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
99	0.003254	0.1114	b2839	lysR	-9.43	0.148712	276 -- 282	1 -- 7	transcriptional activator of lysA; autorepressor	_____________275_____283\n_____________\|_______\|\n5'-GGC...CGGCA_______UACAC...CAA-3'\n______________CACCUGC\n______________\|\|\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	276 -- 282	1 -- 7	-13.2779 kcal/mol	1.51062 kcal/mol	2.34039 kcal/mol	275 283@LB@ \| \|@LB@5'-GGC...CGGCA UACAC...CAA-3'@LB@ CACCUGC@LB@ \|\|\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -13.2779 kcal/mol@LB@Unfolding Energy - mRNA 1.51062 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 276 -- 282@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 1 -- 7@LB@
65	0.001098	0.05953	b1479	maeA	-10.62	0.077885	180 -- 205	37 -- 65	malate dehydrogenase decarboxylating NAD-requiring; malic enzyme	_____________179___________________________206\n_____________\|_____________________________\|\n5'-UAG...UGGAU_______________________C_____ACCAA...GCA-3'\n______________AUUCAAAAAAG__AGUGAG_UGA_AUGGA\n______________\|\|\|\|\|\|\|\|\|\|\|__\|\|\|:\|\|_::\|_\|\|\|\|\|\n______________UAAGUUUUUUC__UCAUUC_GUU_UACCU\n3'-UUU...GUCAU___________CU______U___A_____CGCGU...ACG-5'\n_____________\|_____________________________\|\n_____________66____________________________36\n	184 -- 190	55 -- 61	-21.4117 kcal/mol	4.89609 kcal/mol	5.88101 kcal/mol	179 206@LB@ \| \|@LB@5'-UAG...UGGAU C ACCAA...GCA-3'@LB@ AUUCAAAAAAG AGUGAG UGA AUGGA@LB@ \|\|\|\|\|\|\|\|\|\|\| \|\|\|:\|\| ::\| \|\|\|\|\|@LB@ UAAGUUUUUUC UCAUUC GUU UACCU@LB@3'-UUU...GUCAU CU U A CGCGU...ACG-5'@LB@ \| \|@LB@ 66 36@LB@@LB@@LB@Energy -10.62 kcal/mol@LB@Hybridization Energy -21.4117 kcal/mol@LB@Unfolding Energy - mRNA 4.89609 kcal/mol@LB@Unfolding Energy - sRNA 5.88101 kcal/mol@LB@@LB@Position - mRNA 180 -- 205@LB@Position - sRNA 37 -- 65@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 55 -- 61@LB@
45	0.0004696	0.03623	b4035	malK	-9.83	0.120497	188 -- 201	44 -- 57	maltose ABC transportor ATPase	_____________187____________202\n_____________\|______________\|\n5'-CGC...UUACA_______A______UGGCG...UGU-3'\n______________AAGGGAG_AGGGCA\n______________\|\|\|\|:\|\|_\|:\|:\|\|\n______________UUCCUUC_UUCUGU\n3'-UUU...GUUUU_______A______UAUAC...ACG-5'\n_____________\|______________\|\n_____________58_____________43\n	188 -- 194	51 -- 57	-14.5332 kcal/mol	2.95068 kcal/mol	1.74831 kcal/mol	187 202@LB@ \| \|@LB@5'-CGC...UUACA A UGGCG...UGU-3'@LB@ AAGGGAG AGGGCA@LB@ \|\|\|\|:\|\| \|:\|:\|\|@LB@ UUCCUUC UUCUGU@LB@3'-UUU...GUUUU A UAUAC...ACG-5'@LB@ \| \|@LB@ 58 43@LB@@LB@@LB@Energy -9.83 kcal/mol@LB@Hybridization Energy -14.5332 kcal/mol@LB@Unfolding Energy - mRNA 2.95068 kcal/mol@LB@Unfolding Energy - sRNA 1.74831 kcal/mol@LB@@LB@Position - mRNA 188 -- 201@LB@Position - sRNA 44 -- 57@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 51 -- 57@LB@
