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
172	0.007014	0.1437	b3430	glgC	-13.14	0.016567	21 -- 80	1 -- 39	glucose-1-phosphate adenylyltransferase	_____________20______________________________________________________________81\n_____________\|_______________________________________________________________\|\n5'-CAG...CUCUC___U___UUUUUGAUCGCAAUU______A_________G__AACAGAGAU_____________UGGGG...UGA-3'\n______________GGA_CGC_______________AACGCC___CGCUUGA_GU_________UGU_UUUACCUGC\n______________\|\|\|_\|\|\|_______________\|\|\|\|\|\|___\|\|\|\|\|\|\|_\|\|_________\|\|:_\|\|:\|\|\|\|\|\|\n______________CCU_GCG_______________UUGCGG___GCGAACU_CA_________ACG_AAGUGGACG\n3'-UUU...UUAUA___C________________________GUA_______G______________U_________-5'\n_____________\|______________________________________________________________\|\n_____________40_____________________________________________________________1\n	74 -- 80	1 -- 7	-41.5646 kcal/mol	13.1395 kcal/mol	15.291 kcal/mol	20 81@LB@ \| \|@LB@5'-CAG...CUCUC U UUUUUGAUCGCAAUU A G AACAGAGAU UGGGG...UGA-3'@LB@ GGA CGC AACGCC CGCUUGA GU UGU UUUACCUGC@LB@ \|\|\| \|\|\| \|\|\|\|\|\| \|\|\|\|\|\|\| \|\| \|\|: \|\|:\|\|\|\|\|\|@LB@ CCU GCG UUGCGG GCGAACU CA ACG AAGUGGACG@LB@3'-UUU...UUAUA C GUA G U -5'@LB@ \| \|@LB@ 40 1@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -41.5646 kcal/mol@LB@Unfolding Energy - mRNA 13.1395 kcal/mol@LB@Unfolding Energy - sRNA 15.291 kcal/mol@LB@@LB@Position - mRNA 21 -- 80@LB@Position - sRNA 1 -- 39@LB@Position Seed - mRNA 74 -- 80@LB@Position Seed - sRNA 1 -- 7@LB@
117	0.00395	0.1189	b3447	ggt	-7.92	0.307079	7 -- 34	69 -- 94	gamma-glutamyltranspeptidase	_____________6____________________________35\n_____________\|____________________________\|\n_____5'-GUUAGG_____UCA____AUUAA__G________AAGCC...CGU-3'\n______________GUUGU___GAGU_____UG_GCUGUGCA\n______________\|\|:\|\|___\|\|:\|_____\|\|_\|\|\|:\|\|\|\|\n______________CAGCA___CUUA_____AC_CGAUACGU\n3'-UUU...AGCCG_____UG_____GUUA___A________CAUUA...ACG-5'\n_____________\|____________________________\|\n_____________95___________________________68\n	28 -- 34	69 -- 75	-19.4914 kcal/mol	6.89072 kcal/mol	4.68367 kcal/mol	6 35@LB@ \| \|@LB@ 5'-GUUAGG UCA AUUAA G AAGCC...CGU-3'@LB@ GUUGU GAGU UG GCUGUGCA@LB@ \|\|:\|\| \|\|:\| \|\| \|\|\|:\|\|\|\|@LB@ CAGCA CUUA AC CGAUACGU@LB@3'-UUU...AGCCG UG GUUA A CAUUA...ACG-5'@LB@ \| \|@LB@ 95 68@LB@@LB@@LB@Energy -7.92 kcal/mol@LB@Hybridization Energy -19.4914 kcal/mol@LB@Unfolding Energy - mRNA 6.89072 kcal/mol@LB@Unfolding Energy - sRNA 4.68367 kcal/mol@LB@@LB@Position - mRNA 7 -- 34@LB@Position - sRNA 69 -- 94@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 69 -- 75@LB@
29	0.0001601	0.01945	b3472	dcrB	-12.60	0.023536	186 -- 203	41 -- 59	putative lipoprotein	_____________185_________________204\n_____________\|___________________\|\n5'-UGG...UUAUC_____________U_____CGCAA...UCG-3'\n______________GAAAGGAAG_AAG_CAAUG\n______________:\|\|\|\|\|\|\|\|_\|\|\|_\|\|\|\|:\n______________UUUUCCUUC_UUC_GUUAU\n3'-UUU...AAGUU_________A___U_____ACCUC...ACG-5'\n_____________\|___________________\|\n_____________60__________________40\n	188 -- 194	51 -- 57	-16.362 kcal/mol	