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	Additional homologs
110	0.003505	0.1114	b4111	proP	-11.30	0.052648	186 -- 222	48 -- 93	proline/glycine betaine transporter		_____________185________________________________________________223\n_____________\|__________________________________________________\|\n5'-CAC...CCAAC_________GA_____________U________________AAAA_____AACCG...GUA-3'\n______________UC_UGCGAG__AA____GCUAUGC_________GAAAAGGA____AGUAA\n______________\|\|_\|:\|\|\|:__\|\|____\|\|\|\|\|\|\|_________:\|\|\|\|\|\|\|____\|\|\|\|\|\n______________AG_AUGCUU__UU____CGAUACG_________UUUUUCCU____UCAUU\n3'-UUU...GCCGC__C______AG__AACA_______UCAUUAAGU_________________CUGUU...ACG-5'\n_____________\|__________________________________________________\|\n_____________94_________________________________________________47\n	198 -- 204	70 -- 76	-22.6159 kcal/mol	6.45165 kcal/mol	4.87071 kcal/mol	185 223@LB@ \| \|@LB@5'-CAC...CCAAC GA U AAAA AACCG...GUA-3'@LB@ UC UGCGAG AA GCUAUGC GAAAAGGA AGUAA@LB@ \|\| \|:\|\|\|: \|\| \|\|\|\|\|\|\| :\|\|\|\|\|\|\| \|\|\|\|\|@LB@ AG AUGCUU UU CGAUACG UUUUUCCU UCAUU@LB@3'-UUU...GCCGC C AG AACA UCAUUAAGU CUGUU...ACG-5'@LB@ \| \|@LB@ 94 47@LB@@LB@@LB@Energy -11.30 kcal/mol@LB@Hybridization Energy -22.6159 kcal/mol@LB@Unfolding Energy - mRNA 6.45165 kcal/mol@LB@Unfolding Energy - sRNA 4.87071 kcal/mol@LB@@LB@Position - mRNA 186 -- 222@LB@Position - sRNA 48 -- 93@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 70 -- 76@LB@
64	0.001067	0.05874	b3340	fusA	-13.60	0.012173	191 -- 223	21 -- 57	protein chain elongation factor EF-G GTP-binding		_____________190_____________________________________224\n_____________\|_______________________________________\|\n5'-AAC...UAAAC____________________CUC__A____A________ACGCU...ACA-3'\n______________GAGGAA_____ACAA_AUGG___GU_CAAC_CCCAUCGC\n______________:\|\|\|\|\|_____\|\|\|\|_\|\|\|\|___\|:_\|\|\|\|_\|\|\|\|\|\|\|\|\n______________UUCCUU_____UGUU_UACC___CG_GUUG_GGGUAGCG\n3'-UUU...GUUUU______CAUUC____A____U____C____C________AACUG...ACG-5'\n_____________\|_______________________________________\|\n_____________58______________________________________20\n	217 -- 223	21 -- 27	-33.2696 kcal/mol	6.00361 kcal/mol	13.6712 kcal/mol	190 224@LB@ \| \|@LB@5'-AAC...UAAAC CUC A A ACGCU...ACA-3'@LB@ GAGGAA ACAA AUGG GU CAAC CCCAUCGC@LB@ :\|\|\|\|\| \|\|\|\| \|\|\|\| \|: \|\|\|\| \|\|\|\|\|\|\|\|@LB@ UUCCUU UGUU UACC CG GUUG GGGUAGCG@LB@3'-UUU...GUUUU CAUUC A U C C AACUG...ACG-5'@LB@ \| \|@LB@ 58 20@LB@@LB@@LB@Energy -13.60 kcal/mol@LB@Hybridization Energy -33.2696 kcal/mol@LB@Unfolding Energy - mRNA 6.00361 kcal/mol@LB@Unfolding Energy - sRNA 13.6712 kcal/mol@LB@@LB@Position - mRNA 191 -- 223@LB@Position - sRNA 21 -- 57@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 21 -- 27@LB@
