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
64	0.004032	0.2071	bsu23050	fmnP	-11.92	0.108419	30 -- 48	32 -- 51	riboflavin transporter FmnP	_____________29___________________49\n_____________\|____________________\|\n5'-GUG...AGUCU____GG___GAA________UUCAU...UAA-3'\n______________GGAU___GA___GAUGGAGG\n______________\|\|\|\|___\|\|___\|\|\|:\|\|\|\|\n______________CCUA___CU___CUAUCUCC\n3'-UUU...AAAAG____GAA__AGA________CCAAC...AUA-5'\n_____________\|____________________\|\n_____________52___________________31\n	42 -- 48	32 -- 38	-18.1391 kcal/mol	5.24431 kcal/mol	0.97021 kcal/mol	29 49@LB@ \| \|@LB@5'-GUG...AGUCU GG GAA UUCAU...UAA-3'@LB@ GGAU GA GAUGGAGG@LB@ \|\|\|\| \|\| \|\|\|:\|\|\|\|@LB@ CCUA CU CUAUCUCC@LB@3'-UUU...AAAAG GAA AGA CCAAC...AUA-5'@LB@ \| \|@LB@ 52 31@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -18.1391 kcal/mol@LB@Unfolding Energy - mRNA 5.24431 kcal/mol@LB@Unfolding Energy - sRNA 0.97021 kcal/mol@LB@@LB@Position - mRNA 30 -- 48@LB@Position - sRNA 32 -- 51@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 32 -- 38@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@
100	0.008436	0.2778	bsu35250	ftsX	-12.75	0.078592	182 -- 188	30 -- 36	cell division protein FtsX	_____________181_____189\n_____________\|_______\|\n5'-UGC...AGUCA_______AGUAU...CGC-3'\n______________AGAGGGG\n______________\|\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	182 -- 188	30 -- 36	-13.7147 kcal/mol	0.82624 kcal/mol	0.133643 kcal/mol	181 189@LB@ \| \|@LB@5'-UGC...AGUCA AGUAU...CGC-3'@LB@ AGAGGGG@LB@ \|\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -12.75 kcal/mol@LB@Hybridization Energy -13.7147 kcal/mol@LB@Unfolding Energy - mRNA 0.82624 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 182 -- 188@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 30 -- 36@LB@
166	0.01583	0.3152	bsu38190	galT	-8.42	0.343831	170 -- 181	16 -- 26	galactose-1-phosphate uridylyltransferase	_____________169__________182\n_____________\|____________\|\n5'-GGG...GGAGA_______A____ACUAA...AUG-3'\n______________GGGAGCG_GAGA\n______________\|\|\|\|:\|:_\|\|\|\|\n______________CCCUUGU_CUCU\n3'-UUU...CCAAC____________CAUCG...AUA-5'\n_____________\|____________\|\n_____________27___________15\n	170 -- 176	20 -- 26	-15.5563 kcal/mol	1.12924 kcal/mol	6.00672 kcal/mol	169 182@LB@ \| \|@LB@5'-GGG...GGAGA A ACUAA...AUG-3'@LB@ GGGAGCG GAGA@LB@ \|\|\|\|:\|: \|\|\|\|@LB@ CCCUUGU CUCU@LB@3'-UUU...CCAAC CAUCG...AUA-5'@LB@ \| \|@LB@ 27 15@LB@@LB@@LB@Energy -8.42 kcal/mol@LB@Hybridization Energy -15.5563 kcal/mol@LB@Unfolding Energy - mRNA 1.12924 kcal/mol@LB@Unfolding Energy - sRNA 6.00672 kcal/mol@LB@@LB@Position - mRNA 170 -- 181@LB@Position - sRNA 16 -- 26@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 20 -- 26@LB@
