Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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
173	0.02105	0.4072	b2840	ygeA	-11.88	0.093670	213 -- 233	44 -- 67	Asp/Glu_racemase family protein	_____________212______________________234\n_____________\|________________________\|\n5'-AAA...CAAUU___U__________G_________UGGGA...UUC-3'\n______________GGU__UGCUGGGAG_AA__UGAGC\n______________:\|\|__\|:\|\|\|\|:\|\|_\|\|__\|\|\|\|\|\n______________UCA__AUGACCUUC_UU__ACUCG\n3'-UUU...CCGAU___UU_________G__AC_____UUACA...GCG-5'\n_____________\|________________________\|\n_____________68_______________________43\n	219 -- 225	54 -- 60	-22.3324 kcal/mol	7.15309 kcal/mol	3.30407 kcal/mol	212 234@LB@ \| \|@LB@5'-AAA...CAAUU U G UGGGA...UUC-3'@LB@ GGU UGCUGGGAG AA UGAGC@LB@ :\|\| \|:\|\|\|\|:\|\| \|\| \|\|\|\|\|@LB@ UCA AUGACCUUC UU ACUCG@LB@3'-UUU...CCGAU UU G AC UUACA...GCG-5'@LB@ \| \|@LB@ 68 43@LB@@LB@@LB@Energy -11.88 kcal/mol@LB@Hybridization Energy -22.3324 kcal/mol@LB@Unfolding Energy - mRNA 7.15309 kcal/mol@LB@Unfolding Energy - sRNA 3.30407 kcal/mol@LB@@LB@Position - mRNA 213 -- 233@LB@Position - sRNA 44 -- 67@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 54 -- 60@LB@
93	0.009691	0.3393	b2959	yggL	-10.23	0.172987	12 -- 59	38 -- 83	DUF469 family protein	_____________11_________________________________________________60\n_____________\|__________________________________________________\|\n5'-GUA...CAUAU___GA___A____GAACCUU____________U___CU__A_________UUCUA...CAU-3'\n______________GGC__CCG_CUGG_______AUGC_GGAA_CA_AUG__UG_AGUGAUGUC\n______________:\|\|__\|\|\|_\|\|\|\|_______\|\|:\|_\|\|\|\|_\|\|_\|\|\|__\|\|_\|\|::\|\|\|\|\|\n______________UCG__GGC_GACC_______UAUG_CCUU_GU_UAC__AC_UCGUUACAG\n____3'-UUUUCGG___UG___C____GAUUCAU____A____C____________________CACGA...GCG-5'\n_____________\|__________________________________________________\|\n_____________84_________________________________________________37\n	53 -- 59	38 -- 44	-35.0381 kcal/mol	9.91615 kcal/mol	14.8888 kcal/mol	11 60@LB@ \| \|@LB@5'-GUA...CAUAU GA A GAACCUU U CU A UUCUA...CAU-3'@LB@ GGC CCG CUGG AUGC GGAA CA AUG UG AGUGAUGUC@LB@ :\|\| \|\|\| \|\|\|\| \|\|:\| \|\|\|\| \|\| \|\|\| \|\| \|\|::\|\|\|\|\|@LB@ UCG GGC GACC UAUG CCUU GU UAC AC UCGUUACAG@LB@ 3'-UUUUCGG UG C GAUUCAU A C CACGA...GCG-5'@LB@ \| \|@LB@ 84 37@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -35.0381 kcal/mol@LB@Unfolding Energy - mRNA 9.91615 kcal/mol@LB@Unfolding Energy - sRNA 14.8888 kcal/mol@LB@@LB@Position - mRNA 12 -- 59@LB@Position - sRNA 38 -- 83@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 38 -- 44@LB@
