Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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_000913 Escherichia coli str. K-12 substr. MG1655

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	Additional homologs
176	0.01279	0.2504	b3980	tufB	-13.59	0.058494	200 -- 216	7 -- 22	translation elongation factor EF-Tu 2	b3339	_____________199_______________217\n_____________\|_________________\|\n5'-UCC...CAAUC______U__________UUGAA...CUA-3'\n______________GAUGUC_AAAGAAAAGU\n______________\|\|::\|\|_\|\|\|\|\|\|\|\|\|:\n______________CUGUAG_UUUCUUUUCG\n3'-UUU...UACCC_________________UCACCG-5'\n_____________\|_________________\|\n_____________23________________6\n	210 -- 216	7 -- 13	-16.0105 kcal/mol	1.82662 kcal/mol	0.590875 kcal/mol	199 217@LB@ \| \|@LB@5'-UCC...CAAUC U UUGAA...CUA-3'@LB@ GAUGUC AAAGAAAAGU@LB@ \|\|::\|\| \|\|\|\|\|\|\|\|\|:@LB@ CUGUAG UUUCUUUUCG@LB@3'-UUU...UACCC UCACCG-5'@LB@ \| \|@LB@ 23 6@LB@@LB@@LB@Energy -13.59 kcal/mol@LB@Hybridization Energy -16.0105 kcal/mol@LB@Unfolding Energy - mRNA 1.82662 kcal/mol@LB@Unfolding Energy - sRNA 0.590875 kcal/mol@LB@@LB@Position - mRNA 200 -- 216@LB@Position - sRNA 7 -- 22@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 7 -- 13@LB@
43	0.00215	0.1648	b4268	idnK	-13.73	0.054596	180 -- 268	1 -- 79	D-gluconate kinase thermosensitive	b3437	_____________179______________________________________________________________________________________________269\n_____________\|________________________________________________________________________________________________\|\n5'-AGG...AGGUA___U______GGA______________________U_AAAGCUUUAUU_________GU____G_______UAAA_______UUGGU____A____UGCCG...AUG-3'\n______________AGA_GAUUCA___GAUUUU______AAAUGGCGGG_G___________UUGAUGGGC__UUCA_GGAGUGG____ACAUUAA_____AGCA__GGU\n______________\|:\|_:\|::\|\|___:\|::\|\|______\|\|\|\|\|\|\|\|\|\|_\|___________\|\|\|\|\|\|\|\|\|__\|:\|\|_::\|:\|\|\|____\|\|\|\|:\|\|_____\|\|\|\|__\|\|:\n______________UUU_UUGGGU___UUGGAA______UUUACCGCCC_C___________AACUACCCG__AGGU_UUUUACC____UGUAGUU_____UCGU__CCG\n___________3'-___U______AG_______CUUGGC______________________________________G_______CC_________UCUUU____CA___-5'\n______________\|______________________________________________________________________________________________\|\n______________79_____________________________________________________________________________________________1\n	249 -- 255	15 -- 21	-57.0668 kcal/mol	16.9855 kcal/mol	26.3515 kcal/mol	179 269@LB@ \| \|@LB@5'-AGG...AGGUA U GGA U AAAGCUUUAUU GU G UAAA UUGGU A UGCCG...AUG-3'@LB@ AGA GAUUCA GAUUUU AAAUGGCGGG G UUGAUGGGC UUCA GGAGUGG ACAUUAA AGCA GGU@LB@ \|:\| :\|::\|\| :\|::\|\| \|\|\|\|\|\|\|\|\|\| \| \|\|\|\|\|\|\|\|\| \|:\|\| ::\|:\|\|\| \|\|\|\|:\|\| \|\|\|\| \|\|:@LB@ UUU UUGGGU UUGGAA UUUACCGCCC C AACUACCCG AGGU UUUUACC UGUAGUU UCGU CCG@LB@ 3'- U AG CUUGGC G CC UCUUU CA -5'@LB@ \| \|@LB@ 79 1@LB@@LB@@LB@Energy -13.73 kcal/mol@LB@Hybridization Energy -57.0668 kcal/mol@LB@Unfolding Energy - mRNA 16.9855 kcal/mol@LB@Unfolding Energy - sRNA 26.3515 kcal/mol@LB@@LB@Position - mRNA 180 -- 268@LB@Position - sRNA 1 -- 79@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 15 -- 21@LB@
