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
191	0.01055	0.1967	stm0634	ybeF	-18.83	0.027435	210 -- 262	35 -- 82	putative LysR family transcriptional regulator	_____________209____________________________________________________________263\n_____________\|______________________________________________________________\|\n5'-GCU...CGUGA____UA_____C_G____AAAG_______________UCAACA____________AAC____AAUUU...UGU-3'\n______________GUGA__AUAAU_A_GCAG____ACAACCG___GCCGA______CCUA_CAGGACA___CGCA\n______________\|::\|__\|:\|\|:_\|_:\|\|:____\|\|\|\|\|\|\|___\|\|\|:\|______\|\|:\|_\|\|\|:\|\|\|___\|\|\|\|\n______________CGUU__UGUUG_U_UGUU____UGUUGGC___CGGUU______GGGU_GUCUUGU___GCGU\n3'-UUU...GUUAA____UG_____U_G____GUAG_______AUU_____UUC_______A______________AAGGC...UCA-5'\n_____________\|______________________________________________________________\|\n_____________83_____________________________________________________________34\n	227 -- 233	62 -- 68	-42.1612 kcal/mol	9.04443 kcal/mol	22.5095 kcal/mol	209 263@LB@ \| \|@LB@5'-GCU...CGUGA UA C G AAAG UCAACA AAC AAUUU...UGU-3'@LB@ GUGA AUAAU A GCAG ACAACCG GCCGA CCUA CAGGACA CGCA@LB@ \|::\| \|:\|\|: \| :\|\|: \|\|\|\|\|\|\| \|\|\|:\| \|\|:\| \|\|\|:\|\|\| \|\|\|\|@LB@ CGUU UGUUG U UGUU UGUUGGC CGGUU GGGU GUCUUGU GCGU@LB@3'-UUU...GUUAA UG U G GUAG AUU UUC A AAGGC...UCA-5'@LB@ \| \|@LB@ 83 34@LB@@LB@@LB@Energy -18.83 kcal/mol@LB@Hybridization Energy -42.1612 kcal/mol@LB@Unfolding Energy - mRNA 9.04443 kcal/mol@LB@Unfolding Energy - sRNA 22.5095 kcal/mol@LB@@LB@Position - mRNA 210 -- 262@LB@Position - sRNA 35 -- 82@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 62 -- 68@LB@
192	0.01067	0.197	stm2650	yfiP	-13.22	0.223534	188 -- 232	36 -- 90	DTW domain-containing protein	_____________187_________________________233\n_____________\|___________________________\|\n5'-UCA...UCUCC________UUUCUAUGACC________UGUCC...GCU-3'\n______________GCAAACGC___________AAUAACGC\n______________\|\|\|\|\|\|:\|___________\|\|:\|\|\|:\|\n______________CGUUUGUG___________UUGUUGUG\n3'-UUU...GUUAA___________________________UUGUA...UCA-5'\n_____________\|___________________________\|\n_____________91__________________________35\n	208 -- 214	75 -- 81	-16.7007 kcal/mol	3.95203 kcal/mol	3.72363 kcal/mol	187 233@LB@ \| \|@LB@5'-UCA...UCUCC UUUCUAUGACC UGUCC...GCU-3'@LB@ GCAAACGC AAUAACGC@LB@ \|\|\|\|\|\|:\| \|\|:\|\|\|:\|@LB@ CGUUUGUG UUGUUGUG@LB@3'-UUU...GUUAA UUGUA...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -13.22 kcal/mol@LB@Hybridization Energy -16.7007 kcal/mol@LB@Unfolding Energy - mRNA 3.95203 kcal/mol@LB@Unfolding Energy - sRNA 3.72363 kcal/mol@LB@@LB@Position - mRNA 188 -- 232@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 75 -- 81@LB@