39	0.003417	0.2776	b4469	ygiQ	-15.58	0.022035	190 -- 206	44 -- 60	Radical SAM superfamily protein	_____________189_______________207\n_____________\|_________________\|\n5'-GCG...CAUUU__________AA_____UCUAU...CUC-3'\n______________CUGGAAGCAA__UGAGC\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\|\|\|\n______________GACCUUCGUU__ACUCG\n3'-UUU...AUUAU__________AC_____UUACA...GCG-5'\n_____________\|_________________\|\n_____________61________________43\n	193 -- 199	51 -- 57	-24.5566 kcal/mol	5.6787 kcal/mol	3.2985 kcal/mol	189 207@LB@ \| \|@LB@5'-GCG...CAUUU AA UCUAU...CUC-3'@LB@ CUGGAAGCAA UGAGC@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ GACCUUCGUU ACUCG@LB@3'-UUU...AUUAU AC UUACA...GCG-5'@LB@ \| \|@LB@ 61 43@LB@@LB@@LB@Energy -15.58 kcal/mol@LB@Hybridization Energy -24.5566 kcal/mol@LB@Unfolding Energy - mRNA 5.6787 kcal/mol@LB@Unfolding Energy - sRNA 3.2985 kcal/mol@LB@@LB@Position - mRNA 190 -- 206@LB@Position - sRNA 44 -- 60@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 51 -- 57@LB@
143	0.01687	0.3964	b3103	yhaH	-11.09	0.125996	208 -- 287	3 -- 67	DUF805 family inner membrane protein	_____________207_________________________________________________________________________________288\n_____________\|___________________________________________________________________________________\|\n5'-AUU...GGACU____U_____A_____CUAAAAAAUU___________C____G__G_G_____CGCAAAGAGUACU__AU____A________AACAU...UUA-3'\n______________GGUA___CUG_AAGUA__________AUGUCG_GUUU_CGGG_UC_U_CGCGG_____________GG__GUUU_UUCUGGUC\n______________:\|\|\|___\|\|\|_\|\|\|:\|__________\|\|\|\|\|\|_\|:\|\|_\|:\|\|_\|\|_\|_\|\|\|\|:_____________\|\|__\|\|:\|_\|:\|\|\|:\|\|\n______________UCAU___GAC_UUCGU__________UACAGC_CGAA_GUCC_AG_A_GCGCU_____________CC__CAGA_AGGACUAG\n3'-UUU...CCGAU____UAU___C_____UACACUCGU_______A____A____A____G___________________________________CG-5'\n_____________\|___________________________________________________________________________________\|\n_____________68__________________________________________________________________________________2\n	281 -- 287	3 -- 9	-42.8726 kcal/mol	17.657 kcal/mol	14.1245 kcal/mol	207 288@LB@ \| \|@LB@5'-AUU...GGACU U A CUAAAAAAUU C G G G CGCAAAGAGUACU AU A AACAU...UUA-3'@LB@ GGUA CUG AAGUA AUGUCG GUUU CGGG UC U CGCGG GG GUUU UUCUGGUC@LB@ :\|\|\| \|\|\| \|\|\|:\| \|\|\|\|\|\| \|:\|\| \|:\|\| \|\| \| \|\|\|\|: \|\| \|\|:\| \|:\|\|\|:\|\|@LB@ UCAU GAC UUCGU UACAGC CGAA GUCC AG A GCGCU CC CAGA AGGACUAG@LB@3'-UUU...CCGAU UAU C UACACUCGU A A A G CG-5'@LB@ \| \|@LB@ 68 2@LB@@LB@@LB@Energy -11.09 kcal/mol@LB@Hybridization Energy -42.8726 kcal/mol@LB@Unfolding Energy - mRNA 17.657 kcal/mol@LB@Unfolding Energy - sRNA 14.1245 kcal/mol@LB@@LB@Position - mRNA 208 -- 287@LB@Position - sRNA 3 -- 67@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 3 -- 9@LB@
