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
54	0.002071	0.1363	stm1429	ydhB	-17.23	0.050879	3 -- 45	36 -- 79	putative LysR family transcriptional regulator	_____________2___________________________________46\n_____________\|___________________________________\|\n5'-CAA...UAUCA________UU__CGCA___________________UUACG...UCA-3'\n______________GACAGACA__GU____GAGUGU__AGGGAGUGAAA\n______________\|\|\|\|\|\|\|\|__\|\|____:\|:\|\|\|__\|\|\|:\|\|\|\|\|\|\|\n______________CUGUCUGU__CA____UUUACA__UCCUUCACUUU\n3'-UUU...GAUAC________CC____________UG___________UUCCC...UCA-5'\n_____________\|___________________________________\|\n_____________80__________________________________35\n	136 -- 142	132 -- 138	-30.0385 kcal/mol	9.87391 kcal/mol	6.0649 kcal/mol	2 46@LB@ \| \|@LB@5'-CAA...UAUCA UU CGCA UUACG...UCA-3'@LB@ GACAGACA GU GAGUGU AGGGAGUGAAA@LB@ \|\|\|\|\|\|\|\| \|\| :\|:\|\|\| \|\|\|:\|\|\|\|\|\|\|@LB@ CUGUCUGU CA UUUACA UCCUUCACUUU@LB@3'-UUU...GAUAC CC UG UUCCC...UCA-5'@LB@ \| \|@LB@ 80 35@LB@@LB@@LB@Energy -17.23 kcal/mol@LB@Hybridization Energy -30.0385 kcal/mol@LB@Unfolding Energy - mRNA 9.87391 kcal/mol@LB@Unfolding Energy - sRNA 6.0649 kcal/mol@LB@@LB@Position - mRNA 3 -- 45@LB@Position - sRNA 36 -- 79@LB@Position Seed - mRNA 136 -- 142@LB@Position Seed - sRNA 132 -- 138@LB@
73	0.003444	0.1596	stm1437	ydhM	-18.33	0.033340	6 -- 47	35 -- 81	TetR family transcriptional regulator	_____________5_______________________48\n_____________\|_______________________\|\n5'-CGG...CAAAC___________CC___G______UGCUG...AGU-3'\n______________CGAACACGAUA__CGC_AACAUC\n______________\|:\|\|\|\|\|:\|:\|__\|:\|_\|\|\|\|\|\|\n______________GUUUGUGUUGU__GUG_UUGUAG\n3'-UUU...UUAAC___________U___________UGUUG...UCA-5'\n_____________\|_______________________\|\n_____________82______________________34\n	219 -- 225	79 -- 85	-19.8292 kcal/mol	2.08213 kcal/mol	4.32311 kcal/mol	5 48@LB@ \| \|@LB@5'-CGG...CAAAC CC G UGCUG...AGU-3'@LB@ CGAACACGAUA CGC AACAUC@LB@ \|:\|\|\|\|\|:\|:\| \|:\| \|\|\|\|\|\|@LB@ GUUUGUGUUGU GUG UUGUAG@LB@3'-UUU...UUAAC U UGUUG...UCA-5'@LB@ \| \|@LB@ 82 34@LB@@LB@@LB@Energy -18.33 kcal/mol@LB@Hybridization Energy -19.8292 kcal/mol@LB@Unfolding Energy - mRNA 2.08213 kcal/mol@LB@Unfolding Energy - sRNA 4.32311 kcal/mol@LB@@LB@Position - mRNA 6 -- 47@LB@Position - sRNA 35 -- 81@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 79 -- 85@LB@
26	0.0006768	0.08814	stm1365	ydiJ	-17.55	0.045121	78 -- 116	57 -- 91	similar to E. coli putative oxidase (AAC74757.1); Blastp hit to AAC74757.1 (1018 aa) 88% identity in aa 1 - 1017	_____________77_________________________117\n_____________\|__________________________\|\n5'-CUA...AAUGU_________AAUA_____________AACGA...CCA-3'\n______________GAUACAACA____ACGCAACA_CGCA\n______________:\|:\|\|\|\|\|\|____\|\|:\|\|\|\|\|_\|:\|\|\n______________UUGUGUUGU____UGUGUUGU_GUGU\n3'-UUU...AACGU_____________________A____UGGCA...UCA-5'\n_____________\|__________________________\|\n_____________92_________________________56\n	95 -- 101	71 -- 77	-21.9961 kcal/mol	1.97147 kcal/mol	5.98953 kcal/mol	77 117@LB@ \| \|@LB@5'-CUA...AAUGU AAUA AACGA...CCA-3'@LB@ GAUACAACA ACGCAACA CGCA@LB@ :\|:\|\|\|\|\|\| \|\|:\|\|\|\|\| \|:\|\|@LB@ UUGUGUUGU UGUGUUGU GUGU@LB@3'-UUU...AACGU A UGGCA...UCA-5'@LB@ \| \|@LB@ 92 56@LB@@LB@@LB@Energy -17.55 kcal/mol@LB@Hybridization Energy -21.9961 kcal/mol@LB@Unfolding Energy - mRNA 1.97147 kcal/mol@LB@Unfolding Energy - sRNA 5.98953 kcal/mol@LB@@LB@Position - mRNA 78 -- 116@LB@Position - sRNA 57 -- 91@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 71 -- 77@LB@
