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	Additional homologs
111	0.004903	0.1545	b1735	chbR	-11.17	0.151186	109 -- 138	30 -- 50	repressor of chb operon for N N'-diacetylchitobiose utilization		_____________108____________________________139\n_____________\|______________________________\|\n5'-GAU...GUCCA________AUCAUUUAAU__CG________UGCGC...CUG-3'\n______________CGCUCAGG__________GA__UCCAUGCU\n______________\|:\|\|\|\|\|\|__________\|\|__\|\|\|\|\|\|\|\|\n______________GUGAGUCC__________CU__AGGUACGA\n3'-UUU...ACAAA________C___________AA________AUAUU...GCA-5'\n_____________\|______________________________\|\n_____________51_____________________________29\n	132 -- 138	30 -- 36	-23.5874 kcal/mol	7.28235 kcal/mol	5.13509 kcal/mol	108 139@LB@ \| \|@LB@5'-GAU...GUCCA AUCAUUUAAU CG UGCGC...CUG-3'@LB@ CGCUCAGG GA UCCAUGCU@LB@ \|:\|\|\|\|\|\| \|\| \|\|\|\|\|\|\|\|@LB@ GUGAGUCC CU AGGUACGA@LB@3'-UUU...ACAAA C AA AUAUU...GCA-5'@LB@ \| \|@LB@ 51 29@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -23.5874 kcal/mol@LB@Unfolding Energy - mRNA 7.28235 kcal/mol@LB@Unfolding Energy - sRNA 5.13509 kcal/mol@LB@@LB@Position - mRNA 109 -- 138@LB@Position - sRNA 30 -- 50@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 30 -- 36@LB@
60	0.002324	0.1363	b0881	clpS	-11.74	0.117068	9 -- 15	40 -- 46	regulatory protein for ClpA substrate specificity		_____________8_______16\n_____________\|_______\|\n___5'-GCAUUUGA_______CAAGG...UCA-3'\n______________CAGGGGA\n______________\|\|\|\|\|\|\|\n______________GUCCCCU\n3'-UUU...AGUGA_______AAAGG...GCA-5'\n_____________\|_______\|\n_____________47______39\n	9 -- 15	40 -- 46	-13.2936 kcal/mol	0.199257 kcal/mol	1.35582 kcal/mol	8 16@LB@ \| \|@LB@ 5'-GCAUUUGA CAAGG...UCA-3'@LB@ CAGGGGA@LB@ \|\|\|\|\|\|\|@LB@ GUCCCCU@LB@3'-UUU...AGUGA AAAGG...GCA-5'@LB@ \| \|@LB@ 47 39@LB@@LB@@LB@Energy -11.74 kcal/mol@LB@Hybridization Energy -13.2936 kcal/mol@LB@Unfolding Energy - mRNA 0.199257 kcal/mol@LB@Unfolding Energy - sRNA 1.35582 kcal/mol@LB@@LB@Position - mRNA 9 -- 15@LB@Position - sRNA 40 -- 46@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 40 -- 46@LB@
124	0.005471	0.1553	b1249	clsA	-8.47	0.418250	164 -- 196	34 -- 71	cardiolipin synthase 1		_____________163____________________________________197\n_____________\|______________________________________\|\n5'-GUC...CGUAA__U____A____G__C_______AAA____________AUCUA...CAG-3'\n______________AC_CAUA_CAAU_CG___UUUCA______GGAUUUCUA\n______________\|\|_\|\|:\|_\|\|\|\|_\|\|___\|\|\|\|\|______\|\|\|\|\|\|\|:\|\n______________UG_GUGU_GUUA_GC___AAAGU______CCUAAAGGU\n3'-UUU...UCUGA__U____C____A__AAC_____GAGUCC_________ACGAA...GCA-5'\n_____________\|______________________________________\|\n_____________72_____________________________________33\n	190 -- 196	34 -- 40	-20.3655 kcal/mol	7.10457 kcal/mol	4.79237 kcal/mol	163 197@LB@ \| \|@LB@5'-GUC...CGUAA U A G C AAA AUCUA...CAG-3'@LB@ AC CAUA CAAU CG UUUCA GGAUUUCUA@LB@ \|\| \|\|:\| \|\|\|\| \|\| \|\|\|\|\| \|\|\|\|\|\|\|:\|@LB@ UG GUGU GUUA GC AAAGU CCUAAAGGU@LB@3'-UUU...UCUGA U C A AAC GAGUCC ACGAA...GCA-5'@LB@ \| \|@LB@ 72 33@LB@@LB@@LB@Energy -8.47 kcal/mol@LB@Hybridization Energy -20.3655 kcal/mol@LB@Unfolding Energy - mRNA 7.10457 kcal/mol@LB@Unfolding Energy - sRNA 4.79237 kcal/mol@LB@@LB@Position - mRNA 164 -- 196@LB@Position - sRNA 34 -- 71@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 34 -- 40@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@