188	0.02302	0.4113	b3105	yhaJ	-12.66	0.069284	224 -- 245	40 -- 61	LysR family putative transcriptional regulator	_____________223____________________246\n_____________\|______________________\|\n5'-CGG...UUAAC__________CUAC____U___GAUGC...GCG-3'\n______________GCUGGAAGCA____GGGU_AUG\n______________:\|\|\|\|\|\|\|\|\|____\|:\|:_\|\|\|\n______________UGACCUUCGU____CUCG_UAC\n3'-UUU...CAUUA__________UACA____U___AGCAC...GCG-5'\n_____________\|______________________\|\n_____________62_____________________39\n	227 -- 233	52 -- 58	-21.8067 kcal/mol	5.84576 kcal/mol	3.30075 kcal/mol	223 246@LB@ \| \|@LB@5'-CGG...UUAAC CUAC U GAUGC...GCG-3'@LB@ GCUGGAAGCA GGGU AUG@LB@ :\|\|\|\|\|\|\|\|\| \|:\|: \|\|\|@LB@ UGACCUUCGU CUCG UAC@LB@3'-UUU...CAUUA UACA U AGCAC...GCG-5'@LB@ \| \|@LB@ 62 39@LB@@LB@@LB@Energy -12.66 kcal/mol@LB@Hybridization Energy -21.8067 kcal/mol@LB@Unfolding Energy - mRNA 5.84576 kcal/mol@LB@Unfolding Energy - sRNA 3.30075 kcal/mol@LB@@LB@Position - mRNA 224 -- 245@LB@Position - sRNA 40 -- 61@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 52 -- 58@LB@
49	0.004671	0.2905	b3184	yhbE	-14.90	0.028775	284 -- 299	49 -- 64	EamA family inner membrane putative transporter	_____________283______________300\n_____________\|________________\|\n5'-AAG...AAGCA________________G-3'\n______________GGUGCUGGAGGUGAUG\n______________::\|:\|\|\|\|\|:\|::\|\|\|\n______________UUAUGACCUUCGUUAC\n3'-UUU...AUUCA________________ACUCG...GCG-5'\n_____________\|________________\|\n_____________65_______________48\n	293 -- 299	49 -- 55	-22.6177 kcal/mol	4.70237 kcal/mol	3.01036 kcal/mol	283 300@LB@ \| \|@LB@5'-AAG...AAGCA G-3'@LB@ GGUGCUGGAGGUGAUG@LB@ ::\|:\|\|\|\|\|:\|::\|\|\|@LB@ UUAUGACCUUCGUUAC@LB@3'-UUU...AUUCA ACUCG...GCG-5'@LB@ \| \|@LB@ 65 48@LB@@LB@@LB@Energy -14.90 kcal/mol@LB@Hybridization Energy -22.6177 kcal/mol@LB@Unfolding Energy - mRNA 4.70237 kcal/mol@LB@Unfolding Energy - sRNA 3.01036 kcal/mol@LB@@LB@Position - mRNA 284 -- 299@LB@Position - sRNA 49 -- 64@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 49 -- 55@LB@
28	0.002335	0.2776	b3248	yhdE	-16.83	0.013392	101 -- 153	6 -- 68	dTTP/UTP pyrophosphatase; m(5)UTP/m(5)CTP/pseudo-UTP pyrophosphatase	_____________100______________________________________________________________154\n_____________\|________________________________________________________________\|\n5'-UUA...ACCGG_____U__________________U_____GG_____CU______________A__________CUGAU...AGC-3'\n______________AAGUG_U_CUGG_AGUAGUGU_AG_CAAUG__GUGCU____GG____CCGUGG___UUUUCUUG\n______________\|\|\|\|:_\|_\|\|\|\|_\|\|:\|:\|\|\|_\|\|_\|\|\|\|\|__\|\|\|\|\|____\|\|____\|\|\|:\|:___\|:\|\|\|:\|\|\n______________UUCAU_A_GACC_UCGUUACA_UC_GUUAC__CACGA____CC____GGCGCU___AGAAGGAC\n3'-UUU...ACCGA_____U_U____U________C________AG_____AAGU__AAGA______CCC________UAGCG-5'\n_____________\|________________________________________________________________\|\n_____________69_______________________________________________________________5\n	147 -- 153	6 -- 12	-47.0166 kcal/mol	16.0597 kcal/mol	14.1245 kcal/mol	100 154@LB@ \| \|@LB@5'-UUA...ACCGG U U GG