Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
169	0.006985	0.1454	b0384	psiF	-5.27	0.543574	221 -- 228	1 -- 8	PsiF family protein	_____________220______229\n_____________\|________\|\n5'-CCC...CUGGU________UUUUC...UGA-3'\n______________UACCUUGC\n______________\|\|\|\|:\|:\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	222 -- 228	1 -- 7	-9.62499 kcal/mol	2.26355 kcal/mol	2.11603 kcal/mol	220 229@LB@ \| \|@LB@5'-CCC...CUGGU UUUUC...UGA-3'@LB@ UACCUUGC@LB@ \|\|\|\|:\|:\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -5.27 kcal/mol@LB@Hybridization Energy -9.62499 kcal/mol@LB@Unfolding Energy - mRNA 2.26355 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 221 -- 228@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 1 -- 7@LB@
151	0.006118	0.1406	b1103	hinT	-6.52	0.328434	216 -- 241	45 -- 70	purine nucleoside phosphoramidase dadA activator protein	_____________215________________________242\n_____________\|__________________________\|\n5'-CAA...AAACU_________A_____AUUCGU_____GAUCC...CGC-3'\n______________AUAUUCAGC_AAAUU______CGUGA\n______________\|\|\|\|\|\|\|\|\|_\|\|\|\|:______\|\|\|\|\|\n______________UAUAAGUCG_UUUAG______GCACU\n3'-AUU...GAUUU_________G_____GCUAAU_____UCAUU...AUG-5'\n_____________\|__________________________\|\n_____________71_________________________44\n	218 -- 224	62 -- 68	-20.3535 kcal/mol	5.67357 kcal/mol	8.1779 kcal/mol	215 242@LB@ \| \|@LB@5'-CAA...AAACU A AUUCGU GAUCC...CGC-3'@LB@ AUAUUCAGC AAAUU CGUGA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|: \|\|\|\|\|@LB@ UAUAAGUCG UUUAG GCACU@LB@3'-AUU...GAUUU G GCUAAU UCAUU...AUG-5'@LB@ \| \|@LB@ 71 44@LB@@LB@@LB@Energy -6.52 kcal/mol@LB@Hybridization Energy -20.3535 kcal/mol@LB@Unfolding Energy - mRNA 5.67357 kcal/mol@LB@Unfolding Energy - sRNA 8.1779 kcal/mol@LB@@LB@Position - mRNA 216 -- 241@LB@Position - sRNA 45 -- 70@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 62 -- 68@LB@
59	0.0008996	0.0531	b1310	ycjN	-10.87	0.024752	113 -- 129	42 -- 59	putative ABC sugar transporter periplasmic binding protein	_____________112________________130\n_____________\|__________________\|\n5'-UUC...GUCGG__________________UGAUA...UUA-3'\n______________GAUCUGAUUA_GUGAAGU\n______________:\|\|\|:\|\|\|\|\|_\|\|\|\|\|\|\|\n______________UUAGGCUAAU_CACUUCA\n3'-AUU...UCGGU__________G_______UUUUC...AUG-5'\n_____________\|__________________\|\n_____________60_________________41\n	123 -- 129	42 -- 48	-20.0101 kcal/mol	5.87569 kcal/mol	3.27976 kcal/mol	112 130@LB@ \| \|@LB@5'-UUC...GUCGG UGAUA...UUA-3'@LB@ GAUCUGAUUA GUGAAGU@LB@ :\|\|\|:\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UUAGGCUAAU CACUUCA@LB@3'-AUU...UCGGU G UUUUC...AUG-5'@LB@ \| \|@LB@ 60 41@LB@@LB@@LB@Energy -10.87 kcal/mol@LB@Hybridization Energy -20.0101 kcal/mol@LB@Unfolding Energy - mRNA 5.87569 kcal/mol@LB@Unfolding Energy - sRNA 3.27976 kcal/mol@LB@@LB@Position - mRNA 113 -- 129@LB@Position - sRNA 42 -- 59@LB@Position Seed - mRNA 123 -- 129@LB@Position Seed - sRNA 42 -- 48@LB@
