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	Additional homologs
136	0.01205	0.2883	bsu35319	yvzG	-14.21	0.042782	258 -- 272	27 -- 43	Evidence 4: Homologs of previously reported genes of unknown function		_____________257_______________273\n_____________\|_________________\|\n5'-AAG...UUACC_________________UGUUA...AUU-3'\n______________AUC_GA_AGAGGGGUUG\n______________\|\|\|_\|\|_\|\|\|\|\|\|\|\|\|\|\n______________UAG_CU_UCUCCCCAAC\n3'-UUU...AGAAC___A__A__________CCCUU...AUA-5'\n_____________\|_________________\|\n_____________44________________26\n	266 -- 272	27 -- 33	-20.1473 kcal/mol	4.96591 kcal/mol	0.966729 kcal/mol	257 273@LB@ \| \|@LB@5'-AAG...UUACC UGUUA...AUU-3'@LB@ AUC GA AGAGGGGUUG@LB@ \|\|\| \|\| \|\|\|\|\|\|\|\|\|\|@LB@ UAG CU UCUCCCCAAC@LB@3'-UUU...AGAAC A A CCCUU...AUA-5'@LB@ \| \|@LB@ 44 26@LB@@LB@@LB@Energy -14.21 kcal/mol@LB@Hybridization Energy -20.1473 kcal/mol@LB@Unfolding Energy - mRNA 4.96591 kcal/mol@LB@Unfolding Energy - sRNA 0.966729 kcal/mol@LB@@LB@Position - mRNA 258 -- 272@LB@Position - sRNA 27 -- 43@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 27 -- 33@LB@
195	0.01942	0.3269	bsu00690	ftsH	-11.53	0.125763	258 -- 269	21 -- 33	ATP-dependent zinc metalloprotease FtsH		_____________257___________270\n_____________\|_____________\|\n5'-AGU...UAAUC_______U_____UACUU...AAA-3'\n______________GGGGUUG__GAGC\n______________\|\|\|\|\|\|\|__\|\|:\|\n______________CCCCAAC__CUUG\n3'-UUU...UAUCU_______CC____UCUCU...AUA-5'\n_____________\|_____________\|\n_____________34____________20\n	258 -- 264	27 -- 33	-15.4755 kcal/mol	2.12746 kcal/mol	1.8225 kcal/mol	257 270@LB@ \| \|@LB@5'-AGU...UAAUC U UACUU...AAA-3'@LB@ GGGGUUG GAGC@LB@ \|\|\|\|\|\|\| \|\|:\|@LB@ CCCCAAC CUUG@LB@3'-UUU...UAUCU CC UCUCU...AUA-5'@LB@ \| \|@LB@ 34 20@LB@@LB@@LB@Energy -11.53 kcal/mol@LB@Hybridization Energy -15.4755 kcal/mol@LB@Unfolding Energy - mRNA 2.12746 kcal/mol@LB@Unfolding Energy - sRNA 1.8225 kcal/mol@LB@@LB@Position - mRNA 258 -- 269@LB@Position - sRNA 21 -- 33@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 27 -- 33@LB@
38	0.001645	0.1432	bsu19540	yodB	-7.66	0.420262	259 -- 271	37 -- 51	ArsR family transcriptional regulator		_____________258_____________272\n_____________\|_______________\|\n5'-GAG...ACGAU___AC__________CAUCC...AAC-3'\n______________GGA____GGUCUGAU\n______________\|\|\|____\|:\|\|\|\|\|\|\n______________CCU____CUAGACUA\n3'-UUU...AAAAG___AGAA________UCUCC...AUA-5'\n_____________\|_______________\|\n_____________52______________36\n	265 -- 271	37 -- 43	-11.6813 kcal/mol	3.05786 kcal/mol	0.959935 kcal/mol	258 272@LB@ \| \|@LB@5'-GAG...ACGAU AC CAUCC...AAC-3'@LB@ GGA GGUCUGAU@LB@ \|\|\| \|:\|\|\|\|\|\|@LB@ CCU CUAGACUA@LB@3'-UUU...AAAAG AGAA UCUCC...AUA-5'@LB@ \| \|@LB@ 52 36@LB@@LB@@LB@Energy -7.66 kcal/mol@LB@Hybridization Energy -11.6813 kcal/mol@LB@Unfolding Energy - mRNA 3.05786 kcal/mol@LB@Unfolding Energy - sRNA 0.959935 kcal/mol@LB@@LB@Position - mRNA 259 -- 271@LB@Position - sRNA 37 -- 51@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 37 -- 43@LB@
