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: http://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	Additional homologs
64	0.003108	0.1596	stm4162	thiF	-13.53	0.200092	247 -- 294	34 -- 76	molybdopterin/thiamine biosynthesis adenylyltransferase		_____________246___________________295\n_____________\|_____________________\|\n5'-GCA...GCUCG_______________A_____AGCAA...UUG-3'\n______________GCGAUAUCGCGAUUG_AGGCC\n______________:\|:\|:\|\|\|:\|:\|::\|_\|:\|\|\|\n______________UGUUGUAGUGUUGGC_UUCGG\n3'-UUU...UGUUG_______________A_____UUUUC...UCA-5'\n_____________\|_____________________\|\n_____________77____________________33\n	248 -- 254	69 -- 75	-25.2172 kcal/mol	7.66984 kcal/mol	8.92374 kcal/mol	246 295@LB@ \| \|@LB@5'-GCA...GCUCG A AGCAA...UUG-3'@LB@ GCGAUAUCGCGAUUG AGGCC@LB@ :\|:\|:\|\|\|:\|:\|::\| \|:\|\|\|@LB@ UGUUGUAGUGUUGGC UUCGG@LB@3'-UUU...UGUUG A UUUUC...UCA-5'@LB@ \| \|@LB@ 77 33@LB@@LB@@LB@Energy -13.53 kcal/mol@LB@Hybridization Energy -25.2172 kcal/mol@LB@Unfolding Energy - mRNA 7.66984 kcal/mol@LB@Unfolding Energy - sRNA 8.92374 kcal/mol@LB@@LB@Position - mRNA 247 -- 294@LB@Position - sRNA 34 -- 76@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 69 -- 75@LB@
75	0.003517	0.1596	stm1214	ycfR	-14.36	0.148951	168 -- 212	35 -- 81	multiple stress resistance protein BhsA	stm0823	_____________167______________213\n_____________\|________________\|\n5'-AAA...ACCAC_________CA_____AUUCA...AAC-3'\n______________UUCUGGCUC___GAGU\n______________\|\|\|:\|\|\|\|\|___:\|\|\|\n______________AAGGCCGAG___UUCA\n3'-UUU...AAAGC_________UCC____-5'\n_____________\|_______________\|\n_____________82______________35\n	15 -- 21	8 -- 14	-15.9373 kcal/mol	4.12962 kcal/mol	4.82557 kcal/mol	167 213@LB@ \| \|@LB@5'-AAA...ACCAC CA AUUCA...AAC-3'@LB@ UUCUGGCUC GAGU@LB@ \|\|\|:\|\|\|\|\| :\|\|\|@LB@ AAGGCCGAG UUCA@LB@3'-UUU...AAAGC UCC -5'@LB@ \| \|@LB@ 82 35@LB@@LB@@LB@Energy -14.36 kcal/mol@LB@Hybridization Energy -15.9373 kcal/mol@LB@Unfolding Energy - mRNA 4.12962 kcal/mol@LB@Unfolding Energy - sRNA 4.82557 kcal/mol@LB@@LB@Position - mRNA 168 -- 212@LB@Position - sRNA 35 -- 81@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 8 -- 14@LB@
83	0.003855	0.1596	stm1680	ycjI	-14.22	0.156552	151 -- 200	34 -- 86	murein peptide amidase A		_____________150_________201\n_____________\|___________\|\n5'-GAA...CUGAA___________UUCGC...CGG-3'\n______________CAUUAUGGACG\n______________\|\|:\|\|\|\|\|\|\|:\n______________GUGAUACCUGU\n3'-UUU...AAUUA___________CUGUC...UCA-5'\n_____________\|___________\|\n_____________87__________33\n	259 -- 265	159 -- 165	-14.9153 kcal/mol	1.6295 kcal/mol	3.40995 kcal/mol	150 201@LB@ \| \|@LB@5'-GAA...CUGAA UUCGC...CGG-3'@LB@ CAUUAUGGACG@LB@ \|\|:\|\|\|\|\|\|\|:@LB@ GUGAUACCUGU@LB@3'-UUU...AAUUA CUGUC...UCA-5'@LB@ \| \|@LB@ 87 33@LB@@LB@@LB@Energy -14.22 kcal/mol@LB@Hybridization Energy -14.9153 kcal/mol@LB@Unfolding Energy - mRNA 1.6295 kcal/mol@LB@Unfolding Energy - sRNA 3.40995 kcal/mol@LB@@LB@Position - mRNA 151 -- 200@LB@Position - sRNA 34 -- 86@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 159 -- 165@LB@