104	0.006761	0.2281	b1671	ydhX	-13.25	0.069212	145 -- 167	2 -- 25	putative 4Fe-4S ferridoxin-type protein; FNR Nar NarP-regulated protein; putative subunit of YdhYVWXUT oxidoreductase complex	b4072	_____________144_______________________168\n_____________\|_________________________\|\n5'-CAC...UUUCA___A_______U___U_________ACAGU...AGG-3'\n______________GGG_GAUGUCA_GGA__AG_GGUGG\n______________\|\|\|_\|\|::\|\|\|_:\|\|__\|\|_:\|\|\|\|\n______________CCC_CUGUAGU_UCU__UC_UCACC\n3'-UUU...UUUUA___________U___UU__G_____G-5'\n_____________\|_________________________\|\n_____________26________________________1\n	149 -- 155	16 -- 22	-23.0825 kcal/mol	7.31216 kcal/mol	2.51746 kcal/mol	144 168@LB@ \| \|@LB@5'-CAC...UUUCA A U U ACAGU...AGG-3'@LB@ GGG GAUGUCA GGA AG GGUGG@LB@ \|\|\| \|\|::\|\|\| :\|\| \|\| :\|\|\|\|@LB@ CCC CUGUAGU UCU UC UCACC@LB@3'-UUU...UUUUA U UU G G-5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -13.25 kcal/mol@LB@Hybridization Energy -23.0825 kcal/mol@LB@Unfolding Energy - mRNA 7.31216 kcal/mol@LB@Unfolding Energy - sRNA 2.51746 kcal/mol@LB@@LB@Position - mRNA 145 -- 167@LB@Position - sRNA 2 -- 25@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 16 -- 22@LB@
115	0.007886	0.2401	b2890	lysS	-11.64	0.144658	161 -- 186	1 -- 20	lysine tRNA synthetase constitutive	b4129	_____________160_________________________187\n_____________\|___________________________\|\n5'-AAA...CAAUU________CAAGUUU____________UAUGA...GGA-3'\n______________UAUCGAAG_______GAAAGCAG_GGU\n______________:\|\|\|:\|\|\|_______:\|\|\|\|\|\|\|_\|\|:\n______________GUAGUUUC_______UUUUCGUC_CCG\n3'-UUU...CCCCU_______________________A___-5'\n_____________\|__________________________\|\n_____________21_________________________1\n	177 -- 183	5 -- 11	-18.6981 kcal/mol	5.60124 kcal/mol	1.45855 kcal/mol	160 187@LB@ \| \|@LB@5'-AAA...CAAUU CAAGUUU UAUGA...GGA-3'@LB@ UAUCGAAG GAAAGCAG GGU@LB@ :\|\|\|:\|\|\| :\|\|\|\|\|\|\| \|\|:@LB@ GUAGUUUC UUUUCGUC CCG@LB@3'-UUU...CCCCU A -5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -11.64 kcal/mol@LB@Hybridization Energy -18.6981 kcal/mol@LB@Unfolding Energy - mRNA 5.60124 kcal/mol@LB@Unfolding Energy - sRNA 1.45855 kcal/mol@LB@@LB@Position - mRNA 161 -- 186@LB@Position - sRNA 1 -- 20@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 5 -- 11@LB@
106	0.007048	0.2333	b4512	ybdD	-9.12	0.369799	33 -- 54	1 -- 25	DUF466 family protein	b4353	_____________32________________________55\n_____________\|_________________________\|\n5'-GCA...GAGGG___________C___U_________UUAGU...GGG-3'\n______________GGGGAUGUUGG_GAA__GU__UGGC\n______________\|\|\|\|\|::\|:::_\|\|\|__\|:__\|\|\|\|\n______________CCCCUGUAGUU_CUU__CG__ACCG\n3'-UUU...UUUUA___________U___UU__UC____-5'\n_____________\|________________________\|\n_____________26_______________________1\n	36 -- 42	16 -- 22	-21.5624 kcal/mol	9.92515 kcal/mol	2.51748 kcal/mol	32 55@LB@ \| \|@LB@5'-GCA...GAGGG C U UUAGU...GGG-3'@LB@ GGGGAUGUUGG GAA GU UGGC@LB@ \|\|\|\|\|::\|::: \|\|\| \|: \|\|\|\|@LB@ CCCCUGUAGUU CUU CG ACCG@LB@3'-UUU...UUUUA U UU UC -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -9.12 kcal/mol@LB@Hybridization Energy -21.5624 kcal/mol@LB@Unfolding Energy - mRNA 9.92515 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 33 -- 54@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 16 -- 22@LB@
