Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
188	0.02326	0.4145	b2501	ppk	-10.84	0.080977	186 -- 203	48 -- 65	polyphosphate kinase component of RNA degradosome	_____________185________________204\n_____________\|__________________\|\n5'-CGC...AAAAC____UAAA__________GGUCA...UUG-3'\n______________GGAG____AGUGGUAAUG\n______________\|\|\|:____\|\|\|\|\|:\|\|\|\|\n______________CCUU____UCACCGUUAC\n3'-UUU...UACAA____UUAG__________GUUAC...UUG-5'\n_____________\|__________________\|\n_____________66_________________47\n	197 -- 203	48 -- 54	-18.775 kcal/mol	3.93073 kcal/mol	4.00814 kcal/mol	185 204@LB@ \| \|@LB@5'-CGC...AAAAC UAAA GGUCA...UUG-3'@LB@ GGAG AGUGGUAAUG@LB@ \|\|\|: \|\|\|\|\|:\|\|\|\|@LB@ CCUU UCACCGUUAC@LB@3'-UUU...UACAA UUAG GUUAC...UUG-5'@LB@ \| \|@LB@ 66 47@LB@@LB@@LB@Energy -10.84 kcal/mol@LB@Hybridization Energy -18.775 kcal/mol@LB@Unfolding Energy - mRNA 3.93073 kcal/mol@LB@Unfolding Energy - sRNA 4.00814 kcal/mol@LB@@LB@Position - mRNA 186 -- 203@LB@Position - sRNA 48 -- 65@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 48 -- 54@LB@
98	0.009218	0.3118	b3391	hofQ	-10.83	0.081241	8 -- 57	7 -- 65	DNA catabolic putative fimbrial transporter	_____________7_____________________________________________________________58\n_____________\|_____________________________________________________________\|\n____5'-CUAUCAG____UGG_________G____GC__A___U___UGU_________________________AAAGA...UAG-3'\n______________GGGA___UAG_GGCGA_GCGA__GC_UCA_CGG___AAUAAAA_____GAC_____GGGCA\n______________\|\|:\|___:\|\|_\|\|\|:\|_\|\|:\|__\|\|_:\|\|_\|:\|___\|\|\|\|\|\|\|_____\|\|\|_____:\|\|\|\|\n______________CCUU___GUC_CCGUU_CGUU__CG_GGU_GUC___UUAUUUU_____CUG_____UCCGU\n3'-UUU...UACAA____UUA___A_____A____AC______U___UU________AGACA___UUAUU_____AUAUUG-5'\n_____________\|_____________________________________________________________\|\n_____________66____________________________________________________________6\n	43 -- 49	25 -- 31	-34.6984 kcal/mol	11.715 kcal/mol	12.1538 kcal/mol	7 58@LB@ \| \|@LB@ 5'-CUAUCAG UGG G GC A U UGU AAAGA...UAG-3'@LB@ GGGA UAG GGCGA GCGA GC UCA CGG AAUAAAA GAC GGGCA@LB@ \|\|:\| :\|\| \|\|\|:\| \|\|:\| \|\| :\|\| \|:\| \|\|\|\|\|\|\| \|\|\| :\|\|\|\|@LB@ CCUU GUC CCGUU CGUU CG GGU GUC UUAUUUU CUG UCCGU@LB@3'-UUU...UACAA UUA A A AC U UU AGACA UUAUU AUAUUG-5'@LB@ \| \|@LB@ 66 6@LB@@LB@@LB@Energy -10.83 kcal/mol@LB@Hybridization Energy -34.6984 kcal/mol@LB@Unfolding Energy - mRNA 11.715 kcal/mol@LB@Unfolding Energy - sRNA 12.1538 kcal/mol@LB@@LB@Position - mRNA 8 -- 57@LB@Position - sRNA 7 -- 65@LB@Position Seed - mRNA 43 -- 49@LB@Position Seed - sRNA 25 -- 31@LB@
91	0.007817	0.2889	b3380	yhfW	-10.82	0.081759	179 -- 205	41 -- 67	phosphopentomutase-related metalloenzyme superfamily protein	_____________178_________________________206\n_____________\|___________________________\|\n5'-CUC...CAGUC_______C__UC___G__C________GCGAU...GUG-3'\n______________UUGGAAA_UC__UGG_GG_GUAAUGGC\n______________\|\|\|\|\|\|\|_\|\|__\|\|\|_::_\|:\|\|\|\|\|\|\n______________AACCUUU_AG__ACC_UU_CGUUACCG\n3'-UUU...UAUAC_______U__UC___G__A________GGUUG...UUG-5'\n_____________\|___________________________\|\n_____________68__________________________40\n	