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
111	0.003511	0.1114	b0077	ilvI	-11.05	0.061087	188 -- 206	36 -- 52	acetolactate synthase 3 large subunit	_____________187_________________207\n_____________\|___________________\|\n5'-AAA...CAAAC__________GCC______AUGUU...UUU-3'\n______________AGUGAGGCAG___AUGGAG\n______________\|\|\|:\|\|:\|\|:___\|\|\|\|\|\|\n______________UCAUUCUGUU___UACCUC\n3'-UUU...UUCCU__________A________GCGUU...ACG-5'\n_____________\|___________________\|\n_____________53__________________35\n	191 -- 197	43 -- 49	-19.2253 kcal/mol	4.72052 kcal/mol	3.43382 kcal/mol	187 207@LB@ \| \|@LB@5'-AAA...CAAAC GCC AUGUU...UUU-3'@LB@ AGUGAGGCAG AUGGAG@LB@ \|\|\|:\|\|:\|\|: \|\|\|\|\|\|@LB@ UCAUUCUGUU UACCUC@LB@3'-UUU...UUCCU A GCGUU...ACG-5'@LB@ \| \|@LB@ 53 35@LB@@LB@@LB@Energy -11.05 kcal/mol@LB@Hybridization Energy -19.2253 kcal/mol@LB@Unfolding Energy - mRNA 4.72052 kcal/mol@LB@Unfolding Energy - sRNA 3.43382 kcal/mol@LB@@LB@Position - mRNA 188 -- 206@LB@Position - sRNA 36 -- 52@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 43 -- 49@LB@
112	0.003634	0.1131	b1473	yddG	-8.08	0.286569	177 -- 226	24 -- 55	aromatic amino acid exporter	_____________176________________________________________________227\n_____________\|__________________________________________________\|\n5'-GCG...UUAAC__C___A_______AACA_C____AUGACACGACAAAAA___________AGGGC...CGG-3'\n______________GG_AAG_GAGACAA____G_GAGC_______________GCAACGCUCAU\n______________\|\|_\|\|\|_:\|\|\|\|\|\|____\|_\|\|\|\|_______________\|\|\|\|\|\|\|:\|\|\|\n______________CC_UUC_UUCUGUU____C_CUCG_______________CGUUGCGGGUA\n3'-UUU...UUUUU______A_______AUA_________________________________GCGAA...ACG-5'\n_____________\|__________________________________________________\|\n_____________56_________________________________________________23\n	216 -- 222	28 -- 34	-30.4707 kcal/mol	9.38627 kcal/mol	13.0079 kcal/mol	176 227@LB@ \| \|@LB@5'-GCG...UUAAC C A AACA C AUGACACGACAAAAA AGGGC...CGG-3'@LB@ GG AAG GAGACAA G GAGC GCAACGCUCAU@LB@ \|\| \|\|\| :\|\|\|\|\|\| \| \|\|\|\| \|\|\|\|\|\|\|:\|\|\|@LB@ CC UUC UUCUGUU C CUCG CGUUGCGGGUA@LB@3'-UUU...UUUUU A AUA GCGAA...ACG-5'@LB@ \| \|@LB@ 56 23@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -30.4707 kcal/mol@LB@Unfolding Energy - mRNA 9.38627 kcal/mol@LB@Unfolding Energy - sRNA 13.0079 kcal/mol@LB@@LB@Position - mRNA 177 -- 226@LB@Position - sRNA 24 -- 55@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 28 -- 34@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@
114	0.00366	0.1131	b0162	cdaR	-8.46	0.240590	33 -- 47	64 -- 77	carbohydrate diacid regulon transcriptional regulator; autoregulator	_____________32______________48\n_____________\|_______________\|\n5'-CAA...CUACC____A__________CUCCC...GGC-3'\n______________UGUU_AUGCAGUAAU\n______________\|\|:\|_\|\|\|\|\|\|\|\|\|\|\n______________ACGA_UACGUCAUUA\n3'-UUU...UUAAC_______________AGUUU...ACG-5'\n_____________\|_______________\|\n_____________78______________63\n	41 -- 47	64 -- 70	-14.8052 kcal/mol	3.39589 kcal/mol	2.94867 kcal/mol	32 48@LB@ \| \|@LB@5'-CAA...CUACC A CUCCC...GGC-3'@LB@ UGUU AUGCAGUAAU@LB@ \|\|:\| \|\|\|\|\|\|\|\|\|\|@LB@ ACGA UACGUCAUUA@LB@3'-UUU...UUAAC AGUUU...ACG-5'@LB@ \| \|@LB@ 78 63@LB@@LB@@LB@Energy -8.46 kcal/mol@LB@Hybridization Energy -14.8052 kcal/mol@LB@Unfolding Energy - mRNA 3.39589 kcal/mol@LB@Unfolding Energy - sRNA 2.94867 kcal/mol@LB@@LB@Position - mRNA 33 -- 47@LB@Position - sRNA 64 -- 77@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 64 -- 70@LB@