7	8.283e-05	0.04123	stm1953	yedO	-23.64	0.004188	172 -- 228	31 -- 88	D-cysteine desulfhydrase	_____________171__________________________________________________________229\n_____________\|____________________________________________________________\|\n5'-UAA...AAAAA___________________________GA___U___U____ACUA_____CUU_______UUCCC...GUG-3'\n______________GAACAC_AC__CACAACGUU___ACCG__GGC_CAA__GCC____CAUCA___AACGCGC\n______________:\|\|\|\|\|_\|\|__\|\|\|\|\|\|:\|:___\|\|\|\|__:\|\|_\|\|\|__\|\|\|____\|\|\|\|\|___\|\|\|:\|\|\|\n______________UUUGUG_UG__GUGUUGUAG___UGGC__UCG_GUU__CGG____GUAGU___UUGUGCG\n3'-UUU...UAACG______U__UU_________UGU____AU_______UU____________C_________UAAGG...UCA-5'\n_____________\|____________________________________________________________\|\n_____________89___________________________________________________________30\n	218 -- 224	36 -- 42	-46.0183 kcal/mol	9.00749 kcal/mol	22.3196 kcal/mol	171 229@LB@ \| \|@LB@5'-UAA...AAAAA GA U U ACUA CUU UUCCC...GUG-3'@LB@ GAACAC AC CACAACGUU ACCG GGC CAA GCC CAUCA AACGCGC@LB@ :\|\|\|\|\| \|\| \|\|\|\|\|\|:\|: \|\|\|\| :\|\| \|\|\| \|\|\| \|\|\|\|\| \|\|\|:\|\|\|@LB@ UUUGUG UG GUGUUGUAG UGGC UCG GUU CGG GUAGU UUGUGCG@LB@3'-UUU...UAACG U UU UGU AU UU C UAAGG...UCA-5'@LB@ \| \|@LB@ 89 30@LB@@LB@@LB@Energy -23.64 kcal/mol@LB@Hybridization Energy -46.0183 kcal/mol@LB@Unfolding Energy - mRNA 9.00749 kcal/mol@LB@Unfolding Energy - sRNA 22.3196 kcal/mol@LB@@LB@Position - mRNA 172 -- 228@LB@Position - sRNA 31 -- 88@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 36 -- 42@LB@
117	0.005749	0.1738	stm2562	yfhA	-19.31	0.022783	16 -- 66	47 -- 100	two-component system response regulator GlrR	_____________15____________67\n_____________\|_____________\|\n5'-CUG...AGGCC_____________UCGAU...UCG-3'\n______________UUGCAAACGCAGC\n______________\|\|\|\|\|\|\|\|:\|\|:\|\n______________AACGUUUGUGUUG\n3'-UUU...UGGUU_____________UUGUG...UCA-5'\n_____________\|_____________\|\n_____________101___________46\n	28 -- 34	80 -- 86	-18.759 kcal/mol	3.6583 kcal/mol	3.5889 kcal/mol	15 67@LB@ \| \|@LB@5'-CUG...AGGCC UCGAU...UCG-3'@LB@ UUGCAAACGCAGC@LB@ \|\|\|\|\|\|\|\|:\|\|:\|@LB@ AACGUUUGUGUUG@LB@3'-UUU...UGGUU UUGUG...UCA-5'@LB@ \| \|@LB@ 101 46@LB@@LB@@LB@Energy -19.31 kcal/mol@LB@Hybridization Energy -18.759 kcal/mol@LB@Unfolding Energy - mRNA 3.6583 kcal/mol@LB@Unfolding Energy - sRNA 3.5889 kcal/mol@LB@@LB@Position - mRNA 16 -- 66@LB@Position - sRNA 47 -- 100@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 80 -- 86@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@