CU A CUGAU...AGC-3'@LB@ AAGUG U CUGG AGUAGUGU AG CAAUG GUGCU GG CCGUGG UUUUCUUG@LB@ \|\|\|\|: \| \|\|\|\| \|\|:\|:\|\|\| \|\| \|\|\|\|\| \|\|\|\|\| \|\| \|\|\|:\|: \|:\|\|\|:\|\|@LB@ UUCAU A GACC UCGUUACA UC GUUAC CACGA CC GGCGCU AGAAGGAC@LB@3'-UUU...ACCGA U U U C AG AAGU AAGA CCC UAGCG-5'@LB@ \| \|@LB@ 69 5@LB@@LB@@LB@Energy -16.83 kcal/mol@LB@Hybridization Energy -47.0166 kcal/mol@LB@Unfolding Energy - mRNA 16.0597 kcal/mol@LB@Unfolding Energy - sRNA 14.1245 kcal/mol@LB@@LB@Position - mRNA 101 -- 153@LB@Position - sRNA 6 -- 68@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 6 -- 12@LB@
46	0.004112	0.2905	b3263	yhdU	-13.66	0.046979	167 -- 251	6 -- 86	putative membrane protein	_____________166______________________________________________________________________________________________252\n_____________\|________________________________________________________________________________________________\|\n5'-GAU...UUCCU______________AAACAUGCACA____C________AUUC_C_____U__GU___________C_______CUG____________________UUUGA...CAG-3'\n______________GCCAG_ACUUGGUU___________GGCU_AGGUAAUG____G_AAGUA_UG__GGC____UCGU_GUUUUCG___UCUUCGU______UUUUCUG\n______________\|\|\|\|\|_\|\|::\|\|:\|___________\|\|\|\|_\|:\|\|\|\|\|:____\|_\|\|\|:\|_\|\|__:\|\|____\|\|\|\|_\|:\|\|\|\|:___\|\|\|:\|\|:______:\|\|:\|\|\|\n______________CGGUC_UGGGCCGA___________CCGA_UUCAUUAU____C_UUCGU_AC__UCG____AGCA_CGAAAGU___AGAGGCG______GAAGGAC\n_______3'-UUUU_____G________________________________GAC________U__AC___UUAC____________CCA_______CUCCCA_______UAGCG-5'\n_____________\|________________________________________________________________________________________________\|\n_____________87_______________________________________________________________________________________________5\n	245 -- 251	6 -- 12	-59.7696 kcal/mol	20.3812 kcal/mol	25.7297 kcal/mol	166 252@LB@ \| \|@LB@5'-GAU...UUCCU AAACAUGCACA C AUUC C U GU C CUG UUUGA...CAG-3'@LB@ GCCAG ACUUGGUU GGCU AGGUAAUG G AAGUA UG GGC UCGU GUUUUCG UCUUCGU UUUUCUG@LB@ \|\|\|\|\| \|\|::\|\|:\| \|\|\|\| \|:\|\|\|\|\|: \| \|\|\|:\| \|\| :\|\| \|\|\|\| \|:\|\|\|\|: \|\|\|:\|\|: :\|\|:\|\|\|@LB@ CGGUC UGGGCCGA CCGA UUCAUUAU C UUCGU AC UCG AGCA CGAAAGU AGAGGCG GAAGGAC@LB@ 3'-UUUU G GAC U AC UUAC CCA CUCCCA UAGCG-5'@LB@ \| \|@LB@ 87 5@LB@@LB@@LB@Energy -13.66 kcal/mol@LB@Hybridization Energy -59.7696 kcal/mol@LB@Unfolding Energy - mRNA 20.3812 kcal/mol@LB@Unfolding Energy - sRNA 25.7297 kcal/mol@LB@@LB@Position - mRNA 167 -- 251@LB@Position - sRNA 6 -- 86@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 6 -- 12@LB@
