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
51	0.002362	0.1545	bsu28450	sdhC	-14.17	0.043697	178 -- 219	14 -- 47	succinate dehydrogenase cytochrome b558 subunit	_____________177_________________________________________220\n_____________\|___________________________________________\|\n5'-AAA...UCGCA_______AAAC______UAAAGUAAU__CU_____________UUUAU...AGU-3'\n______________CUU_AUC____AGGGGG_________GU__GGGAACAGAGAGU\n______________\|\|\|_\|\|\|____\|\|:\|\|\|_________\|\|__\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________GAA_UAG____UCUCCC_________CA__CCCUUGUCUCUCA\n3'-UUU...GCCUA___C___ACUA_________________AC_____________UCGAA...AUA-5'\n_____________\|___________________________________________\|\n_____________48__________________________________________13\n	213 -- 219	14 -- 20	-33.4599 kcal/mol	9.41028 kcal/mol	9.88362 kcal/mol	177 220@LB@ \| \|@LB@5'-AAA...UCGCA AAAC UAAAGUAAU CU UUUAU...AGU-3'@LB@ CUU AUC AGGGGG GU GGGAACAGAGAGU@LB@ \|\|\| \|\|\| \|\|:\|\|\| \|\| \|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ GAA UAG UCUCCC CA CCCUUGUCUCUCA@LB@3'-UUU...GCCUA C ACUA AC UCGAA...AUA-5'@LB@ \| \|@LB@ 48 13@LB@@LB@@LB@Energy -14.17 kcal/mol@LB@Hybridization Energy -33.4599 kcal/mol@LB@Unfolding Energy - mRNA 9.41028 kcal/mol@LB@Unfolding Energy - sRNA 9.88362 kcal/mol@LB@@LB@Position - mRNA 178 -- 219@LB@Position - sRNA 14 -- 47@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 14 -- 20@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@
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@
125	0.01105	0.2883	bsu27350	yrrN	-18.26	0.005831	285 -- 299	16 -- 30	protease YrrN	_____________284_____________300\n_____________\|_______________\|\n5'-GGG...UUUUA_______________U-3'\n______________GUUGGGGAACAGAGA\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________CAACCCCUUGUCUCU\n3'-UUU...CUCCC_______________CAUCG...AUA-5'\n_____________\|_______________\|\n_____________31______________15\n	293 -- 299	16 -- 22	-28.5342 kcal/mol	4.24145 kcal/mol	6.02784 kcal/mol	284 300@LB@ \| \|@LB@5'-GGG...UUUUA U-3'@LB@ GUUGGGGAACAGAGA@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ CAACCCCUUGUCUCU@LB@3'-UUU...CUCCC CAUCG...AUA-5'@LB@ \| \|@LB@ 31 15@LB@@LB@@LB@Energy -18.26 kcal/mol@LB@Hybridization Energy -28.5342 kcal/mol@LB@Unfolding Energy - mRNA 4.24145 kcal/mol@LB@Unfolding Energy - sRNA 6.02784 kcal/mol@LB@@LB@Position - mRNA 285 -- 299@LB@Position - sRNA 16 -- 30@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 16 -- 22@LB@
161	0.01452	0.3008	bsu04700	rsbU	-15.42	0.024826	142 -- 163	16 -- 38	phosphoserine phosphatase RsbU	_____________141_____________________164\n_____________\|_______________________\|\n5'-CUG...AUUCC____C____GAA___________UACAA...UCA-3'\n______________GUAG_GGGG____GGAACAGAGA\n______________:\|\|\|_\|\|\|\|____\|\|\|\|\|\|\|\|\|\|\n______________UAUC_CCCC____CCUUGUCUCU\n3'-UUU...UAGAC____U____AACC__________CAUCG...AUA-5'\n_____________\|_______________________\|\n_____________39______________________15\n	157 -- 163	16 -- 22	-28.36 kcal/mol	3.46196 kcal/mol	9.47701 kcal/mol	141 164@LB@ \| \|@LB@5'-CUG...AUUCC C GAA UACAA...UCA-3'@LB@ GUAG GGGG GGAACAGAGA@LB@ :\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ UAUC CCCC CCUUGUCUCU@LB@3'-UUU...UAGAC U AACC CAUCG...AUA-5'@LB@ \| \|@LB@ 39 15@LB@@LB@@LB@Energy -15.42 kcal/mol@LB@Hybridization Energy -28.36 kcal/mol@LB@Unfolding Energy - mRNA 3.46196 kcal/mol@LB@Unfolding Energy - sRNA 9.47701 kcal/mol@LB@@LB@Position - mRNA 142 -- 163@LB@Position - sRNA 16 -- 38@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 16 -- 22@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@
