Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
111	0.01894	0.5385	b2600	tyrA	-7.88	0.238290	191 -- 206	74 -- 89	fused chorismate mutase T/prephenate dehydrogenase	_____________190______________207\n_____________\|________________\|\n5'-UCG...CUUAA_________UA_____GCUGA...UGG-3'\n______________GAGGUUUAU__UGGUU\n______________:\|:\|\|\|:\|:__\|\|\|:\|\n______________UUUCAAGUG__ACCGA\n3'-CGC...GGCGU_________CA_____AAUCA...AAG-5'\n_____________\|________________\|\n_____________90_______________73\n	193 -- 199	81 -- 87	-12.4695 kcal/mol	4.06959 kcal/mol	0.517373 kcal/mol	190 207@LB@ \| \|@LB@5'-UCG...CUUAA UA GCUGA...UGG-3'@LB@ GAGGUUUAU UGGUU@LB@ :\|:\|\|\|:\|: \|\|\|:\|@LB@ UUUCAAGUG ACCGA@LB@3'-CGC...GGCGU CA AAUCA...AAG-5'@LB@ \| \|@LB@ 90 73@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -12.4695 kcal/mol@LB@Unfolding Energy - mRNA 4.06959 kcal/mol@LB@Unfolding Energy - sRNA 0.517373 kcal/mol@LB@@LB@Position - mRNA 191 -- 206@LB@Position - sRNA 74 -- 89@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 81 -- 87@LB@
112	0.0191	0.5385	b0854	potF	-9.27	0.140763	36 -- 50	64 -- 78	putrescine ABC transporter periplasmic binding protein	_____________35______________51\n_____________\|_______________\|\n5'-UAC...AACCC_____AA________UUGCG...ACA-3'\n______________UGGCU__AGUUAUUC\n______________\|\|\|\|\|__\|\|\|\|\|\|\|\|\n______________ACCGA__UCAAUAAG\n3'-CGC...GUGCA_____AA________CUCAA...AAG-5'\n_____________\|_______________\|\n_____________79______________63\n	44 -- 50	64 -- 70	-15.0609 kcal/mol	5.5152 kcal/mol	0.273858 kcal/mol	35 51@LB@ \| \|@LB@5'-UAC...AACCC AA UUGCG...ACA-3'@LB@ UGGCU AGUUAUUC@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ ACCGA UCAAUAAG@LB@3'-CGC...GUGCA AA CUCAA...AAG-5'@LB@ \| \|@LB@ 79 63@LB@@LB@@LB@Energy -9.27 kcal/mol@LB@Hybridization Energy -15.0609 kcal/mol@LB@Unfolding Energy - mRNA 5.5152 kcal/mol@LB@Unfolding Energy - sRNA 0.273858 kcal/mol@LB@@LB@Position - mRNA 36 -- 50@LB@Position - sRNA 64 -- 78@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 64 -- 70@LB@
113	0.0192	0.5385	b2573	rpoE	-9.32	0.137991	165 -- 193	49 -- 83	RNA polymerase sigma E factor	_____________164___________________________________194\n_____________\|_____________________________________\|\n5'-ACA...GAUAG________AAA_______UG_________________ACCUC...UGG-3'\n______________CGCG_UGG___UUUGGUU_________GGGAGACUUU\n______________\|:\|\|_\|\|\|___\|\|\|:\|\|\|_________\|:\|\|:\|\|\|:\|\n______________GUGC_ACC___AAAUCAA_________CUCUUUGAGA\n3'-CGC...UUCAA____A___G_________UAAGCUCAA__________GCUUU...AAG-5'\n_____________\|_____________________________________\|\n_____________84____________________________________48\n	184 -- 190	52 -- 58	-21.709 kcal/mol	7.98 kcal/mol	4.40602 kcal/mol	164 194@LB@ \| \|@LB@5'-ACA...GAUAG AAA UG ACCUC...UGG-3'@LB@ CGCG UGG UUUGGUU GGGAGACUUU@LB@ \|:\|\| \|\|\| \|\|\|:\|\|\| \|:\|\|:\|\|\|:\|@LB@ GUGC ACC AAAUCAA CUCUUUGAGA@LB@3'-CGC...UUCAA A G UAAGCUCAA GCUUU...AAG-5'@LB@ \| \|@LB@ 84 48@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -21.709 kcal/mol@LB@Unfolding Energy - mRNA 7.98 kcal/mol@LB@Unfolding Energy - sRNA 4.40602 kcal/mol@LB@@LB@Position - mRNA 165 -- 193@LB@Position - sRNA 49 -- 83@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 52 -- 58@LB@