115	0.003699	0.1133	b3343	tusB	-8.43	0.243717	216 -- 222	20 -- 26	mnm(5)-s(2)U34-tRNA synthesis 2-thiolation protein	_____________215_____223\n_____________\|_______\|\n5'-GCU...CAUUA_______CACCC...GCG-3'\n______________CAUCGCU\n______________\|\|\|\|\|\|\|\n______________GUAGCGA\n3'-UUU...UGCGG_______ACUGC...ACG-5'\n_____________\|_______\|\n_____________27______19\n	216 -- 222	20 -- 26	-9.55221 kcal/mol	1.0434 kcal/mol	0.0768517 kcal/mol	215 223@LB@ \| \|@LB@5'-GCU...CAUUA CACCC...GCG-3'@LB@ CAUCGCU@LB@ \|\|\|\|\|\|\|@LB@ GUAGCGA@LB@3'-UUU...UGCGG ACUGC...ACG-5'@LB@ \| \|@LB@ 27 19@LB@@LB@@LB@Energy -8.43 kcal/mol@LB@Hybridization Energy -9.55221 kcal/mol@LB@Unfolding Energy - mRNA 1.0434 kcal/mol@LB@Unfolding Energy - sRNA 0.0768517 kcal/mol@LB@@LB@Position - mRNA 216 -- 222@LB@Position - sRNA 20 -- 26@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 20 -- 26@LB@
116	0.003923	0.1189	b4515	cydX	-11.57	0.044828	15 -- 31	37 -- 53	cytochrome d (bd-I) ubiquinol oxidase subunit X	_____________14________________32\n_____________\|_________________\|\n5'-ACC...AACGC____CU___________AUGCA...GUC-3'\n______________AAGU__GACAAUGUGGG\n______________\|\|\|\|__\|\|\|\|\|\|:\|\|\|:\n______________UUCA__CUGUUAUACCU\n3'-UUU...UUUCC____UU___________CGCGU...ACG-5'\n_____________\|_________________\|\n_____________54________________36\n	25 -- 31	37 -- 43	-18.6761 kcal/mol	3.6374 kcal/mol	3.44536 kcal/mol	14 32@LB@ \| \|@LB@5'-ACC...AACGC CU AUGCA...GUC-3'@LB@ AAGU GACAAUGUGGG@LB@ \|\|\|\| \|\|\|\|\|\|:\|\|\|:@LB@ UUCA CUGUUAUACCU@LB@3'-UUU...UUUCC UU CGCGU...ACG-5'@LB@ \| \|@LB@ 54 36@LB@@LB@@LB@Energy -11.57 kcal/mol@LB@Hybridization Energy -18.6761 kcal/mol@LB@Unfolding Energy - mRNA 3.6374 kcal/mol@LB@Unfolding Energy - sRNA 3.44536 kcal/mol@LB@@LB@Position - mRNA 15 -- 31@LB@Position - sRNA 37 -- 53@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 37 -- 43@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@
118	0.004043	0.119	b1636	pdxY	-15.07	0.004282	119 -- 169	46 -- 90	pyridoxamine kinase	_____________118___________________________________________________170\n_____________\|_____________________________________________________\|\n5'-UAU...AGAAU___U____U_________GGAAAUA_____U___G_G________________AAUCA...UCU-3'\n______________UAC__GUC_GAUU_UGCU_______AUGCA_UAA_U_GAAAGGGGGAGUGAGA\n______________\|\|\|__:\|\|_:\|\|\|_\|\|\|\|_______\|\|\|\|\|_\|\|\|_\|_:\|\|\|::\|\|:\|\|\|:\|\|\|\n______________AUG__UAG_UUAA_ACGA_______UACGU_AUU_A_UUUUUUCCUUCAUUCU\n3'-UUU...GCAGC___CU________C________________C___A_G________________GUUAU...ACG-5'\n_____________\|_____________________________________________________\|\n_____________91____________________________________________________45\n	163 -- 169	46 -- 52	-32.4349 kcal/mol	11.9314 kcal/mol	5.43414 kcal/mol	118 170@LB@ \| \|@LB@5'-UAU...AGAAU U U GGAAAUA U G G AAUCA...UCU-3'@LB@ UAC GUC GAUU UGCU AUGCA UAA U GAAAGGGGGAGUGAGA@LB@ \|\|\| :\|\| :\|\|\| \|\|\|\| \|\|\|\|\| \|\|\| \| :\|\|\|::\|\|:\|\|\|:\|\|\|@LB@ AUG UAG UUAA ACGA UACGU AUU A UUUUUUCCUUCAUUCU@LB@3'-UUU...GCAGC CU C C A G GUUAU...ACG-5'@LB@ \| \|@LB@ 91 45@LB@@LB@@LB@Energy -15.07 kcal/mol@LB@Hybridization Energy -32.4349 kcal/mol@LB@Unfolding Energy - mRNA 11.9314 kcal/mol@LB@Unfolding Energy - sRNA 5.43414 kcal/mol@LB@@LB@Position - mRNA 119 -- 169@LB@Position - sRNA 46 -- 90@LB@Position Seed - mRNA 163 -- 169@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@
120	0.004053	0.119	b2441	eutB	-6.09	0.606518	293 -- 299	73 -- 79	ethanolamine ammonia-lyase large subunit heavy chain	_____________292_____300\n_____________\|_______\|\n5'-CUG...GGGGA_______G-3'\n______________UGUGCUG\n______________\|\|\|\|\|\|:\n______________ACACGAU\n3'-UUU...AGUUA_______ACGUC...ACG-5'\n_____________\|_______\|\n_____________80______72\n	293 -- 299	73 -- 79	-8.7652 kcal/mol	1.34517 kcal/mol	1.33434 kcal/mol	292 300@LB@ \| \|@LB@5'-CUG...GGGGA G-3'@LB@ UGUGCUG@LB@ \|\|\|\|\|\|:@LB@ ACACGAU@LB@3'-UUU...AGUUA ACGUC...ACG-5'@LB@ \| \|@LB@ 80 72@LB@@LB@@LB@Energy -6.09 kcal/mol@LB@Hybridization Energy -8.7652 kcal/mol@LB@Unfolding Energy - mRNA 1.34517 kcal/mol@LB@Unfolding Energy - sRNA 1.33434 kcal/mol@LB@@LB@Position - mRNA 293 -- 299@LB@Position - sRNA 73 -- 79@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 73 -- 79@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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