Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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_000913 Escherichia coli str. K-12 substr. MG1655

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
155	0.009115	0.2059	b1531	marA	-9.94	0.142609	213 -- 231	72 -- 89	multiple antibiotic resistance transcriptional regulator	_____________212_________________232\n_____________\|___________________\|\n5'-AAG...GACGC_______A_____U_____UUCAU...AGC-3'\n______________AAUACUG_CGCUA_UACCA\n______________\|\|\|\|\|\|\|_\|\|\|:\|_:\|\|\|\|\n______________UUAUGAC_GCGGU_GUGGU\n3'-UUU...CGCGC_____________U_____CCCUU...GUG-5'\n_____________\|___________________\|\n_____________90__________________71\n	213 -- 219	83 -- 89	-21.2611 kcal/mol	3.54366 kcal/mol	7.77515 kcal/mol	212 232@LB@ \| \|@LB@5'-AAG...GACGC A U UUCAU...AGC-3'@LB@ AAUACUG CGCUA UACCA@LB@ \|\|\|\|\|\|\| \|\|\|:\| :\|\|\|\|@LB@ UUAUGAC GCGGU GUGGU@LB@3'-UUU...CGCGC U CCCUU...GUG-5'@LB@ \| \|@LB@ 90 71@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -21.2611 kcal/mol@LB@Unfolding Energy - mRNA 3.54366 kcal/mol@LB@Unfolding Energy - sRNA 7.77515 kcal/mol@LB@@LB@Position - mRNA 213 -- 231@LB@Position - sRNA 72 -- 89@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 83 -- 89@LB@
18	0.001002	0.1727	b2284	nuoF	-9.91	0.144715	4 -- 28	1 -- 36	NADH:ubiquinone oxidoreductase chain F	_____________3____________________________________29\n_____________\|____________________________________\|\n________5'-AAC______C________________________G____UCGAG...ACG-3'\n______________GGUUAU_AGGGUAU___________UCAGGC_GCGC\n______________:\|\|\|\|:_\|\|\|\|:\|:___________\|\|\|\|\|\|_\|\|:\|\n______________UCAAUG_UCCCGUG___________AGUCCG_CGUG\n3'-UUU...ACUAC______U_______UCGUGACAAAA______G____-5'\n_____________\|___________________________________\|\n_____________37__________________________________1\n	11 -- 17	23 -- 29	-32.4986 kcal/mol	7.53826 kcal/mol	15.052 kcal/mol	3 29@LB@ \| \|@LB@ 5'-AAC C G UCGAG...ACG-3'@LB@ GGUUAU AGGGUAU UCAGGC GCGC@LB@ :\|\|\|\|: \|\|\|\|:\|: \|\|\|\|\|\| \|\|:\|@LB@ UCAAUG UCCCGUG AGUCCG CGUG@LB@3'-UUU...ACUAC U UCGUGACAAAA G -5'@LB@ \| \|@LB@ 37 1@LB@@LB@@LB@Energy -9.91 kcal/mol@LB@Hybridization Energy -32.4986 kcal/mol@LB@Unfolding Energy - mRNA 7.53826 kcal/mol@LB@Unfolding Energy - sRNA 15.052 kcal/mol@LB@@LB@Position - mRNA 4 -- 28@LB@Position - sRNA 1 -- 36@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 23 -- 29@LB@
