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
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@
129	0.009293	0.2491	b0428	cyoE	-12.51	0.098557	18 -- 26	1 -- 9	protoheme IX farnesyltransferase		_____________17________27\n_____________\|_________\|\n5'-GGA...GCAAU_________ACAGG...GCA-3'\n______________GGCAGUGGU\n______________:\|\|\|\|\|\|\|:\n______________UCGUCACCG\n3'-UUU...UCUUU_________-5'\n_____________\|________\|\n_____________10_______1\n	20 -- 26	1 -- 7	-15.8954 kcal/mol	2.13019 kcal/mol	1.2588 kcal/mol	17 27@LB@ \| \|@LB@5'-GGA...GCAAU ACAGG...GCA-3'@LB@ GGCAGUGGU@LB@ :\|\|\|\|\|\|\|:@LB@ UCGUCACCG@LB@3'-UUU...UCUUU -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -12.51 kcal/mol@LB@Hybridization Energy -15.8954 kcal/mol@LB@Unfolding Energy - mRNA 2.13019 kcal/mol@LB@Unfolding Energy - sRNA 1.2588 kcal/mol@LB@@LB@Position - mRNA 18 -- 26@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 1 -- 7@LB@
150	0.01097	0.2504	b1878	flhE	-16.24	0.013409	257 -- 279	3 -- 25	proton seal during flagellar secretion		_____________256_____________________280\n_____________\|_______________________\|\n5'-CGU...GGGGA________G_C___C________UAGGA...AUC-3'\n______________GGGGAUGU_G_AGG_AAGUAGUG\n______________\|\|\|\|\|::\|_:_\|\|:_\|\|\|:\|\|\|\|\n______________CCCCUGUA_U_UCU_UUCGUCAC\n3'-UUU...UUUUA________G_U___U________CG-5'\n_____________\|_______________________\|\n_____________26______________________2\n	273 -- 279	3 -- 9	-26.0465 kcal/mol	7.2914 kcal/mol	2.5166 kcal/mol	256 280@LB@ \| \|@LB@5'-CGU...GGGGA G C C UAGGA...AUC-3'@LB@ GGGGAUGU G AGG AAGUAGUG@LB@ \|\|\|\|\|::\| : \|\|: \|\|\|:\|\|\|\|@LB@ CCCCUGUA U UCU UUCGUCAC@LB@3'-UUU...UUUUA G U U CG-5'@LB@ \| \|@LB@ 26 2@LB@@LB@@LB@Energy -16.24 kcal/mol@LB@Hybridization Energy -26.0465 kcal/mol@LB@Unfolding Energy - mRNA 7.2914 kcal/mol@LB@Unfolding Energy - sRNA 2.5166 kcal/mol@LB@@LB@Position - mRNA 257 -- 279@LB@Position - sRNA 3 -- 25@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 3 -- 9@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@
41	0.002071	0.1648	b0992	yccM	-9.88	0.287125	161 -- 167	1 -- 7	putative 4Fe-4S membrane protein		_____________160_____168\n_____________\|_______\|\n5'-AUC...UAGAA_______AUUUG...AAG-3'\n______________UAGUGGC\n______________:\|\|\|\|\|\|\n______________GUCACCG\n3'-UUU...UUUUC_______-5'\n_____________\|______\|\n_____________8______1\n	161 -- 167	1 -- 7	-11.7646 kcal/mol	0.660682 kcal/mol	1.22779 kcal/mol	160 168@LB@ \| \|@LB@5'-AUC...UAGAA AUUUG...AAG-3'@LB@ UAGUGGC@LB@ :\|\|\|\|\|\|@LB@ GUCACCG@LB@3'-UUU...UUUUC -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -11.7646 kcal/mol@LB@Unfolding Energy - mRNA 0.660682 kcal/mol@LB@Unfolding Energy - sRNA 1.22779 kcal/mol@LB@@LB@Position - mRNA 161 -- 167@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 1 -- 7@LB@
