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
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@
178	0.02201	0.4113	b4176	yjeT	-16.79	0.013635	217 -- 249	54 -- 87	DUF2065 family protein	_____________216_________________________________250\n_____________\|___________________________________\|\n5'-UCA...AAUCU____________CC______U______________GUUUA...CGA-3'\n______________GGCUGGCGCUUG__CUGGUU___UGGUACUGGAAG\n______________:\|\|::\|\|:\|::\|__\|\|\|\|:\|___\|::\|\|\|\|\|\|\|\|\|\n______________UCGGUCGUGGGC__GACCGA___AUUAUGACCUUC\n________3'-UUU____________C_______UUC____________GUUAC...GCG-5'\n_____________\|___________________________________\|\n_____________88__________________________________53\n	243 -- 249	54 -- 60	-41.1583 kcal/mol	10.0538 kcal/mol	14.3172 kcal/mol	216 250@LB@ \| \|@LB@5'-UCA...AAUCU CC U GUUUA...CGA-3'@LB@ GGCUGGCGCUUG CUGGUU UGGUACUGGAAG@LB@ :\|\|::\|\|:\|::\| \|\|\|\|:\| \|::\|\|\|\|\|\|\|\|\|@LB@ UCGGUCGUGGGC GACCGA AUUAUGACCUUC@LB@ 3'-UUU C UUC GUUAC...GCG-5'@LB@ \| \|@LB@ 88 53@LB@@LB@@LB@Energy -16.79 kcal/mol@LB@Hybridization Energy -41.1583 kcal/mol@LB@Unfolding Energy - mRNA 10.0538 kcal/mol@LB@Unfolding Energy - sRNA 14.3172 kcal/mol@LB@@LB@Position - mRNA 217 -- 249@LB@Position - sRNA 54 -- 87@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 54 -- 60@LB@
79	0.007454	0.3134	b1912	pgsA	-16.66	0.014365	232 -- 294	1 -- 48	phosphatidylglycerophosphate synthetase	_____________231_____________________________________________________________295\n_____________\|_______________________________________________________________\|\n5'-GUC...UACAC__UU_C_____AUC___A__CCA________AUU______UUAUCUGCCUGUCA_________CGUUUG-3'\n______________UG__C_GUGUC___CUU_UC___UUCUUUGU___GGUCUU______________CCUGGUCGC\n______________\|\|__\|_:\|\|\|\|___\|\|\|_\|\|___\|\|\|\|::\|:___\|\|\|\|\|\|______________\|\|\|\|:\|\|\|\|\n______________AC__G_UACAG___GAA_AG___AAGAGGCG___CCAGAA______________GGACUAGCG\n3'-UUU...GUUAC__UC_U_____CAC______UCC________CUC_____________________________-5'\n_____________\|______________________________________________________________\|\n_____________49_____________________________________________________________1\n	288 -- 294	1 -- 7	-35.4585 kcal/mol	5.43289 kcal/mol	13.3693 kcal/mol	231 295@LB@ \| \|@LB@5'-GUC...UACAC UU C AUC A CCA AUU UUAUCUGCCUGUCA CGUUUG-3'@LB@ UG C GUGUC CUU UC UUCUUUGU GGUCUU CCUGGUCGC@LB@ \|\| \| :\|\|\|\| \|\|\| \|\| \|\|\|\|::\|: \|\|\|\|\|\| \|\|\|\|:\|\|\|\|@LB@ AC G UACAG GAA AG AAGAGGCG CCAGAA GGACUAGCG@LB@3'-UUU...GUUAC UC U CAC UCC CUC -5'@LB@ \| \|@LB@ 49 1@LB@@LB@@LB@Energy -16.66 kcal/mol@LB@Hybridization Energy -35.4585 kcal/mol@LB@Unfolding Energy - mRNA 5.43289 kcal/mol@LB@Unfolding Energy - sRNA 13.3693 kcal/mol@LB@@LB@Position - mRNA 232 -- 294@LB@Position - sRNA 1 -- 48@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 1 -- 7@LB@