147	0.005701	0.1366	b1622	malY	-7.52	0.364460	44 -- 91	35 -- 85	PLP-dependent beta-cystathionase and maltose regulon regulator	_____________43____________________________________________________92\n_____________\|_____________________________________________________\|\n5'-UCG...GAUAU____C____UAA_______GCACU__________CAAUC___________C__AGUAC...UCA-3'\n______________GUCG_UUGU___UGUGCAG_________GAAGGA_____GGGCAAU_UGG_GU\n______________:\|\|:_\|\|\|\|___\|:\|\|\|\|\|_________:\|\|\|\|\|_____:\|:\|\|\|\|_\|\|\|_\|:\n______________UAGU_AACA___AUACGUC_________UUUCCU_____UCUGUUA_ACC_CG\n3'-UUU...AUGCU____U____CG________AUUAAGUUU______UCAU________U___U__CGUUG...ACG-5'\n_____________\|_____________________________________________________\|\n_____________86____________________________________________________34\n	79 -- 85	42 -- 48	-29.3049 kcal/mol	13.5755 kcal/mol	8.20283 kcal/mol	43 92@LB@ \| \|@LB@5'-UCG...GAUAU C UAA GCACU CAAUC C AGUAC...UCA-3'@LB@ GUCG UUGU UGUGCAG GAAGGA GGGCAAU UGG GU@LB@ :\|\|: \|\|\|\| \|:\|\|\|\|\| :\|\|\|\|\| :\|:\|\|\|\| \|\|\| \|:@LB@ UAGU AACA AUACGUC UUUCCU UCUGUUA ACC CG@LB@3'-UUU...AUGCU U CG AUUAAGUUU UCAU U U CGUUG...ACG-5'@LB@ \| \|@LB@ 86 34@LB@@LB@@LB@Energy -7.52 kcal/mol@LB@Hybridization Energy -29.3049 kcal/mol@LB@Unfolding Energy - mRNA 13.5755 kcal/mol@LB@Unfolding Energy - sRNA 8.20283 kcal/mol@LB@@LB@Position - mRNA 44 -- 91@LB@Position - sRNA 35 -- 85@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 42 -- 48@LB@
7	8.167e-06	0.003921	b1531	marA	-12.70	0.022098	183 -- 204	40 -- 62	multiple antibiotic resistance transcriptional regulator	_____________182_____________________205\n_____________\|_______________________\|\n5'-AAG...GUAAA______________U________CCAGA...AGC-3'\n______________CAAAAAA_GAGGUA_GACGAUGU\n______________\|\|\|\|\|\|\|_\|\|:\|\|\|_\|\|\|:\|\|:\|\n______________GUUUUUU_CUUCAU_CUGUUAUA\n3'-UUU...AUUAA_______C______U________CCUCG...ACG-5'\n_____________\|_______________________\|\n_____________63______________________39\n	198 -- 204	40 -- 46	-19.9636 kcal/mol	3.18051 kcal/mol	4.08673 kcal/mol	182 205@LB@ \| \|@LB@5'-AAG...GUAAA U CCAGA...AGC-3'@LB@ CAAAAAA GAGGUA GACGAUGU@LB@ \|\|\|\|\|\|\| \|\|:\|\|\| \|\|\|:\|\|:\|@LB@ GUUUUUU CUUCAU CUGUUAUA@LB@3'-UUU...AUUAA C U CCUCG...ACG-5'@LB@ \| \|@LB@ 63 39@LB@@LB@@LB@Energy -12.70 kcal/mol@LB@Hybridization Energy -19.9636 kcal/mol@LB@Unfolding Energy - mRNA 3.18051 kcal/mol@LB@Unfolding Energy - sRNA 4.08673 kcal/mol@LB@@LB@Position - mRNA 183 -- 204@LB@Position - sRNA 40 -- 62@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 40 -- 46@LB@
63	0.00104	0.05816	b1856	mepM	-14.49	0.006560	139 -- 249	1 -- 88	murein DD-endopeptidase space-maker hydrolase septation protein	