124	0.01102	0.2883	bsu36860	atpE	-15.23	0.027175	263 -- 293	30 -- 52	ATP synthase subunit c		_____________262_______________________________294\n_____________\|_________________________________\|\n5'-AAA...GGUAA____________GUUUCACGUAC__________AUUGCCC-3'\n______________CGG__UUUGAUU___________GGUAGAGGGG\n______________\|\|\|__:\|\|\|\|\|:___________\|:\|\|\|\|\|\|\|\|\n______________GCC__GAACUAG___________CUAUCUCCCC\n3'-UUU...AAAAA___UA_______A____________________AACCC...AUA-5'\n_____________\|_________________________________\|\n_____________53________________________________29\n	287 -- 293	30 -- 36	-22.7251 kcal/mol	6.51858 kcal/mol	0.979974 kcal/mol	262 294@LB@ \| \|@LB@5'-AAA...GGUAA GUUUCACGUAC AUUGCCC-3'@LB@ CGG UUUGAUU GGUAGAGGGG@LB@ \|\|\| :\|\|\|\|\|: \|:\|\|\|\|\|\|\|\|@LB@ GCC GAACUAG CUAUCUCCCC@LB@3'-UUU...AAAAA UA A AACCC...AUA-5'@LB@ \| \|@LB@ 53 29@LB@@LB@@LB@Energy -15.23 kcal/mol@LB@Hybridization Energy -22.7251 kcal/mol@LB@Unfolding Energy - mRNA 6.51858 kcal/mol@LB@Unfolding Energy - sRNA 0.979974 kcal/mol@LB@@LB@Position - mRNA 263 -- 293@LB@Position - sRNA 30 -- 52@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 30 -- 36@LB@
102	0.008773	0.2778	bsu06170	ydjE	-10.58	0.175640	264 -- 284	30 -- 50	sugar kinase YdjE		_____________263___________________285\n_____________\|_____________________\|\n5'-GGG...AUGUU__CG_______A_____A___CGCCA...AAA-3'\n______________GA__UUGAUUU_AUGGA_GGG\n______________\|\|__\|\|\|\|\|:\|_\|\|:\|\|_\|\|\|\n______________CU__AACUAGA_UAUCU_CCC\n3'-UUU...AAAGC__AG_______C_____C___AACCC...AUA-5'\n_____________\|_____________________\|\n_____________51____________________29\n	268 -- 274	40 -- 46	-17.5575 kcal/mol	6.00068 kcal/mol	0.974272 kcal/mol	263 285@LB@ \| \|@LB@5'-GGG...AUGUU CG A A CGCCA...AAA-3'@LB@ GA UUGAUUU AUGGA GGG@LB@ \|\| \|\|\|\|\|:\| \|\|:\|\| \|\|\|@LB@ CU AACUAGA UAUCU CCC@LB@3'-UUU...AAAGC AG C C AACCC...AUA-5'@LB@ \| \|@LB@ 51 29@LB@@LB@@LB@Energy -10.58 kcal/mol@LB@Hybridization Energy -17.5575 kcal/mol@LB@Unfolding Energy - mRNA 6.00068 kcal/mol@LB@Unfolding Energy - sRNA 0.974272 kcal/mol@LB@@LB@Position - mRNA 264 -- 284@LB@Position - sRNA 30 -- 50@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 40 -- 46@LB@
