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
182	0.01014	0.1966	stm3011	galR	-12.96	0.243649	22 -- 54	60 -- 90	transcriptional regulator GalR	_____________21_________________________________________55\n_____________\|__________________________________________\|\n_________5'-AC____C____U____UGCCA______AAUC__________UU_GCAAA...GGC-3'\n______________CUGA_UCGC_GGCC_____GCAGAC____GCAACAGCGC__C\n______________\|\|\|\|_\|\|\|\|_\|:\|\|_____\|\|\|:\|\|____:\|\|\|\|\|:\|:\|__\|\n______________GACU_AGCG_CUGG_____CGUUUG____UGUUGUUGUG__G\n3'-UUU...CACCA____U____U____UUAA_____________________UU_UAGUG...UCA-5'\n_____________\|__________________________________________\|\n_____________91_________________________________________59\n	35 -- 41	75 -- 81	-39.0068 kcal/mol	12.9734 kcal/mol	13.5432 kcal/mol	21 55@LB@ \| \|@LB@ 5'-AC C U UGCCA AAUC UU GCAAA...GGC-3'@LB@ CUGA UCGC GGCC GCAGAC GCAACAGCGC C@LB@ \|\|\|\| \|\|\|\| \|:\|\| \|\|\|:\|\| :\|\|\|\|\|:\|:\| \|@LB@ GACU AGCG CUGG CGUUUG UGUUGUUGUG G@LB@3'-UUU...CACCA U U UUAA UU UAGUG...UCA-5'@LB@ \| \|@LB@ 91 59@LB@@LB@@LB@Energy -12.96 kcal/mol@LB@Hybridization Energy -39.0068 kcal/mol@LB@Unfolding Energy - mRNA 12.9734 kcal/mol@LB@Unfolding Energy - sRNA 13.5432 kcal/mol@LB@@LB@Position - mRNA 22 -- 54@LB@Position - sRNA 60 -- 90@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 75 -- 81@LB@
76	0.003538	0.1596	stm3058	pepP	-14.75	0.129287	129 -- 167	36 -- 78	Xaa-Pro aminopeptidase	_____________128_________________168\n_____________\|___________________\|\n5'-CGA...CUGGC___________CCG_____GCCGC...GCA-3'\n______________GCAAAUGCAGC___GCAGC\n______________\|\|\|\|\|::\|\|:\|___:\|\|:\|\n______________CGUUUGUGUUG___UGUUG\n3'-UUU...GUUAA___________UUG_____UAGUG...UCA-5'\n_____________\|___________________\|\n_____________79__________________35\n	249 -- 255	80 -- 86	-18.5262 kcal/mol	6.77337 kcal/mol	3.80362 kcal/mol	128 168@LB@ \| \|@LB@5'-CGA...CUGGC CCG GCCGC...GCA-3'@LB@ GCAAAUGCAGC GCAGC@LB@ \|\|\|\|\|::\|\|:\| :\|\|:\|@LB@ CGUUUGUGUUG UGUUG@LB@3'-UUU...GUUAA UUG UAGUG...UCA-5'@LB@ \| \|@LB@ 79 35@LB@@LB@@LB@Energy -14.75 kcal/mol@LB@Hybridization Energy -18.5262 kcal/mol@LB@Unfolding Energy - mRNA 6.77337 kcal/mol@LB@Unfolding Energy - sRNA 3.80362 kcal/mol@LB@@LB@Position - mRNA 129 -- 167@LB@Position - sRNA 36 -- 78@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 80 -- 86@LB@
109	0.005328	0.1728	stm3082	N/A	-12.60	0.275269	106 -- 154	38 -- 90	galactonate oxidoreductase	_____________105________________________155\n_____________\|__________________________\|\n5'-AAU...ACAAC______UUUUUA_______UU_____GGCCU...CGG-3'\n______________GCAGAC______AACAACA__CAGCA\n______________\|\|\|:\|\|______\|\|\|\|\|\|\|__\|\|:\|\|\n______________CGUUUG______UUGUUGU__GUUGU\n3'-UUU...GUUAA______UG__________________AGUGU...UCA-5'\n_____________\|__________________________\|\n_____________91_________________________37\n	118 -- 124	76 -- 82	-16.9817 kcal/mol	2.50135 kcal/mol	3.80671 kcal/mol	105 155@LB@ \| \|@LB@5'-AAU...ACAAC UUUUUA UU GGCCU...CGG-3'@LB@ GCAGAC AACAACA CAGCA@LB@ \|\|\|:\|\| \|\|\|\|\|\|\| \|\|:\|\|@LB@ CGUUUG UUGUUGU GUUGU@LB@3'-UUU...GUUAA UG AGUGU...UCA-5'@LB@ \| \|@LB@ 91 37@LB@@LB@@LB@Energy -12.60 kcal/mol@LB@Hybridization Energy -16.9817 kcal/mol@LB@Unfolding Energy - mRNA 2.50135 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 106 -- 154@LB@Position - sRNA 38 -- 90@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 76 -- 82@LB@