124	0.01356	0.3627	b2232	ubiG	-16.56	0.014945	261 -- 300	44 -- 89	bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase	_____________260_____________________________________________300\n_____________\|_______________________________________________\|\n5'-CUU...AAUUU_______U_____CCC______GG________________________-3'\n______________GAAGCCG_CGCCU___GCUGGU_____GAU_CUGGAAG____GUGAGU\n______________:\|\|\|\|\|:_\|:\|\|:___\|\|\|\|\|:_____:\|\|_\|\|\|\|\|\|\|____\|\|\|\|\|:\n______________UUUCGGU_GUGGG___CGACCG_____UUA_GACCUUC____CACUCG\n__________3'-U_______C_____C________AUUCA___U_______GUUA______UUACA...GCG-5'\n_____________\|________________________________________________\|\n_____________90_______________________________________________43\n	288 -- 294	54 -- 60	-44.5757 kcal/mol	13.1093 kcal/mol	14.9095 kcal/mol	260 300@LB@ \| \|@LB@5'-CUU...AAUUU U CCC GG -3'@LB@ GAAGCCG CGCCU GCUGGU GAU CUGGAAG GUGAGU@LB@ :\|\|\|\|\|: \|:\|\|: \|\|\|\|\|: :\|\| \|\|\|\|\|\|\| \|\|\|\|\|:@LB@ UUUCGGU GUGGG CGACCG UUA GACCUUC CACUCG@LB@ 3'-U C C AUUCA U GUUA UUACA...GCG-5'@LB@ \| \|@LB@ 90 43@LB@@LB@@LB@Energy -16.56 kcal/mol@LB@Hybridization Energy -44.5757 kcal/mol@LB@Unfolding Energy - mRNA 13.1093 kcal/mol@LB@Unfolding Energy - sRNA 14.9095 kcal/mol@LB@@LB@Position - mRNA 261 -- 300@LB@Position - sRNA 44 -- 89@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 54 -- 60@LB@
74	0.006788	0.3082	b3525	yhjH	-16.42	0.015793	272 -- 288	44 -- 60	cyclic-di-GMP phosphodiesterase FlhDC-regulated	_____________271_______________289\n_____________\|_________________\|\n5'-UUA...CGUUU____UU___________GUGCU...CCU-3'\n______________UUGG__GCAGUGUGAGC\n______________:\|\|\|__\|\|\|:\|\|\|\|\|\|\|\n______________GACC__CGUUACACUCG\n3'-UUU...AUUAU____UU___________UUACA...GCG-5'\n_____________\|_________________\|\n_____________61________________43\n	279 -- 285	47 -- 53	-25.6078 kcal/mol	5.89114 kcal/mol	3.2985 kcal/mol	271 289@LB@ \| \|@LB@5'-UUA...CGUUU UU GUGCU...CCU-3'@LB@ UUGG GCAGUGUGAGC@LB@ :\|\|\| \|\|\|:\|\|\|\|\|\|\|@LB@ GACC CGUUACACUCG@LB@3'-UUU...AUUAU UU UUACA...GCG-5'@LB@ \| \|@LB@ 61 43@LB@@LB@@LB@Energy -16.42 kcal/mol@LB@Hybridization Energy -25.6078 kcal/mol@LB@Unfolding Energy - mRNA 5.89114 kcal/mol@LB@Unfolding Energy - sRNA 3.2985 kcal/mol@LB@@LB@Position - mRNA 272 -- 288@LB@Position - sRNA 44 -- 60@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 47 -- 53@LB@
38	0.003171	0.2776	b0033	carB	-16.38	0.016045	157 -- 203	40 -- 88	carbamoyl-phosphate synthase large subunit	_____________156_________________________________________________204\n_____________\|___________________________________________________\|\n5'-GCA...UAAUU___________GUAAAACC____________A________AA_____C___CCAAA...CGU-3'\n______________GAG_CAGUACC________GCUAAGUAAU_C_GG_AGUAA___GAGC_AUG\n______________:\|\|_\|\|\|:\|\|\|________\|\|\|\|\|\|\|\|\|\|_\|_\|\|_\|\|:\|\|___\|\|\|\|_\|\|\|\n______________UUC_GUCGUGG________CGAUUCAUUA_G_CC_UCGUU___CUCG_UAC\n_________3'-UU___G_______GCCGAC____________U_A__U_____ACA____U___AGCAC...GCG-5'\n_____________\|___________________________________________________\|\n_____________89__________________________________________________39\n	