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
149	0.01325	0.2966	bsu07610	citM	-7.43	0.445360	149 -- 162	15 -- 27	Mg(2+)/citrate complex secondary transporter	_____________148____________163\n_____________\|______________\|\n5'-AUU...AAAAA_______A______AAAAA...UUG-3'\n______________GGGGAGU_AGGGAG\n______________\|\|\|\|\|::_\|\|:\|\|\|\n______________CCCCUUG_UCUCUC\n3'-UUU...CCCAA______________AUCGA...AUA-5'\n_____________\|______________\|\n_____________28_____________14\n	149 -- 155	21 -- 27	-17.4184 kcal/mol	3.9771 kcal/mol	6.01129 kcal/mol	148 163@LB@ \| \|@LB@5'-AUU...AAAAA A AAAAA...UUG-3'@LB@ GGGGAGU AGGGAG@LB@ \|\|\|\|\|:: \|\|:\|\|\|@LB@ CCCCUUG UCUCUC@LB@3'-UUU...CCCAA AUCGA...AUA-5'@LB@ \| \|@LB@ 28 14@LB@@LB@@LB@Energy -7.43 kcal/mol@LB@Hybridization Energy -17.4184 kcal/mol@LB@Unfolding Energy - mRNA 3.9771 kcal/mol@LB@Unfolding Energy - sRNA 6.01129 kcal/mol@LB@@LB@Position - mRNA 149 -- 162@LB@Position - sRNA 15 -- 27@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 21 -- 27@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@
84	0.006671	0.2588	bsu14270	moeB	-18.74	0.004465	187 -- 207	32 -- 51	molybdopterin-synthase adenylyltransferase	_____________186___________________208\n_____________\|_____________________\|\n5'-UUG...GAUAA___GAACA_____________AACGU...GAG-3'\n______________GGA_____GGUUUGAUGGAGG\n______________\|\|\|_____\|:\|:\|\|\|\|:\|\|\|\|\n______________CCU_____CUAGACUAUCUCC\n3'-UUU...AAAAG___AGAA______________CCAAC...AUA-5'\n_____________\|_____________________\|\n_____________52____________________31\n	201 -- 207	32 -- 38	-23.059 kcal/mol	3.35069 kcal/mol	0.97021 kcal/mol	186 208@LB@ \| \|@LB@5'-UUG...GAUAA GAACA AACGU...GAG-3'@LB@ GGA GGUUUGAUGGAGG@LB@ \|\|\| \|:\|:\|\|\|\|:\|\|\|\|@LB@ CCU CUAGACUAUCUCC@LB@3'-UUU...AAAAG AGAA CCAAC...AUA-5'@LB@ \| \|@LB@ 52 31@LB@@LB@@LB@Energy -18.74 kcal/mol@LB@Hybridization Energy -23.059 kcal/mol@LB@Unfolding Energy - mRNA 3.35069 kcal/mol@LB@Unfolding Energy - sRNA 0.97021 kcal/mol@LB@@LB@Position - mRNA 187 -- 207@LB@Position - sRNA 32 -- 51@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 32 -- 38@LB@
170	0.0164	0.3152	bsu13090	ykkC	-8.27	0.358617	162 -- 212	23 -- 55	multidrug resistance protein	_____________161__________________________________________________213\n_____________\|____________________________________________________\|\n5'-UCA...UUUGU_______GAA____A__A_______AA__AAUGACUCAAAAU_AAA______UUGGU...CCA-3'\n______________UUUCGGA___UCUU_AU__GAUAGA__GG_____________G___UGGGGA\n______________\|\|\|\|\|\|\|___\|\|\|\|_\|\|__\|\|\|\|\|\|__\|\|_____________\|___\|\|\|\|\|\|\n______________AAAGCCU___AGAA_UA__CUAUCU__CC_____________C___ACCCCU\n3'-UUU...UCAAA______________C__GA______C_________________A________UGUCU...AUA-5'\n_____________\|____________________________________________________\|\n_____________56___________________________________________________22\n	