126	0.0111	0.2883	bsu16220	fliG	-14.68	0.034861	264 -- 293	1 -- 29	flagellar motor switch protein FliG		_____________263_____________________________294\n_____________\|_______________________________\|\n5'-GGG...UUUCC______U_____U_U__C_______G_____AAGCACU-3'\n______________UUGGGG__UAGA_G_GU_AGCUUCU_UCUAU\n______________\|\|\|\|\|\|__:\|\|\|_\|_\|\|_\|\|\|\|\|\|\|_\|\|\|\|\|\n______________AACCCC__GUCU_C_CA_UCGAAGA_AGAUA\n3'-UUU...UCCCC______UU______U__________G_____-5'\n_____________\|______________________________\|\n_____________30_____________________________1\n	281 -- 287	7 -- 13	-31.0613 kcal/mol	7.38869 kcal/mol	8.9939 kcal/mol	263 294@LB@ \| \|@LB@5'-GGG...UUUCC U U U C G AAGCACU-3'@LB@ UUGGGG UAGA G GU AGCUUCU UCUAU@LB@ \|\|\|\|\|\| :\|\|\| \| \|\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ AACCCC GUCU C CA UCGAAGA AGAUA@LB@3'-UUU...UCCCC UU U G -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -14.68 kcal/mol@LB@Hybridization Energy -31.0613 kcal/mol@LB@Unfolding Energy - mRNA 7.38869 kcal/mol@LB@Unfolding Energy - sRNA 8.9939 kcal/mol@LB@@LB@Position - mRNA 264 -- 293@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 7 -- 13@LB@
112	0.009326	0.2778	bsu13200	rsbRB	-15.32	0.026068	265 -- 282	32 -- 51	RsbT co-antagonist protein RsbRB	bsu19450	_____________264__________________283\n_____________\|____________________\|\n5'-CUU...GGAAU_________AAC________AAAGU...CGC-3'\n______________GGAU__UGA___GAUGGAGG\n______________\|\|\|\|__\|\|\|___\|\|\|:\|\|\|\|\n______________CCUA__ACU___CUAUCUCC\n3'-UUU...AAAAG____GA___AGA________CCAAC...AUA-5'\n_____________\|____________________\|\n_____________52___________________31\n	276 -- 282	32 -- 38	-18.0013 kcal/mol	1.71479 kcal/mol	0.97021 kcal/mol	264 283@LB@ \| \|@LB@5'-CUU...GGAAU AAC AAAGU...CGC-3'@LB@ GGAU UGA GAUGGAGG@LB@ \|\|\|\| \|\|\| \|\|\|:\|\|\|\|@LB@ CCUA ACU CUAUCUCC@LB@3'-UUU...AAAAG GA AGA CCAAC...AUA-5'@LB@ \| \|@LB@ 52 31@LB@@LB@@LB@Energy -15.32 kcal/mol@LB@Hybridization Energy -18.0013 kcal/mol@LB@Unfolding Energy - mRNA 1.71479 kcal/mol@LB@Unfolding Energy - sRNA 0.97021 kcal/mol@LB@@LB@Position - mRNA 265 -- 282@LB@Position - sRNA 32 -- 51@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 32 -- 38@LB@
81	0.005945	0.2448	bsu06390	yebD	-16.11	0.017881	267 -- 291	30 -- 53	Evidence 5: No homology to any previously reported sequences		_____________266_______________________292\n_____________\|_________________________\|\n5'-UUU...UGCUC_____A___U___AA__A_______AACAG...UUG-3'\n______________UCGGA_UUU_AUC__GG_AGAGGGG\n______________\|\|\|\|\|_:\|\|_\|\|\|__\|:_\|\|\|\|\|\|\|\n______________AGCCU_GAA_UAG__CU_UCUCCCC\n3'-UUU...AAAAA_____A___C___A___A_______AACCC...AUA-5'\n_____________\|_________________________\|\n_____________54________________________29\n	285 -- 291	30 -- 36	