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
35	0.001389	0.1324	bsu24570	gcvT	-12.27	0.095214	256 -- 273	25 -- 46	aminomethyltransferase	_____________255____________________274\n_____________\|______________________\|\n5'-CUC...AACGA_______C_______C______AGCUU...UAA-3'\n______________UUGAUUU___GGAGG___UGGG\n______________\|\|\|\|\|:\|___:\|\|\|\|___\|\|\|\|\n______________AACUAGA___UCUCC___ACCC\n3'-UUU...CCUAG_______CUA_____CCA____CUUGU...AUA-5'\n_____________\|______________________\|\n_____________47_____________________24\n	256 -- 262	40 -- 46	-17.62 kcal/mol	4.38211 kcal/mol	0.972727 kcal/mol	255 274@LB@ \| \|@LB@5'-CUC...AACGA C C AGCUU...UAA-3'@LB@ UUGAUUU GGAGG UGGG@LB@ \|\|\|\|\|:\| :\|\|\|\| \|\|\|\|@LB@ AACUAGA UCUCC ACCC@LB@3'-UUU...CCUAG CUA CCA CUUGU...AUA-5'@LB@ \| \|@LB@ 47 24@LB@@LB@@LB@Energy -12.27 kcal/mol@LB@Hybridization Energy -17.62 kcal/mol@LB@Unfolding Energy - mRNA 4.38211 kcal/mol@LB@Unfolding Energy - sRNA 0.972727 kcal/mol@LB@@LB@Position - mRNA 256 -- 273@LB@Position - sRNA 25 -- 46@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 40 -- 46@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@
200	0.01989	0.3269	bsu30150	ytdP	-13.03	0.070310	188 -- 210	28 -- 52	AraC family transcriptional regulator	_____________187________________________211\n_____________\|__________________________\|\n5'-UUU...UGAAG_____G_UA______AAU________UUAUG...UAU-3'\n______________UGGAU_U_____UGA___GGGGGGUU\n______________:\|\|\|\|_\|_____\|\|\|___\|:\|\|\|\|\|\|\n______________GCCUA_A_____ACU___CUCCCCAA\n3'-UUU...AAAAA_____G_ACUAG___AU_________CCCCU...AUA-5'\n_____________\|__________________________\|\n_____________53_________________________27\n	204 -- 210	28 -- 34	-18.7355 kcal/mol	4.72292 kcal/mol	0.980555 kcal/mol	187 211@LB@ \| \|@LB@5'-UUU...UGAAG G UA AAU UUAUG...UAU-3'@LB@ UGGAU U UGA GGGGGGUU@LB@ :\|\|\|\| \| \|\|\| \|:\|\|\|\|\|\|@LB@ GCCUA A ACU CUCCCCAA@LB@3'-UUU...AAAAA G ACUAG AU CCCCU...AUA-5'@LB@ \| \|@LB@ 53 27@LB@@LB@@LB@Energy -13.03 kcal/mol@LB@Hybridization Energy -18.7355 kcal/mol@LB@Unfolding Energy - mRNA 4.72292 kcal/mol@LB@Unfolding Energy - sRNA 0.980555 kcal/mol@LB@@LB@Position - mRNA 188 -- 210@LB@Position - sRNA 28 -- 52@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 28 -- 34@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@
38	0.001645	0.1432	bsu19540	yodB	-7.66	0.420262	259 -- 271	37 -- 51	ArsR family transcriptional regulator	_____________258_____________272\n_____________\|_______________\|\n5'-GAG...ACGAU___AC__________CAUCC...AAC-3'\n______________GGA____GGUCUGAU\n______________\|\|\|____\|:\|\|\|\|\|\|\n______________CCU____CUAGACUA\n3'-UUU...AAAAG___AGAA________UCUCC...AUA-5'\n_____________\|_______________\|\n_____________52______________36\n	265 -- 271	37 -- 43	-11.6813 kcal/mol	3.05786 kcal/mol	0.959935 kcal/mol	258 272@LB@ \| \|@LB@5'-GAG...ACGAU AC CAUCC...AAC-3'@LB@ GGA GGUCUGAU@LB@ \|\|\| \|:\|\|\|\|\|\|@LB@ CCU CUAGACUA@LB@3'-UUU...AAAAG AGAA UCUCC...AUA-5'@LB@ \| \|@LB@ 52 36@LB@@LB@@LB@Energy -7.66 kcal/mol@LB@Hybridization Energy -11.6813 kcal/mol@LB@Unfolding Energy - mRNA 3.05786 kcal/mol@LB@Unfolding Energy - sRNA 0.959935 kcal/mol@LB@@LB@Position - mRNA 259 -- 271@LB@Position - sRNA 37 -- 51@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 37 -- 43@LB@