178 -- 184	62 -- 68	-37.8454 kcal/mol	6.5567 kcal/mol	14.9104 kcal/mol	156 204@LB@ \| \|@LB@5'-GCA...UAAUU GUAAAACC A AA C CCAAA...CGU-3'@LB@ GAG CAGUACC GCUAAGUAAU C GG AGUAA GAGC AUG@LB@ :\|\| \|\|\|:\|\|\| \|\|\|\|\|\|\|\|\|\| \| \|\| \|\|:\|\| \|\|\|\| \|\|\|@LB@ UUC GUCGUGG CGAUUCAUUA G CC UCGUU CUCG UAC@LB@ 3'-UU G GCCGAC U A U ACA U AGCAC...GCG-5'@LB@ \| \|@LB@ 89 39@LB@@LB@@LB@Energy -16.38 kcal/mol@LB@Hybridization Energy -37.8454 kcal/mol@LB@Unfolding Energy - mRNA 6.5567 kcal/mol@LB@Unfolding Energy - sRNA 14.9104 kcal/mol@LB@@LB@Position - mRNA 157 -- 203@LB@Position - sRNA 40 -- 88@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 62 -- 68@LB@
15	0.001024	0.2294	b2822	recC	-16.38	0.016046	234 -- 264	37 -- 63	exonuclease V (RecBCD complex) gamma chain	_____________233______________________________265\n_____________\|________________________________\|\n5'-AGU...UGGAC___________GUU_________UUAU_____AACGC...AGA-3'\n______________GUGCUGGAAGC___GAUG_GAGU____UGUCG\n______________:\|:\|\|\|\|\|\|\|\|___:\|\|\|_\|\|\|:____\|\|\|\|\|\n______________UAUGACCUUCG___UUAC_CUCG____ACAGC\n3'-UUU...UUCAU__________________A____UU_______ACGAA...GCG-5'\n_____________\|________________________________\|\n_____________64_______________________________36\n	238 -- 244	53 -- 59	-30.8262 kcal/mol	11.1454 kcal/mol	3.30267 kcal/mol	233 265@LB@ \| \|@LB@5'-AGU...UGGAC GUU UUAU AACGC...AGA-3'@LB@ GUGCUGGAAGC GAUG GAGU UGUCG@LB@ :\|:\|\|\|\|\|\|\|\| :\|\|\| \|\|\|: \|\|\|\|\|@LB@ UAUGACCUUCG UUAC CUCG ACAGC@LB@3'-UUU...UUCAU A UU ACGAA...GCG-5'@LB@ \| \|@LB@ 64 36@LB@@LB@@LB@Energy -16.38 kcal/mol@LB@Hybridization Energy -30.8262 kcal/mol@LB@Unfolding Energy - mRNA 11.1454 kcal/mol@LB@Unfolding Energy - sRNA 3.30267 kcal/mol@LB@@LB@Position - mRNA 234 -- 264@LB@Position - sRNA 37 -- 63@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 53 -- 59@LB@
25	0.002073	0.2692	b3163	nlpI	-16.34	0.016289	1 -- 45	38 -- 89	lipoprotein involved in osmotic sensitivity and filamentation	______________1____________________________________________________46\n______________\|____________________________________________________\|\n___________5'-______________U___A__AUUAAA_____________C_________C__AACCU...CAU-3'\n______________AGGGCC_GUAUCCG_CUG_GC____________GAAGCGA__UGAGCAGU_UC\n______________\|::\|\|\|_\|:\|:\|\|\|_\|\|\|_\|\|____________\|\|\|\|\|:\|__\|\|\|\|\|\|:\|_\|\|\n______________UUUCGG_CGUGGGC_GAC_CG____________CUUCGUU__ACUCGUUA_AG\n__________3'-U______U_______C______AUUCAUUAUGAC_______AC________C__CACGA...GCG-5'\n_____________\|_____________________________________________________\|\n_____________90____________________________________________________37\n	36 -- 42	41 -- 47	-40.4977 kcal/mol	9.24688 kcal/mol	14.9106 kcal/mol	1 46@LB@ \| \|@LB@ 5'- U A AUUAAA C C AACCU...CAU-3'@LB@ AGGGCC GUAUCCG CUG GC GAAGCGA UGAGCAGU UC@LB@ \|::\|\|\| \|:\|:\|\|\| \|\|\| \|\| \|\|\|\|\|:\| \|\|\|\|\|\|:\| \|\|@LB@ UUUCGG CGUGGGC GAC CG CUUCGUU ACUCGUUA AG@LB@ 3'-U U C AUUCAUUAUGAC AC C CACGA...GCG-5'@LB@ \| \|@LB@ 90 37@LB@@LB@@LB@Energy -16.34 kcal/mol@LB@Hybridization Energy -40.4977 kcal/mol@LB@Unfolding Energy - mRNA 9.24688 kcal/mol@LB@Unfolding Energy - sRNA 14.9106 kcal/mol@LB@@LB@Position - mRNA 1 -- 45@LB@Position - sRNA 38 -- 89@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 41 -- 47@LB@
