Input and runtime details for job 5774122 (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 5774122 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:30:38 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:16:08 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 23:32:42 CET 2018
	Post-Processing Finished		@ Fri Feb 16 23:32:50 CET 2018
	Job Completed		@ Fri Feb 16 23:33:10 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5774122&toolName=CopraRNA ( 30 days expiry )

Description of the job

FsrA

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_000964 Bacillus subtilis subsp. subtilis str. 168

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
58	0.003185	0.1832	bsu24100	bkdR	-13.90	0.048953	199 -- 241	21 -- 51	sigma L-dependent transcriptional regulator YqiR	_____________198_________________________________________242\n_____________\|___________________________________________\|\n5'-AAU...UAUCG____GCAAAA___A_______U___UGCC__CAAAA_______GGCGU...ACA-3'\n______________GGAU______GGU_CUGAUAG_AGG____GG_____GGGGAAC\n______________\|\|\|\|______\|:\|_\|\|\|\|\|\|\|_\|\|\|____\|\|_____\|\|\|\|\|\|\|\n______________CCUA______CUA_GACUAUC_UCC____CC_____CCCCUUG\n3'-UUU...AAAAG____GAA________________________AA__________UCUCU...AUA-5'\n_____________\|___________________________________________\|\n_____________52__________________________________________20\n	235 -- 241	21 -- 27	-28.1295 kcal/mol	11.4588 kcal/mol	2.76846 kcal/mol	198 242@LB@ \| \|@LB@5'-AAU...UAUCG GCAAAA A U UGCC CAAAA GGCGU...ACA-3'@LB@ GGAU GGU CUGAUAG AGG GG GGGGAAC@LB@ \|\|\|\| \|:\| \|\|\|\|\|\|\| \|\|\| \|\| \|\|\|\|\|\|\|@LB@ CCUA CUA GACUAUC UCC CC CCCCUUG@LB@3'-UUU...AAAAG GAA AA UCUCU...AUA-5'@LB@ \| \|@LB@ 52 20@LB@@LB@@LB@Energy -13.90 kcal/mol@LB@Hybridization Energy -28.1295 kcal/mol@LB@Unfolding Energy - mRNA 11.4588 kcal/mol@LB@Unfolding Energy - sRNA 2.76846 kcal/mol@LB@@LB@Position - mRNA 199 -- 241@LB@Position - sRNA 21 -- 51@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 21 -- 27@LB@
134	0.01184	0.2883	bsu01450	cbiO	-8.85	0.304208	221 -- 231	32 -- 43	energy-coupling factor transporter ATP-binding protein EcfA1	_____________220__________232\n_____________\|____________\|\n5'-AUA...UUGAU____________AUAUC...AUG-3'\n______________AUC_GGUAGAGG\n______________\|\|\|_\|:\|\|\|\|\|\|\n______________UAG_CUAUCUCC\n3'-UUU...AGAAC___A________CCAAC...AUA-5'\n_____________\|____________\|\n_____________44___________31\n	225 -- 231	32 -- 38	-12.7681 kcal/mol	2.95776 kcal/mol	0.959872 kcal/mol	220 232@LB@ \| \|@LB@5'-AUA...UUGAU AUAUC...AUG-3'@LB@ AUC GGUAGAGG@LB@ \|\|\| \|:\|\|\|\|\|\|@LB@ UAG CUAUCUCC@LB@3'-UUU...AGAAC A CCAAC...AUA-5'@LB@ \| \|@LB@ 44 31@LB@@LB@@LB@Energy -8.85 kcal/mol@LB@Hybridization Energy -12.7681 kcal/mol@LB@Unfolding Energy - mRNA 2.95776 kcal/mol@LB@Unfolding Energy - sRNA 0.959872 kcal/mol@LB@@LB@Position - mRNA 221 -- 231@LB@Position - sRNA 32 -- 43@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 32 -- 38@LB@