35	0.001389	0.1324	bsu24570	gcvT	-12.27	0.095214	256 -- 273	25 -- 46	aminomethyltransferase	_____________255____________________274\n_____________\|______________________\|\n5'-CUC...AACGA_______C_______C______AGCUU...UAA-3'\n______________UUGAUUU___GGAGG___UGGG\n______________\|\|\|\|\|:\|___:\|\|\|\|___\|\|\|\|\n______________AACUAGA___UCUCC___ACCC\n3'-UUU...CCUAG_______CUA_____CCA____CUUGU...AUA-5'\n_____________\|______________________\|\n_____________47_____________________24\n	256 -- 262	40 -- 46	-17.62 kcal/mol	4.38211 kcal/mol	0.972727 kcal/mol	255 274@LB@ \| \|@LB@5'-CUC...AACGA C C AGCUU...UAA-3'@LB@ UUGAUUU GGAGG UGGG@LB@ \|\|\|\|\|:\| :\|\|\|\| \|\|\|\|@LB@ AACUAGA UCUCC ACCC@LB@3'-UUU...CCUAG CUA CCA CUUGU...AUA-5'@LB@ \| \|@LB@ 47 24@LB@@LB@@LB@Energy -12.27 kcal/mol@LB@Hybridization Energy -17.62 kcal/mol@LB@Unfolding Energy - mRNA 4.38211 kcal/mol@LB@Unfolding Energy - sRNA 0.972727 kcal/mol@LB@@LB@Position - mRNA 256 -- 273@LB@Position - sRNA 25 -- 46@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 40 -- 46@LB@
70	0.004864	0.2318	bsu03720	gerKB	-15.05	0.029438	176 -- 191	30 -- 44	spore germination protein KB	_____________175_______________192\n_____________\|_________________\|\n5'-UUA...GAUUA___________AA____AAGUG...GCA-3'\n______________GGUCUGA_AGA__GGGG\n______________\|:\|\|\|\|\|_\|\|\|__\|\|\|\|\n______________CUAGACU_UCU__CCCC\n3'-UUU...UAGAA_______A_________AACCC...AUA-5'\n_____________\|_________________\|\n_____________45________________29\n	176 -- 182	38 -- 44	-18.3492 kcal/mol	2.32731 kcal/mol	0.969452 kcal/mol	175 192@LB@ \| \|@LB@5'-UUA...GAUUA AA AAGUG...GCA-3'@LB@ GGUCUGA AGA GGGG@LB@ \|:\|\|\|\|\| \|\|\| \|\|\|\|@LB@ CUAGACU UCU CCCC@LB@3'-UUU...UAGAA A AACCC...AUA-5'@LB@ \| \|@LB@ 45 29@LB@@LB@@LB@Energy -15.05 kcal/mol@LB@Hybridization Energy -18.3492 kcal/mol@LB@Unfolding Energy - mRNA 2.32731 kcal/mol@LB@Unfolding Energy - sRNA 0.969452 kcal/mol@LB@@LB@Position - mRNA 176 -- 191@LB@Position - sRNA 30 -- 44@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 38 -- 44@LB@
180	0.01704	0.3152	bsu28380	gerM	-9.54	0.246988	269 -- 291	32 -- 52	spore germination protein GerM	_____________268______________________292\n_____________\|________________________\|\n5'-AGU...GGAUG___UUU____CA____________CAGCC...AGG-3'\n______________CGG___GUUU__AUCUGAUA_AGG\n______________\|\|\|___:\|:\|__\|\|\|\|\|\|\|\|_\|\|\|\n______________GCC___UAGA__UAGACUAU_UCC\n3'-UUU...AAAAA__________AC________C___CCAAC...AUA-5'\n_____________\|________________________\|\n_____________53_______________________31\n	282 -- 288	36 -- 42	-15.6565 kcal/mol	5.13957 kcal/mol	0.976384 kcal/mol	268 292@LB@ \| \|@LB@5'-AGU...GGAUG UUU CA CAGCC...AGG-3'@LB@ CGG GUUU AUCUGAUA AGG@LB@ \|\|\| :\|:\| \|\|\|\|\|\|\|\| \|\|\|@LB@ GCC UAGA UAGACUAU UCC@LB@3'-UUU...AAAAA AC C CCAAC...AUA-5'@LB@ \| \|@LB@ 53 31@LB@@LB@@LB@Energy -9.54 kcal/mol@LB@Hybridization Energy -15.6565 kcal/mol@LB@Unfolding Energy - mRNA 5.13957 kcal/mol@LB@Unfolding Energy - sRNA 0.976384 kcal/mol@LB@@LB@Position - mRNA 269 -- 291@LB@Position - sRNA 32 -- 52@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 36 -- 42@LB@
