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
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@
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@
32	0.001154	0.119	bsu32820	fadE	-9.01	0.290043	236 -- 252	32 -- 52	acyl-CoA dehydrogenase	_____________235____________________253\n_____________\|______________________\|\n5'-AUU...GGCGG________UA____________AUGUC...AGC-3'\n______________CGGAUUUU__AUC_____GAGG\n______________\|\|\|\|\|:\|\|__\|\|\|_____\|\|\|\|\n______________GCCUAGAA__UAG_____CUCC\n3'-UUU...AAAAA________C____ACUAU____CCAAC...AUA-5'\n_____________\|______________________\|\n_____________53_____________________31\n	237 -- 243	45 -- 51	-13.909 kcal/mol	3.91995 kcal/mol	0.976384 kcal/mol	235 253@LB@ \| \|@LB@5'-AUU...GGCGG UA AUGUC...AGC-3'@LB@ CGGAUUUU AUC GAGG@LB@ \|\|\|\|\|:\|\| \|\|\| \|\|\|\|@LB@ GCCUAGAA UAG CUCC@LB@3'-UUU...AAAAA C ACUAU CCAAC...AUA-5'@LB@ \| \|@LB@ 53 31@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -13.909 kcal/mol@LB@Unfolding Energy - mRNA 3.91995 kcal/mol@LB@Unfolding Energy - sRNA 0.976384 kcal/mol@LB@@LB@Position - mRNA 236 -- 252@LB@Position - sRNA 32 -- 52@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 45 -- 51@LB@
78	0.005707	0.2441	bsu18040	yneP	-11.92	0.108570	96 -- 119	24 -- 45	acyl-CoA thioesterase	_____________95_______________________120\n_____________\|________________________\|\n5'-UUG...CUUUC_________UAU__UAAAA_____CUAAA...AAA-3'\n______________UGAUUUGAU___GG_____UGGGG\n______________\|\|\|\|:\|\|\|\|___\|\|_____\|\|\|\|\|\n______________ACUAGACUA___CC_____ACCCC\n3'-UUU...CUAGA_________UCU__CCA_______UUGUC...AUA-5'\n_____________\|________________________\|\n_____________46_______________________23\n	98 -- 104	37 -- 43	-18.893 kcal/mol	5.99443 kcal/mol	0.977634 kcal/mol	95 120@LB@ \| \|@LB@5'-UUG...CUUUC UAU UAAAA CUAAA...AAA-3'@LB@ UGAUUUGAU GG UGGGG@LB@ \|\|\|\|:\|\|\|\| \|\| \|\|\|\|\|@LB@ ACUAGACUA CC ACCCC@LB@3'-UUU...CUAGA UCU CCA UUGUC...AUA-5'@LB@ \| \|@LB@ 46 23@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -18.893 kcal/mol@LB@Unfolding Energy - mRNA 5.99443 kcal/mol@LB@Unfolding Energy - sRNA 0.977634 kcal/mol@LB@@LB@Position - mRNA 96 -- 119@LB@Position - sRNA 24 -- 45@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 37 -- 43@LB@
123	0.01093	0.2883	bsu22970	ypbH	-15.60	0.022809	254 -- 275	27 -- 45	adapter protein MecA	_____________253____________________276\n_____________\|______________________\|\n5'-GAG...CUCGA________C___CC____A___ACAAA...ACU-3'\n______________UGAUUUGA_AGA__GGGG_UUG\n______________\|\|\|\|:\|\|\|_\|\|\|__\|\|\|\|_\|\|\|\n______________ACUAGACU_UCU__CCCC_AAC\n3'-UUU...CUAGA________A_____________CCCUU...AUA-5'\n_____________\|______________________\|\n_____________46_____________________26\n	255 -- 261	38 -- 44	-20.0369 kcal/mol	3.46393 kcal/mol	0.971562 kcal/mol	253 276@LB@ \| \|@LB@5'-GAG...CUCGA C CC A ACAAA...ACU-3'@LB@ UGAUUUGA AGA GGGG UUG@LB@ \|\|\|\|:\|\|\| \|\|\| \|\|\|\| \|\|\|@LB@ ACUAGACU UCU CCCC AAC@LB@3'-UUU...CUAGA A CCCUU...AUA-5'@LB@ \| \|@LB@ 46 26@LB@@LB@@LB@Energy -15.60 kcal/mol@LB@Hybridization Energy -20.0369 kcal/mol@LB@Unfolding Energy - mRNA 3.46393 kcal/mol@LB@Unfolding Energy - sRNA 0.971562 kcal/mol@LB@@LB@Position - mRNA 254 -- 275@LB@Position - sRNA 27 -- 45@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 38 -- 44@LB@
43	0.00194	0.1492	bsu01370	adk	-12.74	0.079154	128 -- 149	32 -- 52	adenylate kinase	_____________127____________________150\n_____________\|______________________\|\n5'-UUU...UACCG_______A___AAAAC______AAAUG...AUA-3'\n______________UGGAUUU_UGA_____UAGAGG\n______________:\|\|\|\|:\|_\|\|\|_____\|\|\|\|\|\|\n______________GCCUAGA_ACU_____AUCUCC\n3'-UUU...AAAAA___________AGACU______CCAAC...AUA-5'\n_____________\|______________________\|\n_____________53_____________________31\n	128 -- 134	46 -- 52	-16.4639 kcal/mol	2.75066 kcal/mol	0.976384 kcal/mol	127 150@LB@ \| \|@LB@5'-UUU...UACCG A AAAAC AAAUG...AUA-3'@LB@ UGGAUUU UGA UAGAGG@LB@ :\|\|\|\|:\| \|\|\| \|\|\|\|\|\|@LB@ GCCUAGA ACU AUCUCC@LB@3'-UUU...AAAAA AGACU CCAAC...AUA-5'@LB@ \| \|@LB@ 53 31@LB@@LB@@LB@Energy -12.74 kcal/mol@LB@Hybridization Energy -16.4639 kcal/mol@LB@Unfolding Energy - mRNA 2.75066 kcal/mol@LB@Unfolding Energy - sRNA 0.976384 kcal/mol@LB@@LB@Position - mRNA 128 -- 149@LB@Position - sRNA 32 -- 52@LB@Position Seed - mRNA 128 -- 134@LB@Position Seed - sRNA 46 -- 52@LB@
