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
195	0.01942	0.3269	bsu00690	ftsH	-11.53	0.125763	258 -- 269	21 -- 33	ATP-dependent zinc metalloprotease FtsH	_____________257___________270\n_____________\|_____________\|\n5'-AGU...UAAUC_______U_____UACUU...AAA-3'\n______________GGGGUUG__GAGC\n______________\|\|\|\|\|\|\|__\|\|:\|\n______________CCCCAAC__CUUG\n3'-UUU...UAUCU_______CC____UCUCU...AUA-5'\n_____________\|_____________\|\n_____________34____________20\n	258 -- 264	27 -- 33	-15.4755 kcal/mol	2.12746 kcal/mol	1.8225 kcal/mol	257 270@LB@ \| \|@LB@5'-AGU...UAAUC U UACUU...AAA-3'@LB@ GGGGUUG GAGC@LB@ \|\|\|\|\|\|\| \|\|:\|@LB@ CCCCAAC CUUG@LB@3'-UUU...UAUCU CC UCUCU...AUA-5'@LB@ \| \|@LB@ 34 20@LB@@LB@@LB@Energy -11.53 kcal/mol@LB@Hybridization Energy -15.4755 kcal/mol@LB@Unfolding Energy - mRNA 2.12746 kcal/mol@LB@Unfolding Energy - sRNA 1.8225 kcal/mol@LB@@LB@Position - mRNA 258 -- 269@LB@Position - sRNA 21 -- 33@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 27 -- 33@LB@
129	0.01144	0.2883	bsu36230	ywqF	-11.45	0.129133	185 -- 195	31 -- 41	UDP-glucose 6-dehydrogenase YwqF	_____________184_________196\n_____________\|___________\|\n5'-UUU...UUUAA___U_______AAACA...CUC-3'\n______________CUG_UGGAGGG\n______________\|\|\|_\|:\|\|\|\|\|\n______________GAC_AUCUCCC\n3'-UUU...AACUA___U_______CAACC...AUA-5'\n_____________\|___________\|\n_____________42__________30\n	189 -- 195	31 -- 37	-16.042 kcal/mol	3.66073 kcal/mol	0.928126 kcal/mol	184 196@LB@ \| \|@LB@5'-UUU...UUUAA U AAACA...CUC-3'@LB@ CUG UGGAGGG@LB@ \|\|\| \|:\|\|\|\|\|@LB@ GAC AUCUCCC@LB@3'-UUU...AACUA U CAACC...AUA-5'@LB@ \| \|@LB@ 42 30@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -16.042 kcal/mol@LB@Unfolding Energy - mRNA 3.66073 kcal/mol@LB@Unfolding Energy - sRNA 0.928126 kcal/mol@LB@@LB@Position - mRNA 185 -- 195@LB@Position - sRNA 31 -- 41@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 31 -- 37@LB@
141	0.01225	0.2883	bsu32310	yutD	-11.41	0.131333	145 -- 158	24 -- 40	Evidence 4: Homologs of previously reported genes of unknown function; PubMedId: 12770717	_____________144_______________159\n_____________\|_________________\|\n5'-ACA...GCAAU________AC_______CAAUG...AUA-3'\n______________UGAUGGGG_____GGGG\n______________\|\|\|\|:\|:\|_____\|\|\|\|\n______________ACUAUCUC_____CCCC\n3'-UUU...ACUAG________CCCAA____UUGUC...AUA-5'\n_____________\|_________________\|\n_____________41________________23\n	146 -- 152	33 -- 39	-14.827 kcal/mol	2.62921 kcal/mol	0.790979 kcal/mol	144 159@LB@ \| \|@LB@5'-ACA...GCAAU AC CAAUG...AUA-3'@LB@ UGAUGGGG GGGG@LB@ \|\|\|\|:\|:\| \|\|\|\|@LB@ ACUAUCUC CCCC@LB@3'-UUU...ACUAG CCCAA UUGUC...AUA-5'@LB@ \| \|@LB@ 41 23@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -14.827 kcal/mol@LB@Unfolding Energy - mRNA 2.62921 kcal/mol@LB@Unfolding Energy - sRNA 0.790979 kcal/mol@LB@@LB@Position - mRNA 145 -- 158@LB@Position - sRNA 24 -- 40@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 33 -- 39@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@