193	0.01075	0.197	stm3734	rph	-15.48	0.098722	165 -- 206	34 -- 78	ribonuclease PH	_____________164____________________________207\n_____________\|______________________________\|\n5'-GCG...AUAAU_____________U___UUU__________AUCUC...GAG-3'\n______________GCGCAGC__CACA_UCG___UAAGCCGGAG\n______________:\|:\|\|:\|__\|\|\|\|_:\|\|___\|\|\|\|\|\|::\|:\n______________UGUGUUG__GUGU_GGC___AUUCGGUUUU\n3'-UUU...GUUGU_______UA____U________________CGGGU...UCA-5'\n_____________\|______________________________\|\n_____________79_____________________________33\n	183 -- 189	55 -- 61	-24.9708 kcal/mol	4.11178 kcal/mol	11.3295 kcal/mol	164 207@LB@ \| \|@LB@5'-GCG...AUAAU U UUU AUCUC...GAG-3'@LB@ GCGCAGC CACA UCG UAAGCCGGAG@LB@ :\|:\|\|:\| \|\|\|\| :\|\| \|\|\|\|\|\|::\|:@LB@ UGUGUUG GUGU GGC AUUCGGUUUU@LB@3'-UUU...GUUGU UA U CGGGU...UCA-5'@LB@ \| \|@LB@ 79 33@LB@@LB@@LB@Energy -15.48 kcal/mol@LB@Hybridization Energy -24.9708 kcal/mol@LB@Unfolding Energy - mRNA 4.11178 kcal/mol@LB@Unfolding Energy - sRNA 11.3295 kcal/mol@LB@@LB@Position - mRNA 165 -- 206@LB@Position - sRNA 34 -- 78@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 55 -- 61@LB@
194	0.01081	0.197	stm1954	fliY	-13.82	0.181182	183 -- 228	153 -- 193	cystine ABC transporter substrate-binding protein	_____________182________________________229\n_____________\|__________________________\|\n5'-CAG...GUCUA_________AC____AUAUU______UACUA...UGC-3'\n______________UGGUCAUUA__GGCA_____CGGGGU\n______________\|::\|\|\|:\|\|__\|:\|\|_____\|:\|\|\|\|\n______________AUUAGUGAU__CUGU_____GUCCCA\n3'-UUU...AUGUA_________AC____CU_________UUUAC...UCA-5'\n_____________\|__________________________\|\n_____________194________________________152\n	173 -- 179	165 -- 171	-18.5851 kcal/mol	4.12345 kcal/mol	4.10259 kcal/mol	182 229@LB@ \| \|@LB@5'-CAG...GUCUA AC AUAUU UACUA...UGC-3'@LB@ UGGUCAUUA GGCA CGGGGU@LB@ \|::\|\|\|:\|\| \|:\|\| \|:\|\|\|\|@LB@ AUUAGUGAU CUGU GUCCCA@LB@3'-UUU...AUGUA AC CU UUUAC...UCA-5'@LB@ \| \|@LB@ 194 152@LB@@LB@@LB@Energy -13.82 kcal/mol@LB@Hybridization Energy -18.5851 kcal/mol@LB@Unfolding Energy - mRNA 4.12345 kcal/mol@LB@Unfolding Energy - sRNA 4.10259 kcal/mol@LB@@LB@Position - mRNA 183 -- 228@LB@Position - sRNA 153 -- 193@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 165 -- 171@LB@
195	0.01085	0.197	stm0549	fimZ	-13.17	0.226725	219 -- 235	155 -- 171	DNA-binding response regulator	_____________218___________236\n_____________\|_____________\|\n5'-CAG...CUGUU_____________AACAC...UGA-3'\n______________AUCAUUAUGGACG\n______________\|\|\|\|:\|\|\|\|\|\|\|:\n______________UAGUGAUACCUGU\n3'-UUU...GUAAU_____________CUGUC...UCA-5'\n_____________\|_____________\|\n_____________172___________154\n	225 -- 231	159 -- 165	-17.3187 kcal/mol	3.33371 kcal/mol	3.42647 kcal/mol	218 236@LB@ \| \|@LB@5'-CAG...CUGUU AACAC...UGA-3'@LB@ AUCAUUAUGGACG@LB@ \|\|\|\|:\|\|\|\|\|\|\|:@LB@ UAGUGAUACCUGU@LB@3'-UUU...GUAAU CUGUC...UCA-5'@LB@ \| \|@LB@ 172 154@LB@@LB@@LB@Energy -13.17 kcal/mol@LB@Hybridization Energy -17.3187 kcal/mol@LB@Unfolding Energy - mRNA 3.33371 kcal/mol@LB@Unfolding Energy - sRNA 3.42647 kcal/mol@LB@@LB@Position - mRNA 219 -- 235@LB@Position - sRNA 155 -- 171@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 159 -- 165@LB@
