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
143	0.01244	0.2883	bsu13980	pbpH	-18.09	0.006437	121 -- 135	29 -- 45	penicillin-binding enzyme for formation of rod-shaped peptidoglycan cell wall	_____________120_______________136\n_____________\|_________________\|\n5'-UUU...UUGAA_________________AACCA...ACG-3'\n______________UGAUUUGA__GAGGGGU\n______________\|\|\|\|:\|\|\|__\|\|\|\|\|\|\|\n______________ACUAGACU__CUCCCCA\n3'-UUU...CUAGA________AU_______ACCCC...AUA-5'\n_____________\|_________________\|\n_____________46________________28\n	129 -- 135	29 -- 35	-21.9726 kcal/mol	2.91712 kcal/mol	0.969832 kcal/mol	120 136@LB@ \| \|@LB@5'-UUU...UUGAA AACCA...ACG-3'@LB@ UGAUUUGA GAGGGGU@LB@ \|\|\|\|:\|\|\| \|\|\|\|\|\|\|@LB@ ACUAGACU CUCCCCA@LB@3'-UUU...CUAGA AU ACCCC...AUA-5'@LB@ \| \|@LB@ 46 28@LB@@LB@@LB@Energy -18.09 kcal/mol@LB@Hybridization Energy -21.9726 kcal/mol@LB@Unfolding Energy - mRNA 2.91712 kcal/mol@LB@Unfolding Energy - sRNA 0.969832 kcal/mol@LB@@LB@Position - mRNA 121 -- 135@LB@Position - sRNA 29 -- 45@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 29 -- 35@LB@
171	0.01646	0.3152	bsu04650	endB	-11.87	0.110785	167 -- 193	29 -- 53	antitoxin EndoAI	_____________166_________________________194\n_____________\|___________________________\|\n5'-UUC...AAGAG___U___CGUAA____________U__AUGUU...GAA-3'\n______________UCG_AUC_____GUUUGGUGGAGG_GU\n______________\|\|\|_\|\|\|_____:\|:\|\|:\|:\|\|\|\|_\|\|\n______________AGC_UAG_____UAGACUAUCUCC_CA\n3'-UUU...AAAAA___C___AAC______________C__ACCCC...AUA-5'\n_____________\|___________________________\|\n_____________54__________________________28\n	184 -- 190	32 -- 38	-19.891 kcal/mol	7.03825 kcal/mol	0.985603 kcal/mol	166 194@LB@ \| \|@LB@5'-UUC...AAGAG U CGUAA U AUGUU...GAA-3'@LB@ UCG AUC GUUUGGUGGAGG GU@LB@ \|\|\| \|\|\| :\|:\|\|:\|:\|\|\|\| \|\|@LB@ AGC UAG UAGACUAUCUCC CA@LB@3'-UUU...AAAAA C AAC C ACCCC...AUA-5'@LB@ \| \|@LB@ 54 28@LB@@LB@@LB@Energy -11.87 kcal/mol@LB@Hybridization Energy -19.891 kcal/mol@LB@Unfolding Energy - mRNA 7.03825 kcal/mol@LB@Unfolding Energy - sRNA 0.985603 kcal/mol@LB@@LB@Position - mRNA 167 -- 193@LB@Position - sRNA 29 -- 53@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 32 -- 38@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@
12	0.0001633	0.0454	bsu11410	yjbA	-19.25	0.003321	222 -- 243	30 -- 52	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type pf: factor'	_____________221_______________________244\n_____________\|_________________________\|\n5'-GAA...AUGUG______AA_________________AAGAA...UUG-3'\n______________UGGGUC__UUGGUUUGA___AGGGG\n______________:\|\|:\|\|__\|\|\|:\|:\|\|\|___\|\|\|\|\|\n______________GCCUAG__AACUAGACU___UCCCC\n3'-UUU...AAAAA_________________AUC_____AACCC...AUA-5'\n_____________\|_________________________\|\n_____________53________________________29\n	232 -- 238	38 -- 44	-23.9108 kcal/mol	3.6845 kcal/mol	0.979974 kcal/mol	221 244@LB@ \| \|@LB@5'-GAA...AUGUG AA AAGAA...UUG-3'@LB@ UGGGUC UUGGUUUGA AGGGG@LB@ :\|\|:\|\| \|\|\|:\|:\|\|\| \|\|\|\|\|@LB@ GCCUAG AACUAGACU UCCCC@LB@3'-UUU...AAAAA AUC AACCC...AUA-5'@LB@ \| \|@LB@ 53 29@LB@@LB@@LB@Energy -19.25 kcal/mol@LB@Hybridization Energy -23.9108 kcal/mol@LB@Unfolding Energy - mRNA 3.6845 kcal/mol@LB@Unfolding Energy - sRNA 0.979974 kcal/mol@LB@@LB@Position - mRNA 222 -- 243@LB@Position - sRNA 30 -- 52@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 38 -- 44@LB@