19	0.001375	0.2431	b0722	sdhD	-16.32	0.016452	168 -- 195	12 -- 41	succinate dehydrogenase membrane subunit binds cytochrome b556	_____________167_____________________________196\n_____________\|_______________________________\|\n5'-UCC...AUUAC_____________C_____________A___CUCGU...UGG-3'\n______________UGUCGUGCUUUCA__UUCU_CGC_AGG_GUC\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|__\|\|\|\|_\|\|\|_\|\|\|_\|\|\|\n______________ACAGCACGAAAGU__AAGA_GCG_UCC_CAG\n3'-UUU...UCGUU_____________CC____G___C_______AAGGA...GCG-5'\n_____________\|_______________________________\|\n_____________42______________________________11\n	174 -- 180	29 -- 35	-35.0246 kcal/mol	7.60237 kcal/mol	11.1071 kcal/mol	167 196@LB@ \| \|@LB@5'-UCC...AUUAC C A CUCGU...UGG-3'@LB@ UGUCGUGCUUUCA UUCU CGC AGG GUC@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|\| \|\|\| \|\|\| \|\|\|@LB@ ACAGCACGAAAGU AAGA GCG UCC CAG@LB@3'-UUU...UCGUU CC G C AAGGA...GCG-5'@LB@ \| \|@LB@ 42 11@LB@@LB@@LB@Energy -16.32 kcal/mol@LB@Hybridization Energy -35.0246 kcal/mol@LB@Unfolding Energy - mRNA 7.60237 kcal/mol@LB@Unfolding Energy - sRNA 11.1071 kcal/mol@LB@@LB@Position - mRNA 168 -- 195@LB@Position - sRNA 12 -- 41@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 29 -- 35@LB@
192	0.02457	0.4226	b2689	yqaA	-16.30	0.016522	258 -- 300	44 -- 85	COG1238 family inner membrane protein	_____________257_________________________________________300\n_____________\|___________________________________________\|\n5'-CAC...CUACA___U________AACUCCG____C_______U________U___-3'\n______________CUA_UACCCGGC_______AAGU_GUGCUGG_GGCAAUGU__GC\n______________\|:\|_:\|\|\|\|\|\|\|_______\|\|\|\|_:\|:\|\|\|\|_:\|\|\|\|\|\|\|__\|\|\n______________GGU_GUGGGCCG_______UUCA_UAUGACC_UCGUUACA__CG\n______3'-UUUUC___C________ACCGA______U_______U________CU__UUACA...GCG-5'\n_____________\|____________________________________________\|\n_____________86___________________________________________43\n	291 -- 297	48 -- 54	-43.3701 kcal/mol	12.1561 kcal/mol	14.9093 kcal/mol	257 300@LB@ \| \|@LB@5'-CAC...CUACA U AACUCCG C U U -3'@LB@ CUA UACCCGGC AAGU GUGCUGG GGCAAUGU GC@LB@ \|:\| :\|\|\|\|\|\|\| \|\|\|\| :\|:\|\|\|\| :\|\|\|\|\|\|\| \|\|@LB@ GGU GUGGGCCG UUCA UAUGACC UCGUUACA CG@LB@ 3'-UUUUC C ACCGA U U CU UUACA...GCG-5'@LB@ \| \|@LB@ 86 43@LB@@LB@@LB@Energy -16.30 kcal/mol@LB@Hybridization Energy -43.3701 kcal/mol@LB@Unfolding Energy - mRNA 12.1561 kcal/mol@LB@Unfolding Energy - sRNA 14.9093 kcal/mol@LB@@LB@Position - mRNA 258 -- 300@LB@Position - sRNA 44 -- 85@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 48 -- 54@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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