120	0.01063	0.2883	bsu25190	cccA	-10.44	0.184184	169 -- 199	18 -- 38	cytochrome c-550	_____________168_____________________________200\n_____________\|_______________________________\|\n5'-CCA...UUUAC________AAGGAUCAAAAAG______G___AAUGA...AGA-3'\n______________AUAGGGGG_____________GGGGAA_GGA\n______________\|\|\|\|:\|\|\|_____________\|\|\|\|\|\|_:\|\|\n______________UAUCUCCC_____________CCCCUU_UCU\n3'-UUU...UAGAC________CAA________________G___CUCAU...AUA-5'\n_____________\|_______________________________\|\n_____________39______________________________17\n	170 -- 176	31 -- 37	-23.3565 kcal/mol	5.07512 kcal/mol	7.8385 kcal/mol	168 200@LB@ \| \|@LB@5'-CCA...UUUAC AAGGAUCAAAAAG G AAUGA...AGA-3'@LB@ AUAGGGGG GGGGAA GGA@LB@ \|\|\|\|:\|\|\| \|\|\|\|\|\| :\|\|@LB@ UAUCUCCC CCCCUU UCU@LB@3'-UUU...UAGAC CAA G CUCAU...AUA-5'@LB@ \| \|@LB@ 39 17@LB@@LB@@LB@Energy -10.44 kcal/mol@LB@Hybridization Energy -23.3565 kcal/mol@LB@Unfolding Energy - mRNA 5.07512 kcal/mol@LB@Unfolding Energy - sRNA 7.8385 kcal/mol@LB@@LB@Position - mRNA 169 -- 199@LB@Position - sRNA 18 -- 38@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 31 -- 37@LB@
97	0.008118	0.2778	bsu16450	cheC	-9.97	0.215069	178 -- 195	28 -- 47	Chey-P phosphatase CheC	_____________177__________________196\n_____________\|____________________\|\n5'-CGA...UCAAG___A________A_______AUGAC...UGU-3'\n______________CUU_AUCU__UA_AGGGGUU\n______________\|\|\|_\|\|\|\|__\|\|_\|\|\|\|\|\|\|\n______________GAA_UAGA__AU_UCCCCAA\n3'-UUU...GCCUA___C____CU__C_______CCCCU...AUA-5'\n_____________\|____________________\|\n_____________48___________________27\n	189 -- 195	28 -- 34	-14.5799 kcal/mol	3.63028 kcal/mol	0.974663 kcal/mol	177 196@LB@ \| \|@LB@5'-CGA...UCAAG A A AUGAC...UGU-3'@LB@ CUU AUCU UA AGGGGUU@LB@ \|\|\| \|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ GAA UAGA AU UCCCCAA@LB@3'-UUU...GCCUA C CU C CCCCU...AUA-5'@LB@ \| \|@LB@ 48 27@LB@@LB@@LB@Energy -9.97 kcal/mol@LB@Hybridization Energy -14.5799 kcal/mol@LB@Unfolding Energy - mRNA 3.63028 kcal/mol@LB@Unfolding Energy - sRNA 0.974663 kcal/mol@LB@@LB@Position - mRNA 178 -- 195@LB@Position - sRNA 28 -- 47@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 28 -- 34@LB@
3	5.299e-07	0.0005893	bsu18000	citB	-22.45	0.000394	173 -- 202	21 -- 50	aconitate hydratase	_____________172______________________________203\n_____________\|________________________________\|\n5'-UCU...AGAAU____________________AUU____A____GGCAA...CGU-3'\n______________GAUC_UGAUCUGA_AGGGGG___UUGG_GAAU\n______________\|\|\|\|_\|\|\|\|\|\|\|\|_\|\|:\|\|\|___\|\|\|\|_\|\|\|:\n______________CUAG_ACUAGACU_UCUCCC___AACC_CUUG\n3'-UUU...AAAGC____A________A______C______C____UCUCU...AUA-5'\n_____________\|________________________________\|\n_____________51_______________________________20\n	178 -- 184	38 -- 44	-32.0259 kcal/mol	6.8093 kcal/mol	2.76846 kcal/mol	172 203@LB@ \| \|@LB@5'-UCU...AGAAU AUU A