-22.0812 kcal/mol	4.98677 kcal/mol	0.985344 kcal/mol	266 292@LB@ \| \|@LB@5'-UUU...UGCUC A U AA A AACAG...UUG-3'@LB@ UCGGA UUU AUC GG AGAGGGG@LB@ \|\|\|\|\| :\|\| \|\|\| \|: \|\|\|\|\|\|\|@LB@ AGCCU GAA UAG CU UCUCCCC@LB@3'-UUU...AAAAA A C A A AACCC...AUA-5'@LB@ \| \|@LB@ 54 29@LB@@LB@@LB@Energy -16.11 kcal/mol@LB@Hybridization Energy -22.0812 kcal/mol@LB@Unfolding Energy - mRNA 4.98677 kcal/mol@LB@Unfolding Energy - sRNA 0.985344 kcal/mol@LB@@LB@Position - mRNA 267 -- 291@LB@Position - sRNA 30 -- 53@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 30 -- 36@LB@
172	0.01654	0.3152	bsu29680	acsA	-11.36	0.133506	267 -- 288	32 -- 52	acetyl-CoA synthetase		_____________266____________________289\n_____________\|______________________\|\n5'-UUU...CGUAC___C_________G__CC____CAGAG...AUU-3'\n______________CGG_AUUUUGAUU_GG__GAGG\n______________\|\|\|_\|\|:\|\|\|\|\|:_\|:__\|\|\|\|\n______________GCC_UAGAACUAG_CU__CUCC\n3'-UUU...AAAAA_____________A__AU____CCAAC...AUA-5'\n_____________\|______________________\|\n_____________53_____________________31\n	273 -- 279	41 -- 47	-18.8322 kcal/mol	6.49419 kcal/mol	0.976384 kcal/mol	266 289@LB@ \| \|@LB@5'-UUU...CGUAC C G CC CAGAG...AUU-3'@LB@ CGG AUUUUGAUU GG GAGG@LB@ \|\|\| \|\|:\|\|\|\|\|: \|: \|\|\|\|@LB@ GCC UAGAACUAG CU CUCC@LB@3'-UUU...AAAAA A AU CCAAC...AUA-5'@LB@ \| \|@LB@ 53 31@LB@@LB@@LB@Energy -11.36 kcal/mol@LB@Hybridization Energy -18.8322 kcal/mol@LB@Unfolding Energy - mRNA 6.49419 kcal/mol@LB@Unfolding Energy - sRNA 0.976384 kcal/mol@LB@@LB@Position - mRNA 267 -- 288@LB@Position - sRNA 32 -- 52@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 41 -- 47@LB@
191	0.01913	0.3269	bsu37760	rocC	-14.43	0.038902	267 -- 280	26 -- 36	amino acid permease RocC		_____________266____________281\n_____________\|______________\|\n5'-CCG...CUUUG________GAU___CACUG...GCU-3'\n______________GGAGGGGU___UGG\n______________:\|\|\|\|\|\|\|___\|\|\|\n______________UCUCCCCA___ACC\n3'-UUU...GACUA______________CCUUG...AUA-5'\n_____________\|______________\|\n_____________37_____________25\n	268 -- 274	29 -- 35	-16.8756 kcal/mol	2.30826 kcal/mol	0.135623 kcal/mol	266 281@LB@ \| \|@LB@5'-CCG...CUUUG GAU CACUG...GCU-3'@LB@ GGAGGGGU UGG@LB@ :\|\|\|\|\|\|\| \|\|\|@LB@ UCUCCCCA ACC@LB@3'-UUU...GACUA CCUUG...AUA-5'@LB@ \| \|@LB@ 37 25@LB@@LB@@LB@Energy -14.43 kcal/mol@LB@Hybridization Energy -16.8756 kcal/mol@LB@Unfolding Energy - mRNA 2.30826 kcal/mol@LB@Unfolding Energy - sRNA 0.135623 kcal/mol@LB@@LB@Position - mRNA 267 -- 280@LB@Position - sRNA 26 -- 36@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 29 -- 35@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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