Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
130	0.00465	0.126	b2916	argP	-9.43	0.148863	238 -- 266	47 -- 73	transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor	_____________237___________________________267\n_____________\|_____________________________\|\n5'-GGC...ACUGG__________ACG____C_____UU____CGCGC...CAG-3'\n______________AUGCGGUGAU___UGAA_GAGGA__UGAG\n______________\|\|\|\|:\|\|:\|\|___::\|\|_:\|\|\|\|__\|:\|\|\n______________UACGUCAUUA___GUUU_UUCCU__AUUC\n3'-UUU...CACGA__________A______U_____UC____UGUUA...ACG-5'\n_____________\|_____________________________\|\n_____________74____________________________46\n	240 -- 246	65 -- 71	-19.9139 kcal/mol	5.97985 kcal/mol	4.50495 kcal/mol	237 267@LB@ \| \|@LB@5'-GGC...ACUGG ACG C UU CGCGC...CAG-3'@LB@ AUGCGGUGAU UGAA GAGGA UGAG@LB@ \|\|\|\|:\|\|:\|\| ::\|\| :\|\|\|\| \|:\|\|@LB@ UACGUCAUUA GUUU UUCCU AUUC@LB@3'-UUU...CACGA A U UC UGUUA...ACG-5'@LB@ \| \|@LB@ 74 46@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -19.9139 kcal/mol@LB@Unfolding Energy - mRNA 5.97985 kcal/mol@LB@Unfolding Energy - sRNA 4.50495 kcal/mol@LB@@LB@Position - mRNA 238 -- 266@LB@Position - sRNA 47 -- 73@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 65 -- 71@LB@
73	0.001571	0.0758	b3746	ravA	-8.41	0.246327	240 -- 262	54 -- 75	hexameric AAA+ MoxR family ATPase putative molecular chaperone	_____________239_____________________263\n_____________\|_______________________\|\n5'-UGA...CCCGC___A_____UC___G________GCUUU...UAU-3'\n______________CUG_GCAGU__GUU_GAAAAGGG\n______________\|\|:_\|\|\|\|\|__:\|\|_:\|\|\|\|:\|\|\n______________GAU_CGUCA__UAA_UUUUUUCC\n3'-UUU...AACAC___A_____U____G________UUCAU...ACG-5'\n_____________\|_______________________\|\n_____________76______________________53\n	256 -- 262	54 -- 60	-19.2007 kcal/mol	7.09588 kcal/mol	3.69534 kcal/mol	239 263@LB@ \| \|@LB@5'-UGA...CCCGC A UC G GCUUU...UAU-3'@LB@ CUG GCAGU GUU GAAAAGGG@LB@ \|\|: \|\|\|\|\| :\|\| :\|\|\|\|:\|\|@LB@ GAU CGUCA UAA UUUUUUCC@LB@3'-UUU...AACAC A U G UUCAU...ACG-5'@LB@ \| \|@LB@ 76 53@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -19.2007 kcal/mol@LB@Unfolding Energy - mRNA 7.09588 kcal/mol@LB@Unfolding Energy - sRNA 3.69534 kcal/mol@LB@@LB@Position - mRNA 240 -- 262@LB@Position - sRNA 54 -- 75@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 54 -- 60@LB@
89	0.002455	0.09689	b0466	ybaM	-10.99	0.063193	248 -- 263	68 -- 82	DUF2496 family protein	_____________247______________264\n_____________\|________________\|\n5'-GCA...GAUUU__________C__G__GAAAA...CGC-3'\n______________GAUUGUGCUG_UG_AG\n______________:\|\|\|\|\|\|\|\|:_\|\|_\|\|\n______________UUAACACGAU_AC_UC\n3'-UUU...CUUAG_____________G__AUUAA...ACG-5'\n_____________\|________________\|\n_____________83_______________67\n	251 -- 257	73 -- 79	-16.1643 kcal/mol	2.45269 kcal/mol	2.72435 kcal/mol	247 264@LB@ \| \|@LB@5'-GCA...GAUUU C G