163	0.008532	0.1864	stm3093	endA	-16.58	0.065141	135 -- 160	72 -- 101	deoxyribonuclease I	_____________134___________________________________161\n_____________\|_____________________________________\|\n5'-CCA...CUUUC_____________________U_______________UUUCG...CGG-3'\n______________CUGA___GCGGACUGAUUGCA_ACA____GACACAAC\n______________\|\|\|\|___\|\|:\|\|\|::\|\|\|\|\|\|_\|\|\|____:\|\|\|\|\|\|\|\n______________GACU___CGUCUGGUUAACGU_UGU____UUGUGUUG\n3'-UUU...CACCA____UAG______________U___GUUG________UAGUG...UCA-5'\n_____________\|_____________________________________\|\n_____________102___________________________________71\n	154 -- 160	72 -- 78	-36.4155 kcal/mol	5.60666 kcal/mol	13.5432 kcal/mol	134 161@LB@ \| \|@LB@5'-CCA...CUUUC U UUUCG...CGG-3'@LB@ CUGA GCGGACUGAUUGCA ACA GACACAAC@LB@ \|\|\|\| \|\|:\|\|\|::\|\|\|\|\|\| \|\|\| :\|\|\|\|\|\|\|@LB@ GACU CGUCUGGUUAACGU UGU UUGUGUUG@LB@3'-UUU...CACCA UAG U GUUG UAGUG...UCA-5'@LB@ \| \|@LB@ 102 71@LB@@LB@@LB@Energy -16.58 kcal/mol@LB@Hybridization Energy -36.4155 kcal/mol@LB@Unfolding Energy - mRNA 5.60666 kcal/mol@LB@Unfolding Energy - sRNA 13.5432 kcal/mol@LB@@LB@Position - mRNA 135 -- 160@LB@Position - sRNA 72 -- 101@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 72 -- 78@LB@
125	0.006333	0.1774	stm3094	yggJ	-12.37	0.297521	35 -- 55	69 -- 89	putative cytoplasmic protein	_____________34____________________56\n_____________\|_____________________\|\n5'-GCG...GCCAA__________UUUU_______UGGGA...AGA-3'\n______________CAAACGCAGC____UAACGUC\n______________\|\|\|\|\|:\|\|:\|____:\|\|\|:\|\|\n______________GUUUGUGUUG____GUUGUAG\n3'-UUU...UUAAC__________UUGU_______UGUUG...UCA-5'\n_____________\|_____________________\|\n_____________90____________________68\n	49 -- 55	69 -- 75	-19.7914 kcal/mol	1.34113 kcal/mol	4.32311 kcal/mol	34 56@LB@ \| \|@LB@5'-GCG...GCCAA UUUU UGGGA...AGA-3'@LB@ CAAACGCAGC UAACGUC@LB@ \|\|\|\|\|:\|\|:\| :\|\|\|:\|\|@LB@ GUUUGUGUUG GUUGUAG@LB@3'-UUU...UUAAC UUGU UGUUG...UCA-5'@LB@ \| \|@LB@ 90 68@LB@@LB@@LB@Energy -12.37 kcal/mol@LB@Hybridization Energy -19.7914 kcal/mol@LB@Unfolding Energy - mRNA 1.34113 kcal/mol@LB@Unfolding Energy - sRNA 4.32311 kcal/mol@LB@@LB@Position - mRNA 35 -- 55@LB@Position - sRNA 69 -- 89@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 69 -- 75@LB@
29	0.0007392	0.08814	stm3096	yqgE	-16.45	0.068552	198 -- 251	37 -- 84	DUF179 domain-containing protein	_____________197___________252\n_____________\|_____________\|\n5'-UGG...UAUAU_____________CAGGA...GCG-3'\n______________UUGCGAGCACAAC\n______________\|\|\|\|:\|:\|\|\|\|\|\|\n______________AACGUUUGUGUUG\n3'-UUU...UGGUU_____________UUGUG...UCA-5'\n_____________\|_____________\|\n_____________85____________36\n	284 -- 290	80 -- 86	-18.5161 kcal/mol	2.82597 kcal/mol	3.5889 kcal/mol	197 252@LB@ \| \|@LB@5'-UGG...UAUAU CAGGA...GCG-3'@LB@ UUGCGAGCACAAC@LB@ \|\|\|\|:\|:\|\|\|\|\|\|@LB@ AACGUUUGUGUUG@LB@3'-UUU...UGGUU UUGUG...UCA-5'@LB@ \| \|@LB@ 85 36@LB@@LB@@LB@Energy -16.45 kcal/mol@LB@Hybridization Energy -18.5161 kcal/mol@LB@Unfolding Energy - mRNA 2.82597 kcal/mol@LB@Unfolding Energy - sRNA 3.5889 kcal/mol@LB@@LB@Position - mRNA 198 -- 251@LB@Position - sRNA 37 -- 84@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 80 -- 86@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@
