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
104	0.009018	0.2778	bsu08080	acoC	-12.10	0.101314	188 -- 194	30 -- 36	dihydrolipoyllysine-residue acetyltransferase component of acetoin cleaving system	_____________187_____195\n_____________\|_______\|\n5'-UGC...AUUAA_______ACACA...GAG-3'\n______________AGGGGGG\n______________\|\|:\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	188 -- 194	30 -- 36	-13.004 kcal/mol	0.767034 kcal/mol	0.133643 kcal/mol	187 195@LB@ \| \|@LB@5'-UGC...AUUAA ACACA...GAG-3'@LB@ AGGGGGG@LB@ \|\|:\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -12.10 kcal/mol@LB@Hybridization Energy -13.004 kcal/mol@LB@Unfolding Energy - mRNA 0.767034 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@
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@
128	0.01143	0.2883	bsu29690	acuA	-15.81	0.020690	248 -- 269	30 -- 52	acetoin utilization protein AcuA	_____________247_____________________270\n_____________\|_______________________\|\n5'-UAU...GCAAC___C____UA_________A___CCUGU...AUG-3'\n______________CGG_UCUU___CUGAUAGA_GGG\n______________\|\|\|_\|\|\|\|___\|\|\|\|\|\|\|\|_\|\|\|\n______________GCC_AGAA___GACUAUCU_CCC\n3'-UUU...AAAAA___U____CUA________C___AACCC...AUA-5'\n_____________\|_______________________\|\n_____________53______________________29\n	259 -- 265	34 -- 40	-22.8929 kcal/mol	6.10629 kcal/mol	0.979974 kcal/mol	247 270@LB@ \| \|@LB@5'-UAU...GCAAC C UA A CCUGU...AUG-3'@LB@ CGG UCUU CUGAUAGA GGG@LB@ \|\|\| \|\|\|\| \|\|\|\|\|\|\|\| \|\|\|@LB@ GCC AGAA GACUAUCU CCC@LB@3'-UUU...AAAAA U CUA C AACCC...AUA-5'@LB@ \| \|@LB@ 53 29@LB@@LB@@LB@Energy -15.81 kcal/mol@LB@Hybridization Energy -22.8929 kcal/mol@LB@Unfolding Energy - mRNA 6.10629 kcal/mol@LB@Unfolding Energy - sRNA 0.979974 kcal/mol@LB@@LB@Position - mRNA 248 -- 269@LB@Position - sRNA 30 -- 52@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 34 -- 40@LB@
47	0.002107	0.1496	bsu10620	addB	-16.79	0.012734	176 -- 222	12 -- 44	ATP-dependent helicase/deoxyribonuclease subunit B	_____________175_____________________________________________223\n_____________\|_______________________________________________\|\n5'-UAG...AGAGA___AAAAAG________CUUCUAAUUU__________UUUUU_____GCAGG...AGC-3'\n______________GAU______AGAGGGGU__________GGGAGCAGAG_____AGUAG\n______________\|\|\|______\|\|\|\|\|\|\|\|__________\|\|\|\|:\|\|\|\|\|_____\|\|\|\|\|\n______________CUA______UCUCCCCA__________CCCUUGUCUC_____UCAUC\n3'-UUU...UAGAA___GACUA_________AC____________________________GAAGA...AUA-5'\n_____________\|_______________________________________________\|\n_____________45______________________________________________11\n	206 -- 212	17 -- 23	-35.2405 kcal/mol	8.50165 kcal/mol	9.94637 kcal/mol	175 223@LB@ \| \|@LB@5'-UAG...AGAGA AAAAAG CUUCUAAUUU UUUUU GCAGG...AGC-3'@LB@ GAU AGAGGGGU GGGAGCAGAG AGUAG@LB@ \|\|\| \|\|\|\|\|\|\|\| \|\|\|\|:\|\|\|\|\| \|\|\|\|\|@LB@ CUA UCUCCCCA CCCUUGUCUC UCAUC@LB@3'-UUU...UAGAA GACUA AC GAAGA...AUA-5'@LB@ \| \|@LB@ 45 11@LB@@LB@@LB@Energy -16.79 kcal/mol@LB@Hybridization Energy -35.2405 kcal/mol@LB@Unfolding Energy - mRNA 8.50165 kcal/mol@LB@Unfolding Energy - sRNA 9.94637 kcal/mol@LB@@LB@Position - mRNA 176 -- 222@LB@Position - sRNA 12 -- 44@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 17 -- 23@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@
62	0.003827	0.2059	bsu11360	appD	-16.60	0.014008	157 -- 196	21 -- 48	oligopeptide transport ATP-binding protein AppD	_____________156______________________________________197\n_____________\|________________________________________\|\n5'-AUG...CUUUC______AAACG_____CAACA_______GGAAA_______UAGCA...AAG-3'\n______________UCUUGA_____UUUGA_____AGAGGGG_____GGGGAGC\n______________\|\|\|\|\|\|_____\|:\|\|\|_____\|\|\|\|\|\|\|_____\|\|\|\|\|:\|\n______________AGAACU_____AGACU_____UCUCCCC_____CCCCUUG\n3'-UUU...AGCCU________________A___________AA__________UCUCU...AUA-5'\n_____________\|________________________________________\|\n_____________49_______________________________________20\n	