155	0.008213	0.1845	stm3112	mltC	-21.66	0.009126	170 -- 198	62 -- 90	murein transglycosylase C		_____________169____________________________199\n_____________\|______________________________\|\n5'-UAA...ACAUG___UA________________G___UC___GAAUG...UCA-3'\n______________GCA___ACGACAACACAACAU_CAC__CCG\n______________\|\|\|___\|\|:\|\|\|\|\|\|\|\|\|\|\|\|_\|\|\|__\|\|\|\n______________CGU___UGUUGUUGUGUUGUA_GUG__GGC\n3'-UUU...GUUAA___UUG___________________UU___AUUCG...UCA-5'\n_____________\|______________________________\|\n_____________91_____________________________61\n	183 -- 189	70 -- 76	-33.7206 kcal/mol	4.25464 kcal/mol	8.62576 kcal/mol	169 199@LB@ \| \|@LB@5'-UAA...ACAUG UA G UC GAAUG...UCA-3'@LB@ GCA ACGACAACACAACAU CAC CCG@LB@ \|\|\| \|\|:\|\|\|\|\|\|\|\|\|\|\|\| \|\|\| \|\|\|@LB@ CGU UGUUGUUGUGUUGUA GUG GGC@LB@3'-UUU...GUUAA UUG UU AUUCG...UCA-5'@LB@ \| \|@LB@ 91 61@LB@@LB@@LB@Energy -21.66 kcal/mol@LB@Hybridization Energy -33.7206 kcal/mol@LB@Unfolding Energy - mRNA 4.25464 kcal/mol@LB@Unfolding Energy - sRNA 8.62576 kcal/mol@LB@@LB@Position - mRNA 170 -- 198@LB@Position - sRNA 62 -- 90@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 70 -- 76@LB@
74	0.003449	0.1596	stm1129	N/A	-19.64	0.020096	190 -- 238	139 -- 186	N-acetylmannosamine-6-phosphate 2-epimerase	stm3337	_____________189__________________________________239\n_____________\|____________________________________\|\n5'-AUA...UGGAU________UAGC_____U__AACA_________C__AAACG...AAA-3'\n______________GUCACUAU____CAGGC_GG____AAGUGUACA_GA\n______________:\|\|\|\|\|\|\|____\|\|\|:\|_\|\|____\|\|:\|\|\|\|\|\|_\|\|\n______________UAGUGAUA____GUCUG_CC____UUUACAUGU_CU\n3'-UUU...GUAAU________CCU______U__CA___________C__UCACU...UCA-5'\n_____________\|____________________________________\|\n_____________187__________________________________138\n	229 -- 235	142 -- 148	-26.4502 kcal/mol	8.56913 kcal/mol	5.67007 kcal/mol	189 239@LB@ \| \|@LB@5'-AUA...UGGAU UAGC U AACA C AAACG...AAA-3'@LB@ GUCACUAU CAGGC GG AAGUGUACA GA@LB@ :\|\|\|\|\|\|\| \|\|\|:\| \|\| \|\|:\|\|\|\|\|\| \|\|@LB@ UAGUGAUA GUCUG CC UUUACAUGU CU@LB@3'-UUU...GUAAU CCU U CA C UCACU...UCA-5'@LB@ \| \|@LB@ 187 138@LB@@LB@@LB@Energy -19.64 kcal/mol@LB@Hybridization Energy -26.4502 kcal/mol@LB@Unfolding Energy - mRNA 8.56913 kcal/mol@LB@Unfolding Energy - sRNA 5.67007 kcal/mol@LB@@LB@Position - mRNA 190 -- 238@LB@Position - sRNA 139 -- 186@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 142 -- 148@LB@
27	0.0006872	0.08814	stm1806	nhaB	-13.59	0.196266	64 -- 136	66 -- 135	Na+/H+ antiporter NhaB		_____________63___________________________________________________________________________137\n_____________\|____________________________________________________________________________\|\n5'-AGC...AUGAA_________GAUCAAG______AUU______U_____CU______AUC_U____G__UU__UU____U________CUCGC...CAU-3'\n______________GAAAAAGGG_______GC_ACC____UCUGA_AUCGC__GCCAAU___G_UAAG_AC__GC__GCAU__CGUCGCG\n______________\|\|\|\|\|\|\|\|\|_______\|\|_\|\|\|____\|\|\|\|\|_\|\|\|\|\|__:\|\|\|\|\|___\|_:\|\|:_\|\|__:\|__:\|\|:__\|:\|\|:\|:\n______________CUUUUUCCC_______CG_UGG____AGACU_UAGCG__UGGUUA___C_GUUU_UG__UG__UGUG__GUAGUGU\n3'-UUU...CUUCA_________AUCAGAG__A___CACC___________UC______A________G__U___U_____UU_______UGGCA...UCA-5'\n_____________\|____________________________________________________________________________\|\n_____________136__________________________________________________________________________65\n	