149	0.005854	0.1368	b2166	psuK	-12.08	0.032688	265 -- 298	54 -- 89	pseudouridine kinase		_____________264___________________________________299\n_____________\|_____________________________________\|\n5'-UUU...UUCAC________UUAAA__________________UCC___UA-3'\n______________AUGAAUCA______UUAUGCGG__AUUCAAA___AGG\n______________\|:\|\|\|\|\|\|______:\|\|\|\|\|:\|__\|\|\|\|\|\|\|___\|\|\|\n______________UGCUUAGU______GAUACGUC__UAAGUUU___UCC\n3'-UUU...CAGCA________UAACAC________AU_______UU____UUCAU...ACG-5'\n_____________\|_____________________________________\|\n_____________90____________________________________53\n	279 -- 285	68 -- 74	-22.7366 kcal/mol	5.9989 kcal/mol	4.66068 kcal/mol	264 299@LB@ \| \|@LB@5'-UUU...UUCAC UUAAA UCC UA-3'@LB@ AUGAAUCA UUAUGCGG AUUCAAA AGG@LB@ \|:\|\|\|\|\|\| :\|\|\|\|\|:\| \|\|\|\|\|\|\| \|\|\|@LB@ UGCUUAGU GAUACGUC UAAGUUU UCC@LB@3'-UUU...CAGCA UAACAC AU UU UUCAU...ACG-5'@LB@ \| \|@LB@ 90 53@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -22.7366 kcal/mol@LB@Unfolding Energy - mRNA 5.9989 kcal/mol@LB@Unfolding Energy - sRNA 4.66068 kcal/mol@LB@@LB@Position - mRNA 265 -- 298@LB@Position - sRNA 54 -- 89@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 68 -- 74@LB@
92	0.002723	0.1042	b1413	hrpA	-14.20	0.008055	24 -- 69	1 -- 41	putative ATP-dependent helicase		_____________23_______________________________________________70\n_____________\|________________________________________________\|\n5'-GGU...UUUGA________AU____________UGU____ACUU______CAAU_____CACAG...GCG-3'\n______________AUGG_GCG__GC_CCCGUUGCU___UGAC____UAUUCA____CCUGC\n______________\|\|\|\|_\|\|\|__:\|_\|\|\|:\|:\|\|\|___\|\|\|\|____:\|\|\|\|\|____\|\|\|\|\|\n______________UACC_CGC__UG_GGGUAGCGA___ACUG____GUAAGU____GGACG\n3'-UUU...UGUUA____U___GU__C________________CAAC_______________-5'\n_____________\|_______________________________________________\|\n_____________42______________________________________________1\n	37 -- 43	20 -- 26	-41.3168 kcal/mol	11.8333 kcal/mol	15.2922 kcal/mol	23 70@LB@ \| \|@LB@5'-GGU...UUUGA AU UGU ACUU CAAU CACAG...GCG-3'@LB@ AUGG GCG GC CCCGUUGCU UGAC UAUUCA CCUGC@LB@ \|\|\|\| \|\|\| :\| \|\|\|:\|:\|\|\| \|\|\|\| :\|\|\|\|\| \|\|\|\|\|@LB@ UACC CGC UG GGGUAGCGA ACUG GUAAGU GGACG@LB@3'-UUU...UGUUA U GU C CAAC -5'@LB@ \| \|@LB@ 42 1@LB@@LB@@LB@Energy -14.20 kcal/mol@LB@Hybridization Energy -41.3168 kcal/mol@LB@Unfolding Energy - mRNA 11.8333 kcal/mol@LB@Unfolding Energy - sRNA 15.2922 kcal/mol@LB@@LB@Position - mRNA 24 -- 69@LB@Position - sRNA 1 -- 41@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 20 -- 26@LB@
133	0.004969	0.1313	b0148	hrpB	-12.31	0.028366	190 -- 234	2 -- 40	putative ATP-dependent helicase		_____________189___________________________________________235\n_____________\|_____________________________________________\|\n5'-GCA...CCCUC________UU___G________GCC______UGCCGUC_______AAUUA...AAU-3'\n______________UGGAGCGU__UGU_UCGUCGUU___CGUUGC_______UUACCUG\n______________\|\|\|\|\|\|\|:__:\|:_:\|:\|\|\|:\|___\|\|\|\|\|\|_______\|:\|\|\|\|\|\n______________ACCUCGCG__GCG_GGUAGCGA___GCAACG_______AGUGGAC\n3'-UUU...GUUAU________UU____________ACU______UA____________G-5'\n_____________\|_____________________________________________\|\n_____________41____________________________________________1\n	228 -- 234	2 -- 8	-41.1674 kcal/mol	13.5737 kcal/mol	15.2914 kcal/mol	189 235@LB@ \| \|@LB@5'-GCA...CCCUC UU G GCC UGCCGUC AAUUA...AAU-3'@LB@ UGGAGCGU UGU UCGUCGUU CGUUGC UUACCUG@LB@ \|\|\|\|\|\|\|: :\|: :\|:\|\|\|:\| \|\|\|\|\|\| \|:\|\|\|\|\|@LB@ ACCUCGCG GCG GGUAGCGA GCAACG AGUGGAC@LB@3'-UUU...GUUAU UU ACU UA G-5'@LB@ \| \|@LB@ 41 1@LB@@LB@@LB@Energy -12.31 kcal/mol@LB@Hybridization Energy -41.1674 kcal/mol@LB@Unfolding Energy - mRNA 13.5737 kcal/mol@LB@Unfolding Energy - sRNA 15.2914 kcal/mol@LB@@LB@Position - mRNA 190 -- 234@LB@Position - sRNA 2 -- 40@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 2 -- 8@LB@
