Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
101	0.004534	0.1538	b2079	baeR	-10.16	0.230535	155 -- 191	34 -- 71	response regulator in two-component regulatory system with BaeS	_____________154_______________________________________192\n_____________\|_________________________________________\|\n5'-CAG...GGUAA___U________A_____AC______G_AAC______UA__GAGAG...CGA-3'\n______________GCA_UACAGUAG___GUU____CGCU_G___GGGAUU__CA\n______________:\|\|_:\|\|\|\|:\|:___\|\|\|____\|:\|\|_:___\|\|\|\|\|\|__\|\|\n______________UGU_GUGUCGUU___CAA____GUGA_U___CCCUAA__GU\n3'-UUU...UCUGA____________AAG___CAAA____G_C________AG__ACGAA...GCA-5'\n_____________\|_________________________________________\|\n_____________72________________________________________33\n	160 -- 166	61 -- 67	-23.4603 kcal/mol	8.51419 kcal/mol	4.79237 kcal/mol	154 192@LB@ \| \|@LB@5'-CAG...GGUAA U A AC G AAC UA GAGAG...CGA-3'@LB@ GCA UACAGUAG GUU CGCU G GGGAUU CA@LB@ :\|\| :\|\|\|\|:\|: \|\|\| \|:\|\| : \|\|\|\|\|\| \|\|@LB@ UGU GUGUCGUU CAA GUGA U CCCUAA GU@LB@3'-UUU...UCUGA AAG CAAA G C AG ACGAA...GCA-5'@LB@ \| \|@LB@ 72 33@LB@@LB@@LB@Energy -10.16 kcal/mol@LB@Hybridization Energy -23.4603 kcal/mol@LB@Unfolding Energy - mRNA 8.51419 kcal/mol@LB@Unfolding Energy - sRNA 4.79237 kcal/mol@LB@@LB@Position - mRNA 155 -- 191@LB@Position - sRNA 34 -- 71@LB@Position Seed - mRNA 160 -- 166@LB@Position Seed - sRNA 61 -- 67@LB@
92	0.004122	0.1538	b3912	cpxR	-15.13	0.019325	106 -- 130	39 -- 76	response regulator in two-component regulatory system with CpxA	_____________105_____________________________________131\n_____________\|_______________________________________\|\n5'-UGA...GAUUC________A___U__________________________GUAAA...AUG-3'\n______________AGGCUGCA_ACA_GCG______________UCAGGGGGU\n______________\|\|:\|\|:\|\|_\|\|\|_\|\|:______________\|\|\|\|\|\|\|:\|\n______________UCUGAUGU_UGU_CGU______________AGUCCCCUA\n3'-UUU...CCGUU________G_______UAAGCAACAAAGUG_________AAGGU...GCA-5'\n_____________\|_______________________________________\|\n_____________77______________________________________38\n	124 -- 130	39 -- 45	-28.779 kcal/mol	8.86764 kcal/mol	4.77949 kcal/mol	105 131@LB@ \| \|@LB@5'-UGA...GAUUC A U GUAAA...AUG-3'@LB@ AGGCUGCA ACA GCG UCAGGGGGU@LB@ \|\|:\|\|:\|\| \|\|\| \|\|: \|\|\|\|\|\|\|:\|@LB@ UCUGAUGU UGU CGU AGUCCCCUA@LB@3'-UUU...CCGUU G UAAGCAACAAAGUG AAGGU...GCA-5'@LB@ \| \|@LB@ 77 38@LB@@LB@@LB@Energy -15.13 kcal/mol@LB@Hybridization Energy -28.779 kcal/mol@LB@Unfolding Energy - mRNA 8.86764 kcal/mol@LB@Unfolding Energy - sRNA 4.77949 kcal/mol@LB@@LB@Position - mRNA 106 -- 130@LB@Position - sRNA 39 -- 76@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 39 -- 45@LB@
104	0.004609	0.1538	b3405	ompR	-12.19	0.094658	154 -- 190	42 -- 77	response regulator in two-component regulatory system with EnvZ	_____________153___________________________________191\n_____________\|_____________________________________\|\n5'-AAU...UUUUU____A_______UUA___A______CGAAC___U___AGUAC...GCG-3'\n______________AAGA_UACACGC___CAA_UUGUUG_____CUU_GGG\n______________\|\|\|\|_\|\|\|\|\|:\|___\|\|\|_\|:\|\|\|\|_____\|\|:_\|\|\|\n______________UUCU_AUGUGUG___GUU_AGCAAC_____GAG_CCC\n3'-UUU...CCCGU____G_______UC____A______AAAGU___U___CUAAA...GCA-5'\n_____________\|_____________________________________\|\n_____________78____________________________________41\n	