1	0	0	b3752	rbsK	-20.54	0.000534	137 -- 155	1 -- 21	ribokinase		_____________136___________________156\n_____________\|_____________________\|\n5'-GCA...GUGUA_____________________ACGCG...GUA-3'\n______________AUA_UAAAGAAAAGCAG_GGC\n______________\|:\|_:\|\|\|\|\|\|\|\|\|\|\|\|_\|\|\|\n______________UGU_GUUUCUUUUCGUC_CCG\n3'-UUU...ACCCC___A_____________A___-5'\n_____________\|____________________\|\n_____________22___________________1\n	146 -- 152	5 -- 11	-23.5677 kcal/mol	1.51892 kcal/mol	1.51103 kcal/mol	136 156@LB@ \| \|@LB@5'-GCA...GUGUA ACGCG...GUA-3'@LB@ AUA UAAAGAAAAGCAG GGC@LB@ \|:\| :\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|@LB@ UGU GUUUCUUUUCGUC CCG@LB@3'-UUU...ACCCC A A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -20.54 kcal/mol@LB@Hybridization Energy -23.5677 kcal/mol@LB@Unfolding Energy - mRNA 1.51892 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 137 -- 155@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 5 -- 11@LB@
2	5.107e-11	8.961e-08	b2314	dedD	-25.37	0.000001	176 -- 205	1 -- 30	membrane-anchored periplasmic protein involved in septation		_____________175_____________________________206\n_____________\|_______________________________\|\n5'-UUG...UCAUG______AUU______________________AAGUA...AUU-3'\n______________GAAGUG___GACG_CGAGGAGAAGCGGUGGC\n______________:\|\|:\|\|___\|\|\|:_\|:\|:\|\|:\|\|\|\|:\|\|\|\|\|\n______________UUUUAC___CUGU_GUUUCUUUUCGUCACCG\n3'-UUU...AGGUG______CC_____A_________________-5'\n_____________\|______________________________\|\n_____________31_____________________________1\n	199 -- 205	1 -- 7	-36.5756 kcal/mol	8.68219 kcal/mol	2.51911 kcal/mol	175 206@LB@ \| \|@LB@5'-UUG...UCAUG AUU AAGUA...AUU-3'@LB@ GAAGUG GACG CGAGGAGAAGCGGUGGC@LB@ :\|\|:\|\| \|\|\|: \|:\|:\|\|:\|\|\|\|:\|\|\|\|\|@LB@ UUUUAC CUGU GUUUCUUUUCGUCACCG@LB@3'-UUU...AGGUG CC A -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -25.37 kcal/mol@LB@Hybridization Energy -36.5756 kcal/mol@LB@Unfolding Energy - mRNA 8.68219 kcal/mol@LB@Unfolding Energy - sRNA 2.51911 kcal/mol@LB@@LB@Position - mRNA 176 -- 205@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 1 -- 7@LB@