130 -- 136	66 -- 72	-51.3167 kcal/mol	14.8404 kcal/mol	22.5826 kcal/mol	63 137@LB@ \| \|@LB@5'-AGC...AUGAA GAUCAAG AUU U CU AUC U G UU UU U CUCGC...CAU-3'@LB@ GAAAAAGGG GC ACC UCUGA AUCGC GCCAAU G UAAG AC GC GCAU CGUCGCG@LB@ \|\|\|\|\|\|\|\|\| \|\| \|\|\| \|\|\|\|\| \|\|\|\|\| :\|\|\|\|\| \| :\|\|: \|\| :\| :\|\|: \|:\|\|:\|:@LB@ CUUUUUCCC CG UGG AGACU UAGCG UGGUUA C GUUU UG UG UGUG GUAGUGU@LB@3'-UUU...CUUCA AUCAGAG A CACC UC A G U U UU UGGCA...UCA-5'@LB@ \| \|@LB@ 136 65@LB@@LB@@LB@Energy -13.59 kcal/mol@LB@Hybridization Energy -51.3167 kcal/mol@LB@Unfolding Energy - mRNA 14.8404 kcal/mol@LB@Unfolding Energy - sRNA 22.5826 kcal/mol@LB@@LB@Position - mRNA 64 -- 136@LB@Position - sRNA 66 -- 135@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 66 -- 72@LB@
111	0.005436	0.1728	stm2683	yfjB	-15.36	0.103307	255 -- 299	43 -- 90	NAD(+) kinase		_____________254___________________________________________________________________300\n_____________\|_____________________________________________________________________\|\n5'-CUC...UUCGC__________GAU____UU______UUCAA__________ACUCACAUU_____AUCAAUCU_______AAGGA...AGG-3'\n______________UUAUUAUGGG___CAGA__CAGGGU________GGGAAGU___________GUC________UCGCUAC\n______________\|:\|:\|\|\|\|\|:___\|\|\|\|__\|\|\|\|\|\|________:\|\|\|\|\|\|___________\|\|\|________\|\|\|\|\|\|\|\n______________AGUGAUACCU___GUCU__GUCCCA________UCCUUCA___________CAG________AGCGAUG\n3'-UUU...UAAUU_________________________UUUACAUG_______CUUUUUCCCAU__________________GCACC...UCA-5'\n_____________\|_____________________________________________________________________\|\n_____________91____________________________________________________________________42\n	179 -- 185	115 -- 121	-40.6869 kcal/mol	14.2494 kcal/mol	12.858 kcal/mol	254 300@LB@ \| \|@LB@5'-CUC...UUCGC GAU UU UUCAA ACUCACAUU AUCAAUCU AAGGA...AGG-3'@LB@ UUAUUAUGGG CAGA CAGGGU GGGAAGU GUC UCGCUAC@LB@ \|:\|:\|\|\|\|\|: \|\|\|\| \|\|\|\|\|\| :\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ AGUGAUACCU GUCU GUCCCA UCCUUCA CAG AGCGAUG@LB@3'-UUU...UAAUU UUUACAUG CUUUUUCCCAU GCACC...UCA-5'@LB@ \| \|@LB@ 91 42@LB@@LB@@LB@Energy -15.36 kcal/mol@LB@Hybridization Energy -40.6869 kcal/mol@LB@Unfolding Energy - mRNA 14.2494 kcal/mol@LB@Unfolding Energy - sRNA 12.858 kcal/mol@LB@@LB@Position - mRNA 255 -- 299@LB@Position - sRNA 43 -- 90@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 115 -- 121@LB@
9	0.0001316	0.05206	stm1221	cobB	-19.79	0.018892	28 -- 73	51 -- 101	NAD-dependent protein deacylase		_____________27__________________74\n_____________\|___________________\|\n5'-UCG...UUACG___________________UGGCG...UGG-3'\n______________GCA___AUAACAACGCAAC\n______________\|\|\|___\|:\|\|\|\|\|\|:\|\|\|\|\n______________CGU___UGUUGUUGUGUUG\n3'-UUU...GUUAA___UUG_____________UAGUG...UCA-5'\n_____________\|___________________\|\n_____________102_________________50\n	57 -- 63	72 -- 78	-19.3364 kcal/mol	2.6852 kcal/mol	3.80362 kcal/mol	27 74@LB@ \| \|@LB@5'-UCG...UUACG UGGCG...UGG-3'@LB@ GCA AUAACAACGCAAC@LB@ \|\|\| \|:\|\|\|\|\|\|:\|\|\|\|@LB@ CGU UGUUGUUGUGUUG@LB@3'-UUU...GUUAA UUG UAGUG...UCA-5'@LB@ \| \|@LB@ 102 50@LB@@LB@@LB@Energy -19.79 kcal/mol@LB@Hybridization Energy -19.3364 kcal/mol@LB@Unfolding Energy - mRNA 2.6852 kcal/mol@LB@Unfolding Energy - sRNA 3.80362 kcal/mol@LB@@LB@Position - mRNA 28 -- 73@LB@Position - sRNA 51 -- 101@LB@Position Seed - mRNA 57 -- 63@LB@Position Seed - sRNA 72 -- 78@LB@
