Input and runtime details for job 3202356 (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 3202356 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:02 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:03:47 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:03:55 CET 2018
	Job Completed		@ Sat Feb 17 02:04:28 CET 2018

DIRECT ACCESS: https://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

Description of the job

GcvB

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_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

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
127	0.006343	0.1774	stm1751	hns	-12.42	0.292757	1 -- 14	147 -- 162	transcriptional regulator	______________1_______________15\n______________\|_______________\|\n___________5'-________________AUCCC...UAG-3'\n______________GACAGAC__GGUGAGU\n______________\|\|\|\|\|\|\|__\|\|\|:\|:\|\n______________CUGUCUG__CCAUUUA\n3'-UUU...GAUAC_______UC_______CAUGU...UCA-5'\n_____________\|________________\|\n_____________163______________146\n	8 -- 14	147 -- 153	-17.2475 kcal/mol	3.56352 kcal/mol	3.32093 kcal/mol	1 15@LB@ \| \|@LB@ 5'- AUCCC...UAG-3'@LB@ GACAGAC GGUGAGU@LB@ \|\|\|\|\|\|\| \|\|\|:\|:\|@LB@ CUGUCUG CCAUUUA@LB@3'-UUU...GAUAC UC CAUGU...UCA-5'@LB@ \| \|@LB@ 163 146@LB@@LB@@LB@Energy -12.42 kcal/mol@LB@Hybridization Energy -17.2475 kcal/mol@LB@Unfolding Energy - mRNA 3.56352 kcal/mol@LB@Unfolding Energy - sRNA 3.32093 kcal/mol@LB@@LB@Position - mRNA 1 -- 14@LB@Position - sRNA 147 -- 162@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 147 -- 153@LB@
128	0.006467	0.1774	stm3907	N/A	-18.55	0.030594	118 -- 173	37 -- 89		_____________117__________________________174\n_____________\|____________________________\|\n5'-UCA...AAAAA____________ACCAGU______G___AAAAC...UUU-3'\n______________CAGACGCAACAA______CAGCAU_AUA\n______________\|\|:\|\|:\|\|\|\|\|\|______\|\|:\|\|\|_\|:\|\n______________GUUUGUGUUGUU______GUUGUA_UGU\n3'-UUU...UUAAC____________GU__________G___UGGCA...UCA-5'\n_____________\|____________________________\|\n_____________90___________________________36\n	123 -- 129	78 -- 84	-22.8944 kcal/mol	3.16008 kcal/mol	6.30461 kcal/mol	117 174@LB@ \| \|@LB@5'-UCA...AAAAA ACCAGU G AAAAC...UUU-3'@LB@ CAGACGCAACAA CAGCAU AUA@LB@ \|\|:\|\|:\|\|\|\|\|\| \|\|:\|\|\| \|:\|@LB@ GUUUGUGUUGUU GUUGUA UGU@LB@3'-UUU...UUAAC GU G UGGCA...UCA-5'@LB@ \| \|@LB@ 90 36@LB@@LB@@LB@Energy -18.55 kcal/mol@LB@Hybridization Energy -22.8944 kcal/mol@LB@Unfolding Energy - mRNA 3.16008 kcal/mol@LB@Unfolding Energy - sRNA 6.30461 kcal/mol@LB@@LB@Position - mRNA 118 -- 173@LB@Position - sRNA 37 -- 89@LB@Position Seed - mRNA 123 -- 129@LB@Position Seed - sRNA 78 -- 84@LB@
129	0.006472	0.1774	stm0158	acnB	-11.80	0.356459	140 -- 172	33 -- 60	bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase	_____________139________________173\n_____________\|__________________\|\n5'-AUU...CUUUU_________G_U______UUAAA...UGC-3'\n______________UUGUAAACA_A_UAACAC\n______________\|\|\|:\|\|\|\|\|_\|_:\|\|\|\|\|\n______________AACGUUUGU_U_GUUGUG\n3'-UUU...UGGUU_________G_U______UUGUA...UCA-5'\n_____________\|__________________\|\n_____________61_________________32\n	48 -- 54	84 -- 90	-17.8051 kcal/mol	3.41045 kcal/mol	3.73018 kcal/mol	139 173@LB@ \| \|@LB@5'-AUU...CUUUU G U UUAAA...UGC-3'@LB@ UUGUAAACA A UAACAC@LB@ \|\|\|:\|\|\|\|\| \| :\|\|\|\|\|@LB@ AACGUUUGU U GUUGUG@LB@3'-UUU...UGGUU G U UUGUA...UCA-5'@LB@ \| \|@LB@ 61 32@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -17.8051 kcal/mol@LB@Unfolding Energy - mRNA 3.41045 kcal/mol@LB@Unfolding Energy - sRNA 3.73018 kcal/mol@LB@@LB@Position - mRNA 140 -- 172@LB@Position - sRNA 33 -- 60@LB@Position Seed - mRNA 48 -- 54@LB@Position Seed - sRNA 84 -- 90@LB@