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@
169	0.01639	0.3152	bsu07850	yfkM	-11.33	0.135062	186 -- 208	22 -- 34	general stress protein 18	_____________185_____________________209\n_____________\|_______________________\|\n5'-UGU...AAAGC___A___UAUGAAUCA_______AAAAA...CUG-3'\n______________GGG_GGU_________UGGGGAA\n______________:\|\|_\|\|\|_________\|\|\|\|\|\|\|\n______________UCC_CCA_________ACCCCUU\n3'-UUU...CUAUC_______________________GUCUC...AUA-5'\n_____________\|_______________________\|\n_____________35______________________21\n	202 -- 208	22 -- 28	-15.0114 kcal/mol	2.66027 kcal/mol	1.02154 kcal/mol	185 209@LB@ \| \|@LB@5'-UGU...AAAGC A UAUGAAUCA AAAAA...CUG-3'@LB@ GGG GGU UGGGGAA@LB@ :\|\| \|\|\| \|\|\|\|\|\|\|@LB@ UCC CCA ACCCCUU@LB@3'-UUU...CUAUC GUCUC...AUA-5'@LB@ \| \|@LB@ 35 21@LB@@LB@@LB@Energy -11.33 kcal/mol@LB@Hybridization Energy -15.0114 kcal/mol@LB@Unfolding Energy - mRNA 2.66027 kcal/mol@LB@Unfolding Energy - sRNA 1.02154 kcal/mol@LB@@LB@Position - mRNA 186 -- 208@LB@Position - sRNA 22 -- 34@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 22 -- 28@LB@
98	0.008247	0.2778	bsu19360	odhB	-11.30	0.136272	146 -- 191	23 -- 51	dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex	_____________145____________________________________________192\n_____________\|______________________________________________\|\n5'-AAG...GAACA___ACGUA___U_________CUU_ACUCGCAAAAACUAAG_____AAUGA...AAU-3'\n______________GGA_____UUG_AUCUGAUAG___G________________GGGGA\n______________\|\|\|_____\|\|\|_\|\|\|\|\|\|\|\|\|___\|________________\|\|\|\|\|\n______________CCU_____AAC_UAGACUAUC___C________________CCCCU\n3'-UUU...AAAAG___AG________________UCC_CAA__________________UGUCU...AUA-5'\n_____________\|______________________________________________\|\n_____________52_____________________________________________22\n	160 -- 166	35 -- 41	-19.511 kcal/mol	7.22607 kcal/mol	0.980049 kcal/mol	145 192@LB@ \| \|@LB@5'-AAG...GAACA ACGUA U CUU ACUCGCAAAAACUAAG AAUGA...AAU-3'@LB@ GGA UUG AUCUGAUAG G GGGGA@LB@ \|\|\| \|\|\| \|\|\|\|\|\|\|\|\| \| \|\|\|\|\|@LB@ CCU AAC UAGACUAUC C CCCCU@LB@3'-UUU...AAAAG AG UCC CAA UGUCU...AUA-5'@LB@ \| \|@LB@ 52 22@LB@@LB@@LB@Energy -11.30 kcal/mol@LB@Hybridization Energy -19.511 kcal/mol@LB@Unfolding Energy - mRNA 7.22607 kcal/mol@LB@Unfolding Energy - sRNA 0.980049 kcal/mol@LB@@LB@Position - mRNA 146 -- 191@LB@Position - sRNA 23 -- 51@LB@Position Seed - mRNA 160 -- 166@LB@Position Seed - sRNA 35 -- 41@LB@
139	0.01217	0.2883	bsu30960	glgD	-11.28	0.137516	171 -- 191	30 -- 50	glycogen biosynthesis protein GlgD	_____________170____________________192\n_____________\|______________________\|\n5'-ACU...GAAUU_____AAUUA____________GCAGA...UUG-3'\n______________GAUUU_____CUGA_AGAGGGG\n______________\|\|\|:\|_____\|\|\|\|_\|\|\|\|\|\|\|\n______________CUAGA_____GACU_UCUCCCC\n3'-UUU...AAAGC_____ACUA_____A_______AACCC...AUA-5'\n_____________\|______________________\|\n_____________51_____________________29\n	