190 -- 196	21 -- 27	-30.7931 kcal/mol	11.4214 kcal/mol	2.76831 kcal/mol	156 197@LB@ \| \|@LB@5'-AUG...CUUUC AAACG CAACA GGAAA UAGCA...AAG-3'@LB@ UCUUGA UUUGA AGAGGGG GGGGAGC@LB@ \|\|\|\|\|\| \|:\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|:\|@LB@ AGAACU AGACU UCUCCCC CCCCUUG@LB@3'-UUU...AGCCU A AA UCUCU...AUA-5'@LB@ \| \|@LB@ 49 20@LB@@LB@@LB@Energy -16.60 kcal/mol@LB@Hybridization Energy -30.7931 kcal/mol@LB@Unfolding Energy - mRNA 11.4214 kcal/mol@LB@Unfolding Energy - sRNA 2.76831 kcal/mol@LB@@LB@Position - mRNA 157 -- 196@LB@Position - sRNA 21 -- 48@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 21 -- 27@LB@
85	0.006705	0.2588	bsu28790	araB	-13.91	0.048694	184 -- 192	30 -- 38	ribulokinase	_____________183_______193\n_____________\|_________\|\n5'-GGA...CAAAA_________GAUGU...AAU-3'\n______________GUAGAGGGG\n______________:\|\|\|\|\|\|\|\|\n______________UAUCUCCCC\n3'-UUU...UAGAC_________AACCC...AUA-5'\n_____________\|_________\|\n_____________39________29\n	186 -- 192	30 -- 36	-16.4519 kcal/mol	1.87822 kcal/mol	0.6591 kcal/mol	183 193@LB@ \| \|@LB@5'-GGA...CAAAA GAUGU...AAU-3'@LB@ GUAGAGGGG@LB@ :\|\|\|\|\|\|\|\|@LB@ UAUCUCCCC@LB@3'-UUU...UAGAC AACCC...AUA-5'@LB@ \| \|@LB@ 39 29@LB@@LB@@LB@Energy -13.91 kcal/mol@LB@Hybridization Energy -16.4519 kcal/mol@LB@Unfolding Energy - mRNA 1.87822 kcal/mol@LB@Unfolding Energy - sRNA 0.6591 kcal/mol@LB@@LB@Position - mRNA 184 -- 192@LB@Position - sRNA 30 -- 38@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 30 -- 36@LB@
42	0.001862	0.1479	bsu40320	argI	-8.56	0.330283	1 -- 17	32 -- 48	arginase	______________1_________________18\n______________\|_________________\|\n___________5'-_____C_______CC___AGCAG...UGA-3'\n______________UCUUG_AUUUGAU___GG\n______________\|\|\|\|\|_\|\|:\|\|\|\|___\|\|\n______________AGAAC_UAGACUA___CC\n3'-UUU...AGCCU_____________UCU__CCAAC...AUA-5'\n_____________\|__________________\|\n_____________49_________________31\n	7 -- 13	37 -- 43	-12.1859 kcal/mol	2.6521 kcal/mol	0.970016 kcal/mol	1 18@LB@ \| \|@LB@ 5'- C CC AGCAG...UGA-3'@LB@ UCUUG AUUUGAU GG@LB@ \|\|\|\|\| \|\|:\|\|\|\| \|\|@LB@ AGAAC UAGACUA CC@LB@3'-UUU...AGCCU UCU CCAAC...AUA-5'@LB@ \| \|@LB@ 49 31@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -12.1859 kcal/mol@LB@Unfolding Energy - mRNA 2.6521 kcal/mol@LB@Unfolding Energy - sRNA 0.970016 kcal/mol@LB@@LB@Position - mRNA 1 -- 17@LB@Position - sRNA 32 -- 48@LB@Position Seed - mRNA 7 -- 13@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@
25	0.0005172	0.06638	bsu30210	bioD	-10.94	0.155183	179 -- 210	28 -- 53	ATP-dependent dethiobiotin synthetase BioD	_____________178_______________________________211\n_____________\|_________________________________\|\n5'-GUC...UUCAA_____AAG___G___CACAUCAUUU________UUUUU...UCG-3'\n______________UCGGA____GA_CUG__________GAGGGGUU\n______________\|\|\|\|\|____\|\|_\|\|\|__________\|\|\|\|\|\|\|\|\n______________AGCCU____CU_GAC__________CUCCCCAA\n3'-UUU...AAAAA_____AGAA__A___UAU_______________CCCCU...AUA-5'\n_____________\|_________________________________\|\n_____________54________________________________27\n	204 -- 210	28 -- 34	-21.1469 kcal/mol	9.22099 kcal/mol	0.985925 kcal/mol	178 211@LB@ \| \|@LB@5'-GUC...UUCAA AAG G CACAUCAUUU UUUUU...UCG-3'@LB@ UCGGA GA CUG GAGGGGUU@LB@ \|\|\|\|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ AGCCU CU GAC CUCCCCAA@LB@3'-UUU...AAAAA AGAA A UAU CCCCU...AUA-5'@LB@ \| \|@LB@ 54 27@LB@@LB@@LB@Energy -10.94 kcal/mol@LB@Hybridization Energy -21.1469 kcal/mol@LB@Unfolding Energy - mRNA 9.22099 kcal/mol@LB@Unfolding Energy - sRNA 0.985925 kcal/mol@LB@@LB@Position - mRNA 179 -- 210@LB@Position - sRNA 28 -- 53@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 28 -- 34@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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