185	0.008022	0.1528	b1813	nudL	-20.51	0.000035	188 -- 228	15 -- 56	putative CoA pyrophosphohydrolase weak 3-phosphohydroxypyruvate phosphatase		_____________187____________________________________________229\n_____________\|______________________________________________\|\n5'-CCU...CAACU__A__________________AUAC_________G___________AUUUU...CUG-3'\n______________GG_GAAGUAAGAC___GUGGA____CGUAGC_CU_A_CGCUUGAUG\n______________:\|_\|\|\|\|\|\|\|\|\|\|___:\|\|\|\|____\|\|:\|:\|_\|:_\|_\|\|\|\|\|\|\|:\|\n______________UC_CUUCAUUCUG___UACCU____GCGUUG_GG_U_GCGAACUGC\n3'-UUU...UUUUU_____________UUA_____C_________C__G_A_________AACGU...ACG-5'\n_____________\|______________________________________________\|\n_____________57_____________________________________________14\n	221 -- 227	16 -- 22	-41.758 kcal/mol	7.45502 kcal/mol	13.7937 kcal/mol	187 229@LB@ \| \|@LB@5'-CCU...CAACU A AUAC G AUUUU...CUG-3'@LB@ GG GAAGUAAGAC GUGGA CGUAGC CU A CGCUUGAUG@LB@ :\| \|\|\|\|\|\|\|\|\|\| :\|\|\|\| \|\|:\|:\| \|: \| \|\|\|\|\|\|\|:\|@LB@ UC CUUCAUUCUG UACCU GCGUUG GG U GCGAACUGC@LB@3'-UUU...UUUUU UUA C C G A AACGU...ACG-5'@LB@ \| \|@LB@ 57 14@LB@@LB@@LB@Energy -20.51 kcal/mol@LB@Hybridization Energy -41.758 kcal/mol@LB@Unfolding Energy - mRNA 7.45502 kcal/mol@LB@Unfolding Energy - sRNA 13.7937 kcal/mol@LB@@LB@Position - mRNA 188 -- 228@LB@Position - sRNA 15 -- 56@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 16 -- 22@LB@
48	0.0005049	0.03706	b2331	smrB	-12.55	0.024312	152 -- 200	43 -- 92	putative DNA endonuclease		_____________151__________________________________________________201\n_____________\|____________________________________________________\|\n5'-UCA...GAUUG__C__________GUAAAC_______GAAAA_______UA___AC_______AUGAA...GAC-3'\n______________CG_UACGAGUCGG________UGUAG_____UUAGAAA__GAG___AGAUAA\n______________\|\|_\|\|\|\|\|:\|\|::________\|\|:\|\|_____\|:\|:\|\|\|__\|\|:___\|\|\|:\|\|\n______________GC_AUGCUUAGUU________ACGUC_____AGUUUUU__CUU___UCUGUU\n3'-UUU...CCGCA_____________AACACGAU_____AUUA________UC___CAU______AUACC...ACG-5'\n_____________\|____________________________________________________\|\n_____________93___________________________________________________42\n	158 -- 164	81 -- 87	-25.319 kcal/mol	6.91043 kcal/mol	5.86211 kcal/mol	151 201@LB@ \| \|@LB@5'-UCA...GAUUG C GUAAAC GAAAA UA AC AUGAA...GAC-3'@LB@ CG UACGAGUCGG UGUAG UUAGAAA GAG AGAUAA@LB@ \|\| \|\|\|\|\|:\|\|:: \|\|:\|\| \|:\|:\|\|\| \|\|: \|\|\|:\|\|@LB@ GC AUGCUUAGUU ACGUC AGUUUUU CUU UCUGUU@LB@3'-UUU...CCGCA AACACGAU AUUA UC CAU AUACC...ACG-5'@LB@ \| \|@LB@ 93 42@LB@@LB@@LB@Energy -12.55 kcal/mol@LB@Hybridization Energy -25.319 kcal/mol@LB@Unfolding Energy - mRNA 6.91043 kcal/mol@LB@Unfolding Energy - sRNA 5.86211 kcal/mol@LB@@LB@Position - mRNA 152 -- 200@LB@Position - sRNA 43 -- 92@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 81 -- 87@LB@