140	0.007169	0.182	stm3126	N/A	-18.02	0.037639	66 -- 114	39 -- 91	putative amino acid transporter	_____________65_______________________________115\n_____________\|________________________________\|\n5'-AUU...GCGCA______G______U___________UU_____UAUCC...UGA-3'\n______________UGCGGG_ACGGCG_CACAACGUUAU__ACCGU\n______________\|\|\|:::_\|\|::\|:_\|\|\|\|\|\|:\|:\|:__\|\|\|\|\|\n______________ACGUUU_UGUUGU_GUGUUGUAGUG__UGGCA\n3'-UUU...GGUUA______G______U___________U______UUCGG...UCA-5'\n_____________\|________________________________\|\n_____________92_______________________________38\n	82 -- 88	69 -- 75	-33.8851 kcal/mol	10.4253 kcal/mol	9.42541 kcal/mol	65 115@LB@ \| \|@LB@5'-AUU...GCGCA G U UU UAUCC...UGA-3'@LB@ UGCGGG ACGGCG CACAACGUUAU ACCGU@LB@ \|\|\|::: \|\|::\|: \|\|\|\|\|\|:\|:\|: \|\|\|\|\|@LB@ ACGUUU UGUUGU GUGUUGUAGUG UGGCA@LB@3'-UUU...GGUUA G U U UUCGG...UCA-5'@LB@ \| \|@LB@ 92 38@LB@@LB@@LB@Energy -18.02 kcal/mol@LB@Hybridization Energy -33.8851 kcal/mol@LB@Unfolding Energy - mRNA 10.4253 kcal/mol@LB@Unfolding Energy - sRNA 9.42541 kcal/mol@LB@@LB@Position - mRNA 66 -- 114@LB@Position - sRNA 39 -- 91@LB@Position Seed - mRNA 82 -- 88@LB@Position Seed - sRNA 69 -- 75@LB@
25	0.0006298	0.08814	stm3161	metC	-13.21	0.223681	190 -- 249	35 -- 90	cystathionine beta-lyase	_____________189__________________250\n_____________\|____________________\|\n5'-CAA...AACUG_________G__________AAAAA...CAC-3'\n______________GUAAACGCA__GACGCAGCA\n______________\|:\|\|\|\|:\|\|__:\|\|:\|\|:\|\|\n______________CGUUUGUGU__UUGUGUUGU\n3'-UUU...GUUAA_________UG_________AGUGU...UCA-5'\n_____________\|____________________\|\n_____________91___________________34\n	243 -- 249	71 -- 77	-21.5854 kcal/mol	5.07977 kcal/mol	3.80671 kcal/mol	189 250@LB@ \| \|@LB@5'-CAA...AACUG G AAAAA...CAC-3'@LB@ GUAAACGCA GACGCAGCA@LB@ \|:\|\|\|\|:\|\| :\|\|:\|\|:\|\|@LB@ CGUUUGUGU UUGUGUUGU@LB@3'-UUU...GUUAA UG AGUGU...UCA-5'@LB@ \| \|@LB@ 91 34@LB@@LB@@LB@Energy -13.21 kcal/mol@LB@Hybridization Energy -21.5854 kcal/mol@LB@Unfolding Energy - mRNA 5.07977 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 190 -- 249@LB@Position - sRNA 35 -- 90@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 71 -- 77@LB@
50	0.001812	0.1291	stm3207	ygiH	-15.41	0.101358	70 -- 101	63 -- 93	acyl-phosphate--glycerol-3-phosphate O-acyltransferase	_____________69___________________________________102\n_____________\|____________________________________\|\n5'-UAU...CGAAA_____UCUAU__________U_______________UGCCU...CGC-3'\n______________GUUGC_____AAAUACAAUA_C____CAUCACGACC\n______________:\|\|\|\|_____\|\|\|:\|\|\|\|:\|_\|____\|\|\|\|\|\|:\|\|\|\n______________UAACG_____UUUGUGUUGU_G____GUAGUGUUGG\n3'-UUU...CUGGU____________________U_UGUU__________CAUUC...UCA-5'\n_____________\|____________________________________\|\n_____________94___________________________________62\n	95 -- 101	63 -- 69	-25.69 kcal/mol	1.94006 kcal/mol	8.62086 kcal/mol	69 102@LB@ \| \|@LB@5'-UAU...CGAAA UCUAU U UGCCU...CGC-3'@LB@ GUUGC AAAUACAAUA C CAUCACGACC@LB@ :\|\|\|\| \|\|\|:\|\|\|\|:\| \| \|\|\|\|\|\|:\|\|\|@LB@ UAACG UUUGUGUUGU G GUAGUGUUGG@LB@3'-UUU...CUGGU U UGUU CAUUC...UCA-5'@LB@ \| \|@LB@ 94 62@LB@@LB@@LB@Energy -15.41 kcal/mol@LB@Hybridization Energy -25.69 kcal/mol@LB@Unfolding Energy - mRNA 1.94006 kcal/mol@LB@Unfolding Energy - sRNA 8.62086 kcal/mol@LB@@LB@Position - mRNA 70 -- 101@LB@Position - sRNA 63 -- 93@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 63 -- 69@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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