53	0.004949	0.2905	b3353	yheT	-17.66	0.009631	104 -- 164	43 -- 88	UPF0017 family putative hydrolase	_____________103____________________________________________________________165\n_____________\|______________________________________________________________\|\n5'-GAG...ACAGC__________CAAAU____C____AA_____CGAAAUGGCAUG_________CCAG______GCUUG...UGC-3'\n______________AAGCCAGCGC_____CCGG_CUGG__GAGUG____________GCUGGAAGC_____GAGCA\n______________\|\|\|\|\|\|\|\|:\|_____\|\|\|\|_\|\|\|\|__:\|\|\|:____________:\|\|\|\|\|\|\|\|_____\|\|\|\|\|\n______________UUCGGUCGUG_____GGCC_GACC__UUCAU____________UGACCUUCG_____CUCGU\n_________3'-UU________________________GA_____UA___________________UUACA_____UACAG...GCG-5'\n_____________\|______________________________________________________________\|\n_____________89_____________________________________________________________42\n	149 -- 155	53 -- 59	-55.8349 kcal/mol	23.2651 kcal/mol	14.9102 kcal/mol	103 165@LB@ \| \|@LB@5'-GAG...ACAGC CAAAU C AA CGAAAUGGCAUG CCAG GCUUG...UGC-3'@LB@ AAGCCAGCGC CCGG CUGG GAGUG GCUGGAAGC GAGCA@LB@ \|\|\|\|\|\|\|\|:\| \|\|\|\| \|\|\|\| :\|\|\|: :\|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ UUCGGUCGUG GGCC GACC UUCAU UGACCUUCG CUCGU@LB@ 3'-UU GA UA UUACA UACAG...GCG-5'@LB@ \| \|@LB@ 89 42@LB@@LB@@LB@Energy -17.66 kcal/mol@LB@Hybridization Energy -55.8349 kcal/mol@LB@Unfolding Energy - mRNA 23.2651 kcal/mol@LB@Unfolding Energy - sRNA 14.9102 kcal/mol@LB@@LB@Position - mRNA 104 -- 164@LB@Position - sRNA 43 -- 88@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 53 -- 59@LB@
162	0.02022	0.4072	b3354	yheU	-12.65	0.069641	153 -- 196	51 -- 89	UPF0270 family protein	_____________152__________________________________________197\n_____________\|____________________________________________\|\n5'-CUG...UGGCU_______C___UU____A________CAAC___U__________AAUCA...GUA-3'\n______________GGAGUCA_GCA__CCUG_CUGGUUAA____GUA_CUGGAGGCGA\n______________::\|\|:\|\|_\|\|\|__\|\|:\|_\|\|\|\|:\|\|\|____:\|\|_\|\|\|\|\|:\|\|:\|\n______________UUUCGGU_CGU__GGGC_GACCGAUU____UAU_GACCUUCGUU\n__________3'-U_________________C________CAU_______________ACACU...GCG-5'\n_____________\|____________________________________________\|\n_____________90___________________________________________50\n	189 -- 195	52 -- 58	-41.3188 kcal/mol	14.1702 kcal/mol	14.5017 kcal/mol	152 197@LB@ \| \|@LB@5'-CUG...UGGCU C UU A CAAC U AAUCA...GUA-3'@LB@ GGAGUCA GCA CCUG CUGGUUAA GUA CUGGAGGCGA@LB@ ::\|\|:\|\| \|\|\| \|\|:\| \|\|\|\|:\|\|\| :\|\| \|\|\|\|\|:\|\|:\|@LB@ UUUCGGU CGU GGGC GACCGAUU UAU GACCUUCGUU@LB@ 3'-U C CAU ACACU...GCG-5'@LB@ \| \|@LB@ 90 50@LB@@LB@@LB@Energy -12.65 kcal/mol@LB@Hybridization Energy -41.3188 kcal/mol@LB@Unfolding Energy - mRNA 14.1702 kcal/mol@LB@Unfolding Energy - sRNA 14.5017 kcal/mol@LB@@LB@Position - mRNA 153 -- 196@LB@Position - sRNA 51 -- 89@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 52 -- 58@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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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

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