GAAAA...CGC-3'@LB@ GAUUGUGCUG UG AG@LB@ :\|\|\|\|\|\|\|\|: \|\| \|\|@LB@ UUAACACGAU AC UC@LB@3'-UUU...CUUAG G AUUAA...ACG-5'@LB@ \| \|@LB@ 83 67@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -16.1643 kcal/mol@LB@Unfolding Energy - mRNA 2.45269 kcal/mol@LB@Unfolding Energy - sRNA 2.72435 kcal/mol@LB@@LB@Position - mRNA 248 -- 263@LB@Position - sRNA 68 -- 82@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 73 -- 79@LB@
93	0.002751	0.1042	b3407	yhgF	-15.01	0.004479	248 -- 282	1 -- 31	putative transcriptional accessory protein	_____________247_________________________________283\n_____________\|___________________________________\|\n5'-CCC...CAGGC_______GAACA_G______C__C___________UUGAC...CCG-3'\n______________GCGCCCG_____G_UUGACG_UG_CGUUCGCCUGC\n______________:\|\|\|\|\|:_____\|_\|\|\|\|\|\|_\|\|_\|:\|\|\|:\|\|\|\|\|\n______________UGCGGGU_____C_AACUGC_AC_GUAAGUGGACG\n3'-UUU...CGCGU_______AG____G______A______________-5'\n_____________\|__________________________________\|\n_____________32_________________________________1\n	276 -- 282	1 -- 7	-43.3047 kcal/mol	13.2535 kcal/mol	15.0438 kcal/mol	247 283@LB@ \| \|@LB@5'-CCC...CAGGC GAACA G C C UUGAC...CCG-3'@LB@ GCGCCCG G UUGACG UG CGUUCGCCUGC@LB@ :\|\|\|\|\|: \| \|\|\|\|\|\| \|\| \|:\|\|\|:\|\|\|\|\|@LB@ UGCGGGU C AACUGC AC GUAAGUGGACG@LB@3'-UUU...CGCGU AG G A -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -15.01 kcal/mol@LB@Hybridization Energy -43.3047 kcal/mol@LB@Unfolding Energy - mRNA 13.2535 kcal/mol@LB@Unfolding Energy - sRNA 15.0438 kcal/mol@LB@@LB@Position - mRNA 248 -- 282@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 1 -- 7@LB@
85	0.002164	0.08969	b0910	cmk	-11.54	0.045559	249 -- 300	1 -- 56	cytidylate kinase	_____________248________________________________________________________300\n_____________\|__________________________________________________________\|\n5'-CCG...GUGCA_____________CCUU_________G______G__GGAA________AUGG_______-3'\n______________GGGA___AAGGCA_______GUGUAA_G_CUAU_GC____GCGUUGCA____CAUCUGC\n______________:\|\|\|___\|\|\|:\|\|_______\|:\|:\|\|_\|_\|:\|\|_\|\|____:\|\|\|\|\|\|\|____\|\|:\|\|\|\|\n______________UCCU___UUCUGU_______CGCGUU_C_GGUA_CG____UGCAACGU____GUGGACG\n3'-UUU...UUUUU____UCA______UAUACCU______G_G____G__AAC_________AA_________-5'\n_____________\|__________________________________________________________\|\n_____________57_________________________________________________________1\n	294 -- 300	1 -- 7	-44.7718 kcal/mol	16.3932 kcal/mol	16.8439 kcal/mol	248 300@LB@ \| \|@LB@5'-CCG...GUGCA CCUU G G GGAA AUGG -3'@LB@ GGGA AAGGCA GUGUAA G CUAU GC GCGUUGCA CAUCUGC@LB@ :\|\|\| \|\|\|:\|\| \|:\|:\|\| \| \|:\|\| \|\| :\|\|\|\|\|\|\| \|\|:\|\|\|\|@LB@ UCCU UUCUGU CGCGUU C GGUA CG UGCAACGU GUGGACG@LB@3'-UUU...UUUUU UCA UAUACCU G G G AAC AA -5'@LB@ \| \|@LB@ 57 1@LB@@LB@@LB@Energy -11.54 kcal/mol@LB@Hybridization Energy -44.7718 kcal/mol@LB@Unfolding Energy - mRNA 16.3932 kcal/mol@LB@Unfolding Energy - sRNA 16.8439 kcal/mol@LB@@LB@Position - mRNA 249 -- 300@LB@Position - sRNA 1 -- 56@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 1 -- 7@LB@