33	0.0002072	0.02212	b2101	yegW	-12.62	0.023301	188 -- 205	37 -- 56	putative DNA-binding transcriptional regulator		_____________187__________________206\n_____________\|____________________\|\n5'-CGG...CCGGC_____A______________ACAAG...AAA-3'\n______________AGGAA__AAGACAA_AUGGA\n______________\|\|\|\|\|__\|\|\|\|\|\|\|_\|\|\|\|\|\n______________UCCUU__UUCUGUU_UACCU\n3'-UUU...UUUUU_____CA_______A_____CGCGU...ACG-5'\n_____________\|____________________\|\n_____________57___________________36\n	194 -- 200	43 -- 49	-17.4469 kcal/mol	1.13054 kcal/mol	3.6645 kcal/mol	187 206@LB@ \| \|@LB@5'-CGG...CCGGC A ACAAG...AAA-3'@LB@ AGGAA AAGACAA AUGGA@LB@ \|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ UCCUU UUCUGUU UACCU@LB@3'-UUU...UUUUU CA A CGCGU...ACG-5'@LB@ \| \|@LB@ 57 36@LB@@LB@@LB@Energy -12.62 kcal/mol@LB@Hybridization Energy -17.4469 kcal/mol@LB@Unfolding Energy - mRNA 1.13054 kcal/mol@LB@Unfolding Energy - sRNA 3.6645 kcal/mol@LB@@LB@Position - mRNA 188 -- 205@LB@Position - sRNA 37 -- 56@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 43 -- 49@LB@
142	0.005444	0.1351	b3950	frwB	-10.99	0.063119	13 -- 50	47 -- 86	putative enzyme IIB component of PTS	b3899	_____________12__________________________________________51\n_____________\|___________________________________________\|\n5'-GCA...GGGGU____U__________C__________________C___C____UUAUA...GGG-3'\n______________GGUC_GAUUGUGCUG__CGGUGGUU____GAAGG_AAG_UGGG\n______________::\|\|_:\|\|\|\|\|\|\|\|:__\|:\|\|::\|\|____:\|\|\|\|_\|\|\|_\|::\|\n______________UUAG_UUAACACGAU__GUCAUUAA____UUUCC_UUC_AUUC\n3'-UUU...CAUGC_______________AC________GUUU______________UGUUA...ACG-5'\n_____________\|___________________________________________\|\n_____________87__________________________________________46\n	30 -- 36	63 -- 69	-27.1662 kcal/mol	11.4404 kcal/mol	4.74035 kcal/mol	12 51@LB@ \| \|@LB@5'-GCA...GGGGU U C C C UUAUA...GGG-3'@LB@ GGUC GAUUGUGCUG CGGUGGUU GAAGG AAG UGGG@LB@ ::\|\| :\|\|\|\|\|\|\|\|: \|:\|\|::\|\| :\|\|\|\| \|\|\| \|::\|@LB@ UUAG UUAACACGAU GUCAUUAA UUUCC UUC AUUC@LB@3'-UUU...CAUGC AC GUUU UGUUA...ACG-5'@LB@ \| \|@LB@ 87 46@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -27.1662 kcal/mol@LB@Unfolding Energy - mRNA 11.4404 kcal/mol@LB@Unfolding Energy - sRNA 4.74035 kcal/mol@LB@@LB@Position - mRNA 13 -- 50@LB@Position - sRNA 47 -- 86@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 63 -- 69@LB@
53	0.0006788	0.04512	b3949	frwC	-10.17	0.100438	200 -- 218	68 -- 90	putative enzyme IIC component of PTS		_____________199_____________________219\n_____________\|_______________________\|\n5'-UUG...CAGCU_______G_______________AUCCU...UGG-3'\n______________UAUGAAU_AGUUG____GUGCAG\n______________\|\|:\|\|\|\|_\|:\|\|\|____:\|\|\|\|\|\n______________AUGCUUA_UUAAC____UACGUC\n3'-UUU...GCAGC_______G_____ACGA______AUUAA...ACG-5'\n_____________\|_______________________\|\n_____________91______________________67\n	200 -- 206	84 -- 90	-18.2816 kcal/mol	3.60123 kcal/mol	4.51505 kcal/mol	199 219@LB@ \| \|@LB@5'-UUG...CAGCU G AUCCU...UGG-3'@LB@ UAUGAAU AGUUG GUGCAG@LB@ \|\|:\|\|\|\| \|:\|\|\| :\|\|\|\|\|@LB@ AUGCUUA UUAAC UACGUC@LB@3'-UUU...GCAGC G ACGA AUUAA...ACG-5'@LB@ \| \|@LB@ 91 67@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -18.2816 kcal/mol@LB@Unfolding Energy - mRNA 3.60123 kcal/mol@LB@Unfolding Energy - sRNA 4.51505 kcal/mol@LB@@LB@Position - mRNA 200 -- 218@LB@Position - sRNA 68 -- 90@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 84 -- 90@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