196	0.01089	0.197	stm3904	ilvD	-14.14	0.161583	237 -- 253	179 -- 194	dihydroxy-acid dehydratase	_____________236___________254\n_____________\|_____________\|\n5'-CGA...UGAAG___AA________AGUAA...GCA-3'\n______________GGA__AGAUGGGG\n______________\|\|\|__\|\|\|::\|\|\|\n______________CCU__UCUGUCCC\n3'-UUU...UGAUA___G_________AUUUA...UCA-5'\n_____________\|_____________\|\n_____________195___________178\n	182 -- 188	152 -- 158	-15.6614 kcal/mol	1.17371 kcal/mol	3.10307 kcal/mol	236 254@LB@ \| \|@LB@5'-CGA...UGAAG AA AGUAA...GCA-3'@LB@ GGA AGAUGGGG@LB@ \|\|\| \|\|\|::\|\|\|@LB@ CCU UCUGUCCC@LB@3'-UUU...UGAUA G AUUUA...UCA-5'@LB@ \| \|@LB@ 195 178@LB@@LB@@LB@Energy -14.14 kcal/mol@LB@Hybridization Energy -15.6614 kcal/mol@LB@Unfolding Energy - mRNA 1.17371 kcal/mol@LB@Unfolding Energy - sRNA 3.10307 kcal/mol@LB@@LB@Position - mRNA 237 -- 253@LB@Position - sRNA 179 -- 194@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 152 -- 158@LB@
197	0.01093	0.197	stm2924	rpoS	-16.80	0.060020	191 -- 216	36 -- 60	RNA polymerase sigma factor RpoS	_____________190________________________________217\n_____________\|__________________________________\|\n___5'-CGGGAACA_________U____C___GCAAAAAA________AUGGG...AGG-3'\n______________ACAGGAAGU_AAGG_GGG________UCGCUACU\n______________\|\|\|\|\|\|\|\|\|_\|\|::_\|\|\|________\|\|\|\|\|\|\|:\n______________UGUCCUUCA_UUUU_CCC________AGCGAUGG\n3'-UUU...UUACA_________C____U___AUCAG___________CACCA...UCA-5'\n_____________\|__________________________________\|\n_____________61_________________________________35\n	36 -- 42	114 -- 120	-31.3768 kcal/mol	8.74888 kcal/mol	8.99738 kcal/mol	190 217@LB@ \| \|@LB@ 5'-CGGGAACA U C GCAAAAAA AUGGG...AGG-3'@LB@ ACAGGAAGU AAGG GGG UCGCUACU@LB@ \|\|\|\|\|\|\|\|\| \|\|:: \|\|\| \|\|\|\|\|\|\|:@LB@ UGUCCUUCA UUUU CCC AGCGAUGG@LB@3'-UUU...UUACA C U AUCAG CACCA...UCA-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -16.80 kcal/mol@LB@Hybridization Energy -31.3768 kcal/mol@LB@Unfolding Energy - mRNA 8.74888 kcal/mol@LB@Unfolding Energy - sRNA 8.99738 kcal/mol@LB@@LB@Position - mRNA 191 -- 216@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 114 -- 120@LB@
198	0.01098	0.197	stm2803	N/A	-14.51	0.140962	192 -- 262	36 -- 101	DNA-binding transcriptional regulator	_____________191___________________________263\n_____________\|_____________________________\|\n5'-GCU...AAAAA________UA___C_____UAU_______UCGCU...CGC-3'\n______________GCAGACCA__UGC__GCGC___CAGCACA\n______________\|\|\|\|\|\|\|\|__\|\|\|__:\|:\|___\|\|:\|\|\|\|\n______________CGUCUGGU__ACG__UGUG___GUUGUGU\n3'-UUU...CUUAG________UA___UU____UU________UGUAG...UCA-5'\n_____________\|_____________________________\|\n_____________102___________________________35\n	213 -- 219	74 -- 80	-31.0005 kcal/mol	8.41541 kcal/mol	13.1066 kcal/mol	191 263@LB@ \| \|@LB@5'-GCU...AAAAA