13	4.485e-05	0.01183	b0511	ybbW	-13.60	0.002717	173 -- 210	18 -- 58	putative allantoin transporter	_____________172________________________________________211\n_____________\|__________________________________________\|\n5'-UGG...ACGUU_______________AU____________UUU__________AGAGA...UUA-3'\n______________AUUCGA_UACGUGAA__UAAGAGG___GA___AUGGAACAUC\n______________\|\|:\|\|\|_\|\|\|\|\|\|\|\|__\|\|\|:\|\|\|___\|\|___\|\|:\|\|\|\|\|\|\|\n______________UAGGCU_AUGCACUU__AUUUUCC___CU___UAUCUUGUAG\n3'-AUU...CGGUU______A________C________AGA__UUC__________AAUGG...AUG-5'\n_____________\|__________________________________________\|\n_____________59_________________________________________17\n	204 -- 210	18 -- 24	-34.0515 kcal/mol	8.25655 kcal/mol	12.1809 kcal/mol	172 211@LB@ \| \|@LB@5'-UGG...ACGUU AU UUU AGAGA...UUA-3'@LB@ AUUCGA UACGUGAA UAAGAGG GA AUGGAACAUC@LB@ \|\|:\|\|\| \|\|\|\|\|\|\|\| \|\|\|:\|\|\| \|\| \|\|:\|\|\|\|\|\|\|@LB@ UAGGCU AUGCACUU AUUUUCC CU UAUCUUGUAG@LB@3'-AUU...CGGUU A C AGA UUC AAUGG...AUG-5'@LB@ \| \|@LB@ 59 17@LB@@LB@@LB@Energy -13.60 kcal/mol@LB@Hybridization Energy -34.0515 kcal/mol@LB@Unfolding Energy - mRNA 8.25655 kcal/mol@LB@Unfolding Energy - sRNA 12.1809 kcal/mol@LB@@LB@Position - mRNA 173 -- 210@LB@Position - sRNA 18 -- 58@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 18 -- 24@LB@
145	0.005462	0.1325	b3239	yhcO	-10.93	0.023720	179 -- 225	2 -- 55	putative barnase inhibitor	_____________178______________________________________________________226\n_____________\|________________________________________________________\|\n5'-CUA...CGCCG___A_______C___________AAC______________A_______________AUGAG...GCG-3'\n______________CGA__ACGUGA_GGU____GG_C____AGAU_GAAUAUUU_UACCUUUG_AUUUUG\n______________\|\|\|__\|\|\|\|\|\|_:\|\|____\|\|_\|____\|\|\|\|_\|\|\|:\|\|:\|_\|\|\|\|\|:\|\|_\|:::\|:\n______________GCU__UGCACU_UCA____CC_G____UCUA_CUUGUAGA_AUGGAGAC_UGGGAU\n3'-AUU...UUUAG___AA__________UUUU__A_ACUU____U_________________A______G-5'\n_____________\|________________________________________________________\|\n_____________56_______________________________________________________1\n	213 -- 219	9 -- 15	-30.2735 kcal/mol	6.67064 kcal/mol	12.6986 kcal/mol	178 226@LB@ \| \|@LB@5'-CUA...CGCCG A C AAC A AUGAG...GCG-3'@LB@ CGA ACGUGA GGU GG C AGAU GAAUAUUU UACCUUUG AUUUUG@LB@ \|\|\| \|\|\|\|\|\| :\|\| \|\| \| \|\|\|\| \|\|\|:\|\|:\| \|\|\|\|\|:\|\| \|:::\|:@LB@ GCU UGCACU UCA CC G UCUA CUUGUAGA AUGGAGAC UGGGAU@LB@3'-AUU...UUUAG AA UUUU A ACUU U A G-5'@LB@ \| \|@LB@ 56 1@LB@@LB@@LB@Energy -10.93 kcal/mol@LB@Hybridization Energy -30.2735 kcal/mol@LB@Unfolding Energy - mRNA 6.67064 kcal/mol@LB@Unfolding Energy - sRNA 12.6986 kcal/mol@LB@@LB@Position - mRNA 179 -- 225@LB@Position - sRNA 2 -- 55@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 9 -- 15@LB@
171	0.00718	0.1466	b1708	nlpC	-9.44	0.065343	288 -- 298	49 -- 59	putative C40 clan peptidase lipoprotein	_____________287_________299\n_____________\|___________\|\n5'-AAA...UUUCU___________CG-3'\n______________GAUUCGAUUAC\n______________:\|\|:\|\|\|\|\|\|\|\n______________UUAGGCUAAUG\n3'-AUU...UCGGU___________CACUU...AUG-5'\n_____________\|___________\|\n_____________60__________48\n	292 -- 298	49 -- 55	-11.5278 kcal/mol	1.77565 kcal/mol	0.318405 kcal/mol	287 299@LB@ \| \|@LB@5'-AAA...UUUCU CG-3'@LB@ GAUUCGAUUAC@LB@ :\|\|:\|\|\|\|\|\|\|@LB@ UUAGGCUAAUG@LB@3'-AUU...UCGGU CACUU...AUG-5'@LB@ \| \|@LB@ 60 48@LB@@LB@@LB@Energy -9.44 kcal/mol@LB@Hybridization Energy -11.5278 kcal/mol@LB@Unfolding Energy - mRNA 1.77565 kcal/mol@LB@Unfolding Energy - sRNA 0.318405 kcal/mol@LB@@LB@Position - mRNA 288 -- 298@LB@Position - sRNA 49 -- 59@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 49 -- 55@LB@