92	0.007313	0.2652	bsu34470	yveA	-16.72	0.013215	240 -- 265	25 -- 47	aspartate-proton symporter	_____________239________________________266\n_____________\|__________________________\|\n5'-CCU...CGCUG___________UUU__UU___A____AGCCA...UCA-3'\n______________UUUGAUCUGAU___GA__GGG_UGGG\n______________:\|\|\|\|\|\|\|\|\|\|___\|\|__\|\|\|_\|\|\|\|\n______________GAACUAGACUA___CU__CCC_ACCC\n3'-UUU...GCCUA___________U____C____A____CUUGU...AUA-5'\n_____________\|__________________________\|\n_____________48_________________________24\n	244 -- 250	37 -- 43	-24.6158 kcal/mol	6.92071 kcal/mol	0.975871 kcal/mol	239 266@LB@ \| \|@LB@5'-CCU...CGCUG UUU UU A AGCCA...UCA-3'@LB@ UUUGAUCUGAU GA GGG UGGG@LB@ :\|\|\|\|\|\|\|\|\|\| \|\| \|\|\| \|\|\|\|@LB@ GAACUAGACUA CU CCC ACCC@LB@3'-UUU...GCCUA U C A CUUGU...AUA-5'@LB@ \| \|@LB@ 48 24@LB@@LB@@LB@Energy -16.72 kcal/mol@LB@Hybridization Energy -24.6158 kcal/mol@LB@Unfolding Energy - mRNA 6.92071 kcal/mol@LB@Unfolding Energy - sRNA 0.975871 kcal/mol@LB@@LB@Position - mRNA 240 -- 265@LB@Position - sRNA 25 -- 47@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 37 -- 43@LB@
52	0.002415	0.1549	bsu03320	nasB	-8.41	0.344801	188 -- 199	36 -- 51	assimilatory nitrate reductase electron transfer subunit	_____________187______________200\n_____________\|________________\|\n5'-UUU...CCAAA________________CAUGA...UCA-3'\n______________GGA____GGUCUGAUA\n______________\|\|\|____\|:\|\|\|\|\|\|\|\n______________CCU____CUAGACUAU\n3'-UUU...AAAAG___AGAA_________CUCCC...AUA-5'\n_____________\|________________\|\n_____________52_______________35\n	193 -- 199	36 -- 42	-13.3061 kcal/mol	3.93547 kcal/mol	0.960469 kcal/mol	187 200@LB@ \| \|@LB@5'-UUU...CCAAA CAUGA...UCA-3'@LB@ GGA GGUCUGAUA@LB@ \|\|\| \|:\|\|\|\|\|\|\|@LB@ CCU CUAGACUAU@LB@3'-UUU...AAAAG AGAA CUCCC...AUA-5'@LB@ \| \|@LB@ 52 35@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -13.3061 kcal/mol@LB@Unfolding Energy - mRNA 3.93547 kcal/mol@LB@Unfolding Energy - sRNA 0.960469 kcal/mol@LB@@LB@Position - mRNA 188 -- 199@LB@Position - sRNA 36 -- 51@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 36 -- 42@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@
13	0.0002088	0.05257	bsu22150	ypvA	-19.04	0.003759	161 -- 194	26 -- 53	ATP-dependent helicase YpvA	_____________160____________________________________195\n_____________\|______________________________________\|\n5'-GUG...UAUUA________________AUGUCGAA___UU_________AACUA...CCG-3'\n______________UUGG____UGGUCUGA________UAG__GGGGGUUGG\n______________\|:\|\|____\|\|:\|\|\|\|\|________\|\|\|__:\|\|\|\|\|\|\|\|\n______________AGCC____ACUAGACU________AUC__UCCCCAACC\n3'-UUU...AAAAA____UAGA______________________________CCUUG...AUA-5'\n_____________\|______________________________________\|\n_____________54_____________________________________25\n	188 -- 194	26 -- 32	-27.605 kcal/mol	7.58324 kcal/mol	0.986187 kcal/mol	160 195@LB@ \| \|@LB@5'-GUG...UAUUA AUGUCGAA UU AACUA...CCG-3'@LB@ UUGG UGGUCUGA UAG GGGGGUUGG@LB@ \|:\|\| \|\|:\|\|\|\|\| \|\|\| :\|\|\|\|\|\|\|\|@LB@ AGCC ACUAGACU AUC UCCCCAACC@LB@3'-UUU...AAAAA UAGA CCUUG...AUA-5'@LB@ \| \|@LB@ 54 25@LB@@LB@@LB@Energy -19.04 kcal/mol@LB@Hybridization Energy -27.605 kcal/mol@LB@Unfolding Energy - mRNA 7.58324 kcal/mol@LB@Unfolding Energy - sRNA 0.986187 kcal/mol@LB@@LB@Position - mRNA 161 -- 194@LB@Position - sRNA 26 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 26 -- 32@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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