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
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@
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@
135	0.01203	0.2883	bsu09920	yhaN	-10.31	0.192319	8 -- 29	28 -- 47	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; PubMedId: 16267290; Product type pe : enzyme'	_____________7______________________30\n_____________\|______________________\|\n____5'-AACAAAC_______CUUUUUUU__C____UAUUU...ACG-3'\n______________CUUGAUC________GG_GGUU\n______________\|\|\|\|\|\|\|________\|\|_\|\|\|\|\n______________GAACUAG________CC_CCAA\n3'-UUU...GCCUA_______ACUAUCU________CCCCU...AUA-5'\n_____________\|______________________\|\n_____________48_____________________27\n	8 -- 14	41 -- 47	-14.5368 kcal/mol	3.24797 kcal/mol	0.974663 kcal/mol	7 30@LB@ \| \|@LB@ 5'-AACAAAC CUUUUUUU C UAUUU...ACG-3'@LB@ CUUGAUC GG GGUU@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|@LB@ GAACUAG CC CCAA@LB@3'-UUU...GCCUA ACUAUCU CCCCU...AUA-5'@LB@ \| \|@LB@ 48 27@LB@@LB@@LB@Energy -10.31 kcal/mol@LB@Hybridization Energy -14.5368 kcal/mol@LB@Unfolding Energy - mRNA 3.24797 kcal/mol@LB@Unfolding Energy - sRNA 0.974663 kcal/mol@LB@@LB@Position - mRNA 8 -- 29@LB@Position - sRNA 28 -- 47@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 41 -- 47@LB@
155	0.01391	0.2994	bsu24780	yqgY	-10.29	0.193646	188 -- 194	30 -- 36	Evidence 4: Homologs of previously reported genes of unknown function	_____________187_____195\n_____________\|_______\|\n5'-UGU...UCUCG_______AUAAA...GAC-3'\n______________GGAGGGG\n______________:\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	188 -- 194	30 -- 36	-13.7207 kcal/mol	3.29345 kcal/mol	0.133643 kcal/mol	187 195@LB@ \| \|@LB@5'-UGU...UCUCG AUAAA...GAC-3'@LB@ GGAGGGG@LB@ :\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -10.29 kcal/mol@LB@Hybridization Energy -13.7207 kcal/mol@LB@Unfolding Energy - mRNA 3.29345 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 188 -- 194@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 30 -- 36@LB@
96	0.00803	0.2778	bsu39710	iolF	-10.11	0.206009	172 -- 191	30 -- 53	minor myo-inositol transporter IolF	_____________171______________________192\n_____________\|________________________\|\n5'-GGC...AGUUG__________________AU____AAUGA...CCG-3'\n______________UUGGAUCU_GG_CU__UA__GGGG\n______________\|:\|\|\|\|\|\|_\|:_\|\|__\|\|__\|\|\|\|\n______________AGCCUAGA_CU_GA__AU__CCCC\n3'-UUU...AAAAA________A__A__CU__CU____AACCC...AUA-5'\n_____________\|________________________\|\n_____________54_______________________29\n	173 -- 179	46 -- 52	-17.6548 kcal/mol	6.56277 kcal/mol	0.985344 kcal/mol	171 192@LB@ \| \|@LB@5'-GGC...AGUUG AU AAUGA...CCG-3'@LB@ UUGGAUCU GG CU UA GGGG@LB@ \|:\|\|\|\|\|\| \|: \|\| \|\| \|\|\|\|@LB@ AGCCUAGA CU GA AU CCCC@LB@3'-UUU...AAAAA A A CU CU AACCC...AUA-5'@LB@ \| \|@LB@ 54 29@LB@@LB@@LB@Energy -10.11 kcal/mol@LB@Hybridization Energy -17.6548 kcal/mol@LB@Unfolding Energy - mRNA 6.56277 kcal/mol@LB@Unfolding Energy - sRNA 0.985344 kcal/mol@LB@@LB@Position - mRNA 172 -- 191@LB@Position - sRNA 30 -- 53@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 46 -- 52@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@