159 -- 165	66 -- 72	-25.6517 kcal/mol	8.69679 kcal/mol	4.7648 kcal/mol	153 191@LB@ \| \|@LB@5'-AAU...UUUUU A UUA A CGAAC U AGUAC...GCG-3'@LB@ AAGA UACACGC CAA UUGUUG CUU GGG@LB@ \|\|\|\| \|\|\|\|\|:\| \|\|\| \|:\|\|\|\| \|\|: \|\|\|@LB@ UUCU AUGUGUG GUU AGCAAC GAG CCC@LB@3'-UUU...CCCGU G UC A AAAGU U CUAAA...GCA-5'@LB@ \| \|@LB@ 78 41@LB@@LB@@LB@Energy -12.19 kcal/mol@LB@Hybridization Energy -25.6517 kcal/mol@LB@Unfolding Energy - mRNA 8.69679 kcal/mol@LB@Unfolding Energy - sRNA 4.7648 kcal/mol@LB@@LB@Position - mRNA 154 -- 190@LB@Position - sRNA 42 -- 77@LB@Position Seed - mRNA 159 -- 165@LB@Position Seed - sRNA 66 -- 72@LB@
98	0.004518	0.1538	b2193	narP	-14.47	0.028569	155 -- 204	31 -- 74	response regulator in two-component regulatory system with NarQ	_____________154________________________________________________205\n_____________\|__________________________________________________\|\n5'-UUG...CCAAC_______UCAA___UAA______UAAUAAAAC______A__CUA______CUGAA...AAG-3'\n______________GCUACGC____ACA___UGAUUC_________CUCAGG_GA___CUAUGC\n______________:\|\|\|\|:\|____\|\|\|___::\|\|\|\|_________\|\|\|\|\|\|_\|\|___\|:\|\|\|\|\n______________UGAUGUG____UGU___GUUAAG_________GAGUCC_CU___GGUACG\n3'-UUU...GUUUC______________C________CAACAAAGU______C__AAA______AAUAU...GCA-5'\n_____________\|__________________________________________________\|\n_____________75_________________________________________________30\n	155 -- 161	68 -- 74	-27.903 kcal/mol	6.17297 kcal/mol	7.26183 kcal/mol	154 205@LB@ \| \|@LB@5'-UUG...CCAAC UCAA UAA UAAUAAAAC A CUA CUGAA...AAG-3'@LB@ GCUACGC ACA UGAUUC CUCAGG GA CUAUGC@LB@ :\|\|\|\|:\| \|\|\| ::\|\|\|\| \|\|\|\|\|\| \|\| \|:\|\|\|\|@LB@ UGAUGUG UGU GUUAAG GAGUCC CU GGUACG@LB@3'-UUU...GUUUC C CAACAAAGU C AAA AAUAU...GCA-5'@LB@ \| \|@LB@ 75 30@LB@@LB@@LB@Energy -14.47 kcal/mol@LB@Hybridization Energy -27.903 kcal/mol@LB@Unfolding Energy - mRNA 6.17297 kcal/mol@LB@Unfolding Energy - sRNA 7.26183 kcal/mol@LB@@LB@Position - mRNA 155 -- 204@LB@Position - sRNA 31 -- 74@LB@Position Seed - mRNA 155 -- 161@LB@Position Seed - sRNA 68 -- 74@LB@
106	0.004704	0.1538	b0995	torR	-15.76	0.013096	243 -- 292	33 -- 70	response regulator in two-component regulatory system with TorS	_____________242_________________________________________________293\n_____________\|___________________________________________________\|\n5'-CCA...UUACC__G_________ACAAUCCUAC__________A__GGUAUACC________UACGGCGA-3'\n______________CA_GC_GCGAUU__________UUCACUCAGG_GG________GUUUCCGU\n______________\|\|_:\|_\|\|:\|\|\|__________\|\|\|\|\|\|\|\|\|\|_\|\|________:\|\|\|\|\|:\|\n______________GU_UG_CGUUAA__________AAGUGAGUCC_CC________UAAAGGUA\n3'-UUU...CUGAU__G__U______GCAACA_________________________________CGAAU...GCA-5'\n_____________\|___________________________________________________\|\n_____________71__________________________________________________32\n	286 -- 292	33 -- 39	-31.2367 kcal/mol	10.6838 kcal/mol	4.7924 kcal/mol	242 293@LB@ \| \|@LB@5'-CCA...UUACC G ACAAUCCUAC A GGUAUACC