113	0.00365	0.1131	b3154	yhbP	-10.91	0.065979	249 -- 297	26 -- 85	UPF0306 family protein	_____________248___________________________________________________________298\n_____________\|_____________________________________________________________\|\n5'-AAA...AUGUU____C___GUG_______C_____________________ACUC____U____U_______UUU-3'\n______________GUCA_UUG___UGUGCAG___________AGGAAG_GGGA_____UGG_GCGC_AAUGCCU\n______________:\|\|\|_\|\|\|___\|:\|\|\|\|\|___________\|\|\|\|\|\|_::\|\|_____\|\|\|_\|\|\|\|_\|\|:\|\|\|:\n______________UAGU_AAC___AUACGUC___________UCCUUC_UUCU_____ACC_CGCG_UUGCGGG\n3'-UUU...AUGCU____U___ACG_______AUUAAGUUUUU______A____GUUAU___U____________UAGCG...ACG-5'\n_____________\|_____________________________________________________________\|\n_____________86____________________________________________________________25\n	260 -- 266	68 -- 74	-42.816 kcal/mol	18.2405 kcal/mol	13.6657 kcal/mol	248 298@LB@ \| \|@LB@5'-AAA...AUGUU C GUG C ACUC U U UUU-3'@LB@ GUCA UUG UGUGCAG AGGAAG GGGA UGG GCGC AAUGCCU@LB@ :\|\|\| \|\|\| \|:\|\|\|\|\| \|\|\|\|\|\| ::\|\| \|\|\| \|\|\|\| \|\|:\|\|\|:@LB@ UAGU AAC AUACGUC UCCUUC UUCU ACC CGCG UUGCGGG@LB@3'-UUU...AUGCU U ACG AUUAAGUUUUU A GUUAU U UAGCG...ACG-5'@LB@ \| \|@LB@ 86 25@LB@@LB@@LB@Energy -10.91 kcal/mol@LB@Hybridization Energy -42.816 kcal/mol@LB@Unfolding Energy - mRNA 18.2405 kcal/mol@LB@Unfolding Energy - sRNA 13.6657 kcal/mol@LB@@LB@Position - mRNA 249 -- 297@LB@Position - sRNA 26 -- 85@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 68 -- 74@LB@
70	0.001371	0.06901	b2989	yghU	-9.78	0.124117	251 -- 269	4 -- 23	putative S-transferase	_____________250__________________270\n_____________\|____________________\|\n5'-UUA...AAAUC_________GC_________AAUAU...CGC-3'\n______________CGC_UGGCG__GCGUUCGCC\n______________\|\|\|_\|\|:\|\|__\|\|:\|\|\|:\|\|\n______________GCG_ACUGC__CGUAAGUGG\n3'-UUU...GGGUA___A_____AA_________ACG-5'\n_____________\|____________________\|\n_____________24___________________3\n	263 -- 269	4 -- 10	-26.6155 kcal/mol	8.73321 kcal/mol	8.10973 kcal/mol	250 270@LB@ \| \|@LB@5'-UUA...AAAUC GC AAUAU...CGC-3'@LB@ CGC UGGCG GCGUUCGCC@LB@ \|\|\| \|\|:\|\| \|\|:\|\|\|:\|\|@LB@ GCG ACUGC CGUAAGUGG@LB@3'-UUU...GGGUA A AA ACG-5'@LB@ \| \|@LB@ 24 3@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -26.6155 kcal/mol@LB@Unfolding Energy - mRNA 8.73321 kcal/mol@LB@Unfolding Energy - sRNA 8.10973 kcal/mol@LB@@LB@Position - mRNA 251 -- 269@LB@Position - sRNA 4 -- 23@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 4 -- 10@LB@
