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
114	0.005004	0.1545	b0025	ribF	-11.63	0.123109	210 -- 237	43 -- 71	bifunctional riboflavin kinase/FAD synthetase	_____________209___________________________238\n_____________\|_____________________________\|\n5'-UGG...AGCUG__________UACAUAAUC____GC____CCCCG...GCG-3'\n______________AUACGCGGCA__________UCA__CAGG\n______________\|:\|\|:\|:\|\|\|__________\|\|\|__\|\|\|\|\n______________UGUGUGUCGU__________AGU__GUCC\n3'-UUU...UCUGA__________UAAGCAACAA___GA____CCUAA...GCA-5'\n_____________\|_____________________________\|\n_____________72____________________________42\n	213 -- 219	62 -- 68	-21.1915 kcal/mol	5.23887 kcal/mol	4.32409 kcal/mol	209 238@LB@ \| \|@LB@5'-UGG...AGCUG UACAUAAUC GC CCCCG...GCG-3'@LB@ AUACGCGGCA UCA CAGG@LB@ \|:\|\|:\|:\|\|\| \|\|\| \|\|\|\|@LB@ UGUGUGUCGU AGU GUCC@LB@3'-UUU...UCUGA UAAGCAACAA GA CCUAA...GCA-5'@LB@ \| \|@LB@ 72 42@LB@@LB@@LB@Energy -11.63 kcal/mol@LB@Hybridization Energy -21.1915 kcal/mol@LB@Unfolding Energy - mRNA 5.23887 kcal/mol@LB@Unfolding Energy - sRNA 4.32409 kcal/mol@LB@@LB@Position - mRNA 210 -- 237@LB@Position - sRNA 43 -- 71@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 62 -- 68@LB@
178	0.008884	0.1747	b0051	rsmA	-9.94	0.250586	2 -- 32	30 -- 58	16S rRNA m(6)A1518 m(6)A1519 dimethyltransferase SAM-dependent	_____________1_______________________________33\n_____________\|_______________________________\|\n__________5'-G__A___AC___GA______UC__C_______AAAAU...UUA-3'\n______________CG_UGU__CAC__UCAGGG__UU_CCGUGCU\n______________\|\|_\|\|\|__\|\|\|__\|\|\|\|\|\|__\|\|_\|\|:\|\|\|\|\n______________GC_ACA__GUG__AGUCCC__AA_GGUACGA\n3'-UUU...GUUAA__A___AA___________CU__A_______AUAUU...GCA-5'\n_____________\|_______________________________\|\n_____________59______________________________29\n	26 -- 32	30 -- 36	-26.3106 kcal/mol	10.5715 kcal/mol	5.79877 kcal/mol	1 33@LB@ \| \|@LB@ 5'-G A AC GA UC C AAAAU...UUA-3'@LB@ CG UGU CAC UCAGGG UU CCGUGCU@LB@ \|\| \|\|\| \|\|\| \|\|\|\|\|\| \|\| \|\|:\|\|\|\|@LB@ GC ACA GUG AGUCCC AA GGUACGA@LB@3'-UUU...GUUAA A AA CU A AUAUU...GCA-5'@LB@ \| \|@LB@ 59 29@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -26.3106 kcal/mol@LB@Unfolding Energy - mRNA 10.5715 kcal/mol@LB@Unfolding Energy - sRNA 5.79877 kcal/mol@LB@@LB@Position - mRNA 2 -- 32@LB@Position - sRNA 30 -- 58@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 30 -- 36@LB@
173	0.008582	0.1745	b0060	polB	-11.19	0.150164	8 -- 23	39 -- 51	DNA polymerase II	_____________7________________24\n_____________\|________________\|\n____5'-GAAGAGG_______UAU______AUUCU...AGG-3'\n______________UCGCUUA___GGGGAU\n______________\|\|:\|\|:\|___\|\|\|\|\|\|\n______________AGUGAGU___CCCCUA\n3'-UUU...AACAA________________AAGGU...GCA-5'\n_____________\|________________\|\n_____________52_______________38\n	8 -- 14	45 -- 51	-16.4647 kcal/mol	3.48224 kcal/mol	1.79807 kcal/mol	7 24@LB@ \| \|@LB@ 5'-GAAGAGG UAU AUUCU...AGG-3'@LB@ UCGCUUA GGGGAU@LB@ \|\|:\|\|:\| \|\|\|\|\|\|@LB@ AGUGAGU CCCCUA@LB@3'-UUU...AACAA AAGGU...GCA-5'@LB@ \| \|@LB@ 52 38@LB@@LB@@LB@Energy -11.19 kcal/mol@LB@Hybridization Energy -16.4647 kcal/mol@LB@Unfolding Energy - mRNA 3.48224 kcal/mol@LB@Unfolding Energy - sRNA 1.79807 kcal/mol@LB@@LB@Position - mRNA 8 -- 23@LB@Position - sRNA 39 -- 51@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 45 -- 51@LB@
197	0.01006	0.1776	b0069	sgrR	-8.41	0.425671	7 -- 22	58 -- 74	transcriptional DNA-binding transcriptional activator of sgrS sRNA	_____________6_________________23\n_____________\|_________________\|\n_____5'-CAUCCC____________CC___AAGCA...UGA-3'\n______________ACUGCAU_CAGU__UUC\n______________\|\|\|:\|\|:_\|\|\|:__\|\|\|\n______________UGAUGUG_GUCG__AAG\n3'-UUU...GUUUC_______U____UU___CAACA...GCA-5'\n_____________\|_________________\|\n_____________75________________57\n	7 -- 13	68 -- 74	-13.3461 kcal/mol	1.63335 kcal/mol	3.3008 kcal/mol	6 23@LB@ \| \|@LB@ 5'-CAUCCC CC AAGCA...UGA-3'@LB@ ACUGCAU CAGU UUC@LB@ \|\|\|:\|\|: \|\|\|: \|\|\|@LB@ UGAUGUG GUCG AAG@LB@3'-UUU...GUUUC U UU CAACA...GCA-5'@LB@ \| \|@LB@ 75 57@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -13.3461 kcal/mol@LB@Unfolding Energy - mRNA 1.63335 kcal/mol@LB@Unfolding Energy - sRNA 3.3008 kcal/mol@LB@@LB@Position - mRNA 7 -- 22@LB@Position - sRNA 58 -- 74@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 68 -- 74@LB@
112	0.004986	0.1545	b0118	acnB	-15.18	0.018766	221 -- 251	38 -- 71	aconitate hydratase 2; aconitase B; 2-methyl-cis-aconitate hydratase	_____________220________________________________252\n_____________\|__________________________________\|\n5'-GAG...CGUAA_________UGAG___GC_______G________GCGCC...UGC-3'\n______________GCACGUAGC____CGU_____CGCU_AGGGGAUU\n______________:\|\|\|::\|\|\|____\|\|\|_____\|:\|\|_\|\|\|\|\|\|\|\|\n______________UGUGUGUCG____GCA_____GUGA_UCCCCUAA\n3'-UUU...UCUGA_________UUAA___ACAAA____G________AGGUA...GCA-5'\n_____________\|__________________________________\|\n_____________72_________________________________37\n	245 -- 251	38 -- 44	-33.2374 kcal/mol	13.3072 kcal/mol	4.74986 kcal/mol	220 252@LB@ \| \|@LB@5'-GAG...CGUAA UGAG GC G GCGCC...UGC-3'@LB@ GCACGUAGC CGU CGCU AGGGGAUU@LB@ :\|\|\|::\|\|\| \|\|\| \|:\|\| \|\|\|\|\|\|\|\|@LB@ UGUGUGUCG GCA GUGA UCCCCUAA@LB@3'-UUU...UCUGA UUAA ACAAA G AGGUA...GCA-5'@LB@ \| \|@LB@ 72 37@LB@@LB@@LB@Energy -15.18 kcal/mol@LB@Hybridization Energy -33.2374 kcal/mol@LB@Unfolding Energy - mRNA 13.3072 kcal/mol@LB@Unfolding Energy - sRNA 4.74986 kcal/mol@LB@@LB@Position - mRNA 221 -- 251@LB@Position - sRNA 38 -- 71@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 38 -- 44@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@
188	0.009562	0.1776	b0147	ligT	-10.24	0.223023	2 -- 33	35 -- 66	2'-5' RNA ligase	_____________1_________________________________34\n_____________\|_________________________________\|\n__________5'-C________GCAGCGG___GC____UU_______CGGCC...CGG-3'\n______________CAGCAGUU________CA__CAGG__GAUUUCC\n______________\|\|\|\|\|:\|\|________\|\|__\|\|\|\|__\|\|\|\|\|\|\|\n______________GUCGUUAA________GU__GUCC__CUAAAGG\n3'-UUU...UGUGU________GCAACAAA__GA____C________UACGA...GCA-5'\n_____________\|_________________________________\|\n_____________67________________________________34\n	27 -- 33	35 -- 41	-25.6384 kcal/mol	10.64 kcal/mol	4.7609 kcal/mol	1 34@LB@ \| \|@LB@ 5'-C GCAGCGG GC UU CGGCC...CGG-3'@LB@ CAGCAGUU CA CAGG GAUUUCC@LB@ \|\|\|\|\|:\|\| \|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ GUCGUUAA GU GUCC CUAAAGG@LB@3'-UUU...UGUGU GCAACAAA GA C UACGA...GCA-5'@LB@ \| \|@LB@ 67 34@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -25.6384 kcal/mol@LB@Unfolding Energy - mRNA 10.64 kcal/mol@LB@Unfolding Energy - sRNA 4.7609 kcal/mol@LB@@LB@Position - mRNA 2 -- 33@LB@Position - sRNA 35 -- 66@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 35 -- 41@LB@
143	0.006558	0.1605	b0161	degP	-10.78	0.178564	159 -- 170	58 -- 69	serine endoprotease (protease Do) membrane-associated	_____________158__________171\n_____________\|____________\|\n5'-AUU...GAAGA____________UGCGU...CGA-3'\n______________ACACAGCAAUUU\n______________\|\|\|\|\|\|\|\|\|\|\|:\n______________UGUGUCGUUAAG\n3'-UUU...UGAUG____________CAACA...GCA-5'\n_____________\|____________\|\n_____________70___________57\n	164 -- 170	58 -- 64	-16.5275 kcal/mol	2.62124 kcal/mol	3.12494 kcal/mol	158 171@LB@ \| \|@LB@5'-AUU...GAAGA UGCGU...CGA-3'@LB@ ACACAGCAAUUU@LB@ \|\|\|\|\|\|\|\|\|\|\|:@LB@ UGUGUCGUUAAG@LB@3'-UUU...UGAUG CAACA...GCA-5'@LB@ \| \|@LB@ 70 57@LB@@LB@@LB@Energy -10.78 kcal/mol@LB@Hybridization Energy -16.5275 kcal/mol@LB@Unfolding Energy - mRNA 2.62124 kcal/mol@LB@Unfolding Energy - sRNA 3.12494 kcal/mol@LB@@LB@Position - mRNA 159 -- 170@LB@Position - sRNA 58 -- 69@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 58 -- 64@LB@
76	0.003141	0.1452	b0187	yaeR	-8.98	0.354982	261 -- 292	48 -- 78	putative lyase	_____________260_______________________________293\n_____________\|_________________________________\|\n5'-AAA...UGAGC_______UUC___U_____AU__UUG_______GCUGCAAA-3'\n______________AAAG_CU___UAC_GCGAU__UC___GUUUCAC\n______________\|\|\|\|_\|\|___:\|\|_\|\|:\|\|__\|\|___\|\|\|\|\|\|\|\n______________UUUC_GA___GUG_CGUUA__AG___CAAAGUG\n3'-UUU...ACCCG____U__UGU___U_________CAA_______AGUCC...GCA-5'\n_____________\|_________________________________\|\n_____________79________________________________47\n	286 -- 292	48 -- 54	-17.4111 kcal/mol	4.74942 kcal/mol	3.68736 kcal/mol	260 293@LB@ \| \|@LB@5'-AAA...UGAGC UUC U AU UUG GCUGCAAA-3'@LB@ AAAG CU UAC GCGAU UC GUUUCAC@LB@ \|\|\|\| \|\| :\|\| \|\|:\|\| \|\| \|\|\|\|\|\|\|@LB@ UUUC GA GUG CGUUA AG CAAAGUG@LB@3'-UUU...ACCCG U UGU U CAA AGUCC...GCA-5'@LB@ \| \|@LB@ 79 47@LB@@LB@@LB@Energy -8.98 kcal/mol@LB@Hybridization Energy -17.4111 kcal/mol@LB@Unfolding Energy - mRNA 4.74942 kcal/mol@LB@Unfolding Energy - sRNA 3.68736 kcal/mol@LB@@LB@Position - mRNA 261 -- 292@LB@Position - sRNA 48 -- 78@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 48 -- 54@LB@
58	0.002015	0.1223	b0189	rof	-8.06	0.473679	29 -- 61	40 -- 71	modulator of Rho-dependent transcription termination	_____________28_________________________________62\n_____________\|__________________________________\|\n5'-AGG...AGUUA_______A_____A__CG_AAA________C___GACUU...GCG-3'\n______________AUACGCA_GCGGU_CG__G___UCGC_CAG_GGA\n______________\|:\|\|:\|\|_\|\|::\|_\|\|__\|___\|\|:\|_\|\|\|_\|\|\|\n______________UGUGUGU_CGUUA_GC__C___AGUG_GUC_CCU\n3'-UUU...UCUGA_____________A__AA_AA_____A___C___AAAGG...GCA-5'\n_____________\|__________________________________\|\n_____________72_________________________________39\n	29 -- 35	65 -- 71	-25.5885 kcal/mol	12.7864 kcal/mol	4.74818 kcal/mol	28 62@LB@ \| \|@LB@5'-AGG...AGUUA A A CG AAA C GACUU...GCG-3'@LB@ AUACGCA GCGGU CG G UCGC CAG GGA@LB@ \|:\|\|:\|\| \|\|::\| \|\| \| \|\|:\| \|\|\| \|\|\|@LB@ UGUGUGU CGUUA GC C AGUG GUC CCU@LB@3'-UUU...UCUGA A AA AA A C AAAGG...GCA-5'@LB@ \| \|@LB@ 72 39@LB@@LB@@LB@Energy -8.06 kcal/mol@LB@Hybridization Energy -25.5885 kcal/mol@LB@Unfolding Energy - mRNA 12.7864 kcal/mol@LB@Unfolding Energy - sRNA 4.74818 kcal/mol@LB@@LB@Position - mRNA 29 -- 61@LB@Position - sRNA 40 -- 71@LB@Position Seed - mRNA 29 -- 35@LB@Position Seed - sRNA 65 -- 71@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)

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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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