115	0.00375	0.1147	b1057	yceJ	-5.38	0.522888	37 -- 59	1 -- 23	putative cytochrome b561	_____________36_______________________60\n_____________\|________________________\|\n5'-UGA...CACCA_______C__AUG___A_______UAAAC...UGU-3'\n______________GACAUCU_UG___CUG_ACCC_AC\n______________:\|\|\|\|\|\|_\|:___\|\|\|_\|\|\|\|_\|\|\n______________UUGUAGA_AU___GAC_UGGG_UG\n3'-AUU...CUAUC__________GGA___A____A__-5'\n_____________\|_______________________\|\n_____________24______________________1\n	37 -- 43	17 -- 23	-17.2281 kcal/mol	3.85652 kcal/mol	8.01506 kcal/mol	36 60@LB@ \| \|@LB@5'-UGA...CACCA C AUG A UAAAC...UGU-3'@LB@ GACAUCU UG CUG ACCC AC@LB@ :\|\|\|\|\|\| \|: \|\|\| \|\|\|\| \|\|@LB@ UUGUAGA AU GAC UGGG UG@LB@3'-AUU...CUAUC GGA A A -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -5.38 kcal/mol@LB@Hybridization Energy -17.2281 kcal/mol@LB@Unfolding Energy - mRNA 3.85652 kcal/mol@LB@Unfolding Energy - sRNA 8.01506 kcal/mol@LB@@LB@Position - mRNA 37 -- 59@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 17 -- 23@LB@
32	0.0003261	0.03519	b2789	gudP	-8.38	0.124980	121 -- 127	1 -- 7	putative D-glucarate transporter	_____________120_____128\n_____________\|_______\|\n5'-UGA...AAAAC_______GUCAC...ACG-3'\n______________ACCCUAC\n______________\|\|\|\|\|\|\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	121 -- 127	1 -- 7	-11.2076 kcal/mol	0.809325 kcal/mol	2.03949 kcal/mol	120 128@LB@ \| \|@LB@5'-UGA...AAAAC GUCAC...ACG-3'@LB@ ACCCUAC@LB@ \|\|\|\|\|\|\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -8.38 kcal/mol@LB@Hybridization Energy -11.2076 kcal/mol@LB@Unfolding Energy - mRNA 0.809325 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 121 -- 127@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 1 -- 7@LB@
84	0.002084	0.08729	b2067	yegE	-5.99	0.414041	137 -- 150	1 -- 15	putative diguanylate cyclase	_____________136_____________151\n_____________\|_______________\|\n5'-AGU...GUAAA___________A___AUAAA...CGC-3'\n______________ACUUUUGUACU__GC\n______________\|\|:\|:\|\|\|\|\|:__:\|\n______________UGGAGACAUGG__UG\n3'-AUU...UAGAA___________GA__-5'\n_____________\|______________\|\n_____________16_____________1\n	141 -- 147	5 -- 11	-13.6769 kcal/mol	1.88278 kcal/mol	5.82808 kcal/mol	136 151@LB@ \| \|@LB@5'-AGU...GUAAA A AUAAA...CGC-3'@LB@ ACUUUUGUACU GC@LB@ \|\|:\|:\|\|\|\|\|: :\|@LB@ UGGAGACAUGG UG@LB@3'-AUU...UAGAA GA -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -5.99 kcal/mol@LB@Hybridization Energy -13.6769 kcal/mol@LB@Unfolding Energy - mRNA 1.88278 kcal/mol@LB@Unfolding Energy - sRNA 5.82808 kcal/mol@LB@@LB@Position - mRNA 137 -- 150@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 5 -- 11@LB@
172	0.007198	0.1466	b2395	yfeA	-7.88	0.166321	272 -- 292	49 -- 69	putative diguanylate cyclase	_____________271____________________293\n_____________\|______________________\|\n5'-ACC...GUACU__________UC____UU____UUCGCCAC-3'\n______________UAUUCAGCUA___CCG__UUAU\n______________\|\|\|\|\|\|\|\|:\|___\|\|\|__\|\|\|:\n______________AUAAGUCGGU___GGC__AAUG\n3'-AUU...AUUUU__________UUA___U_____CACUU...AUG-5'\n_____________\|______________________\|\n_____________70_____________________48\n	275 -- 281	60 -- 66	-16.2546 kcal/mol	2.18624 kcal/mol	6.21499 kcal/mol	271 293@LB@ \| \|@LB@5'-ACC...GUACU UC UU UUCGCCAC-3'@LB@ UAUUCAGCUA CCG UUAU@LB@ \|\|\|\|\|\|\|\|:\| \|\|\| \|\|\|:@LB@ AUAAGUCGGU GGC AAUG@LB@3'-AUU...AUUUU UUA U CACUU...AUG-5'@LB@ \| \|@LB@ 70 48@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -16.2546 kcal/mol@LB@Unfolding Energy - mRNA 2.18624 kcal/mol@LB@Unfolding Energy - sRNA 6.21499 kcal/mol@LB@@LB@Position - mRNA 272 -- 292@LB@Position - sRNA 49 -- 69@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 60 -- 66@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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