19	0.0001526	0.02826	b1040	csgD	-18.47	0.001904	103 -- 117	60 -- 74	csgBAC operon transcriptional regulator	b3520	_____________102_____________118\n_____________\|_______________\|\n5'-UUA...UUAUU_______________GCAAC...CGC-3'\n______________ACUACACACAGCAGU\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|:\|\n______________UGAUGUGUGUCGUUA\n3'-UUU...GUUUC_______________AGCAA...GCA-5'\n_____________\|_______________\|\n_____________75______________59\n	111 -- 117	60 -- 66	-23.4761 kcal/mol	1.72592 kcal/mol	3.27997 kcal/mol	102 118@LB@ \| \|@LB@5'-UUA...UUAUU GCAAC...CGC-3'@LB@ ACUACACACAGCAGU@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\|:\|@LB@ UGAUGUGUGUCGUUA@LB@3'-UUU...GUUUC AGCAA...GCA-5'@LB@ \| \|@LB@ 75 59@LB@@LB@@LB@Energy -18.47 kcal/mol@LB@Hybridization Energy -23.4761 kcal/mol@LB@Unfolding Energy - mRNA 1.72592 kcal/mol@LB@Unfolding Energy - sRNA 3.27997 kcal/mol@LB@@LB@Position - mRNA 103 -- 117@LB@Position - sRNA 60 -- 74@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 60 -- 66@LB@
137	0.006282	0.1605	b0123	cueO	-13.57	0.047118	144 -- 176	48 -- 78	multicopper oxidase (laccase)		_____________143________________________________177\n_____________\|__________________________________\|\n5'-CUG...AGGGG___________U__A_______AUU_________CUGCU...CGU-3'\n______________AAGGACUAUGC_CA_C_GUUUG___UUGUUUCGC\n______________\|\|:\|\|\|\|\|::\|_\|\|_\|_:\|\|:\|___\|\|\|\|\|\|\|:\|\n______________UUUCUGAUGUG_GU_G_UAAGC___AACAAAGUG\n3'-UUU...ACCCG___________U__C_U_________________AGUCC...GCA-5'\n_____________\|__________________________________\|\n_____________79_________________________________47\n	170 -- 176	48 -- 54	-24.1368 kcal/mol	6.88378 kcal/mol	3.68736 kcal/mol	143 177@LB@ \| \|@LB@5'-CUG...AGGGG U A AUU CUGCU...CGU-3'@LB@ AAGGACUAUGC CA C GUUUG UUGUUUCGC@LB@ \|\|:\|\|\|\|\|::\| \|\| \| :\|\|:\| \|\|\|\|\|\|\|:\|@LB@ UUUCUGAUGUG GU G UAAGC AACAAAGUG@LB@3'-UUU...ACCCG U C U AGUCC...GCA-5'@LB@ \| \|@LB@ 79 47@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -24.1368 kcal/mol@LB@Unfolding Energy - mRNA 6.88378 kcal/mol@LB@Unfolding Energy - sRNA 3.68736 kcal/mol@LB@@LB@Position - mRNA 144 -- 176@LB@Position - sRNA 48 -- 78@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 48 -- 54@LB@
8	3.984e-05	0.01752	b2752	cysD	-11.53	0.128779	103 -- 132	45 -- 74	sulfate adenylyltransferase subunit 2		_____________102____________________________133\n_____________\|______________________________\|\n5'-GCC...AAGGA_____U___UC_____G__AA_________UUCUC...UCU-3'\n______________ACUAC_CAU__UAAUU_GU__UUUCAUUCG\n______________\|\|\|\|\|_\|\|:__:\|\|\|\|_\|\|__\|\|\|\|\|:\|\|:\n______________UGAUG_GUG__GUUAA_CA__AAAGUGAGU\n3'-UUU...GUUUC_____U___UC_____G__AC_________CCCCU...GCA-5'\n_____________\|______________________________\|\n_____________75_____________________________44\n	126 -- 132	45 -- 51	-20.8412 kcal/mol	5.57115 kcal/mol	3.74056 kcal/mol	102 133@LB@ \| \|@LB@5'-GCC...AAGGA U UC G AA UUCUC...UCU-3'@LB@ ACUAC CAU UAAUU GU UUUCAUUCG@LB@ \|\|\|\|\| \|\|: :\|\|\|\| \|\| \|\|\|\|\|:\|\|:@LB@ UGAUG GUG GUUAA CA AAAGUGAGU@LB@3'-UUU...GUUUC U UC G AC CCCCU...GCA-5'@LB@ \| \|@LB@ 75 44@LB@@LB@@LB@Energy -11.53 kcal/mol@LB@Hybridization Energy -20.8412 kcal/mol@LB@Unfolding Energy - mRNA 5.57115 kcal/mol@LB@Unfolding Energy - sRNA 3.74056 kcal/mol@LB@@LB@Position - mRNA 103 -- 132@LB@Position - sRNA 45 -- 74@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 45 -- 51@LB@