_____________138________________________________________________________________________________________________________________250\n_____________\|__________________________________________________________________________________________________________________\|\n5'-CAA...AUUCC__________A___CAACCAG______AGCUGCCU_________AU___U__G__A___AUUAC_______AGAUA____GCUCU_____CC_______UAAUA__________GACCA...UCG-3'\n______________UGAGUCAAUU__GC_______UAUGCG_________GAAAGGAG__UAA_GA_GA_GUG_____GUGCAAC_____GCCC_____GUCGC__UGGCGUU_____AUUUACC_GC\n______________:\|\|:\|\|\|\|\|\|__\|\|_______\|\|\|\|\|:_________:\|\|\|\|\|\|:__\|\|\|_\|\|_:\|_:\|\|_____\|:\|\|\|\|\|_____\|\|\|\|_____:\|\|\|\|__\|\|:\|\|\|\|_____\|\|\|:\|\|\|_\|\|\n______________GCUUAGUUAA__CG_______AUACGU_________UUUUCCUU__AUU_CU_UU_UAC_____CGCGUUG_____CGGG_____UAGCG__ACUGCAA_____UAAGUGG_CG\n3'-UUU...AGCAU__________CA_______________CAUUAAGUU________C_______G__A___CU_____________________________A________CG__________A__-5'\n_____________\|_________________________________________________________________________________________________________________\|\n_____________89________________________________________________________________________________________________________________1\n	241 -- 247	4 -- 10	-60.5282 kcal/mol	25.2709 kcal/mol	20.7761 kcal/mol	138 250@LB@ \| \|@LB@5'-CAA...AUUCC A CAACCAG AGCUGCCU AU U G A AUUAC AGAUA GCUCU CC UAAUA GACCA...UCG-3'@LB@ UGAGUCAAUU GC UAUGCG GAAAGGAG UAA GA GA GUG GUGCAAC GCCC GUCGC UGGCGUU AUUUACC GC@LB@ :\|\|:\|\|\|\|\|\| \|\| \|\|\|\|\|: :\|\|\|\|\|\|: \|\|\| \|\| :\| :\|\| \|:\|\|\|\|\| \|\|\|\| :\|\|\|\| \|\|:\|\|\|\| \|\|\|:\|\|\| \|\|@LB@ GCUUAGUUAA CG AUACGU UUUUCCUU AUU CU UU UAC CGCGUUG CGGG UAGCG ACUGCAA UAAGUGG CG@LB@3'-UUU...AGCAU CA CAUUAAGUU C G A CU A CG A -5'@LB@ \| \|@LB@ 89 1@LB@@LB@@LB@Energy -14.49 kcal/mol@LB@Hybridization Energy -60.5282 kcal/mol@LB@Unfolding Energy - mRNA 25.2709 kcal/mol@LB@Unfolding Energy - sRNA 20.7761 kcal/mol@LB@@LB@Position - mRNA 139 -- 249@LB@Position - sRNA 1 -- 88@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 4 -- 10@LB@
22	6.552e-05	0.01049	b3829	metE	-13.68	0.011485	203 -- 246	1 -- 47	5-methyltetrahydropteroyltriglutamate- homocysteine S-methyltransferase	_____________202_____________________________________________247\n_____________\|_______________________________________________\|\n5'-GAG...AAAAU________U__AUC____A_______G__UCCCUC_____G______GUCGC...GUG-3'\n______________GACAAUAU_GA_____AC_CCC_UCG_UU______GCGUU_GCCUGC\n______________\|\|\|\|\|\|\|\|_\|\|_____\|\|_\|\|\|_\|\|\|_\|\|______\|\|:\|\|_:\|\|\|\|\|\n______________CUGUUAUA_CU_____UG_GGG_AGC_AA______CGUAA_UGGACG\n3'-UUU...UCAUU________C__CGCGU__C___U___G__CUGCAA_____G______-5'\n_____________\|______________________________________________\|\n_____________48_____________________________________________1\n	204 -- 210	40 -- 46	-38.0501 kcal/mol	7.59426 kcal/mol	16.7767 kcal/mol	202 247@LB@ \| \|@LB@5'-GAG...AAAAU U AUC A G UCCCUC G GUCGC...GUG-3'@LB@ GACAAUAU GA AC CCC UCG UU GCGUU GCCUGC@LB@ \|\|\|\|\|\|\|\| \|\| \|\| \|\|\| \|\|\| \|\| \|\|:\|\| :\|\|\|\|\|@LB@ CUGUUAUA CU UG GGG AGC AA CGUAA UGGACG@LB@3'-UUU...UCAUU C CGCGU C U G CUGCAA G -5'@LB@ \| \|@LB@ 48 1@LB@@LB@@LB@Energy -13.68 kcal/mol@LB@Hybridization Energy -38.0501 kcal/mol@LB@Unfolding Energy - mRNA 7.59426 kcal/mol@LB@Unfolding Energy - sRNA 16.7767 kcal/mol@LB@@LB@Position - mRNA 203 -- 246@LB@Position - sRNA 1 -- 47@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 40 -- 46@LB@