199 -- 205	41 -- 47	-26.7792 kcal/mol	10.1319 kcal/mol	5.83043 kcal/mol	178 206@LB@ \| \|@LB@5'-CUC...CAGUC C UC G C GCGAU...GUG-3'@LB@ UUGGAAA UC UGG GG GUAAUGGC@LB@ \|\|\|\|\|\|\| \|\| \|\|\| :: \|:\|\|\|\|\|\|@LB@ AACCUUU AG ACC UU CGUUACCG@LB@3'-UUU...UAUAC U UC G A GGUUG...UUG-5'@LB@ \| \|@LB@ 68 40@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -26.7792 kcal/mol@LB@Unfolding Energy - mRNA 10.1319 kcal/mol@LB@Unfolding Energy - sRNA 5.83043 kcal/mol@LB@@LB@Position - mRNA 179 -- 205@LB@Position - sRNA 41 -- 67@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 41 -- 47@LB@
75	0.006388	0.2822	b2813	mltA	-10.80	0.082551	232 -- 252	47 -- 66	membrane-bound lytic murein transglycosylase A	_____________231____________________253\n_____________\|______________________\|\n5'-UGC...UCUUA____CAC_______________UUGCC...AAG-3'\n______________UGGG___GGUU_GUGGCAAUGC\n______________\|\|\|:___::\|:_\|\|\|\|\|\|\|\|\|\|\n______________ACCU___UUAG_CACCGUUACG\n3'-UUU...AUACA____U______U__________UUACC...UUG-5'\n_____________\|______________________\|\n_____________67_____________________46\n	246 -- 252	47 -- 53	-21.5988 kcal/mol	6.72365 kcal/mol	4.0775 kcal/mol	231 253@LB@ \| \|@LB@5'-UGC...UCUUA CAC UUGCC...AAG-3'@LB@ UGGG GGUU GUGGCAAUGC@LB@ \|\|\|: ::\|: \|\|\|\|\|\|\|\|\|\|@LB@ ACCU UUAG CACCGUUACG@LB@3'-UUU...AUACA U U UUACC...UUG-5'@LB@ \| \|@LB@ 67 46@LB@@LB@@LB@Energy -10.80 kcal/mol@LB@Hybridization Energy -21.5988 kcal/mol@LB@Unfolding Energy - mRNA 6.72365 kcal/mol@LB@Unfolding Energy - sRNA 4.0775 kcal/mol@LB@@LB@Position - mRNA 232 -- 252@LB@Position - sRNA 47 -- 66@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 47 -- 53@LB@
66	0.005339	0.2645	b1476	fdnI	-10.79	0.082799	156 -- 194	9 -- 48	formate dehydrogenase-N cytochrome B556 (gamma) subunit nitrate-inducible	_____________155________________________________________195\n_____________\|__________________________________________\|\n5'-CGU...CAUCG___U________AUA_____________GA______G_____AUCAU...UUU-3'\n______________GUA_UGGCCCGA___AGGAAGUGGA__C__UGACGA__GAGG\n______________\|:\|_\|\|\|\|\|\|:\|___\|\|:\|\|:\|::\|__\|__\|\|\|\|:\|__:\|\|\|\n______________CGU_ACCGGGUU___UCUUUUAUUU__G__ACUGUU__UUCC\n3'-UUU...CGUUA___U________G____________UA_AC______AU____GUAUAUUG-5'\n_____________\|__________________________________________\|\n_____________49_________________________________________8\n	161 -- 167	37 -- 43	-34.1322 kcal/mol	12.2398 kcal/mol	11.1008 kcal/mol	155 195@LB@ \| \|@LB@5'-CGU...CAUCG U AUA GA G AUCAU...UUU-3'@LB@ GUA UGGCCCGA AGGAAGUGGA C UGACGA GAGG@LB@ \|:\| \|\|\|\|\|\|:\| \|\|:\|\|:\|::\| \| \|\|\|\|:\| :\|\|\|@LB@ CGU ACCGGGUU UCUUUUAUUU G ACUGUU UUCC@LB@3'-UUU...CGUUA U G UA AC AU GUAUAUUG-5'@LB@ \| \|@LB@ 49 8@LB@@LB@@LB@Energy -10.79 kcal/mol@LB@Hybridization Energy -34.1322 kcal/mol@LB@Unfolding Energy - mRNA 12.2398 kcal/mol@LB@Unfolding Energy - sRNA 11.1008 kcal/mol@LB@@LB@Position - mRNA 156 -- 194@LB@Position - sRNA 9 -- 48@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 37 -- 43@LB@