1.80431 kcal/mol	1.95655 kcal/mol	185 204@LB@ \| \|@LB@5'-UGG...UUAUC U CGCAA...UCG-3'@LB@ GAAAGGAAG AAG CAAUG@LB@ :\|\|\|\|\|\|\|\| \|\|\| \|\|\|\|:@LB@ UUUUCCUUC UUC GUUAU@LB@3'-UUU...AAGUU A U ACCUC...ACG-5'@LB@ \| \|@LB@ 60 40@LB@@LB@@LB@Energy -12.60 kcal/mol@LB@Hybridization Energy -16.362 kcal/mol@LB@Unfolding Energy - mRNA 1.80431 kcal/mol@LB@Unfolding Energy - sRNA 1.95655 kcal/mol@LB@@LB@Position - mRNA 186 -- 203@LB@Position - sRNA 41 -- 59@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 51 -- 57@LB@
103	0.003335	0.1114	b3494	uspB	-9.88	0.117554	193 -- 207	43 -- 57	universal stress (ethanol tolerance) protein B	_____________192_____________208\n_____________\|_______________\|\n5'-AAU...CCGGG_________U_____GCACC...UGC-3'\n______________GAGGAGGUA_GAUAA\n______________:\|\|\|\|:\|\|\|_\|\|:\|\|\n______________UUCCUUCAU_CUGUU\n3'-UUU...GUUUU_________U_____AUACC...ACG-5'\n_____________\|_______________\|\n_____________58______________42\n	195 -- 201	49 -- 55	-16.0492 kcal/mol	4.41466 kcal/mol	1.75421 kcal/mol	192 208@LB@ \| \|@LB@5'-AAU...CCGGG U GCACC...UGC-3'@LB@ GAGGAGGUA GAUAA@LB@ :\|\|\|\|:\|\|\| \|\|:\|\|@LB@ UUCCUUCAU CUGUU@LB@3'-UUU...GUUUU U AUACC...ACG-5'@LB@ \| \|@LB@ 58 42@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -16.0492 kcal/mol@LB@Unfolding Energy - mRNA 4.41466 kcal/mol@LB@Unfolding Energy - sRNA 1.75421 kcal/mol@LB@@LB@Position - mRNA 193 -- 207@LB@Position - sRNA 43 -- 57@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 49 -- 55@LB@
182	0.007798	0.1509	b3523	yhjE	-11.78	0.039321	145 -- 165	64 -- 85	putative MFS transporter; membrane protein	_____________144____________________166\n_____________\|______________________\|\n5'-AAC...GAAAU____C__U______________AUGGC...UUG-3'\n______________AUCA_UU_UGCUGUGC_GUAAU\n______________\|\|\|\|_\|\|_\|\|\|\|:\|\|\|_\|\|\|\|\|\n______________UAGU_AA_ACGAUACG_CAUUA\n3'-UUU...AUGCU____U__C________U_____AGUUU...ACG-5'\n_____________\|______________________\|\n_____________86_____________________63\n	154 -- 160	70 -- 76	-18.5967 kcal/mol	3.10692 kcal/mol	3.70798 kcal/mol	144 166@LB@ \| \|@LB@5'-AAC...GAAAU C U AUGGC...UUG-3'@LB@ AUCA UU UGCUGUGC GUAAU@LB@ \|\|\|\| \|\| \|\|\|\|:\|\|\| \|\|\|\|\|@LB@ UAGU AA ACGAUACG CAUUA@LB@3'-UUU...AUGCU U C U AGUUU...ACG-5'@LB@ \| \|@LB@ 86 63@LB@@LB@@LB@Energy -11.78 kcal/mol@LB@Hybridization Energy -18.5967 kcal/mol@LB@Unfolding Energy - mRNA 3.10692 kcal/mol@LB@Unfolding Energy - sRNA 3.70798 kcal/mol@LB@@LB@Position - mRNA 145 -- 165@LB@Position - sRNA 64 -- 85@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 70 -- 76@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@
173	0.007186	0.145	b3554	yiaF	-10.99	0.063148	166 -- 198	46 -- 94	barrier effect co-colonization resistance factor; DUF3053 family lipoprotein	_____________165_______________________________________________199\n_____________\|_________________________________________________\|\n5'-AAU...GUGUC________CU__UU___G_______________________________AAAUG...AGC-3'\n______________GUUGUGCG__UU__UUG_GU_______________GAAAGG_AGUAAGA\n______________\|\|:\|\|:\|\|__\|:__\|\|\|_\|:_______________:\|\|\|\|\|_\|\|\|\|\|\|\|\n______________CAGCAUGC__AG__AAC_CG_______________UUUUCC_UCAUUCU\n3'-UUU...AGCCG________UU__UU___A__AUACGUCAUUAAGUU______U_______GUUAU...ACG-5'\n_____________\|_________________________________________________\|\n_____________95________________________________________________45\n	