75	0.00423	0.1979	b1917	yecC	-10.99	0.188691	288 -- 298	1 -- 11	putative ABC transporter ATPase		_____________287_________299\n_____________\|___________\|\n5'-CUG...CUGGC___________AA-3'\n______________GAAGUGGUGGC\n______________:\|\|\|::\|\|\|\|\|\n______________UUUCGUCACCG\n3'-UUU...UUUCU___________-5'\n_____________\|__________\|\n_____________12_________1\n	292 -- 298	1 -- 7	-16.6045 kcal/mol	4.33348 kcal/mol	1.27751 kcal/mol	287 299@LB@ \| \|@LB@5'-CUG...CUGGC AA-3'@LB@ GAAGUGGUGGC@LB@ :\|\|\|::\|\|\|\|\|@LB@ UUUCGUCACCG@LB@3'-UUU...UUUCU -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -16.6045 kcal/mol@LB@Unfolding Energy - mRNA 4.33348 kcal/mol@LB@Unfolding Energy - sRNA 1.27751 kcal/mol@LB@@LB@Position - mRNA 288 -- 298@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 1 -- 7@LB@
96	0.005909	0.216	b0511	ybbW	-13.57	0.059054	201 -- 236	1 -- 27	putative allantoin transporter		_____________200___________________________________237\n_____________\|_____________________________________\|\n5'-UGG...GAUUU____A_____________ACUAUUCC____AC_C___UAUAG...UUA-3'\n______________AUGG__ACAUCAGAGAAA________AGCA__G_GGC\n______________\|\|\|\|__\|\|\|\|\|\|:\|\|\|\|\|________\|\|\|\|__\|_\|\|\|\n______________UACC__UGUAGUUUCUUU________UCGU__C_CCG\n3'-UUU...UGUUU____CC___________________________A___-5'\n_____________\|____________________________________\|\n_____________28___________________________________1\n	211 -- 217	10 -- 16	-23.7564 kcal/mol	7.66376 kcal/mol	2.51867 kcal/mol	200 237@LB@ \| \|@LB@5'-UGG...GAUUU A ACUAUUCC AC C UAUAG...UUA-3'@LB@ AUGG ACAUCAGAGAAA AGCA G GGC@LB@ \|\|\|\| \|\|\|\|\|\|:\|\|\|\|\| \|\|\|\| \| \|\|\|@LB@ UACC UGUAGUUUCUUU UCGU C CCG@LB@3'-UUU...UGUUU CC A -5'@LB@ \| \|@LB@ 28 1@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -23.7564 kcal/mol@LB@Unfolding Energy - mRNA 7.66376 kcal/mol@LB@Unfolding Energy - sRNA 2.51867 kcal/mol@LB@@LB@Position - mRNA 201 -- 236@LB@Position - sRNA 1 -- 27@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 10 -- 16@LB@
97	0.005972	0.2161	b0768	ybhD	-15.34	0.022873	51 -- 78	6 -- 32	putative DNA-binding transcriptional regulator	b2409	_____________50___________________________79\n_____________\|____________________________\|\n5'-CAG...UUAUU____U____UU__________C______UCUCU...CAU-3'\n______________GCGA_AUGG__ACAUUAAGGG_AAAGCA\n______________:\|:\|_\|\|\|\|__\|\|\|\|:\|\|:\|:_\|\|\|\|\|\|\n______________UGUU_UACC__UGUAGUUUCU_UUUCGU\n3'-UUU...CGAGG____U____CC_________________CACCG-5'\n_____________\|____________________________\|\n_____________33___________________________5\n	64 -- 70	13 -- 19	-24.2506 kcal/mol	6.37495 kcal/mol	2.53457 kcal/mol	50 79@LB@ \| \|@LB@5'-CAG...UUAUU U UU C UCUCU...CAU-3'@LB@ GCGA AUGG ACAUUAAGGG AAAGCA@LB@ :\|:\| \|\|\|\| \|\|\|\|:\|\|:\|: \|\|\|\|\|\|@LB@ UGUU UACC UGUAGUUUCU UUUCGU@LB@3'-UUU...CGAGG U CC CACCG-5'@LB@ \| \|@LB@ 33 5@LB@@LB@@LB@Energy -15.34 kcal/mol@LB@Hybridization Energy -24.2506 kcal/mol@LB@Unfolding Energy - mRNA 6.37495 kcal/mol@LB@Unfolding Energy - sRNA 2.53457 kcal/mol@LB@@LB@Position - mRNA 51 -- 78@LB@Position - sRNA 6 -- 32@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 13 -- 19@LB@