158	0.006224	0.1377	b3553	ghrB	-7.62	0.349627	252 -- 258	1 -- 7	glyoxylate/hydroxypyruvate reductase B	_____________251_____259\n_____________\|_______\|\n5'-UCA...UGCAA_______AAGAG...CAC-3'\n______________CGCCUGC\n______________\|:\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	252 -- 258	1 -- 7	-12.8134 kcal/mol	2.86334 kcal/mol	2.34039 kcal/mol	251 259@LB@ \| \|@LB@5'-UCA...UGCAA AAGAG...CAC-3'@LB@ CGCCUGC@LB@ \|:\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -7.62 kcal/mol@LB@Hybridization Energy -12.8134 kcal/mol@LB@Unfolding Energy - mRNA 2.86334 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 252 -- 258@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 1 -- 7@LB@
159	0.006259	0.1377	b2194	ccmH	-11.29	0.052751	252 -- 296	43 -- 89	heme lyase CcmH subunit	_____________251__________________________________________________297\n_____________\|____________________________________________________\|\n5'-CUG...CGCUG____CC_____________________________U_____CAC___A____CAGU-3'\n______________GCGA__AUCGA_UGUGUUG__CAGU___UUAAAGA__GAAG___AGG_ACAA\n______________:\|\|\|__\|\|\|:\|_\|\|\|\|:\|:__\|\|\|\|___\|:\|\|\|:\|__\|\|\|\|___\|:\|_\|\|\|\|\n______________UGCU__UAGUU_ACACGAU__GUCA___AGUUUUU__CUUC___UUC_UGUU\n3'-UUU...CAGCA___________A_______AC____UUA_______UC____A__________AUACC...ACG-5'\n_____________\|____________________________________________________\|\n_____________90___________________________________________________42\n	263 -- 269	73 -- 79	-25.337 kcal/mol	8.31324 kcal/mol	5.7326 kcal/mol	251 297@LB@ \| \|@LB@5'-CUG...CGCUG CC U CAC A CAGU-3'@LB@ GCGA AUCGA UGUGUUG CAGU UUAAAGA GAAG AGG ACAA@LB@ :\|\|\| \|\|\|:\| \|\|\|\|:\|: \|\|\|\| \|:\|\|\|:\| \|\|\|\| \|:\| \|\|\|\|@LB@ UGCU UAGUU ACACGAU GUCA AGUUUUU CUUC UUC UGUU@LB@3'-UUU...CAGCA A AC UUA UC A AUACC...ACG-5'@LB@ \| \|@LB@ 90 42@LB@@LB@@LB@Energy -11.29 kcal/mol@LB@Hybridization Energy -25.337 kcal/mol@LB@Unfolding Energy - mRNA 8.31324 kcal/mol@LB@Unfolding Energy - sRNA 5.7326 kcal/mol@LB@@LB@Position - mRNA 252 -- 296@LB@Position - sRNA 43 -- 89@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 73 -- 79@LB@
167	0.006646	0.1402	b0007	yaaJ	-8.17	0.274480	254 -- 261	1 -- 8	putative transporter	_____________253______262\n_____________\|________\|\n5'-CAA...AUGAU________UCUUC...GAU-3'\n______________UUACCUGC\n______________\|:\|\|\|\|\|\|\n______________AGUGGACG\n3'-UUU...ACGUA________-5'\n_____________\|_______\|\n_____________9_______1\n	255 -- 261	1 -- 7	-12.8229 kcal/mol	2.29081 kcal/mol	2.36381 kcal/mol	253 262@LB@ \| \|@LB@5'-CAA...AUGAU UCUUC...GAU-3'@LB@ UUACCUGC@LB@ \|:\|\|\|\|\|\|@LB@ AGUGGACG@LB@3'-UUU...ACGUA -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -8.17 kcal/mol@LB@Hybridization Energy -12.8229 kcal/mol@LB@Unfolding Energy - mRNA 2.29081 kcal/mol@LB@Unfolding Energy - sRNA 2.36381 kcal/mol@LB@@LB@Position - mRNA 254 -- 261@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 1 -- 7@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