162 -- 168	49 -- 55	-21.902 kcal/mol	11.1231 kcal/mol	2.51158 kcal/mol	161 213@LB@ \| \|@LB@5'-UCA...UUUGU GAA A A AA AAUGACUCAAAAU AAA UUGGU...CCA-3'@LB@ UUUCGGA UCUU AU GAUAGA GG G UGGGGA@LB@ \|\|\|\|\|\|\| \|\|\|\| \|\| \|\|\|\|\|\| \|\| \| \|\|\|\|\|\|@LB@ AAAGCCU AGAA UA CUAUCU CC C ACCCCU@LB@3'-UUU...UCAAA C GA C A UGUCU...AUA-5'@LB@ \| \|@LB@ 56 22@LB@@LB@@LB@Energy -8.27 kcal/mol@LB@Hybridization Energy -21.902 kcal/mol@LB@Unfolding Energy - mRNA 11.1231 kcal/mol@LB@Unfolding Energy - sRNA 2.51158 kcal/mol@LB@@LB@Position - mRNA 162 -- 212@LB@Position - sRNA 23 -- 55@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 49 -- 55@LB@
34	0.001327	0.1302	bsu23550	mleA	-19.34	0.003138	3 -- 24	31 -- 51	NAD-dependent malic enzyme 1	_____________2______________________25\n_____________\|______________________\|\n_________5'-AU__U_C____________AU___AUUUA...GGG-3'\n______________GG_U_CUUGGUCUGAUA__GGG\n______________\|\|_\|_\|\|\|\|:\|\|\|\|\|\|\|__\|\|\|\n______________CC_A_GAACUAGACUAU__CCC\n3'-UUU...AAAAG__U______________CU___CAACC...AUA-5'\n_____________\|______________________\|\n_____________52_____________________30\n	13 -- 19	36 -- 42	-24.8934 kcal/mol	4.58077 kcal/mol	0.970589 kcal/mol	2 25@LB@ \| \|@LB@ 5'-AU U C AU AUUUA...GGG-3'@LB@ GG U CUUGGUCUGAUA GGG@LB@ \|\| \| \|\|\|\|:\|\|\|\|\|\|\| \|\|\|@LB@ CC A GAACUAGACUAU CCC@LB@3'-UUU...AAAAG U CU CAACC...AUA-5'@LB@ \| \|@LB@ 52 30@LB@@LB@@LB@Energy -19.34 kcal/mol@LB@Hybridization Energy -24.8934 kcal/mol@LB@Unfolding Energy - mRNA 4.58077 kcal/mol@LB@Unfolding Energy - sRNA 0.970589 kcal/mol@LB@@LB@Position - mRNA 3 -- 24@LB@Position - sRNA 31 -- 51@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 36 -- 42@LB@
4	1.471e-05	0.01227	bsu32200	yutJ	-17.92	0.007061	210 -- 239	21 -- 53	NADH dehydrogenase-like protein YutJ	_____________209_______________________________240\n_____________\|_________________________________\|\n5'-UGA...AAAAA________________C_____UUAC_______AUGCG...UAA-3'\n______________UUGG_UCUUGAUC_GG_GGAGG_____GGGAAC\n______________\|:\|\|_\|\|\|\|\|\|\|\|_\|:_:\|\|\|\|_____\|\|\|\|\|\|\n______________AGCC_AGAACUAG_CU_UCUCC_____CCCUUG\n3'-UUU...AAAAA____U________A__A_____CCAAC______UCUCU...AUA-5'\n_____________\|_________________________________\|\n_____________54________________________________20\n	215 -- 221	41 -- 47	-30.8017 kcal/mol	10.1098 kcal/mol	2.77573 kcal/mol	209 240@LB@ \| \|@LB@5'-UGA...AAAAA C UUAC AUGCG...UAA-3'@LB@ UUGG UCUUGAUC GG GGAGG GGGAAC@LB@ \|:\|\| \|\|\|\|\|\|\|\| \|: :\|\|\|\| \|\|\|\|\|\|@LB@ AGCC AGAACUAG CU UCUCC CCCUUG@LB@3'-UUU...AAAAA U A A CCAAC UCUCU...AUA-5'@LB@ \| \|@LB@ 54 20@LB@@LB@@LB@Energy -17.92 kcal/mol@LB@Hybridization Energy -30.8017 kcal/mol@LB@Unfolding Energy - mRNA 10.1098 kcal/mol@LB@Unfolding Energy - sRNA 2.77573 kcal/mol@LB@@LB@Position - mRNA 210 -- 239@LB@Position - sRNA 21 -- 53@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 41 -- 47@LB@