185 -- 191	30 -- 36	-19.1028 kcal/mol	6.84884 kcal/mol	0.974272 kcal/mol	170 192@LB@ \| \|@LB@5'-ACU...GAAUU AAUUA GCAGA...UUG-3'@LB@ GAUUU CUGA AGAGGGG@LB@ \|\|\|:\| \|\|\|\| \|\|\|\|\|\|\|@LB@ CUAGA GACU UCUCCCC@LB@3'-UUU...AAAGC ACUA A AACCC...AUA-5'@LB@ \| \|@LB@ 51 29@LB@@LB@@LB@Energy -11.28 kcal/mol@LB@Hybridization Energy -19.1028 kcal/mol@LB@Unfolding Energy - mRNA 6.84884 kcal/mol@LB@Unfolding Energy - sRNA 0.974272 kcal/mol@LB@@LB@Position - mRNA 171 -- 191@LB@Position - sRNA 30 -- 50@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 30 -- 36@LB@
179	0.01703	0.3152	bsu08425	mprF	-11.09	0.146985	133 -- 167	22 -- 52	phosphatidylglycerol lysyltransferase	_____________132__________________________________168\n_____________\|____________________________________\|\n5'-ACU...AAUAA___UAG___UAUAA___GU_____AUUA________GAGGA...AUC-3'\n______________CGG____UG_____UGA__UGGAG____UUGGGGGA\n______________\|\|\|____\|\|_____\|\|\|__\|:\|\|\|____\|\|\|\|\|\|:\|\n______________GCC____AC_____ACU__AUCUC____AACCCCUU\n3'-UUU...AAAAA___UAGA__UAG____________CCC_________GUCUC...AUA-5'\n_____________\|____________________________________\|\n_____________53___________________________________21\n	161 -- 167	22 -- 28	-20.3953 kcal/mol	7.42087 kcal/mol	1.8808 kcal/mol	132 168@LB@ \| \|@LB@5'-ACU...AAUAA UAG UAUAA GU AUUA GAGGA...AUC-3'@LB@ CGG UG UGA UGGAG UUGGGGGA@LB@ \|\|\| \|\| \|\|\| \|:\|\|\| \|\|\|\|\|\|:\|@LB@ GCC AC ACU AUCUC AACCCCUU@LB@3'-UUU...AAAAA UAGA UAG CCC GUCUC...AUA-5'@LB@ \| \|@LB@ 53 21@LB@@LB@@LB@Energy -11.09 kcal/mol@LB@Hybridization Energy -20.3953 kcal/mol@LB@Unfolding Energy - mRNA 7.42087 kcal/mol@LB@Unfolding Energy - sRNA 1.8808 kcal/mol@LB@@LB@Position - mRNA 133 -- 167@LB@Position - sRNA 22 -- 52@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 22 -- 28@LB@
101	0.008451	0.2778	bsu32150	paiA	-11.07	0.148459	77 -- 92	23 -- 39	protease synthase and sporulation negative regulatory protein PAI 1	_____________76________________93\n_____________\|_________________\|\n5'-AUU...AUCAC_______A______U__UGAAG...CAC-3'\n______________GAUAGGG__GUUGG_GA\n______________\|\|\|\|\|:\|__\|\|\|\|\|_\|\|\n______________CUAUCUC__CAACC_CU\n3'-UUU...CUAGA_______CC_____C__UGUCU...AUA-5'\n_____________\|_________________\|\n_____________40________________22\n	77 -- 83	33 -- 39	-14.8457 kcal/mol	2.98855 kcal/mol	0.791731 kcal/mol	76 93@LB@ \| \|@LB@5'-AUU...AUCAC A U UGAAG...CAC-3'@LB@ GAUAGGG GUUGG GA@LB@ \|\|\|\|\|:\| \|\|\|\|\| \|\|@LB@ CUAUCUC CAACC CU@LB@3'-UUU...CUAGA CC C UGUCU...AUA-5'@LB@ \| \|@LB@ 40 22@LB@@LB@@LB@Energy -11.07 kcal/mol@LB@Hybridization Energy -14.8457 kcal/mol@LB@Unfolding Energy - mRNA 2.98855 kcal/mol@LB@Unfolding Energy - sRNA 0.791731 kcal/mol@LB@@LB@Position - mRNA 77 -- 92@LB@Position - sRNA 23 -- 39@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 33 -- 39@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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