88	0.00402	0.1596	stm2651	yfiQ	-16.02	0.080775	116 -- 159	50 -- 88	protein acetyltransferase	_____________115__________________________160\n_____________\|____________________________\|\n5'-CAA...AGGAA__________UCCGGGA___________AUAAA...GUA-3'\n______________AAACGCAACA_______AACGUCACAGC\n______________\|\|\|\|:\|\|\|\|\|_______\|\|\|:\|\|\|\|\|:\|\n______________UUUGUGUUGU_______UUGUAGUGUUG\n3'-UUU...UAACG__________UGUG______________GCAUU...UCA-5'\n_____________\|____________________________\|\n_____________89___________________________49\n	137 -- 143	64 -- 70	-25.6269 kcal/mol	4.45838 kcal/mol	7.90699 kcal/mol	115 160@LB@ \| \|@LB@5'-CAA...AGGAA UCCGGGA AUAAA...GUA-3'@LB@ AAACGCAACA AACGUCACAGC@LB@ \|\|\|\|:\|\|\|\|\| \|\|\|:\|\|\|\|\|:\|@LB@ UUUGUGUUGU UUGUAGUGUUG@LB@3'-UUU...UAACG UGUG GCAUU...UCA-5'@LB@ \| \|@LB@ 89 49@LB@@LB@@LB@Energy -16.02 kcal/mol@LB@Hybridization Energy -25.6269 kcal/mol@LB@Unfolding Energy - mRNA 4.45838 kcal/mol@LB@Unfolding Energy - sRNA 7.90699 kcal/mol@LB@@LB@Position - mRNA 116 -- 159@LB@Position - sRNA 50 -- 88@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 64 -- 70@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@
164	0.008796	0.191	stm2932	ygbE	-13.54	0.199482	240 -- 279	44 -- 82	putative inner membrane protein	_____________239________________280\n_____________\|__________________\|\n5'-CGC...GCGUA__________________UUUCA...CCA-3'\n______________AUAGC__CAUAACAUUAC\n______________\|:\|:\|__\|\|:\|\|\|\|\|:\|\|\n______________UGUUG__GUGUUGUAGUG\n3'-UUU...GUUUG_____UU___________UUGGC...UCA-5'\n_____________\|__________________\|\n_____________83_________________43\n	250 -- 256	67 -- 73	-14.8194 kcal/mol	1.59581 kcal/mol	5.25507 kcal/mol	239 280@LB@ \| \|@LB@5'-CGC...GCGUA UUUCA...CCA-3'@LB@ AUAGC CAUAACAUUAC@LB@ \|:\|:\| \|\|:\|\|\|\|\|:\|\|@LB@ UGUUG GUGUUGUAGUG@LB@3'-UUU...GUUUG UU UUGGC...UCA-5'@LB@ \| \|@LB@ 83 43@LB@@LB@@LB@Energy -13.54 kcal/mol@LB@Hybridization Energy -14.8194 kcal/mol@LB@Unfolding Energy - mRNA 1.59581 kcal/mol@LB@Unfolding Energy - sRNA 5.25507 kcal/mol@LB@@LB@Position - mRNA 240 -- 279@LB@Position - sRNA 44 -- 82@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 67 -- 73@LB@
89	0.004143	0.1596	stm2957	ygcA	-15.40	0.101796	159 -- 208	35 -- 82	23S rRNA (uracil(1939)-C(5))-methyltransferase	_____________158____________________________________________209\n_____________\|______________________________________________\|\n5'-AUA...UACUC_____AACG____GU_________UCAG___________UA_____AAUGA...GUC-3'\n______________UGCAA____GCGC__GACGACGCG____AUCAUAACCGU__AAGUC\n______________\|\|\|\|\|____:\|:\|__:\|\|:\|\|:\|:____\|\|\|\|:\|\|\|\|\|\|__\|\|\|:\|\n______________ACGUU____UGUG__UUGUUGUGU____UAGUGUUGGCA__UUCGG\n3'-UUU...GGUUA________________________UG____________________UUUUC...UCA-5'\n_____________\|______________________________________________\|\n_____________83_____________________________________________34\n	250 -- 256	61 -- 67	-36.475 kcal/mol	14.3441 kcal/mol	11.8308 kcal/mol	158 209@LB@ \| \|@LB@5'-AUA...UACUC AACG GU UCAG UA AAUGA...GUC-3'@LB@ UGCAA GCGC GACGACGCG AUCAUAACCGU AAGUC@LB@ \|\|\|\|\| :\|:\| :\|\|:\|\|:\|: \|\|\|\|:\|\|\|\|\|\| \|\|\|:\|@LB@ ACGUU UGUG UUGUUGUGU UAGUGUUGGCA UUCGG@LB@3'-UUU...GGUUA UG UUUUC...UCA-5'@LB@ \| \|@LB@ 83 34@LB@@LB@@LB@Energy -15.40 kcal/mol@LB@Hybridization Energy -36.475 kcal/mol@LB@Unfolding Energy - mRNA 14.3441 kcal/mol@LB@Unfolding Energy - sRNA 11.8308 kcal/mol@LB@@LB@Position - mRNA 159 -- 208@LB@Position - sRNA 35 -- 82@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 61 -- 67@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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