113	0.00948	0.2799	bsu31960	dhbF	-9.87	0.222399	16 -- 37	32 -- 53	dimodular nonribosomal peptide synthase	_____________15______________________38\n_____________\|_______________________\|\n5'-AGA...CUCGA___U__________C________AUCAU...CAG-3'\n______________UCG_GGUCUUGAUU_GGUA_AGG\n______________\|\|\|_\|:\|\|\|\|\|\|\|:_\|:\|\|_\|\|\|\n______________AGC_CUAGAACUAG_CUAU_UCC\n3'-UUU...AAAAA______________A____C___CCAAC...AUA-5'\n_____________\|_______________________\|\n_____________54______________________31\n	22 -- 28	42 -- 48	-21.9493 kcal/mol	11.0963 kcal/mol	0.981755 kcal/mol	15 38@LB@ \| \|@LB@5'-AGA...CUCGA U C AUCAU...CAG-3'@LB@ UCG GGUCUUGAUU GGUA AGG@LB@ \|\|\| \|:\|\|\|\|\|\|\|: \|:\|\| \|\|\|@LB@ AGC CUAGAACUAG CUAU UCC@LB@3'-UUU...AAAAA A C CCAAC...AUA-5'@LB@ \| \|@LB@ 54 31@LB@@LB@@LB@Energy -9.87 kcal/mol@LB@Hybridization Energy -21.9493 kcal/mol@LB@Unfolding Energy - mRNA 11.0963 kcal/mol@LB@Unfolding Energy - sRNA 0.981755 kcal/mol@LB@@LB@Position - mRNA 16 -- 37@LB@Position - sRNA 32 -- 53@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 42 -- 48@LB@
116	0.01008	0.2881	bsu32800	yusH	-9.74	0.231897	187 -- 194	31 -- 38	glycine cleavage system H protein	_____________186______195\n_____________\|________\|\n5'-AUC...AAAAA________AUUCA...CCG-3'\n______________AUGGAGGG\n______________\|\|:\|\|\|\|\|\n______________UAUCUCCC\n3'-UUU...UAGAC________CAACC...AUA-5'\n_____________\|________\|\n_____________39_______30\n	188 -- 194	31 -- 37	-12.574 kcal/mol	2.17853 kcal/mol	0.65488 kcal/mol	186 195@LB@ \| \|@LB@5'-AUC...AAAAA AUUCA...CCG-3'@LB@ AUGGAGGG@LB@ \|\|:\|\|\|\|\|@LB@ UAUCUCCC@LB@3'-UUU...UAGAC CAACC...AUA-5'@LB@ \| \|@LB@ 39 30@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -12.574 kcal/mol@LB@Unfolding Energy - mRNA 2.17853 kcal/mol@LB@Unfolding Energy - sRNA 0.65488 kcal/mol@LB@@LB@Position - mRNA 187 -- 194@LB@Position - sRNA 31 -- 38@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 31 -- 37@LB@
118	0.01022	0.2883	bsu19370	sucA	-9.59	0.243554	183 -- 190	23 -- 30	2-oxoglutarate dehydrogenase subunit E1	_____________182______191\n_____________\|________\|\n5'-UUU...UUUAA________UAAUA...AUC-3'\n______________GUUGGGGG\n______________\|\|\|\|\|\|\|:\n______________CAACCCCU\n3'-UUU...CUCCC________UGUCU...AUA-5'\n_____________\|________\|\n_____________31_______22\n	184 -- 190	23 -- 29	-13.0923 kcal/mol	3.48895 kcal/mol	0.018115 kcal/mol	182 191@LB@ \| \|@LB@5'-UUU...UUUAA UAAUA...AUC-3'@LB@ GUUGGGGG@LB@ \|\|\|\|\|\|\|:@LB@ CAACCCCU@LB@3'-UUU...CUCCC UGUCU...AUA-5'@LB@ \| \|@LB@ 31 22@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -13.0923 kcal/mol@LB@Unfolding Energy - mRNA 3.48895 kcal/mol@LB@Unfolding Energy - sRNA 0.018115 kcal/mol@LB@@LB@Position - mRNA 183 -- 190@LB@Position - sRNA 23 -- 30@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 23 -- 29@LB@
152	0.01351	0.2966	bsu25600	comER	-9.59	0.243237	173 -- 194	30 -- 51	ComE operon protein 4	_____________172____________________195\n_____________\|______________________\|\n5'-AGC...UUAGA____AAUAGCUCAAA_______AAACC...CAA-3'\n______________GGAU___________GGAGGGG\n______________\|\|\|\|___________:\|\|\|\|\|\|\n______________CCUA___________UCUCCCC\n3'-UUU...AAAAG____GAACUAGACUA_______AACCC...AUA-5'\n_____________\|______________________\|\n_____________52_____________________29\n	188 -- 194	30 -- 36	-16.7526 kcal/mol	6.18889 kcal/mol	0.974282 kcal/mol	172 195@LB@ \| \|@LB@5'-AGC...UUAGA AAUAGCUCAAA AAACC...CAA-3'@LB@ GGAU GGAGGGG@LB@ \|\|\|\| :\|\|\|\|\|\|@LB@ CCUA UCUCCCC@LB@3'-UUU...AAAAG GAACUAGACUA AACCC...AUA-5'@LB@ \| \|@LB@ 52 29@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -16.7526 kcal/mol@LB@Unfolding Energy - mRNA 6.18889 kcal/mol@LB@Unfolding Energy - sRNA 0.974282 kcal/mol@LB@@LB@Position - mRNA 173 -- 194@LB@Position - sRNA 30 -- 51@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 30 -- 36@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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