54	0.00187	0.1218	b3607	cysE	-14.87	0.022582	98 -- 129	42 -- 78	serine acetyltransferase		_____________97_________________________________________130\n_____________\|__________________________________________\|\n5'-CGG...CACGC______GA__________C_____________AACCC_____AACCU...CGA-3'\n______________AAGGAC___GCGCAGCAG__________CACU_____CAGGG\n______________\|\|:\|\|\|___:\|:\|\|\|\|\|:__________\|\|\|\|_____\|\|\|\|\|\n______________UUUCUG___UGUGUCGUU__________GUGA_____GUCCC\n3'-UUU...ACCCG______AUG_________AAGCAACAAA______________CUAAA...GCA-5'\n_____________\|__________________________________________\|\n_____________79_________________________________________41\n	108 -- 114	61 -- 67	-27.0645 kcal/mol	7.42824 kcal/mol	4.76487 kcal/mol	97 130@LB@ \| \|@LB@5'-CGG...CACGC GA C AACCC AACCU...CGA-3'@LB@ AAGGAC GCGCAGCAG CACU CAGGG@LB@ \|\|:\|\|\| :\|:\|\|\|\|\|: \|\|\|\| \|\|\|\|\|@LB@ UUUCUG UGUGUCGUU GUGA GUCCC@LB@3'-UUU...ACCCG AUG AAGCAACAAA CUAAA...GCA-5'@LB@ \| \|@LB@ 79 41@LB@@LB@@LB@Energy -14.87 kcal/mol@LB@Hybridization Energy -27.0645 kcal/mol@LB@Unfolding Energy - mRNA 7.42824 kcal/mol@LB@Unfolding Energy - sRNA 4.76487 kcal/mol@LB@@LB@Position - mRNA 98 -- 129@LB@Position - sRNA 42 -- 78@LB@Position Seed - mRNA 108 -- 114@LB@Position Seed - sRNA 61 -- 67@LB@
63	0.002639	0.1417	b2751	cysN	-11.35	0.139541	181 -- 198	34 -- 49	sulfate adenylyltransferase subunit 1		_____________180________________199\n_____________\|__________________\|\n5'-AGU...AAAAA__G_______U_______AGAUG...GUG-3'\n______________AC_UCAGGGG_AUUUUUA\n______________\|\|_\|\|\|\|\|\|\|_\|\|\|\|::\|\n______________UG_AGUCCCC_UAAAGGU\n3'-UUU...CAAAG__________________ACGAA...GCA-5'\n_____________\|__________________\|\n_____________50_________________33\n	184 -- 190	41 -- 47	-17.8149 kcal/mol	4.64155 kcal/mol	1.82276 kcal/mol	180 199@LB@ \| \|@LB@5'-AGU...AAAAA G U AGAUG...GUG-3'@LB@ AC UCAGGGG AUUUUUA@LB@ \|\| \|\|\|\|\|\|\| \|\|\|\|::\|@LB@ UG AGUCCCC UAAAGGU@LB@3'-UUU...CAAAG ACGAA...GCA-5'@LB@ \| \|@LB@ 50 33@LB@@LB@@LB@Energy -11.35 kcal/mol@LB@Hybridization Energy -17.8149 kcal/mol@LB@Unfolding Energy - mRNA 4.64155 kcal/mol@LB@Unfolding Energy - sRNA 1.82276 kcal/mol@LB@@LB@Position - mRNA 181 -- 198@LB@Position - sRNA 34 -- 49@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 41 -- 47@LB@
107	0.004745	0.1538	b2413	cysZ	-9.47	0.298503	222 -- 238	58 -- 74	sulfate transporter sulfite inhibited		_____________221_______________239\n_____________\|_________________\|\n5'-ACC...CAUCU__CC_____________UUACU...UUU-3'\n______________GC__CACGCAGCGGUUU\n______________:\|__\|\|\|:\|\|\|\|::\|\|:\n______________UG__GUGUGUCGUUAAG\n3'-UUU...GUUUC__AU_____________CAACA...GCA-5'\n_____________\|_________________\|\n_____________75________________57\n	232 -- 238	58 -- 64	-18.5455 kcal/mol	5.77464 kcal/mol	3.3008 kcal/mol	221 239@LB@ \| \|@LB@5'-ACC...CAUCU CC UUACU...UUU-3'@LB@ GC CACGCAGCGGUUU@LB@ :\| \|\|\|:\|\|\|\|::\|\|:@LB@ UG GUGUGUCGUUAAG@LB@3'-UUU...GUUUC AU CAACA...GCA-5'@LB@ \| \|@LB@ 75 57@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -18.5455 kcal/mol@LB@Unfolding Energy - mRNA 5.77464 kcal/mol@LB@Unfolding Energy - sRNA 3.3008 kcal/mol@LB@@LB@Position - mRNA 222 -- 238@LB@Position - sRNA 58 -- 74@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 58 -- 64@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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