130	0.00652	0.1774	stm4228	malF	-14.47	0.143021	162 -- 175	1 -- 15	maltose ABC transporter permease MalF	_____________161_____________176\n_____________\|_______________\|\n5'-AAC...ACAUC_______________UUCAA...UAA-3'\n______________UCCGGC_CAGGAAGU\n______________\|\|\|\|\|\|_\|\|\|\|\|\|\|\|\n______________AGGCCG_GUCCUUCA\n3'-UUU...AAGCA______A________-5'\n_____________\|______________\|\n_____________16_____________1\n	169 -- 175	1 -- 7	-25.2779 kcal/mol	6.67863 kcal/mol	4.81264 kcal/mol	161 176@LB@ \| \|@LB@5'-AAC...ACAUC UUCAA...UAA-3'@LB@ UCCGGC CAGGAAGU@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ AGGCCG GUCCUUCA@LB@3'-UUU...AAGCA A -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -14.47 kcal/mol@LB@Hybridization Energy -25.2779 kcal/mol@LB@Unfolding Energy - mRNA 6.67863 kcal/mol@LB@Unfolding Energy - sRNA 4.81264 kcal/mol@LB@@LB@Position - mRNA 162 -- 175@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 1 -- 7@LB@
131	0.006551	0.1774	stm3217	aer	-17.88	0.039631	254 -- 298	36 -- 77	senses cellular redox state or proton motive force; similar to E. coli aerotaxis sensor receptor flavoprotein (AAC76107.1); Blastp hit to AAC76107.1 (506 aa) 83% identity in aa 1 - 506	_____________253____________________________________________________________________________________299\n_____________\|______________________________________________________________________________________\|\n5'-UUU...AAGGC______UGA_____________________ACAAA____AA__AUU____________________UC__G______UUUA_____UAAAG...CCA-3'\n______________GCAGGA___GGUGAAAA_________UCGU_____UAUU__GG____AAUCGCA____AAUUGCGA__CA_AGCAAU____ACAAC\n______________:\|\|\|\|\|___:\|\|\|\|\|\|\|_________\|\|\|:_____\|\|::__\|\|____\|\|\|\|\|\|\|____\|\|\|\|\|\|:\|__\|\|_\|:\|\|\|:____\|\|\|\|\|\n______________UGUCCU___UCACUUUU_________AGCG_____AUGG__CC____UUAGCGU____UUAACGUU__GU_UUGUUG____UGUUG\n3'-UUU...UUACA_________________UCCCAUCAG_____________CA__AGAC_______CUGG________U___G_______________UAGUG...UCA-5'\n_____________\|______________________________________________________________________________________\|\n_____________78_____________________________________________________________________________________35\n	89 -- 95	99 -- 105	-43.6348 kcal/mol	13.4466 kcal/mol	20.9633 kcal/mol	253 299@LB@ \| \|@LB@5'-UUU...AAGGC UGA ACAAA AA AUU UC G UUUA UAAAG...CCA-3'@LB@ GCAGGA GGUGAAAA UCGU UAUU GG AAUCGCA AAUUGCGA CA AGCAAU ACAAC@LB@ :\|\|\|\|\| :\|\|\|\|\|\|\| \|\|\|: \|\|:: \|\| \|\|\|\|\|\|\| \|\|\|\|\|\|:\| \|\| \|:\|\|\|: \|\|\|\|\|@LB@ UGUCCU UCACUUUU AGCG AUGG CC UUAGCGU UUAACGUU GU UUGUUG UGUUG@LB@3'-UUU...UUACA UCCCAUCAG CA AGAC CUGG U G UAGUG...UCA-5'@LB@ \| \|@LB@ 78 35@LB@@LB@@LB@Energy -17.88 kcal/mol@LB@Hybridization Energy -43.6348 kcal/mol@LB@Unfolding Energy - mRNA 13.4466 kcal/mol@LB@Unfolding Energy - sRNA 20.9633 kcal/mol@LB@@LB@Position - mRNA 254 -- 298@LB@Position - sRNA 36 -- 77@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 99 -- 105@LB@