130	0.01149	0.2883	bsu02620	phoD	-13.55	0.056825	174 -- 193	30 -- 50	alkaline phosphatase D	_____________173____________________194\n_____________\|______________________\|\n5'-GCC...GAGAC____AA___G____G_______AUCUU...CGG-3'\n______________GAUC__UGA___GA_AGAGGGG\n______________\|\|\|\|__\|\|\|___\|\|_\|\|\|\|\|\|\|\n______________CUAG__ACU___CU_UCUCCCC\n3'-UUU...AAAGC____A____AGA__A_______AACCC...AUA-5'\n_____________\|______________________\|\n_____________51_____________________29\n	187 -- 193	30 -- 36	-18.9864 kcal/mol	4.46268 kcal/mol	0.974272 kcal/mol	173 194@LB@ \| \|@LB@5'-GCC...GAGAC AA G G AUCUU...CGG-3'@LB@ GAUC UGA GA AGAGGGG@LB@ \|\|\|\| \|\|\| \|\| \|\|\|\|\|\|\|@LB@ CUAG ACU CU UCUCCCC@LB@3'-UUU...AAAGC A AGA A AACCC...AUA-5'@LB@ \| \|@LB@ 51 29@LB@@LB@@LB@Energy -13.55 kcal/mol@LB@Hybridization Energy -18.9864 kcal/mol@LB@Unfolding Energy - mRNA 4.46268 kcal/mol@LB@Unfolding Energy - sRNA 0.974272 kcal/mol@LB@@LB@Position - mRNA 174 -- 193@LB@Position - sRNA 30 -- 50@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 30 -- 36@LB@
178	0.01684	0.3152	bsu09460	ctrA	-17.20	0.010320	182 -- 213	20 -- 50	amino acid permease	_____________181_________________________________214\n_____________\|___________________________________\|\n5'-CAA...UAGAU____GG__G____________AA__AAA_______UUUUU...UAA-3'\n______________GAUC__GA_UUGA___AGGGG__UG___GGGAGCG\n______________\|\|\|\|__\|\|_:\|\|\|___\|\|\|\|\|__\|\|___\|\|\|\|:\|:\n______________CUAG__CU_GACU___UCCCC__AC___CCCUUGU\n3'-UUU...AAAGC____AA__A____AUC_____A_____________CUCUC...AUA-5'\n_____________\|___________________________________\|\n_____________51__________________________________19\n	207 -- 213	20 -- 26	-25.5851 kcal/mol	4.15406 kcal/mol	4.22897 kcal/mol	181 214@LB@ \| \|@LB@5'-CAA...UAGAU GG G AA AAA UUUUU...UAA-3'@LB@ GAUC GA UUGA AGGGG UG GGGAGCG@LB@ \|\|\|\| \|\| :\|\|\| \|\|\|\|\| \|\| \|\|\|\|:\|:@LB@ CUAG CU GACU UCCCC AC CCCUUGU@LB@3'-UUU...AAAGC AA A AUC A CUCUC...AUA-5'@LB@ \| \|@LB@ 51 19@LB@@LB@@LB@Energy -17.20 kcal/mol@LB@Hybridization Energy -25.5851 kcal/mol@LB@Unfolding Energy - mRNA 4.15406 kcal/mol@LB@Unfolding Energy - sRNA 4.22897 kcal/mol@LB@@LB@Position - mRNA 182 -- 213@LB@Position - sRNA 20 -- 50@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 20 -- 26@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@
181	0.0171	0.3152	bsu32040	yuiF	-15.17	0.027943	179 -- 194	29 -- 51	amino acid transporter YuiF	_____________178_____________________195\n_____________\|_______________________\|\n5'-ACA...CUAAA_______________________AUCAU...GGU-3'\n______________GGAUUUU_______UGGAGGGGU\n______________\|\|\|\|:\|\|_______\|:\|\|\|\|\|\|\|\n______________CCUAGAA_______AUCUCCCCA\n3'-UUU...AAAAG_______CUAGACU_________ACCCC...AUA-5'\n_____________\|_______________________\|\n_____________52______________________28\n	188 -- 194	29 -- 35	-21.3957 kcal/mol	5.25498 kcal/mol	0.974539 kcal/mol	178 195@LB@ \| \|@LB@5'-ACA...CUAAA AUCAU...GGU-3'@LB@ GGAUUUU UGGAGGGGU@LB@ \|\|\|\|:\|\| \|:\|\|\|\|\|\|\|@LB@ CCUAGAA AUCUCCCCA@LB@3'-UUU...AAAAG CUAGACU ACCCC...AUA-5'@LB@ \| \|@LB@ 52 28@LB@@LB@@LB@Energy -15.17 kcal/mol@LB@Hybridization Energy -21.3957 kcal/mol@LB@Unfolding Energy - mRNA 5.25498 kcal/mol@LB@Unfolding Energy - sRNA 0.974539 kcal/mol@LB@@LB@Position - mRNA 179 -- 194@LB@Position - sRNA 29 -- 51@LB@Position Seed - mRNA 188 -- 194@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)

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching