Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
67	0.01414	0.6177	b0474	adk	-7.17	0.151538	186 -- 198	39 -- 51	adenylate kinase	_____________185___________199\n_____________\|_____________\|\n5'-ACC...AUUUU_______U_____CAAUG...AUA-3'\n______________AAGGGGA_UUUCG\n______________\|\|\|:\|\|\|_\|\|\|\|:\n______________UUCUCCU_AAAGU\n3'-UUU...GCAGU_______U_____AAAAA...ACA-5'\n_____________\|_____________\|\n_____________52____________38\n	186 -- 192	45 -- 51	-12.5937 kcal/mol	4.3836 kcal/mol	1.04441 kcal/mol	185 199@LB@ \| \|@LB@5'-ACC...AUUUU U CAAUG...AUA-3'@LB@ AAGGGGA UUUCG@LB@ \|\|\|:\|\|\| \|\|\|\|:@LB@ UUCUCCU AAAGU@LB@3'-UUU...GCAGU U AAAAA...ACA-5'@LB@ \| \|@LB@ 52 38@LB@@LB@@LB@Energy -7.17 kcal/mol@LB@Hybridization Energy -12.5937 kcal/mol@LB@Unfolding Energy - mRNA 4.3836 kcal/mol@LB@Unfolding Energy - sRNA 1.04441 kcal/mol@LB@@LB@Position - mRNA 186 -- 198@LB@Position - sRNA 39 -- 51@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 45 -- 51@LB@
105	0.0216	0.6177	b2962	yggX	-9.20	0.059738	186 -- 194	45 -- 53	oxidative damage protective factor for iron-sulfur proteins	_____________185_______195\n_____________\|_________\|\n5'-UCA...GUCGA_________UGAUU...AGA-3'\n______________UAAAGAGGA\n______________:\|\|\|\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	188 -- 194	45 -- 51	-10.7665 kcal/mol	0.645872 kcal/mol	0.917553 kcal/mol	185 195@LB@ \| \|@LB@5'-UCA...GUCGA UGAUU...AGA-3'@LB@ UAAAGAGGA@LB@ :\|\|\|\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.20 kcal/mol@LB@Hybridization Energy -10.7665 kcal/mol@LB@Unfolding Energy - mRNA 0.645872 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 186 -- 194@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 45 -- 51@LB@
142	0.02758	0.6177	b3186	rplU	-10.01	0.040887	186 -- 200	38 -- 52	50S ribosomal subunit protein L21	_____________185_____________201\n_____________\|_______________\|\n5'-UUA...GCGCG____C__________AUGUA...UUG-3'\n______________GAAG_GGAGUUUUAU\n______________:\|\|\|_\|\|\|:\|\|\|:\|\|\n______________UUUC_CCUUAAAGUA\n3'-UUU...GGCAG____U__________AAAAA...ACA-5'\n_____________\|_______________\|\n_____________53______________37\n	194 -- 200	38 -- 44	-13.3778 kcal/mol	2.29537 kcal/mol	1.0693 kcal/mol	185 201@LB@ \| \|@LB@5'-UUA...GCGCG C AUGUA...UUG-3'@LB@ GAAG GGAGUUUUAU@LB@ :\|\|\| \|\|\|:\|\|\|:\|\|@LB@ UUUC CCUUAAAGUA@LB@3'-UUU...GGCAG U AAAAA...ACA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -10.01 kcal/mol@LB@Hybridization Energy -13.3778 kcal/mol@LB@Unfolding Energy - mRNA 2.29537 kcal/mol@LB@Unfolding Energy - sRNA 1.0693 kcal/mol@LB@@LB@Position - mRNA 186 -- 200@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 38 -- 44@LB@
147	0.02922	0.6177	b3836	tatA	-6.91	0.169904	186 -- 195	44 -- 53	TatABCE protein translocation system subunit	_____________185________196\n_____________\|__________\|\n5'-CUA...UCUAC__C_______CAUGU...GUG-3'\n______________CA_AGAGGAA\n______________\|\|_\|\|\|\|\|\|\|\n______________GU_UCUCCUU\n3'-UUU...GGGCA__U_______AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	189 -- 195	44 -- 50	-10.6779 kcal/mol	2.84312 kcal/mol	0.927997 kcal/mol	185 196@LB@ \| \|@LB@5'-CUA...UCUAC C CAUGU...GUG-3'@LB@ CA AGAGGAA@LB@ \|\| \|\|\|\|\|\|\|@LB@ GU UCUCCUU@LB@3'-UUU...GGGCA U AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -6.91 kcal/mol@LB@Hybridization Energy -10.6779 kcal/mol@LB@Unfolding Energy - mRNA 2.84312 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 186 -- 195@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
158	0.03174	0.6177	b3185	rpmA	-9.10	0.062717	186 -- 199	39 -- 52	50S ribosomal subunit protein L27	_____________185____________200\n_____________\|______________\|\n5'-GAA...GACCU______A_______AAUGG...CGG-3'\n______________GAGGAG_GAUUUCA\n______________:\|:\|\|\|_:\|\|\|\|\|\|\n______________UUUCUC_UUAAAGU\n3'-UUU...GGCAG______C_______AAAAA...ACA-5'\n_____________\|______________\|\n_____________53_____________38\n	193 -- 199	39 -- 45	-11.8509 kcal/mol	1.7019 kcal/mol	1.05043 kcal/mol	185 200@LB@ \| \|@LB@5'-GAA...GACCU A AAUGG...CGG-3'@LB@ GAGGAG GAUUUCA@LB@ :\|:\|\|\| :\|\|\|\|\|\|@LB@ UUUCUC UUAAAGU@LB@3'-UUU...GGCAG C AAAAA...ACA-5'@LB@ \| \|@LB@ 53 38@LB@@LB@@LB@Energy -9.10 kcal/mol@LB@Hybridization Energy -11.8509 kcal/mol@LB@Unfolding Energy - mRNA 1.7019 kcal/mol@LB@Unfolding Energy - sRNA 1.05043 kcal/mol@LB@@LB@Position - mRNA 186 -- 199@LB@Position - sRNA 39 -- 52@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 39 -- 45@LB@
163	0.03345	0.6177	b1235	rssB	-5.20	0.346272	186 -- 195	44 -- 55	PcnB-degradosome interaction factor; response regulator	_____________185__________196\n_____________\|____________\|\n5'-AAU...AGCCA____________AGAAC...CAA-3'\n______________GUC__AGGGGAG\n______________\|\|\|__\|\|:\|\|\|:\n______________CAG__UCUCCUU\n3'-UUU...CCGGG___UU_______AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	189 -- 195	44 -- 50	-10.1709 kcal/mol	4.02871 kcal/mol	0.941432 kcal/mol	185 196@LB@ \| \|@LB@5'-AAU...AGCCA AGAAC...CAA-3'@LB@ GUC AGGGGAG@LB@ \|\|\| \|\|:\|\|\|:@LB@ CAG UCUCCUU@LB@3'-UUU...CCGGG UU AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -5.20 kcal/mol@LB@Hybridization Energy -10.1709 kcal/mol@LB@Unfolding Energy - mRNA 4.02871 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 186 -- 195@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
166	0.03384	0.6177	b4035	malK	-4.35	0.473183	186 -- 196	44 -- 53	maltose ABC transportor ATPase	_____________185_________197\n_____________\|___________\|\n5'-CGC...UGUUA_______A___GGGCA...UGU-3'\n______________CAAAGGG_GAA\n______________\|\|\|\|\|:\|_\|\|\|\n______________GUUUCUC_CUU\n3'-UUU...GGGCA___________AAAGU...ACA-5'\n_____________\|___________\|\n_____________54__________43\n	186 -- 192	47 -- 53	-9.12531 kcal/mol	3.84302 kcal/mol	0.927997 kcal/mol	185 197@LB@ \| \|@LB@5'-CGC...UGUUA A GGGCA...UGU-3'@LB@ CAAAGGG GAA@LB@ \|\|\|\|\|:\| \|\|\|@LB@ GUUUCUC CUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -4.35 kcal/mol@LB@Hybridization Energy -9.12531 kcal/mol@LB@Unfolding Energy - mRNA 3.84302 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 186 -- 196@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 47 -- 53@LB@
178	0.03627	0.6177	b0924	mukB	-9.59	0.049840	186 -- 195	44 -- 53	chromosome condensin MukBEF ATPase and DNA-binding subunit	_____________185________196\n_____________\|__________\|\n5'-UGG...GAUAG__________GAAUA...CUG-3'\n______________CGGAGAGGAA\n______________\|::\|\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	189 -- 195	44 -- 50	-13.8471 kcal/mol	3.32824 kcal/mol	0.927997 kcal/mol	185 196@LB@ \| \|@LB@5'-UGG...GAUAG GAAUA...CUG-3'@LB@ CGGAGAGGAA@LB@ \|::\|\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -13.8471 kcal/mol@LB@Unfolding Energy - mRNA 3.32824 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 186 -- 195@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
40	0.007925	0.6129	b1109	ndh	-7.04	0.160101	187 -- 195	46 -- 54	respiratory NADH dehydrogenase 2/cupric reductase	_____________186_______196\n_____________\|_________\|\n5'-UGU...UAAAU_________UCACG...AAG-3'\n______________UUAAGGGGG\n______________\|:\|\|:\|:\|\|\n______________AGUUUCUCC\n3'-UUU...CGGGC_________UUAAA...ACA-5'\n_____________\|_________\|\n_____________55________45\n	189 -- 195	46 -- 52	-9.48398 kcal/mol	1.51964 kcal/mol	0.922697 kcal/mol	186 196@LB@ \| \|@LB@5'-UGU...UAAAU UCACG...AAG-3'@LB@ UUAAGGGGG@LB@ \|:\|\|:\|:\|\|@LB@ AGUUUCUCC@LB@3'-UUU...CGGGC UUAAA...ACA-5'@LB@ \| \|@LB@ 55 45@LB@@LB@@LB@Energy -7.04 kcal/mol@LB@Hybridization Energy -9.48398 kcal/mol@LB@Unfolding Energy - mRNA 1.51964 kcal/mol@LB@Unfolding Energy - sRNA 0.922697 kcal/mol@LB@@LB@Position - mRNA 187 -- 195@LB@Position - sRNA 46 -- 54@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 46 -- 52@LB@
61	0.01292	0.6177	b4154	frdA	-9.46	0.053105	187 -- 202	38 -- 54	anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit	_____________186_______________203\n_____________\|_________________\|\n5'-UAA...AACAA__U_________G____GCAAA...UCG-3'\n______________UC__GGAGGAAU_UCGU\n______________\|\|__:\|\|\|\|\|\|\|_\|\|:\|\n______________AG__UCUCCUUA_AGUA\n3'-UUU...CGGGC__UU________A____AAAAA...ACA-5'\n_____________\|_________________\|\n_____________55________________37\n	191 -- 197	43 -- 49	-14.1575 kcal/mol	3.5319 kcal/mol	1.17036 kcal/mol	186 203@LB@ \| \|@LB@5'-UAA...AACAA U G GCAAA...UCG-3'@LB@ UC GGAGGAAU UCGU@LB@ \|\| :\|\|\|\|\|\|\| \|\|:\|@LB@ AG UCUCCUUA AGUA@LB@3'-UUU...CGGGC UU A AAAAA...ACA-5'@LB@ \| \|@LB@ 55 37@LB@@LB@@LB@Energy -9.46 kcal/mol@LB@Hybridization Energy -14.1575 kcal/mol@LB@Unfolding Energy - mRNA 3.5319 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 187 -- 202@LB@Position - sRNA 38 -- 54@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 43 -- 49@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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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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