132	0.006673	0.1774	stm2677	ffh	-17.54	0.045291	232 -- 275	38 -- 86	4.5S-RNP protein	_____________231_________________________________________________________________________________________________276\n_____________\|___________________________________________________________________________________________________\|\n5'-UAG...CAAAA_______UA__U_____CG____UU__CC__________A_A____A___A__G___UACG___C______CU____CC__U____________AA___GGCUU...AAG-3'\n______________ACGGGCA__GU__GUGU__ACAG__GA__AGUGAGAAAG_G_AG_C__GU_UA_CGU____UGA__CGCAG__CCAA__GU__GCAUAACAACA__GAC\n______________\|\|:\|:\|\|__\|\|__:\|\|\|__\|\|\|\|__\|\|__\|\|\|\|\|:\|\|\|\|_\|_\|\|_\|__\|:_\|\|_\|\|\|____\|\|\|__\|\|\|\|\|__\|\|\|\|__\|:__:\|\|:\|\|\|\|\|\|\|__:\|\|\n______________UGUCUGU__CA__UACA__UGUC__CU__UCACUUUUUC_C_UC_G__CG_AU_GCA____ACU__GCGUC__GGUU__CG__UGUGUUGUUGU__UUG\n3'-UUU...AUACC_______CC__UU__________________________C_A__A_AG_____G___CCAG___UA_____U_____AA__UU___________G____UAGUG...UCA-5'\n_____________\|___________________________________________________________________________________________________\|\n_____________87__________________________________________________________________________________________________37\n	110 -- 116	76 -- 82	-60.3799 kcal/mol	23.7315 kcal/mol	24.6218 kcal/mol	231 276@LB@ \| \|@LB@5'-UAG...CAAAA UA U CG UU CC A A A A G UACG C CU CC U AA GGCUU...AAG-3'@LB@ ACGGGCA GU GUGU ACAG GA AGUGAGAAAG G AG C GU UA CGU UGA CGCAG CCAA GU GCAUAACAACA GAC@LB@ \|\|:\|:\|\| \|\| :\|\|\| \|\|\|\| \|\| \|\|\|\|\|:\|\|\|\| \| \|\| \| \|: \|\| \|\|\| \|\|\| \|\|\|\|\| \|\|\|\| \|: :\|\|:\|\|\|\|\|\|\| :\|\|@LB@ UGUCUGU CA UACA UGUC CU UCACUUUUUC C UC G CG AU GCA ACU GCGUC GGUU CG UGUGUUGUUGU UUG@LB@3'-UUU...AUACC CC UU C A A AG G CCAG UA U AA UU G UAGUG...UCA-5'@LB@ \| \|@LB@ 87 37@LB@@LB@@LB@Energy -17.54 kcal/mol@LB@Hybridization Energy -60.3799 kcal/mol@LB@Unfolding Energy - mRNA 23.7315 kcal/mol@LB@Unfolding Energy - sRNA 24.6218 kcal/mol@LB@@LB@Position - mRNA 232 -- 275@LB@Position - sRNA 38 -- 86@LB@Position Seed - mRNA 110 -- 116@LB@Position Seed - sRNA 76 -- 82@LB@
133	0.006689	0.1774	stm0831	dps	-13.05	0.236755	141 -- 176	159 -- 184	DNA starvation/stationary phase protection protein Dps	_____________140________________________177\n_____________\|__________________________\|\n5'-CAU...UUACC___CA_______AACU__________AAUUG...UUA-3'\n______________CAC__AACAGCA____CGUC_UAACC\n______________\|\|\|__\|\|\|\|:\|\|____\|:\|\|_:\|\|\|\|\n______________GUG__UUGUUGU____GUAG_GUUGG\n3'-UUU...CGUUU____________GUU_____U_____CAUUC...UCA-5'\n_____________\|__________________________\|\n_____________185________________________158\n	37 -- 43	76 -- 82	-18.4678 kcal/mol	1.39739 kcal/mol	8.25195 kcal/mol	140 177@LB@ \| \|@LB@5'-CAU...UUACC CA AACU AAUUG...UUA-3'@LB@ CAC AACAGCA CGUC UAACC@LB@ \|\|\| \|\|\|\|:\|\| \|:\|\| :\|\|\|\|@LB@ GUG UUGUUGU GUAG GUUGG@LB@3'-UUU...CGUUU GUU U CAUUC...UCA-5'@LB@ \| \|@LB@ 185 158@LB@@LB@@LB@Energy -13.05 kcal/mol@LB@Hybridization Energy -18.4678 kcal/mol@LB@Unfolding Energy - mRNA 1.39739 kcal/mol@LB@Unfolding Energy - sRNA 8.25195 kcal/mol@LB@@LB@Position - mRNA 141 -- 176@LB@Position - sRNA 159 -- 184@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 76 -- 82@LB@