17	0.0003284	0.06216	bsu08690	ygaD	-15.59	0.022949	198 -- 218	30 -- 49	ABC transporter ATP-binding protein	_____________197___________________219\n_____________\|_____________________\|\n5'-UGA...CACAC___A____AAA__G_______GAAUC...UCG-3'\n______________AUC_UGAU___GA_AGAGGGG\n______________\|\|\|_\|\|\|\|___\|\|_\|\|\|\|\|\|\|\n______________UAG_ACUA___CU_UCUCCCC\n3'-UUU...AAGCC___A____GA___A_______AACCC...AUA-5'\n_____________\|_____________________\|\n_____________50____________________29\n	212 -- 218	30 -- 36	-19.3788 kcal/mol	2.8161 kcal/mol	0.974265 kcal/mol	197 219@LB@ \| \|@LB@5'-UGA...CACAC A AAA G GAAUC...UCG-3'@LB@ AUC UGAU GA AGAGGGG@LB@ \|\|\| \|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ UAG ACUA CU UCUCCCC@LB@3'-UUU...AAGCC A GA A AACCC...AUA-5'@LB@ \| \|@LB@ 50 29@LB@@LB@@LB@Energy -15.59 kcal/mol@LB@Hybridization Energy -19.3788 kcal/mol@LB@Unfolding Energy - mRNA 2.8161 kcal/mol@LB@Unfolding Energy - sRNA 0.974265 kcal/mol@LB@@LB@Position - mRNA 198 -- 218@LB@Position - sRNA 30 -- 49@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 30 -- 36@LB@
31	0.001131	0.119	bsu15020	coaD	-13.71	0.053189	186 -- 192	30 -- 36	phosphopantetheine adenylyltransferase	_____________185_____193\n_____________\|_______\|\n5'-UCC...UAAAA_______GUAGU...AUG-3'\n______________AGAGGGG\n______________\|\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	186 -- 192	30 -- 36	-14.3069 kcal/mol	0.46648 kcal/mol	0.133643 kcal/mol	185 193@LB@ \| \|@LB@5'-UCC...UAAAA GUAGU...AUG-3'@LB@ AGAGGGG@LB@ \|\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -13.71 kcal/mol@LB@Hybridization Energy -14.3069 kcal/mol@LB@Unfolding Energy - mRNA 0.46648 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 186 -- 192@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 30 -- 36@LB@
41	0.001775	0.1444	bsu36710	fdhD	-11.37	0.133163	186 -- 192	30 -- 36	protein FdhD	_____________185_____193\n_____________\|_______\|\n5'-UCG...AUUGC_______AAGAG...CAG-3'\n______________GGAGGGG\n______________:\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	186 -- 192	30 -- 36	-13.1021 kcal/mol	1.59974 kcal/mol	0.133643 kcal/mol	185 193@LB@ \| \|@LB@5'-UCG...AUUGC AAGAG...CAG-3'@LB@ GGAGGGG@LB@ :\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -11.37 kcal/mol@LB@Hybridization Energy -13.1021 kcal/mol@LB@Unfolding Energy - mRNA 1.59974 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 186 -- 192@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 30 -- 36@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@
81	0.005945	0.2448	bsu06390	yebD	-16.11	0.017881	267 -- 291	30 -- 53	Evidence 5: No homology to any previously reported sequences	_____________266_______________________292\n_____________\|_________________________\|\n5'-UUU...UGCUC_____A___U___AA__A_______AACAG...UUG-3'\n______________UCGGA_UUU_AUC__GG_AGAGGGG\n______________\|\|\|\|\|_:\|\|_\|\|\|__\|:_\|\|\|\|\|\|\|\n______________AGCCU_GAA_UAG__CU_UCUCCCC\n3'-UUU...AAAAA_____A___C___A___A_______AACCC...AUA-5'\n_____________\|_________________________\|\n_____________54________________________29\n	285 -- 291	30 -- 36	-22.0812 kcal/mol	4.98677 kcal/mol	0.985344 kcal/mol	266 292@LB@ \| \|@LB@5'-UUU...UGCUC A U AA A AACAG...UUG-3'@LB@ UCGGA UUU AUC GG AGAGGGG@LB@ \|\|\|\|\| :\|\| \|\|\| \|: \|\|\|\|\|\|\|@LB@ AGCCU GAA UAG CU UCUCCCC@LB@3'-UUU...AAAAA A C A A AACCC...AUA-5'@LB@ \| \|@LB@ 54 29@LB@@LB@@LB@Energy -16.11 kcal/mol@LB@Hybridization Energy -22.0812 kcal/mol@LB@Unfolding Energy - mRNA 4.98677 kcal/mol@LB@Unfolding Energy - sRNA 0.985344 kcal/mol@LB@@LB@Position - mRNA 267 -- 291@LB@Position - sRNA 30 -- 53@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 30 -- 36@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@

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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