121	0.004137	0.1205	b0353	mhpT	-11.58	0.044392	170 -- 179	1 -- 10	3-hydroxyphenylpropionic transporter	_____________169________180\n_____________\|__________\|\n5'-CGG...UCGCG__________ACUCG...CGG-3'\n______________AUUCACCUGC\n______________\|\|\|\|\|\|\|\|\|\|\n______________UAAGUGGACG\n3'-UUU...CAACG__________-5'\n_____________\|_________\|\n_____________11________1\n	173 -- 179	1 -- 7	-16.6324 kcal/mol	2.26547 kcal/mol	2.7891 kcal/mol	169 180@LB@ \| \|@LB@5'-CGG...UCGCG ACUCG...CGG-3'@LB@ AUUCACCUGC@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UAAGUGGACG@LB@3'-UUU...CAACG -5'@LB@ \| \|@LB@ 11 1@LB@@LB@@LB@Energy -11.58 kcal/mol@LB@Hybridization Energy -16.6324 kcal/mol@LB@Unfolding Energy - mRNA 2.26547 kcal/mol@LB@Unfolding Energy - sRNA 2.7891 kcal/mol@LB@@LB@Position - mRNA 170 -- 179@LB@Position - sRNA 1 -- 10@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 1 -- 7@LB@
152	0.005935	0.1368	b2701	mltB	-9.57	0.138424	83 -- 107	69 -- 92	membrane-bound lytic murein transglycosylase B	_____________82________________________108\n_____________\|_________________________\|\n5'-AGA...GAUAG__AG_G____G_____A________AAGUC...GAA-3'\n______________CG__G_GAAU_AGUUG_GUUAUGUA\n______________\|\|__:_\|\|\|\|_\|:\|\|\|_\|:\|\|\|\|:\|\n______________GC__U_CUUA_UUAAC_CGAUACGU\n3'-UUU...CCGCA__A__G____G_____A________CAUUA...ACG-5'\n_____________\|_________________________\|\n_____________93________________________68\n	101 -- 107	69 -- 75	-19.8359 kcal/mol	5.60429 kcal/mol	4.66371 kcal/mol	82 108@LB@ \| \|@LB@5'-AGA...GAUAG AG G G A AAGUC...GAA-3'@LB@ CG G GAAU AGUUG GUUAUGUA@LB@ \|\| : \|\|\|\| \|:\|\|\| \|:\|\|\|\|:\|@LB@ GC U CUUA UUAAC CGAUACGU@LB@3'-UUU...CCGCA A G G A CAUUA...ACG-5'@LB@ \| \|@LB@ 93 68@LB@@LB@@LB@Energy -9.57 kcal/mol@LB@Hybridization Energy -19.8359 kcal/mol@LB@Unfolding Energy - mRNA 5.60429 kcal/mol@LB@Unfolding Energy - sRNA 4.66371 kcal/mol@LB@@LB@Position - mRNA 83 -- 107@LB@Position - sRNA 69 -- 92@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 69 -- 75@LB@
163	0.006379	0.1377	b2210	mqo	-11.85	0.037664	161 -- 168	1 -- 8	malate dehydrogenase FAD/NAD(P)-binding domain	_____________160______169\n_____________\|________\|\n5'-GGC...AAAUC________AAUAA...AUG-3'\n______________UCACCUGC\n______________\|\|\|\|\|\|\|\|\n______________AGUGGACG\n3'-UUU...ACGUA________-5'\n_____________\|_______\|\n_____________9_______1\n	162 -- 168	1 -- 7	-15.6271 kcal/mol	1.41654 kcal/mol	2.36381 kcal/mol	160 169@LB@ \| \|@LB@5'-GGC...AAAUC AAUAA...AUG-3'@LB@ UCACCUGC@LB@ \|\|\|\|\|\|\|\|@LB@ AGUGGACG@LB@3'-UUU...ACGUA -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -11.85 kcal/mol@LB@Hybridization Energy -15.6271 kcal/mol@LB@Unfolding Energy - mRNA 1.41654 kcal/mol@LB@Unfolding Energy - sRNA 2.36381 kcal/mol@LB@@LB@Position - mRNA 161 -- 168@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 1 -- 7@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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