172	0.02065	0.4033	b1015	putP	-10.70	0.086688	188 -- 205	52 -- 67	proline:sodium symporter	_____________187________________206\n_____________\|__________________\|\n5'-AGA...AUUUU_______CU____A____UAUUA...ACG-3'\n______________UUGGAGA__UUAG_UGGC\n______________\|\|\|\|\|:\|__\|:\|\|_\|\|\|\|\n______________AACCUUU__AGUC_ACCG\n3'-UUU...UAUAC_______U__________UUACG...UUG-5'\n_____________\|__________________\|\n_____________68_________________51\n	188 -- 194	61 -- 67	-15.9795 kcal/mol	2.37428 kcal/mol	2.90583 kcal/mol	187 206@LB@ \| \|@LB@5'-AGA...AUUUU CU A UAUUA...ACG-3'@LB@ UUGGAGA UUAG UGGC@LB@ \|\|\|\|\|:\| \|:\|\| \|\|\|\|@LB@ AACCUUU AGUC ACCG@LB@3'-UUU...UAUAC U UUACG...UUG-5'@LB@ \| \|@LB@ 68 51@LB@@LB@@LB@Energy -10.70 kcal/mol@LB@Hybridization Energy -15.9795 kcal/mol@LB@Unfolding Energy - mRNA 2.37428 kcal/mol@LB@Unfolding Energy - sRNA 2.90583 kcal/mol@LB@@LB@Position - mRNA 188 -- 205@LB@Position - sRNA 52 -- 67@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 61 -- 67@LB@
5	0.0001064	0.07159	b1784	yeaH	-10.63	0.089613	150 -- 205	1 -- 57	UPF0229 family protein	_____________149________________________________________________________206\n_____________\|__________________________________________________________\|\n5'-UGU...UGAGA__C_____CA_______G_____UACAGUUGGCAAA___AGUACG_____________CUGGU...CGA-3'\n______________AG_GGCAA__CA__GGC_UAGCA_____________UGU______GGGGGCAUAUGAC\n______________\|\|_\|\|\|\|\|__\|\|__\|\|\|_:\|:\|\|_____________\|\|\|______:::\|\|\|\|\|\|\|:\|\|\n______________UC_CCGUU__GU__CCG_GUUGU_____________ACA______UUUCCGUAUAUUG\n3'-UUU...UUUAG__A_____AC__UA___G_____CUUUUAUUUUAG____CUGUUA_____________-5'\n_____________\|_________________________________________________________\|\n_____________58________________________________________________________1\n	198 -- 204	2 -- 8	-36.8439 kcal/mol	14.0882 kcal/mol	12.1233 kcal/mol	149 206@LB@ \| \|@LB@5'-UGU...UGAGA C CA G UACAGUUGGCAAA AGUACG CUGGU...CGA-3'@LB@ AG GGCAA CA GGC UAGCA UGU GGGGGCAUAUGAC@LB@ \|\| \|\|\|\|\| \|\| \|\|\| :\|:\|\| \|\|\| :::\|\|\|\|\|\|\|:\|\|@LB@ UC CCGUU GU CCG GUUGU ACA UUUCCGUAUAUUG@LB@3'-UUU...UUUAG A AC UA G CUUUUAUUUUAG CUGUUA -5'@LB@ \| \|@LB@ 58 1@LB@@LB@@LB@Energy -10.63 kcal/mol@LB@Hybridization Energy -36.8439 kcal/mol@LB@Unfolding Energy - mRNA 14.0882 kcal/mol@LB@Unfolding Energy - sRNA 12.1233 kcal/mol@LB@@LB@Position - mRNA 150 -- 205@LB@Position - sRNA 1 -- 57@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 2 -- 8@LB@
124	0.01277	0.3462	b2812	tcdA	-10.63	0.089790	208 -- 228	41 -- 66	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA	_____________207________________________229\n_____________\|__________________________\|\n5'-GUG...GUCUG___U______________________GUCAG...UUU-3'\n______________UGG__AAUUAGUG___AUGC_AUGGC\n______________\|\|\|__\|\|\|:\|\|\|\|___\|\|\|\|_\|\|\|\|\|\n______________ACC__UUAGUCAC___UACG_UACCG\n3'-UUU...AUACA___UU________CGU____U_____GGUUG...UUG-5'\n_____________\|__________________________\|\n_____________67_________________________40\n	213 -- 219	54 -- 60	-21.2123 kcal/mol	4.76037 kcal/mol	5.82355 kcal/mol	207 229@LB@ \| \|@LB@5'-GUG...GUCUG U GUCAG...UUU-3'@LB@ UGG AAUUAGUG AUGC AUGGC@LB@ \|\|\| \|\|\|:\|\|\|\| \|\|\|\| \|\|\|\|\|@LB@ ACC UUAGUCAC UACG UACCG@LB@3'-UUU...AUACA UU CGU U GGUUG...UUG-5'@LB@ \| \|@LB@ 67 40@LB@@LB@@LB@Energy -10.63 kcal/mol@LB@Hybridization Energy -21.2123 kcal/mol@LB@Unfolding Energy - mRNA 4.76037 kcal/mol@LB@Unfolding Energy - sRNA 5.82355 kcal/mol@LB@@LB@Position - mRNA 208 -- 228@LB@Position - sRNA 41 -- 66@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 54 -- 60@LB@