UACGGCGA-3'@LB@ CA GC GCGAUU UUCACUCAGG GG GUUUCCGU@LB@ \|\| :\| \|\|:\|\|\| \|\|\|\|\|\|\|\|\|\| \|\| :\|\|\|\|\|:\|@LB@ GU UG CGUUAA AAGUGAGUCC CC UAAAGGUA@LB@3'-UUU...CUGAU G U GCAACA CGAAU...GCA-5'@LB@ \| \|@LB@ 71 32@LB@@LB@@LB@Energy -15.76 kcal/mol@LB@Hybridization Energy -31.2367 kcal/mol@LB@Unfolding Energy - mRNA 10.6838 kcal/mol@LB@Unfolding Energy - sRNA 4.7924 kcal/mol@LB@@LB@Position - mRNA 243 -- 292@LB@Position - sRNA 33 -- 70@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 33 -- 39@LB@
142	0.006549	0.1605	b3902	rhaD	-9.93	0.251242	192 -- 218	44 -- 69	rhamnulose-1-phosphate aldolase	_____________191_________________________219\n_____________\|___________________________\|\n5'-AGA...CAGGA______AACAUGCAAAACA________UCCUG...UGA-3'\n______________ACACAG_____________UUACUCAG\n______________\|\|\|\|\|\|_____________\|:\|\|\|\|\|\|\n______________UGUGUC_____________AGUGAGUC\n3'-UUU...UGAUG______GUUAAGCAACAA_________CCCUA...GCA-5'\n_____________\|___________________________\|\n_____________70__________________________43\n	212 -- 218	44 -- 50	-16.231 kcal/mol	2.20309 kcal/mol	4.09554 kcal/mol	191 219@LB@ \| \|@LB@5'-AGA...CAGGA AACAUGCAAAACA UCCUG...UGA-3'@LB@ ACACAG UUACUCAG@LB@ \|\|\|\|\|\| \|:\|\|\|\|\|\|@LB@ UGUGUC AGUGAGUC@LB@3'-UUU...UGAUG GUUAAGCAACAA CCCUA...GCA-5'@LB@ \| \|@LB@ 70 43@LB@@LB@@LB@Energy -9.93 kcal/mol@LB@Hybridization Energy -16.231 kcal/mol@LB@Unfolding Energy - mRNA 2.20309 kcal/mol@LB@Unfolding Energy - sRNA 4.09554 kcal/mol@LB@@LB@Position - mRNA 192 -- 218@LB@Position - sRNA 44 -- 69@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 44 -- 50@LB@
117	0.005152	0.155	b2235	nrdB	-9.05	0.346139	190 -- 222	48 -- 77	ribonucleoside-diphosphate reductase 1 beta subunit ferritin-like protein	_____________189_______________________________223\n_____________\|_________________________________\|\n5'-UCC...CCAAC_____AC__U_______UAUACCACCU______AGACG...AAU-3'\n______________AGGAC__AC_CAUGGCA__________UUUCAC\n______________\|:\|\|\|__\|\|_\|\|::\|\|\|__________\|\|\|\|\|\|\n______________UUCUG__UG_GUGUCGU__________AAAGUG\n3'-UUU...CCCGU_____A___U_______UAAGCAAC________AGUCC...GCA-5'\n_____________\|_________________________________\|\n_____________78________________________________47\n	200 -- 206	62 -- 68	-18.188 kcal/mol	5.45206 kcal/mol	3.68729 kcal/mol	189 223@LB@ \| \|@LB@5'-UCC...CCAAC AC U UAUACCACCU AGACG...AAU-3'@LB@ AGGAC AC CAUGGCA UUUCAC@LB@ \|:\|\|\| \|\| \|\|::\|\|\| \|\|\|\|\|\|@LB@ UUCUG UG GUGUCGU AAAGUG@LB@3'-UUU...CCCGU A U UAAGCAAC AGUCC...GCA-5'@LB@ \| \|@LB@ 78 47@LB@@LB@@LB@Energy -9.05 kcal/mol@LB@Hybridization Energy -18.188 kcal/mol@LB@Unfolding Energy - mRNA 5.45206 kcal/mol@LB@Unfolding Energy - sRNA 3.68729 kcal/mol@LB@@LB@Position - mRNA 190 -- 222@LB@Position - sRNA 48 -- 77@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 62 -- 68@LB@