GGCAA...CGU-3'@LB@ GAUC UGAUCUGA AGGGGG UUGG GAAU@LB@ \|\|\|\| \|\|\|\|\|\|\|\| \|\|:\|\|\| \|\|\|\| \|\|\|:@LB@ CUAG ACUAGACU UCUCCC AACC CUUG@LB@3'-UUU...AAAGC A A C C UCUCU...AUA-5'@LB@ \| \|@LB@ 51 20@LB@@LB@@LB@Energy -22.45 kcal/mol@LB@Hybridization Energy -32.0259 kcal/mol@LB@Unfolding Energy - mRNA 6.8093 kcal/mol@LB@Unfolding Energy - sRNA 2.76846 kcal/mol@LB@@LB@Position - mRNA 173 -- 202@LB@Position - sRNA 21 -- 50@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 38 -- 44@LB@
149	0.01325	0.2966	bsu07610	citM	-7.43	0.445360	149 -- 162	15 -- 27	Mg(2+)/citrate complex secondary transporter	_____________148____________163\n_____________\|______________\|\n5'-AUU...AAAAA_______A______AAAAA...UUG-3'\n______________GGGGAGU_AGGGAG\n______________\|\|\|\|\|::_\|\|:\|\|\|\n______________CCCCUUG_UCUCUC\n3'-UUU...CCCAA______________AUCGA...AUA-5'\n_____________\|______________\|\n_____________28_____________14\n	149 -- 155	21 -- 27	-17.4184 kcal/mol	3.9771 kcal/mol	6.01129 kcal/mol	148 163@LB@ \| \|@LB@5'-AUU...AAAAA A AAAAA...UUG-3'@LB@ GGGGAGU AGGGAG@LB@ \|\|\|\|\|:: \|\|:\|\|\|@LB@ CCCCUUG UCUCUC@LB@3'-UUU...CCCAA AUCGA...AUA-5'@LB@ \| \|@LB@ 28 14@LB@@LB@@LB@Energy -7.43 kcal/mol@LB@Hybridization Energy -17.4184 kcal/mol@LB@Unfolding Energy - mRNA 3.9771 kcal/mol@LB@Unfolding Energy - sRNA 6.01129 kcal/mol@LB@@LB@Position - mRNA 149 -- 162@LB@Position - sRNA 15 -- 27@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 21 -- 27@LB@
87	0.00681	0.2588	bsu29140	citZ	-14.51	0.037644	213 -- 231	27 -- 52	citrate synthase 2	_____________212_________________________232\n_____________\|___________________________\|\n5'-GAG...CGACA__C________________________UAGCA...AUG-3'\n______________CG_GGUCUUGA________AGGGGUUG\n______________\|\|_\|:\|\|\|\|\|\|________\|\|\|\|\|\|\|\|\n______________GC_CUAGAACU________UCCCCAAC\n3'-UUU...AAAAA___________AGACUAUC________CCCUU...AUA-5'\n_____________\|___________________________\|\n_____________53__________________________26\n	225 -- 231	27 -- 33	-23.9033 kcal/mol	8.41647 kcal/mol	0.980744 kcal/mol	212 232@LB@ \| \|@LB@5'-GAG...CGACA C UAGCA...AUG-3'@LB@ CG GGUCUUGA AGGGGUUG@LB@ \|\| \|:\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ GC CUAGAACU UCCCCAAC@LB@3'-UUU...AAAAA AGACUAUC CCCUU...AUA-5'@LB@ \| \|@LB@ 53 26@LB@@LB@@LB@Energy -14.51 kcal/mol@LB@Hybridization Energy -23.9033 kcal/mol@LB@Unfolding Energy - mRNA 8.41647 kcal/mol@LB@Unfolding Energy - sRNA 0.980744 kcal/mol@LB@@LB@Position - mRNA 213 -- 231@LB@Position - sRNA 27 -- 52@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 27 -- 33@LB@