186	0.01872	0.3269	bsu09880	yhaR	-10.74	0.166509	137 -- 152	16 -- 29	enoyl-CoA hydratase/isomerase YhaR	_____________136______________153\n_____________\|________________\|\n5'-CAG...UUUAU_______UG_______AUGUA...AAU-3'\n______________UUGGGGA__GCGGGGA\n______________\|\|\|\|\|\|\|__:\|:\|:\|\|\n______________AACCCCU__UGUCUCU\n3'-UUU...UCCCC________________CAUCG...AUA-5'\n_____________\|________________\|\n_____________30_______________15\n	146 -- 152	16 -- 22	-19.1675 kcal/mol	2.41685 kcal/mol	6.01276 kcal/mol	136 153@LB@ \| \|@LB@5'-CAG...UUUAU UG AUGUA...AAU-3'@LB@ UUGGGGA GCGGGGA@LB@ \|\|\|\|\|\|\| :\|:\|:\|\|@LB@ AACCCCU UGUCUCU@LB@3'-UUU...UCCCC CAUCG...AUA-5'@LB@ \| \|@LB@ 30 15@LB@@LB@@LB@Energy -10.74 kcal/mol@LB@Hybridization Energy -19.1675 kcal/mol@LB@Unfolding Energy - mRNA 2.41685 kcal/mol@LB@Unfolding Energy - sRNA 6.01276 kcal/mol@LB@@LB@Position - mRNA 137 -- 152@LB@Position - sRNA 16 -- 29@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 16 -- 22@LB@
120	0.01063	0.2883	bsu25190	cccA	-10.44	0.184184	169 -- 199	18 -- 38	cytochrome c-550	_____________168_____________________________200\n_____________\|_______________________________\|\n5'-CCA...UUUAC________AAGGAUCAAAAAG______G___AAUGA...AGA-3'\n______________AUAGGGGG_____________GGGGAA_GGA\n______________\|\|\|\|:\|\|\|_____________\|\|\|\|\|\|_:\|\|\n______________UAUCUCCC_____________CCCCUU_UCU\n3'-UUU...UAGAC________CAA________________G___CUCAU...AUA-5'\n_____________\|_______________________________\|\n_____________39______________________________17\n	170 -- 176	31 -- 37	-23.3565 kcal/mol	5.07512 kcal/mol	7.8385 kcal/mol	168 200@LB@ \| \|@LB@5'-CCA...UUUAC AAGGAUCAAAAAG G AAUGA...AGA-3'@LB@ AUAGGGGG GGGGAA GGA@LB@ \|\|\|\|:\|\|\| \|\|\|\|\|\| :\|\|@LB@ UAUCUCCC CCCCUU UCU@LB@3'-UUU...UAGAC CAA G CUCAU...AUA-5'@LB@ \| \|@LB@ 39 17@LB@@LB@@LB@Energy -10.44 kcal/mol@LB@Hybridization Energy -23.3565 kcal/mol@LB@Unfolding Energy - mRNA 5.07512 kcal/mol@LB@Unfolding Energy - sRNA 7.8385 kcal/mol@LB@@LB@Position - mRNA 169 -- 199@LB@Position - sRNA 18 -- 38@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 31 -- 37@LB@
82	0.006245	0.254	bsu12400	yjnA	-14.90	0.031572	235 -- 273	19 -- 53	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; PubMedId: 15849754 16850406; Product type pm: membrane component'	_____________234_____________________________________274\n_____________\|_______________________________________\|\n5'-UUA...GUUUG_____GC___A___G___U__C___A__G__U_______CCUUA...UGC-3'\n______________UCGGA__CUU_GUC_GAU_GA_GGG_GU_GG_GGAGCGG\n______________\|\|\|\|\|__\|\|\|_:\|\|_\|\|\|_\|\|_\|\|\|_\|\|_\|\|_\|\|\|:\|:\|\n______________AGCCU__GAA_UAG_CUA_CU_CCC_CA_CC_CCUUGUC\n3'-UUU...AAAAA_____A____C___A___U_________A__________UCUCA...AUA-5'\n_____________\|_______________________________________\|\n_____________54______________________________________18\n	267 -- 273	19 -- 25	-33.8463 kcal/mol	12.0212 kcal/mol	6.92635 kcal/mol	234 274@LB@ \| \|@LB@5'-UUA...GUUUG GC A G U C A G U CCUUA...UGC-3'@LB@ UCGGA CUU GUC GAU GA GGG GU GG GGAGCGG@LB@ \|\|\|\|\| \|\|\| :\|\| \|\|\| \|\| \|\|\| \|\| \|\| \|\|\|:\|:\|@LB@ AGCCU GAA UAG CUA CU CCC CA CC CCUUGUC@LB@3'-UUU...AAAAA A C A U A UCUCA...AUA-5'@LB@ \| \|@LB@ 54 18@LB@@LB@@LB@Energy -14.90 kcal/mol@LB@Hybridization Energy -33.8463 kcal/mol@LB@Unfolding Energy - mRNA 12.0212 kcal/mol@LB@Unfolding Energy - sRNA 6.92635 kcal/mol@LB@@LB@Position - mRNA 235 -- 273@LB@Position - sRNA 19 -- 53@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 19 -- 25@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@

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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