcal/mol@LB@Unfolding Energy - mRNA 5.35202 kcal/mol@LB@Unfolding Energy - sRNA 7.57357 kcal/mol@LB@@LB@Position - mRNA 184 -- 203@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 10 -- 16@LB@
39	0.00159	0.1292	b1637	tyrS	-8.51	0.043578	178 -- 203	5 -- 27	tyrosyl-tRNA synthetase	_____________177________________________204\n_____________\|__________________________\|\n5'-CAU...UGCAG_________A__U_______U_____GCAAG...CGA-3'\n______________UCGUUAUAU_CA_GGAGAUU_UGAUG\n______________\|\|\|\|\|\|:\|:_\|\|_\|\|\|:\|\|:_\|\|\|\|\|\n______________AGCAAUGUG_GU_CCUUUAG_ACUAC\n3'-UUU...UUUUA__________________________ACAA-5'\n_____________\|__________________________\|\n_____________28_________________________4\n	191 -- 197	10 -- 16	-22.7194 kcal/mol	5.60368 kcal/mol	8.60118 kcal/mol	177 204@LB@ \| \|@LB@5'-CAU...UGCAG A U U GCAAG...CGA-3'@LB@ UCGUUAUAU CA GGAGAUU UGAUG@LB@ \|\|\|\|\|\|:\|: \|\| \|\|\|:\|\|: \|\|\|\|\|@LB@ AGCAAUGUG GU CCUUUAG ACUAC@LB@3'-UUU...UUUUA ACAA-5'@LB@ \| \|@LB@ 28 4@LB@@LB@@LB@Energy -8.51 kcal/mol@LB@Hybridization Energy -22.7194 kcal/mol@LB@Unfolding Energy - mRNA 5.60368 kcal/mol@LB@Unfolding Energy - sRNA 8.60118 kcal/mol@LB@@LB@Position - mRNA 178 -- 203@LB@Position - sRNA 5 -- 27@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 10 -- 16@LB@
98	0.007325	0.239	b4171	miaA	-8.40	0.046782	42 -- 58	5 -- 24	delta(2)-isopentenylpyrophosphate tRNA-adenosine transferase	_____________41___________________59\n_____________\|____________________\|\n5'-GAA...GUGGA____________________AGCGA...UUU-3'\n______________UUGCAC___GAAAUCUGAUG\n______________\|\|:\|\|\|___\|\|\|\|\|\|\|\|\|\|\|\n______________AAUGUG___CUUUAGACUAC\n3'-UUU...UAAGC______GUC___________ACAA-5'\n_____________\|____________________\|\n_____________25___________________4\n	52 -- 58	5 -- 11	-19.996 kcal/mol	4.00751 kcal/mol	7.58501 kcal/mol	41 59@LB@ \| \|@LB@5'-GAA...GUGGA AGCGA...UUU-3'@LB@ UUGCAC GAAAUCUGAUG@LB@ \|\|:\|\|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ AAUGUG CUUUAGACUAC@LB@3'-UUU...UAAGC GUC ACAA-5'@LB@ \| \|@LB@ 25 4@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -19.996 kcal/mol@LB@Unfolding Energy - mRNA 4.00751 kcal/mol@LB@Unfolding Energy - sRNA 7.58501 kcal/mol@LB@@LB@Position - mRNA 42 -- 58@LB@Position - sRNA 5 -- 24@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 5 -- 11@LB@
158	0.01725	0.3504	b3857	mobA	-11.09	0.007545	184 -- 212	5 -- 35	molybdopterin-guanine dinucleotide synthase	_____________183_____________________________213\n_____________\|_______________________________\|\n5'-UCC...CACAA_______GG___________U__________ACGAC...AAC-3'\n______________UAAAAGA__CG__AUAUCGG_GAAUCUGAUG\n______________\|\|\|\|\|:\|__\|\|__\|:\|:\|:\|_:\|\|\|\|\|\|\|\|\|\n______________AUUUUUU__GC__UGUGGUC_UUUAGACUAC\n3'-UUU...CGUGA_______AA__AA_______C__________ACAA-5'\n_____________\|_______________________________\|\n_____________36______________________________4\n	184 -- 190	29 -- 35	-25.0811 kcal/mol	5.24608 kcal/mol	8.74745 kcal/mol	183 213@LB@ \| \|@LB@5'-UCC...CACAA GG U ACGAC...AAC-3'@LB@ UAAAAGA CG AUAUCGG GAAUCUGAUG@LB@ \|\|\|\|\|:\| \|\| \|:\|:\|:\| :\|\|\|\|\|\|\|\|\|@LB@ AUUUUUU GC UGUGGUC UUUAGACUAC@LB@3'-UUU...CGUGA AA AA C ACAA-5'@LB@ \| \|@LB@ 36 4@LB@@LB@@LB@Energy -11.09 kcal/mol@LB@Hybridization Energy -25.0811 kcal/mol@LB@Unfolding Energy - mRNA 5.24608 kcal/mol@LB@Unfolding Energy - sRNA 8.74745 kcal/mol@LB@@LB@Position - mRNA 184 -- 212@LB@Position - sRNA 5 -- 35@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 29 -- 35@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