199	0.01988	0.3269	bsu36590	clsA	-10.32	0.192119	169 -- 195	28 -- 48	cardiolipin synthase	_____________168_________________________196\n_____________\|___________________________\|\n5'-UUA...AAUCU_______AAAUA___AUG__C______ACAAA...CUU-3'\n______________UCUUGAU_____UGA___AG_GGGGUU\n______________\|\|\|\|\|\|\|_____\|\|\|___\|\|_\|\|\|\|\|\|\n______________AGAACUA_____ACU___UC_CCCCAA\n3'-UUU...AGCCU_______G_______A____U______CCCCU...AUA-5'\n_____________\|___________________________\|\n_____________49__________________________27\n	169 -- 175	42 -- 48	-17.4562 kcal/mol	6.16425 kcal/mol	0.974701 kcal/mol	168 196@LB@ \| \|@LB@5'-UUA...AAUCU AAAUA AUG C ACAAA...CUU-3'@LB@ UCUUGAU UGA AG GGGGUU@LB@ \|\|\|\|\|\|\| \|\|\| \|\| \|\|\|\|\|\|@LB@ AGAACUA ACU UC CCCCAA@LB@3'-UUU...AGCCU G A U CCCCU...AUA-5'@LB@ \| \|@LB@ 49 27@LB@@LB@@LB@Energy -10.32 kcal/mol@LB@Hybridization Energy -17.4562 kcal/mol@LB@Unfolding Energy - mRNA 6.16425 kcal/mol@LB@Unfolding Energy - sRNA 0.974701 kcal/mol@LB@@LB@Position - mRNA 169 -- 195@LB@Position - sRNA 28 -- 48@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 42 -- 48@LB@
31	0.001131	0.119	bsu15020	coaD	-13.71	0.053189	186 -- 192	30 -- 36	phosphopantetheine adenylyltransferase	_____________185_____193\n_____________\|_______\|\n5'-UCC...UAAAA_______GUAGU...AUG-3'\n______________AGAGGGG\n______________\|\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	186 -- 192	30 -- 36	-14.3069 kcal/mol	0.46648 kcal/mol	0.133643 kcal/mol	185 193@LB@ \| \|@LB@5'-UCC...UAAAA GUAGU...AUG-3'@LB@ AGAGGGG@LB@ \|\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -13.71 kcal/mol@LB@Hybridization Energy -14.3069 kcal/mol@LB@Unfolding Energy - mRNA 0.46648 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 186 -- 192@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 30 -- 36@LB@
151	0.01347	0.2966	bsu25570	comEC	-9.44	0.254651	59 -- 89	9 -- 50	ComE operon protein 3	_____________58__________________________________________90\n_____________\|___________________________________________\|\n5'-CGC...GAAAU____G_________AA____________________AA_____UCAUU...UCU-3'\n______________GAUC_UUGAUCUGA______________AACAGAGA__AGCUU\n______________\|\|\|\|_\|\|\|\|\|\|\|\|\|______________\|\|\|\|\|\|\|\|__\|\|\|\|\|\n______________CUAG_AACUAGACU______________UUGUCUCU__UCGAA\n3'-UUU...AAAGC______________AUCUCCCCAACCCC________CA_____GAGAGAUA-5'\n_____________\|___________________________________________\|\n_____________51__________________________________________8\n	76 -- 82	16 -- 22	-28.9501 kcal/mol	9.55134 kcal/mol	9.9565 kcal/mol	58 90@LB@ \| \|@LB@5'-CGC...GAAAU G AA AA UCAUU...UCU-3'@LB@ GAUC UUGAUCUGA AACAGAGA AGCUU@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ CUAG AACUAGACU UUGUCUCU UCGAA@LB@3'-UUU...AAAGC AUCUCCCCAACCCC CA GAGAGAUA-5'@LB@ \| \|@LB@ 51 8@LB@@LB@@LB@Energy -9.44 kcal/mol@LB@Hybridization Energy -28.9501 kcal/mol@LB@Unfolding Energy - mRNA 9.55134 kcal/mol@LB@Unfolding Energy - sRNA 9.9565 kcal/mol@LB@@LB@Position - mRNA 59 -- 89@LB@Position - sRNA 9 -- 50@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 16 -- 22@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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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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