UA C UAU UCGCU...CGC-3'@LB@ GCAGACCA UGC GCGC CAGCACA@LB@ \|\|\|\|\|\|\|\| \|\|\| :\|:\| \|\|:\|\|\|\|@LB@ CGUCUGGU ACG UGUG GUUGUGU@LB@3'-UUU...CUUAG UA UU UU UGUAG...UCA-5'@LB@ \| \|@LB@ 102 35@LB@@LB@@LB@Energy -14.51 kcal/mol@LB@Hybridization Energy -31.0005 kcal/mol@LB@Unfolding Energy - mRNA 8.41541 kcal/mol@LB@Unfolding Energy - sRNA 13.1066 kcal/mol@LB@@LB@Position - mRNA 192 -- 262@LB@Position - sRNA 36 -- 101@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 74 -- 80@LB@
199	0.01101	0.197	stm3346	yhcM	-12.83	0.254909	186 -- 228	33 -- 82	cell division protein ZapE	_____________185____________________229\n_____________\|______________________\|\n5'-CAG...UUCAA_G__UA__________UAU___AAGCC...AAA-3'\n______________G_AA__ACAAUAACAU___GCA\n______________\|_\|\|__\|\|\|\|:\|\|\|\|:___:\|\|\n______________C_UU__UGUUGUUGUG___UGU\n3'-UUU...GUUAA_G__UG__________U_____AGUGU...UCA-5'\n_____________\|______________________\|\n_____________83_____________________32\n	193 -- 199	75 -- 81	-14.0954 kcal/mol	2.45302 kcal/mol	3.80671 kcal/mol	185 229@LB@ \| \|@LB@5'-CAG...UUCAA G UA UAU AAGCC...AAA-3'@LB@ G AA ACAAUAACAU GCA@LB@ \| \|\| \|\|\|\|:\|\|\|\|: :\|\|@LB@ C UU UGUUGUUGUG UGU@LB@3'-UUU...GUUAA G UG U AGUGU...UCA-5'@LB@ \| \|@LB@ 83 32@LB@@LB@@LB@Energy -12.83 kcal/mol@LB@Hybridization Energy -14.0954 kcal/mol@LB@Unfolding Energy - mRNA 2.45302 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 186 -- 228@LB@Position - sRNA 33 -- 82@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 75 -- 81@LB@
200	0.01112	0.198	stm2809	proV	-15.77	0.088450	57 -- 94	50 -- 85	glycine betaine/L-proline ABC transporter ATP-binding protein	_____________56______________________________________95\n_____________\|_______________________________________\|\n5'-UUC...AUCAC_____________C__________AUUCAU_________AAAUU...AAA-3'\n______________AGC_CGAUAGCAC____UCGCAAU______GCCAGAAGC\n______________\|:\|_\|:\|:\|:\|\|\|____\|\|:\|\|\|:______\|\|\|\|:\|\|\|\|\n______________UUG_GUUGUUGUG____AGUGUUG______CGGUUUUCG\n3'-UUU...AACGU___U_________UUGU_______GCAUU__________GGUAG...UCA-5'\n_____________\|_______________________________________\|\n_____________86______________________________________49\n	65 -- 71	75 -- 81	-32.303 kcal/mol	6.98444 kcal/mol	14.5427 kcal/mol	56 95@LB@ \| \|@LB@5'-UUC...AUCAC C AUUCAU AAAUU...AAA-3'@LB@ AGC CGAUAGCAC UCGCAAU GCCAGAAGC@LB@ \|:\| \|:\|:\|:\|\|\| \|\|:\|\|\|: \|\|\|\|:\|\|\|\|@LB@ UUG GUUGUUGUG AGUGUUG CGGUUUUCG@LB@3'-UUU...AACGU U UUGU GCAUU GGUAG...UCA-5'@LB@ \| \|@LB@ 86 49@LB@@LB@@LB@Energy -15.77 kcal/mol@LB@Hybridization Energy -32.303 kcal/mol@LB@Unfolding Energy - mRNA 6.98444 kcal/mol@LB@Unfolding Energy - sRNA 14.5427 kcal/mol@LB@@LB@Position - mRNA 57 -- 94@LB@Position - sRNA 50 -- 85@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 75 -- 81@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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