139	0.008022	0.2031	b0311	betA	-9.91	0.144745	36 -- 54	64 -- 80	choline dehydrogenase a flavoprotein	_____________35__________________55\n_____________\|___________________\|\n5'-CGU...CUGGA________U____C_____CCCGG...AAG-3'\n______________UCAACACC_GGGG_GAAUC\n______________:\|\|\|\|\|\|\|_:\|\|\|_:\|\|\|\|\n______________GGUUGUGG_UCCC_UUUAG\n3'-UUU...GACGC___________________AACCG...GUG-5'\n_____________\|___________________\|\n_____________81__________________63\n	37 -- 43	73 -- 79	-20.9821 kcal/mol	4.03056 kcal/mol	7.04361 kcal/mol	35 55@LB@ \| \|@LB@5'-CGU...CUGGA U C CCCGG...AAG-3'@LB@ UCAACACC GGGG GAAUC@LB@ :\|\|\|\|\|\|\| :\|\|\| :\|\|\|\|@LB@ GGUUGUGG UCCC UUUAG@LB@3'-UUU...GACGC AACCG...GUG-5'@LB@ \| \|@LB@ 81 63@LB@@LB@@LB@Energy -9.91 kcal/mol@LB@Hybridization Energy -20.9821 kcal/mol@LB@Unfolding Energy - mRNA 4.03056 kcal/mol@LB@Unfolding Energy - sRNA 7.04361 kcal/mol@LB@@LB@Position - mRNA 36 -- 54@LB@Position - sRNA 64 -- 80@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 73 -- 79@LB@
53	0.002649	0.1727	b2289	lrhA	-9.83	0.149509	112 -- 119	68 -- 75	transcriptional repressor of flagellar motility and chemotaxis genes	_____________111______120\n_____________\|________\|\n5'-CUG...AAACU________GGCAC...CCG-3'\n______________GCCAGGGA\n______________:\|\|\|\|\|\|\|\n______________UGGUCCCU\n3'-UUU...GGUUG________UUAGA...GUG-5'\n_____________\|________\|\n_____________76_______67\n	113 -- 119	68 -- 74	-14.981 kcal/mol	1.464 kcal/mol	3.68273 kcal/mol	111 120@LB@ \| \|@LB@5'-CUG...AAACU GGCAC...CCG-3'@LB@ GCCAGGGA@LB@ :\|\|\|\|\|\|\|@LB@ UGGUCCCU@LB@3'-UUU...GGUUG UUAGA...GUG-5'@LB@ \| \|@LB@ 76 67@LB@@LB@@LB@Energy -9.83 kcal/mol@LB@Hybridization Energy -14.981 kcal/mol@LB@Unfolding Energy - mRNA 1.464 kcal/mol@LB@Unfolding Energy - sRNA 3.68273 kcal/mol@LB@@LB@Position - mRNA 112 -- 119@LB@Position - sRNA 68 -- 75@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 68 -- 74@LB@
189	0.01136	0.2116	b3413	gntX	-9.78	0.152759	211 -- 235	52 -- 76	DNA catabolic protein	_____________210_______________________236\n_____________\|_________________________\|\n5'-CCC...AACAG_______AUU__GC_____A_____AAUGC...AUA-3'\n______________UACCGGG___AU__UGGCU_UGCCG\n______________:\|\|\|:\|\|___\|\|__\|\|\|\|\|_:\|\|\|\|\n______________GUGGUCC___UA__ACCGA_GCGGC\n3'-UUU...CGGUU_______CUU__GA_____C_____AUUUA...GUG-5'\n_____________\|_________________________\|\n_____________77________________________51\n	211 -- 217	70 -- 76	-26.9968 kcal/mol	7.94838 kcal/mol	9.26585 kcal/mol	210 236@LB@ \| \|@LB@5'-CCC...AACAG AUU GC A AAUGC...AUA-3'@LB@ UACCGGG AU UGGCU UGCCG@LB@ :\|\|\|:\|\| \|\| \|\|\|\|\| :\|\|\|\|@LB@ GUGGUCC UA ACCGA GCGGC@LB@3'-UUU...CGGUU CUU GA C AUUUA...GUG-5'@LB@ \| \|@LB@ 77 51@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -26.9968 kcal/mol@LB@Unfolding Energy - mRNA 7.94838 kcal/mol@LB@Unfolding Energy - sRNA 9.26585 kcal/mol@LB@@LB@Position - mRNA 211 -- 235@LB@Position - sRNA 52 -- 76@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 70 -- 76@LB@