60	0.003464	0.1926	bsu03300	nasD	-15.33	0.025906	190 -- 205	34 -- 52	nitrite reductase	_____________189_________________206\n_____________\|___________________\|\n5'-UUU...AGGAG___________________AAAAA...CAA-3'\n______________CGGAUC___AUCUGAUGGG\n______________\|\|\|\|\|\|___\|\|\|\|\|\|\|:\|:\n______________GCCUAG___UAGACUAUCU\n3'-UUU...AAAAA______AAC__________CCCCA...AUA-5'\n_____________\|___________________\|\n_____________53__________________33\n	199 -- 205	34 -- 40	-21.0079 kcal/mol	4.70189 kcal/mol	0.976339 kcal/mol	189 206@LB@ \| \|@LB@5'-UUU...AGGAG AAAAA...CAA-3'@LB@ CGGAUC AUCUGAUGGG@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|:\|:@LB@ GCCUAG UAGACUAUCU@LB@3'-UUU...AAAAA AAC CCCCA...AUA-5'@LB@ \| \|@LB@ 53 33@LB@@LB@@LB@Energy -15.33 kcal/mol@LB@Hybridization Energy -21.0079 kcal/mol@LB@Unfolding Energy - mRNA 4.70189 kcal/mol@LB@Unfolding Energy - sRNA 0.976339 kcal/mol@LB@@LB@Position - mRNA 190 -- 205@LB@Position - sRNA 34 -- 52@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 34 -- 40@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@
187	0.01872	0.3269	bsu10530	ntdC	-12.62	0.082941	177 -- 192	32 -- 53	NTD biosynthesis operon putative oxidoreductase NtdC	_____________176____________________193\n_____________\|______________________\|\n5'-CCU...AUUAA_______A______________AAAUA...ACA-3'\n______________UUGGAUC_UGA______GGAGG\n______________\|:\|\|\|\|\|_\|\|\|______:\|\|\|\|\n______________AGCCUAG_ACU______UCUCC\n3'-UUU...AAAAA_______A___AGACUA_____CCAAC...AUA-5'\n_____________\|______________________\|\n_____________54_____________________31\n	177 -- 183	47 -- 53	-16.8717 kcal/mol	3.27102 kcal/mol	0.981755 kcal/mol	176 193@LB@ \| \|@LB@5'-CCU...AUUAA A AAAUA...ACA-3'@LB@ UUGGAUC UGA GGAGG@LB@ \|:\|\|\|\|\| \|\|\| :\|\|\|\|@LB@ AGCCUAG ACU UCUCC@LB@3'-UUU...AAAAA A AGACUA CCAAC...AUA-5'@LB@ \| \|@LB@ 54 31@LB@@LB@@LB@Energy -12.62 kcal/mol@LB@Hybridization Energy -16.8717 kcal/mol@LB@Unfolding Energy - mRNA 3.27102 kcal/mol@LB@Unfolding Energy - sRNA 0.981755 kcal/mol@LB@@LB@Position - mRNA 177 -- 192@LB@Position - sRNA 32 -- 53@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 47 -- 53@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@

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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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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