135	0.006184	0.1605	b0637	rsfS	-13.92	0.038847	179 -- 195	40 -- 56	ribosomal silencing factor	_____________178_______________196\n_____________\|_________________\|\n5'-AUU...UCUAU___A_____C_______AAAAC...UCA-3'\n______________UUG_UUCAC_CAGGGGG\n______________\|\|\|_\|\|\|\|\|_\|\|\|\|\|\|:\n______________AAC_AAGUG_GUCCCCU\n3'-UUU...UAAGC___A_____A_______AAAGG...GCA-5'\n_____________\|_________________\|\n_____________57________________39\n	189 -- 195	40 -- 46	-20.5369 kcal/mol	4.69018 kcal/mol	1.92548 kcal/mol	178 196@LB@ \| \|@LB@5'-AUU...UCUAU A C AAAAC...UCA-3'@LB@ UUG UUCAC CAGGGGG@LB@ \|\|\| \|\|\|\|\| \|\|\|\|\|\|:@LB@ AAC AAGUG GUCCCCU@LB@3'-UUU...UAAGC A A AAAGG...GCA-5'@LB@ \| \|@LB@ 57 39@LB@@LB@@LB@Energy -13.92 kcal/mol@LB@Hybridization Energy -20.5369 kcal/mol@LB@Unfolding Energy - mRNA 4.69018 kcal/mol@LB@Unfolding Energy - sRNA 1.92548 kcal/mol@LB@@LB@Position - mRNA 179 -- 195@LB@Position - sRNA 40 -- 56@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 40 -- 46@LB@
2	1.464e-07	0.0002576	b2741	rpoS	-16.90	0.006155	67 -- 107	33 -- 71	RNA polymerase sigma S (sigma 38) factor	_____________66______________________________________________108\n_____________\|_______________________________________________\|\n5'-CGG...GUUCA______UU___UUUUGAA______________A_______AA_____AAACC...AGG-3'\n______________ACACGC__GCA_______AUUCGUU_____AC__AGGGGA__UCCGU\n______________\|\|\|\|:\|__\|\|\|_______\|\|\|\|\|\|\|_____\|\|__\|\|\|\|\|\|__\|\|\|:\|\n______________UGUGUG__CGU_______UAAGCAA_____UG__UCCCCU__AGGUA\n3'-UUU...UCUGA______U__________________CAAAG__AG______AA_____CGAAU...GCA-5'\n_____________\|_______________________________________________\|\n_____________72______________________________________________32\n	85 -- 91	55 -- 61	-29.972 kcal/mol	8.28292 kcal/mol	4.7924 kcal/mol	66 108@LB@ \| \|@LB@5'-CGG...GUUCA UU UUUUGAA A AA AAACC...AGG-3'@LB@ ACACGC GCA AUUCGUU AC AGGGGA UCCGU@LB@ \|\|\|\|:\| \|\|\| \|\|\|\|\|\|\| \|\| \|\|\|\|\|\| \|\|\|:\|@LB@ UGUGUG CGU UAAGCAA UG UCCCCU AGGUA@LB@3'-UUU...UCUGA U CAAAG AG AA CGAAU...GCA-5'@LB@ \| \|@LB@ 72 32@LB@@LB@@LB@Energy -16.90 kcal/mol@LB@Hybridization Energy -29.972 kcal/mol@LB@Unfolding Energy - mRNA 8.28292 kcal/mol@LB@Unfolding Energy - sRNA 4.7924 kcal/mol@LB@@LB@Position - mRNA 67 -- 107@LB@Position - sRNA 33 -- 71@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 55 -- 61@LB@
13	0.0001005	0.0245	b1921	fliZ	-13.92	0.038869	246 -- 263	63 -- 78	RpoS antagonist; putative regulator of FliA activity	_____________245________________264\n_____________\|__________________\|\n5'-UGC...AUCUU_______UUAA_______CAGAC...AUC-3'\n______________AAAGACU____ACACAGC\n______________\|\|\|\|\|\|\|____\|\|\|\|\|\|\|\n______________UUUCUGA____UGUGUCG\n3'-UUU...ACCCG_______UG_________UUAAG...GCA-5'\n_____________\|__________________\|\n_____________79_________________62\n	257 -- 263	63 -- 69	-17.8578 kcal/mol	0.69523 kcal/mol	3.24195 kcal/mol	245 264@LB@ \| \|@LB@5'-UGC...AUCUU UUAA CAGAC...AUC-3'@LB@ AAAGACU ACACAGC@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UUUCUGA UGUGUCG@LB@3'-UUU...ACCCG UG UUAAG...GCA-5'@LB@ \| \|@LB@ 79 62@LB@@LB@@LB@Energy -13.92 kcal/mol@LB@Hybridization Energy -17.8578 kcal/mol@LB@Unfolding Energy - mRNA 0.69523 kcal/mol@LB@Unfolding Energy - sRNA 3.24195 kcal/mol@LB@@LB@Position - mRNA 246 -- 263@LB@Position - sRNA 63 -- 78@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 63 -- 69@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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