182	0.01317	0.2504	b2101	yegW	-15.40	0.022099	126 -- 162	3 -- 28	putative DNA-binding transcriptional regulator		_____________125______________________________________163\n_____________\|________________________________________\|\n5'-CGG...UCGUU_________________AACGCCUUAAAUAA_________AUAUA...AAA-3'\n______________GAUGGG___AUUAAAGA______________GAAGCAGUG\n______________:\|\|\|\|\|___\|\|:\|\|\|\|\|______________:\|\|\|\|\|\|\|\|\n______________UUACCC___UAGUUUCU______________UUUCGUCAC\n3'-UUU...GUGUU______CUG_______________________________CG-5'\n_____________\|________________________________________\|\n_____________29_______________________________________2\n	156 -- 162	3 -- 9	-24.3736 kcal/mol	6.45453 kcal/mol	2.51813 kcal/mol	125 163@LB@ \| \|@LB@5'-CGG...UCGUU AACGCCUUAAAUAA AUAUA...AAA-3'@LB@ GAUGGG AUUAAAGA GAAGCAGUG@LB@ :\|\|\|\|\| \|\|:\|\|\|\|\| :\|\|\|\|\|\|\|\|@LB@ UUACCC UAGUUUCU UUUCGUCAC@LB@3'-UUU...GUGUU CUG CG-5'@LB@ \| \|@LB@ 29 2@LB@@LB@@LB@Energy -15.40 kcal/mol@LB@Hybridization Energy -24.3736 kcal/mol@LB@Unfolding Energy - mRNA 6.45453 kcal/mol@LB@Unfolding Energy - sRNA 2.51813 kcal/mol@LB@@LB@Position - mRNA 126 -- 162@LB@Position - sRNA 3 -- 28@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 3 -- 9@LB@
24	0.0009771	0.1361	b4295	yjhU	-16.20	0.013710	198 -- 226	5 -- 30	putative DNA-binding transcriptional regulator; KpLE2 phage-like element	b1512	_____________197___________________________227\n_____________\|_____________________________\|\n5'-GUA...AUACA_______AUA__G______C___C_____CCUGU...UUG-3'\n______________AAAGUGG___GA_AUCAAA_AAA_AGCAG\n______________\|\|\|:\|\|\|___\|\|_\|\|\|\|\|\|_\|\|\|_\|\|\|\|\|\n______________UUUUACC___CU_UAGUUU_UUU_UCGUC\n3'-UUU...AGGUG_______C____G______C_________ACCG-5'\n_____________\|_____________________________\|\n_____________31____________________________4\n	198 -- 204	24 -- 30	-21.4023 kcal/mol	2.69702 kcal/mol	2.50278 kcal/mol	197 227@LB@ \| \|@LB@5'-GUA...AUACA AUA G C C CCUGU...UUG-3'@LB@ AAAGUGG GA AUCAAA AAA AGCAG@LB@ \|\|\|:\|\|\| \|\| \|\|\|\|\|\| \|\|\| \|\|\|\|\|@LB@ UUUUACC CU UAGUUU UUU UCGUC@LB@3'-UUU...AGGUG C G C ACCG-5'@LB@ \| \|@LB@ 31 4@LB@@LB@@LB@Energy -16.20 kcal/mol@LB@Hybridization Energy -21.4023 kcal/mol@LB@Unfolding Energy - mRNA 2.69702 kcal/mol@LB@Unfolding Energy - sRNA 2.50278 kcal/mol@LB@@LB@Position - mRNA 198 -- 226@LB@Position - sRNA 5 -- 30@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 24 -- 30@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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