136	0.006805	0.1774	stm2812	N/A	-16.76	0.060981	84 -- 153	36 -- 90	MFS transporter	_____________83_____________________________________________154\n_____________\|______________________________________________\|\n5'-GGC...AUCCG__C________CUCUCCUCAAAGC______UU_______UC_____UCCCC...UGC-3'\n______________GC_AACGCAAU_____________GCACGA__CAUCACG__ACCGU\n______________\|\|_\|\|\|:\|\|\|:_____________:\|\|\|:\|__\|\|\|\|\|\|:__\|\|\|\|\|\n______________CG_UUGUGUUG_____________UGUGUU__GUAGUGU__UGGCA\n3'-UUU...GUUAA__U________U__________________________________UUCGG...UCA-5'\n_____________\|______________________________________________\|\n_____________91_____________________________________________35\n	116 -- 122	66 -- 72	-26.7431 kcal/mol	6.46375 kcal/mol	9.42239 kcal/mol	83 154@LB@ \| \|@LB@5'-GGC...AUCCG C CUCUCCUCAAAGC UU UC UCCCC...UGC-3'@LB@ GC AACGCAAU GCACGA CAUCACG ACCGU@LB@ \|\| \|\|\|:\|\|\|: :\|\|\|:\| \|\|\|\|\|\|: \|\|\|\|\|@LB@ CG UUGUGUUG UGUGUU GUAGUGU UGGCA@LB@3'-UUU...GUUAA U U UUCGG...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -16.76 kcal/mol@LB@Hybridization Energy -26.7431 kcal/mol@LB@Unfolding Energy - mRNA 6.46375 kcal/mol@LB@Unfolding Energy - sRNA 9.42239 kcal/mol@LB@@LB@Position - mRNA 84 -- 153@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 116 -- 122@LB@Position Seed - sRNA 66 -- 72@LB@
137	0.006825	0.1774	stm1196	acpP	-14.14	0.161333	197 -- 223	36 -- 60	acyl carrier protein	_____________196___________________________________________224\n_____________\|_____________________________________________\|\n5'-ACU...AGAAC_______GAAA_____C____A____CU__GCGUUAA________AAGUA...UGG-3'\n______________GCGUUAA____AUUAU_GGCG_ACAG__GG_______GCAGGAAG\n______________:\|:\|\|\|\|____\|:\|\|\|_\|:\|:_\|\|\|\|__\|\|_______:\|\|\|\|\|\|\|\n______________UGUAAUU____UGAUA_CUGU_UGUC__CC_______UGUCCUUC\n3'-UUU...CACGA_______AG_______C____C________AUUUACA________ACUUU...UCA-5'\n_____________\|_____________________________________________\|\n_____________61____________________________________________35\n	258 -- 264	137 -- 143	-28.6095 kcal/mol	10.3633 kcal/mol	7.13805 kcal/mol	196 224@LB@ \| \|@LB@5'-ACU...AGAAC GAAA C A CU GCGUUAA AAGUA...UGG-3'@LB@ GCGUUAA AUUAU GGCG ACAG GG GCAGGAAG@LB@ :\|:\|\|\|\| \|:\|\|\| \|:\|: \|\|\|\| \|\| :\|\|\|\|\|\|\|@LB@ UGUAAUU UGAUA CUGU UGUC CC UGUCCUUC@LB@3'-UUU...CACGA AG C C AUUUACA ACUUU...UCA-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -14.14 kcal/mol@LB@Hybridization Energy -28.6095 kcal/mol@LB@Unfolding Energy - mRNA 10.3633 kcal/mol@LB@Unfolding Energy - sRNA 7.13805 kcal/mol@LB@@LB@Position - mRNA 197 -- 223@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 137 -- 143@LB@
139	0.007115	0.182	stm0826	ybiN	-18.61	0.029895	232 -- 282	36 -- 90	23S rRNA (adenine(1618)-N(6))-methyltransferase	_____________231___________________283\n_____________\|_____________________\|\n5'-CUC...GAGCC_____AACGAGCG________AAUUC...UUC-3'\n______________GAUCA________AGGCAGGG\n______________:\|\|\|\|________\|\|:\|\|\|\|\|\n______________UUAGU________UCUGUCCC\n3'-UUU...UGUAA_____GAUACCUG________AUUUA...UCA-5'\n_____________\|_____________________\|\n_____________91____________________35\n	124 -- 130	152 -- 158	-17.5433 kcal/mol	4.82059 kcal/mol	3.53427 kcal/mol	231 283@LB@ \| \|@LB@5'-CUC...GAGCC AACGAGCG AAUUC...UUC-3'@LB@ GAUCA AGGCAGGG@LB@ :\|\|\|\| \|\|:\|\|\|\|\|@LB@ UUAGU UCUGUCCC@LB@3'-UUU...UGUAA GAUACCUG AUUUA...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -18.61 kcal/mol@LB@Hybridization Energy -17.5433 kcal/mol@LB@Unfolding Energy - mRNA 4.82059 kcal/mol@LB@Unfolding Energy - sRNA 3.53427 kcal/mol@LB@@LB@Position - mRNA 232 -- 282@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 152 -- 158@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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usability assessment

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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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