3	3.973e-07	0.0004647	b0081	mraZ	-16.47	0.011640	172 -- 200	1 -- 32	RsmH methytransferase inhibitor		_____________171______________________________201\n_____________\|________________________________\|\n5'-GAU...GUGGG__________A___A_____U___________AUGUU...AAA-3'\n______________GCAAAGUGGG_AUA__GGGG_GAGGC__UGGC\n______________:\|\|\|\|:\|\|\|\|_\|:\|__:::\|_:\|:\|\|__\|\|\|\|\n______________UGUUUUACCC_UGU__UUUC_UUUCG__ACCG\n3'-UUU...CGAGG__________C___AG____U_____UC____-5'\n_____________\|_______________________________\|\n_____________33______________________________1\n	175 -- 181	23 -- 29	-28.2943 kcal/mol	9.28897 kcal/mol	2.53929 kcal/mol	171 201@LB@ \| \|@LB@5'-GAU...GUGGG A A U AUGUU...AAA-3'@LB@ GCAAAGUGGG AUA GGGG GAGGC UGGC@LB@ :\|\|\|\|:\|\|\|\| \|:\| :::\| :\|:\|\| \|\|\|\|@LB@ UGUUUUACCC UGU UUUC UUUCG ACCG@LB@3'-UUU...CGAGG C AG U UC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -16.47 kcal/mol@LB@Hybridization Energy -28.2943 kcal/mol@LB@Unfolding Energy - mRNA 9.28897 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 172 -- 200@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 23 -- 29@LB@
4	1.99e-05	0.01653	b4255	rraB	-17.36	0.006479	180 -- 205	1 -- 23	protein inhibitor of RNase E		_____________179________________________206\n_____________\|__________________________\|\n5'-GAG...CGGCA_________GA____U____CA____AAACC...CCA-3'\n______________GGACAUUAA__GGAA_GAGC__UGGC\n______________\|\|\|\|\|\|:\|\|__:\|\|\|_:\|\|\|__\|\|\|\|\n______________CCUGUAGUU__UCUU_UUCG__ACCG\n3'-UUU...UUACC____________________UC____-5'\n_____________\|_________________________\|\n_____________24________________________1\n	182 -- 188	15 -- 21	-24.3176 kcal/mol	5.37332 kcal/mol	1.57928 kcal/mol	179 206@LB@ \| \|@LB@5'-GAG...CGGCA GA U CA AAACC...CCA-3'@LB@ GGACAUUAA GGAA GAGC UGGC@LB@ \|\|\|\|\|\|:\|\| :\|\|\| :\|\|\| \|\|\|\|@LB@ CCUGUAGUU UCUU UUCG ACCG@LB@3'-UUU...UUACC UC -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -17.36 kcal/mol@LB@Hybridization Energy -24.3176 kcal/mol@LB@Unfolding Energy - mRNA 5.37332 kcal/mol@LB@Unfolding Energy - sRNA 1.57928 kcal/mol@LB@@LB@Position - mRNA 180 -- 205@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 15 -- 21@LB@
5	2.356e-05	0.01653	b1123	potD	-19.53	0.001282	190 -- 207	9 -- 25	spermidine/putrescine ABC transporter periplasmic binding protein		_____________189________________208\n_____________\|__________________\|\n5'-GAC...ACACA____________U_____AAUGG...ACU-3'\n______________GGGGACGUUAAA_GAAAA\n______________\|\|\|\|\|\|:\|:\|\|\|_\|\|\|\|\|\n______________CCCCUGUAGUUU_CUUUU\n3'-UUU...UUUUA__________________CGUCACCG-5'\n_____________\|__________________\|\n_____________26_________________8\n	195 -- 201	14 -- 20	-22.5319 kcal/mol	2.32696 kcal/mol	0.671024 kcal/mol	189 208@LB@ \| \|@LB@5'-GAC...ACACA U AAUGG...ACU-3'@LB@ GGGGACGUUAAA GAAAA@LB@ \|\|\|\|\|\|:\|:\|\|\| \|\|\|\|\|@LB@ CCCCUGUAGUUU CUUUU@LB@3'-UUU...UUUUA CGUCACCG-5'@LB@ \| \|@LB@ 26 8@LB@@LB@@LB@Energy -19.53 kcal/mol@LB@Hybridization Energy -22.5319 kcal/mol@LB@Unfolding Energy - mRNA 2.32696 kcal/mol@LB@Unfolding Energy - sRNA 0.671024 kcal/mol@LB@@LB@Position - mRNA 190 -- 207@LB@Position - sRNA 9 -- 25@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 14 -- 20@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)

Job resubmission

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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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