141	0.007251	0.182	stm2325	nuoE	-19.46	0.021521	159 -- 233	56 -- 129	NADH-quinone oxidoreductase subunit E		_____________158_____________________________________________________________________________234\n_____________\|_______________________________________________________________________________\|\n5'-AUG...UAUCU_______A___AUU____UAU___A_____________CUAAUUAU______G_________AC___A___________UUUGA...GUG-3'\n______________GGGUAGU_UCG___UUGU___GUC_GA__UGUGGACCG________GCACGA_AAU_CAACA__CAC_AACCG_AGGCU\n______________\|\|\|\|\|\|\|_\|\|\|___::\|\|___\|\|\|_\|\|__:\|::\|\|\|\|:________:\|\|\|:\|_\|\|:_\|\|\|\|\|__\|\|\|_\|\|\|\|\|_\|:\|\|:\n______________CCCAUCA_AGC___GGCA___CAG_CU__GCGUCUGGU________UGUGUU_UUG_GUUGU__GUG_UUGGC_UUCGG\n3'-UUU...UUUUU_______G___GAU____C_____A__UA_________UAACGUU_______G___U_____A__________A_____UUUUC...UCA-5'\n_____________\|_______________________________________________________________________________\|\n_____________130_____________________________________________________________________________55\n	159 -- 165	123 -- 129	-58.9967 kcal/mol	15.8863 kcal/mol	27.1281 kcal/mol	158 234@LB@ \| \|@LB@5'-AUG...UAUCU A AUU UAU A CUAAUUAU G AC A UUUGA...GUG-3'@LB@ GGGUAGU UCG UUGU GUC GA UGUGGACCG GCACGA AAU CAACA CAC AACCG AGGCU@LB@ \|\|\|\|\|\|\| \|\|\| ::\|\| \|\|\| \|\| :\|::\|\|\|\|: :\|\|\|:\| \|\|: \|\|\|\|\| \|\|\| \|\|\|\|\| \|:\|\|:@LB@ CCCAUCA AGC GGCA CAG CU GCGUCUGGU UGUGUU UUG GUUGU GUG UUGGC UUCGG@LB@3'-UUU...UUUUU G GAU C A UA UAACGUU G U A A UUUUC...UCA-5'@LB@ \| \|@LB@ 130 55@LB@@LB@@LB@Energy -19.46 kcal/mol@LB@Hybridization Energy -58.9967 kcal/mol@LB@Unfolding Energy - mRNA 15.8863 kcal/mol@LB@Unfolding Energy - sRNA 27.1281 kcal/mol@LB@@LB@Position - mRNA 159 -- 233@LB@Position - sRNA 56 -- 129@LB@Position Seed - mRNA 159 -- 165@LB@Position Seed - sRNA 123 -- 129@LB@
148	0.007836	0.1845	stm2318	nuoL	-12.84	0.254324	144 -- 178	37 -- 76	NADH-quinone oxidoreductase subunit L		_____________143___________________179\n_____________\|_____________________\|\n5'-GGG...AGACC_____U____U__________UUCUC...UUG-3'\n______________GAUGG_CAGG___GAUGUACA\n______________\|\|::\|_\|\|\|\|___:\|\|\|\|\|\|\|\n______________CUGUC_GUCC___UUACAUGU\n3'-UUU...GAUAC_____U____CAU________CCUUC...UCA-5'\n_____________\|_____________________\|\n_____________77____________________36\n	82 -- 88	142 -- 148	-19.9967 kcal/mol	7.20144 kcal/mol	3.50251 kcal/mol	143 179@LB@ \| \|@LB@5'-GGG...AGACC U U UUCUC...UUG-3'@LB@ GAUGG CAGG GAUGUACA@LB@ \|\|::\| \|\|\|\| :\|\|\|\|\|\|\|@LB@ CUGUC GUCC UUACAUGU@LB@3'-UUU...GAUAC U CAU CCUUC...UCA-5'@LB@ \| \|@LB@ 77 36@LB@@LB@@LB@Energy -12.84 kcal/mol@LB@Hybridization Energy -19.9967 kcal/mol@LB@Unfolding Energy - mRNA 7.20144 kcal/mol@LB@Unfolding Energy - sRNA 3.50251 kcal/mol@LB@@LB@Position - mRNA 144 -- 178@LB@Position - sRNA 37 -- 76@LB@Position Seed - mRNA 82 -- 88@LB@Position Seed - sRNA 142 -- 148@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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