69	0.004753	0.2298	bsu24850	glcK	-6.97	0.496286	33 -- 46	15 -- 29	glucokinase	_____________32______________47\n_____________\|_______________\|\n5'-GCU...UUAUU____A__________CUUGA...UUC-3'\n______________UUGG__GACAGAGAG\n______________\|\|\|\|__:\|\|\|\|\|\|\|\|\n______________AACC__UUGUCUCUC\n3'-UUU...UCCCC____CC_________AUCGA...AUA-5'\n_____________\|_______________\|\n_____________30______________14\n	40 -- 46	15 -- 21	-16.6304 kcal/mol	3.64593 kcal/mol	6.01316 kcal/mol	32 47@LB@ \| \|@LB@5'-GCU...UUAUU A CUUGA...UUC-3'@LB@ UUGG GACAGAGAG@LB@ \|\|\|\| :\|\|\|\|\|\|\|\|@LB@ AACC UUGUCUCUC@LB@3'-UUU...UCCCC CC AUCGA...AUA-5'@LB@ \| \|@LB@ 30 14@LB@@LB@@LB@Energy -6.97 kcal/mol@LB@Hybridization Energy -16.6304 kcal/mol@LB@Unfolding Energy - mRNA 3.64593 kcal/mol@LB@Unfolding Energy - sRNA 6.01316 kcal/mol@LB@@LB@Position - mRNA 33 -- 46@LB@Position - sRNA 15 -- 29@LB@Position Seed - mRNA 40 -- 46@LB@Position Seed - sRNA 15 -- 21@LB@
139	0.01217	0.2883	bsu30960	glgD	-11.28	0.137516	171 -- 191	30 -- 50	glycogen biosynthesis protein GlgD	_____________170____________________192\n_____________\|______________________\|\n5'-ACU...GAAUU_____AAUUA____________GCAGA...UUG-3'\n______________GAUUU_____CUGA_AGAGGGG\n______________\|\|\|:\|_____\|\|\|\|_\|\|\|\|\|\|\|\n______________CUAGA_____GACU_UCUCCCC\n3'-UUU...AAAGC_____ACUA_____A_______AACCC...AUA-5'\n_____________\|______________________\|\n_____________51_____________________29\n	185 -- 191	30 -- 36	-19.1028 kcal/mol	6.84884 kcal/mol	0.974272 kcal/mol	170 192@LB@ \| \|@LB@5'-ACU...GAAUU AAUUA GCAGA...UUG-3'@LB@ GAUUU CUGA AGAGGGG@LB@ \|\|\|:\| \|\|\|\| \|\|\|\|\|\|\|@LB@ CUAGA GACU UCUCCCC@LB@3'-UUU...AAAGC ACUA A AACCC...AUA-5'@LB@ \| \|@LB@ 51 29@LB@@LB@@LB@Energy -11.28 kcal/mol@LB@Hybridization Energy -19.1028 kcal/mol@LB@Unfolding Energy - mRNA 6.84884 kcal/mol@LB@Unfolding Energy - sRNA 0.974272 kcal/mol@LB@@LB@Position - mRNA 171 -- 191@LB@Position - sRNA 30 -- 50@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 30 -- 36@LB@
91	0.007102	0.2604	bsu36520	glnK	-7.98	0.387566	247 -- 267	32 -- 49	nitrogen regulatory PII-like protein	_____________246____________________268\n_____________\|______________________\|\n5'-GGU...GGCAA_______AAAG_______C___AACUC...CUU-3'\n______________AUUUUGA____CUGA_AG_AGG\n______________\|\|:\|\|\|\|____\|\|\|\|_\|\|_\|\|\|\n______________UAGAACU____GACU_UC_UCC\n3'-UUU...AAGCC_______A_______A______CCAAC...AUA-5'\n_____________\|______________________\|\n_____________50_____________________31\n	247 -- 253	43 -- 49	-11.0905 kcal/mol	2.14263 kcal/mol	0.970192 kcal/mol	246 268@LB@ \| \|@LB@5'-GGU...GGCAA AAAG C AACUC...CUU-3'@LB@ AUUUUGA CUGA AG AGG@LB@ \|\|:\|\|\|\| \|\|\|\| \|\| \|\|\|@LB@ UAGAACU GACU UC UCC@LB@3'-UUU...AAGCC A A CCAAC...AUA-5'@LB@ \| \|@LB@ 50 31@LB@@LB@@LB@Energy -7.98 kcal/mol@LB@Hybridization Energy -11.0905 kcal/mol@LB@Unfolding Energy - mRNA 2.14263 kcal/mol@LB@Unfolding Energy - sRNA 0.970192 kcal/mol@LB@@LB@Position - mRNA 247 -- 267@LB@Position - sRNA 32 -- 49@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 43 -- 49@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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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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