157	0.009216	0.2062	b3361	fic	-9.77	0.153316	103 -- 112	5 -- 14	stationary phase-induced protein putative toxin	_____________102________113\n_____________\|__________\|\n5'-CGC...CGUAA__________AGUCG...AAC-3'\n______________UUUUCAGGCC\n______________\|\|\|\|\|\|\|\|\|\|\n______________AAAAGUCCGG\n3'-UUU...UGACA__________CGUG-5'\n_____________\|__________\|\n_____________15_________4\n	106 -- 112	5 -- 11	-15.6889 kcal/mol	1.64573 kcal/mol	4.24834 kcal/mol	102 113@LB@ \| \|@LB@5'-CGC...CGUAA AGUCG...AAC-3'@LB@ UUUUCAGGCC@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ AAAAGUCCGG@LB@3'-UUU...UGACA CGUG-5'@LB@ \| \|@LB@ 15 4@LB@@LB@@LB@Energy -9.77 kcal/mol@LB@Hybridization Energy -15.6889 kcal/mol@LB@Unfolding Energy - mRNA 1.64573 kcal/mol@LB@Unfolding Energy - sRNA 4.24834 kcal/mol@LB@@LB@Position - mRNA 103 -- 112@LB@Position - sRNA 5 -- 14@LB@Position Seed - mRNA 106 -- 112@LB@Position Seed - sRNA 5 -- 11@LB@
119	0.006508	0.1913	b3834	ubiJ	-9.73	0.156135	145 -- 181	28 -- 78	aerobic ubiquinone synthesis protein SCP2 family protein	_____________144_________________________________________________182\n_____________\|___________________________________________________\|\n5'-GCU...AAUCU____G______UUGUGGC_____A___________________________UUCUG...UGG-3'\n______________GACG_CAGGGG_______GCUGC_UCGU______________GGUUAUAAG\n______________:\|\|:_\|\|\|\|\|:_______\|\|\|\|\|_:\|\|\|______________:\|\|\|\|:\|\|\|\n______________UUGU_GUCCCU_______CGACG_GGCA______________UCAAUGUUC\n3'-UUU...CGCGG____G______UUAGAAC_____C____UUUAAUAAUACUAC_________CCGUG...GUG-5'\n_____________\|___________________________________________________\|\n_____________79__________________________________________________27\n	175 -- 181	28 -- 34	-33.2852 kcal/mol	14.1676 kcal/mol	9.38606 kcal/mol	144 182@LB@ \| \|@LB@5'-GCU...AAUCU G UUGUGGC A UUCUG...UGG-3'@LB@ GACG CAGGGG GCUGC UCGU GGUUAUAAG@LB@ :\|\|: \|\|\|\|\|: \|\|\|\|\| :\|\|\| :\|\|\|\|:\|\|\|@LB@ UUGU GUCCCU CGACG GGCA UCAAUGUUC@LB@3'-UUU...CGCGG G UUAGAAC C UUUAAUAAUACUAC CCGUG...GUG-5'@LB@ \| \|@LB@ 79 27@LB@@LB@@LB@Energy -9.73 kcal/mol@LB@Hybridization Energy -33.2852 kcal/mol@LB@Unfolding Energy - mRNA 14.1676 kcal/mol@LB@Unfolding Energy - sRNA 9.38606 kcal/mol@LB@@LB@Position - mRNA 145 -- 181@LB@Position - sRNA 28 -- 78@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 28 -- 34@LB@