21	0.0009862	0.1579	b2572	rseA	-10.60	0.091224	9 -- 29	44 -- 65	anti-sigma factor	_____________8______________________30\n_____________\|______________________\|\n___5'-UCCCUCCC________UAC____UG_____AACCU...GGG-3'\n______________GGAAGAUU____GCA__GCAAU\n______________\|\|\|\|:\|\|:____\|\|\|__\|\|\|\|\|\n______________CCUUUUAG____CGU__CGUUA\n3'-UUU...UACAA________UCAC___UA_____CCGGG...UUG-5'\n_____________\|______________________\|\n_____________66_____________________43\n	10 -- 16	58 -- 64	-18.0609 kcal/mol	3.14057 kcal/mol	4.32401 kcal/mol	8 30@LB@ \| \|@LB@ 5'-UCCCUCCC UAC UG AACCU...GGG-3'@LB@ GGAAGAUU GCA GCAAU@LB@ \|\|\|\|:\|\|: \|\|\| \|\|\|\|\|@LB@ CCUUUUAG CGU CGUUA@LB@3'-UUU...UACAA UCAC UA CCGGG...UUG-5'@LB@ \| \|@LB@ 66 43@LB@@LB@@LB@Energy -10.60 kcal/mol@LB@Hybridization Energy -18.0609 kcal/mol@LB@Unfolding Energy - mRNA 3.14057 kcal/mol@LB@Unfolding Energy - sRNA 4.32401 kcal/mol@LB@@LB@Position - mRNA 9 -- 29@LB@Position - sRNA 44 -- 65@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 58 -- 64@LB@
184	0.02285	0.4143	b4312	fimB	-10.59	0.091292	169 -- 221	1 -- 58	tyrosine recombinase/inversion of on/off regulator of fimA	_____________168________________________________________________________________222\n_____________\|__________________________________________________________________\|\n5'-AUG...ACAGC_____C___UC______UA_____G________________________AGAAUA____UG_____AAAAA...GUA-3'\n______________UAGUG_GCG__UGUAAU____UAA_GGAAAA___________ACGAUGA______AGGC__AUAAC\n______________:\|\|\|\|_\|\|:__\|\|:\|\|\|____:\|\|_:\|\|\|\|\|___________\|\|:\|\|:\|______\|\|\|\|__\|\|\|\|\|\n______________GUCAC_CGU__ACGUUA____GUU_UCUUUU___________UGUUAUU______UCCG__UAUUG\n3'-UUU...UUUUA_________U_______CCGG___G______AUUUUAGACAC_________________UA_____-5'\n_____________\|_________________________________________________________________\|\n_____________59________________________________________________________________1\n	198 -- 204	12 -- 18	-31.4649 kcal/mol	8.72248 kcal/mol	12.1476 kcal/mol	168 222@LB@ \| \|@LB@5'-AUG...ACAGC C UC UA G AGAAUA UG AAAAA...GUA-3'@LB@ UAGUG GCG UGUAAU UAA GGAAAA ACGAUGA AGGC AUAAC@LB@ :\|\|\|\| \|\|: \|\|:\|\|\| :\|\| :\|\|\|\|\| \|\|:\|\|:\| \|\|\|\| \|\|\|\|\|@LB@ GUCAC CGU ACGUUA GUU UCUUUU UGUUAUU UCCG UAUUG@LB@3'-UUU...UUUUA U CCGG G AUUUUAGACAC UA -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -10.59 kcal/mol@LB@Hybridization Energy -31.4649 kcal/mol@LB@Unfolding Energy - mRNA 8.72248 kcal/mol@LB@Unfolding Energy - sRNA 12.1476 kcal/mol@LB@@LB@Position - mRNA 169 -- 221@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 12 -- 18@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)

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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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