192 -- 198	46 -- 52	-24.2986 kcal/mol	7.73667 kcal/mol	5.5768 kcal/mol	165 199@LB@ \| \|@LB@5'-AAU...GUGUC CU UU G AAAUG...AGC-3'@LB@ GUUGUGCG UU UUG GU GAAAGG AGUAAGA@LB@ \|\|:\|\|:\|\| \|: \|\|\| \|: :\|\|\|\|\| \|\|\|\|\|\|\|@LB@ CAGCAUGC AG AAC CG UUUUCC UCAUUCU@LB@3'-UUU...AGCCG UU UU A AUACGUCAUUAAGUU U GUUAU...ACG-5'@LB@ \| \|@LB@ 95 45@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -24.2986 kcal/mol@LB@Unfolding Energy - mRNA 7.73667 kcal/mol@LB@Unfolding Energy - sRNA 5.5768 kcal/mol@LB@@LB@Position - mRNA 166 -- 198@LB@Position - sRNA 46 -- 94@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 46 -- 52@LB@
119	0.004048	0.119	b3607	cysE	-9.06	0.179616	191 -- 204	40 -- 54	serine acetyltransferase	_____________190_____________205\n_____________\|_______________\|\n5'-CGG...CGUGU_______________CGUGU...CGA-3'\n______________GGAGUAAG_CAAUGU\n______________\|:\|\|\|\|\|\|_\|\|\|\|:\|\n______________CUUCAUUC_GUUAUA\n3'-UUU...UUUUC________U______CCUCG...ACG-5'\n_____________\|_______________\|\n_____________55______________39\n	192 -- 198	47 -- 53	-13.6491 kcal/mol	2.75521 kcal/mol	1.82942 kcal/mol	190 205@LB@ \| \|@LB@5'-CGG...CGUGU CGUGU...CGA-3'@LB@ GGAGUAAG CAAUGU@LB@ \|:\|\|\|\|\|\| \|\|\|\|:\|@LB@ CUUCAUUC GUUAUA@LB@3'-UUU...UUUUC U CCUCG...ACG-5'@LB@ \| \|@LB@ 55 39@LB@@LB@@LB@Energy -9.06 kcal/mol@LB@Hybridization Energy -13.6491 kcal/mol@LB@Unfolding Energy - mRNA 2.75521 kcal/mol@LB@Unfolding Energy - sRNA 1.82942 kcal/mol@LB@@LB@Position - mRNA 191 -- 204@LB@Position - sRNA 40 -- 54@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 47 -- 53@LB@
43	0.0004177	0.03347	b3652	recG	-10.52	0.082371	49 -- 71	17 -- 38	ATP-dependent DNA helicase	_____________48______________________72\n_____________\|_______________________\|\n5'-CAA...AAGCA____AA_________________AGGCG...UGC-3'\n______________GAGC__CAACGCCUGUUGUUUGA\n______________\|\|\|\|__\|\|\|\|\|\|\|::\|:\|:\|\|\|\|\n______________CUCG__GUUGCGGGUAGCGAACU\n3'-UUU...UAUAC____C__________________GCAAC...ACG-5'\n_____________\|_______________________\|\n_____________39______________________16\n	63 -- 69	19 -- 25	-31.2627 kcal/mol	8.52631 kcal/mol	12.2147 kcal/mol	48 72@LB@ \| \|@LB@5'-CAA...AAGCA AA AGGCG...UGC-3'@LB@ GAGC CAACGCCUGUUGUUUGA@LB@ \|\|\|\| \|\|\|\|\|\|\|::\|:\|:\|\|\|\|@LB@ CUCG GUUGCGGGUAGCGAACU@LB@3'-UUU...UAUAC C GCAAC...ACG-5'@LB@ \| \|@LB@ 39 16@LB@@LB@@LB@Energy -10.52 kcal/mol@LB@Hybridization Energy -31.2627 kcal/mol@LB@Unfolding Energy - mRNA 8.52631 kcal/mol@LB@Unfolding Energy - sRNA 12.2147 kcal/mol@LB@@LB@Position - mRNA 49 -- 71@LB@Position - sRNA 17 -- 38@LB@Position Seed - mRNA 63 -- 69@LB@Position Seed - sRNA 19 -- 25@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@

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

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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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