87	0.004792	0.1855	b0476	aes	-9.71	0.157345	34 -- 55	56 -- 76	acetyl esterase	_____________33______________________56\n_____________\|_______________________\|\n5'-CGU...ACGUU______________CA_______UUUUA...CAA-3'\n______________UACC_GGGAAAUUU__UGGUUGU\n______________:\|\|\|_\|\|\|\|\|\|\|:\|__\|\|\|:\|\|:\n______________GUGG_CCCUUUAGA__ACCGACG\n3'-UUU...CGGUU____U__________________CGGCA...GUG-5'\n_____________\|_______________________\|\n_____________77______________________55\n	49 -- 55	56 -- 62	-24.1621 kcal/mol	6.04137 kcal/mol	8.40711 kcal/mol	33 56@LB@ \| \|@LB@5'-CGU...ACGUU CA UUUUA...CAA-3'@LB@ UACC GGGAAAUUU UGGUUGU@LB@ :\|\|\| \|\|\|\|\|\|\|:\| \|\|\|:\|\|:@LB@ GUGG CCCUUUAGA ACCGACG@LB@3'-UUU...CGGUU U CGGCA...GUG-5'@LB@ \| \|@LB@ 77 55@LB@@LB@@LB@Energy -9.71 kcal/mol@LB@Hybridization Energy -24.1621 kcal/mol@LB@Unfolding Energy - mRNA 6.04137 kcal/mol@LB@Unfolding Energy - sRNA 8.40711 kcal/mol@LB@@LB@Position - mRNA 34 -- 55@LB@Position - sRNA 56 -- 76@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 56 -- 62@LB@
176	0.01044	0.208	b0933	ssuB	-9.69	0.158756	203 -- 226	69 -- 90	aliphatic sulfonate ABC transporter ATPase	_____________202______________________227\n_____________\|________________________\|\n5'-AUU...GGUAU_________UC___UGA_______CACGC...AUA-3'\n______________GAAUACUGC__GUC___ACCAGGG\n______________\|\|\|\|\|\|\|\|\|__\|:\|___\|\|\|\|\|\|\|\n______________CUUAUGACG__CGG___UGGUCCC\n3'-UUU...ACGCG______________UUG_______UUUAG...GUG-5'\n_____________\|________________________\|\n_____________91_______________________68\n	220 -- 226	69 -- 75	-28.101 kcal/mol	8.24441 kcal/mol	10.1628 kcal/mol	202 227@LB@ \| \|@LB@5'-AUU...GGUAU UC UGA CACGC...AUA-3'@LB@ GAAUACUGC GUC ACCAGGG@LB@ \|\|\|\|\|\|\|\|\| \|:\| \|\|\|\|\|\|\|@LB@ CUUAUGACG CGG UGGUCCC@LB@3'-UUU...ACGCG UUG UUUAG...GUG-5'@LB@ \| \|@LB@ 91 68@LB@@LB@@LB@Energy -9.69 kcal/mol@LB@Hybridization Energy -28.101 kcal/mol@LB@Unfolding Energy - mRNA 8.24441 kcal/mol@LB@Unfolding Energy - sRNA 10.1628 kcal/mol@LB@@LB@Position - mRNA 203 -- 226@LB@Position - sRNA 69 -- 90@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 69 -- 75@LB@
36	0.001988	0.1727	b2573	rpoE	-9.66	0.161217	247 -- 255	64 -- 72	RNA polymerase sigma E factor	_____________246_______256\n_____________\|_________\|\n5'-ACA...CCAGA_________AGAAA...UGG-3'\n______________AGGGAGAUC\n______________\|\|\|\|\|:\|\|\|\n______________UCCCUUUAG\n3'-UUU...UGUGG_________AACCG...GUG-5'\n_____________\|_________\|\n_____________73________63\n	249 -- 255	64 -- 70	-13.5601 kcal/mol	1.40253 kcal/mol	2.50058 kcal/mol	246 256@LB@ \| \|@LB@5'-ACA...CCAGA AGAAA...UGG-3'@LB@ AGGGAGAUC@LB@ \|\|\|\|\|:\|\|\|@LB@ UCCCUUUAG@LB@3'-UUU...UGUGG AACCG...GUG-5'@LB@ \| \|@LB@ 73 63@LB@@LB@@LB@Energy -9.66 kcal/mol@LB@Hybridization Energy -13.5601 kcal/mol@LB@Unfolding Energy - mRNA 1.40253 kcal/mol@LB@Unfolding Energy - sRNA 2.50058 kcal/mol@LB@@LB@Position - mRNA 247 -- 255@LB@Position - sRNA 64 -- 72@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 64 -- 70@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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