114	0.01931	0.5385	b1951	rcsA	-10.71	0.079523	269 -- 285	16 -- 29	transcriptional regulator of colanic acid capsular biosynthesis	_____________268_______________286\n_____________\|_________________\|\n5'-GUU...AGUAG__________AAA____AAAUC...UUG-3'\n______________AGGGGUUAAA___AGAG\n______________\|:\|\|\|\|\|\|\|\|___\|\|\|\|\n______________UUCCCAAUUU___UCUC\n3'-CGC...UGAAG_________________CACGG...AAG-5'\n_____________\|_________________\|\n_____________30________________15\n	272 -- 278	20 -- 26	-15.5636 kcal/mol	1.76121 kcal/mol	3.08831 kcal/mol	268 286@LB@ \| \|@LB@5'-GUU...AGUAG AAA AAAUC...UUG-3'@LB@ AGGGGUUAAA AGAG@LB@ \|:\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UUCCCAAUUU UCUC@LB@3'-CGC...UGAAG CACGG...AAG-5'@LB@ \| \|@LB@ 30 15@LB@@LB@@LB@Energy -10.71 kcal/mol@LB@Hybridization Energy -15.5636 kcal/mol@LB@Unfolding Energy - mRNA 1.76121 kcal/mol@LB@Unfolding Energy - sRNA 3.08831 kcal/mol@LB@@LB@Position - mRNA 269 -- 285@LB@Position - sRNA 16 -- 29@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 20 -- 26@LB@
115	0.01932	0.5385	b3475	acpT	-9.48	0.130030	187 -- 194	75 -- 82	4'-phosphopantetheinyl transferase	_____________186______195\n_____________\|________\|\n5'-GGG...AUUAA________CCUGA...GCU-3'\n______________ACGUUGGC\n______________\|\|\|\|\|\|\|\|\n______________UGCAACCG\n3'-CGC...UCAAG________AAAUC...AAG-5'\n_____________\|________\|\n_____________83_______74\n	188 -- 194	75 -- 81	-13.2305 kcal/mol	3.41608 kcal/mol	0.339284 kcal/mol	186 195@LB@ \| \|@LB@5'-GGG...AUUAA CCUGA...GCU-3'@LB@ ACGUUGGC@LB@ \|\|\|\|\|\|\|\|@LB@ UGCAACCG@LB@3'-CGC...UCAAG AAAUC...AAG-5'@LB@ \| \|@LB@ 83 74@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -13.2305 kcal/mol@LB@Unfolding Energy - mRNA 3.41608 kcal/mol@LB@Unfolding Energy - sRNA 0.339284 kcal/mol@LB@@LB@Position - mRNA 187 -- 194@LB@Position - sRNA 75 -- 82@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 75 -- 81@LB@
116	0.01945	0.5385	b1175	minD	-9.10	0.150484	222 -- 240	13 -- 34	inhibitor of FtsZ ring polymerization; chromosome-membrane tethering protein; membrane ATPase of the MinCDEE system	_____________221____________________241\n_____________\|______________________\|\n5'-CUG...UUGUU__________C___________UUGGU...AAA-3'\n______________ACUUC__GGG__AAAGGGGGUG\n______________\|\|\|\|\|__\|\|\|__\|\|\|:\|:\|\|\|\|\n______________UGAAG__CCC__UUUUCUCCAC\n3'-CGC...GUCAC_____UU___AA__________GGCGA...AAG-5'\n_____________\|______________________\|\n_____________35_____________________12\n	234 -- 240	13 -- 19	-19.7427 kcal/mol	7.311 kcal/mol	3.33198 kcal/mol	221 241@LB@ \| \|@LB@5'-CUG...UUGUU C UUGGU...AAA-3'@LB@ ACUUC GGG AAAGGGGGUG@LB@ \|\|\|\|\| \|\|\| \|\|\|:\|:\|\|\|\|@LB@ UGAAG CCC UUUUCUCCAC@LB@3'-CGC...GUCAC UU AA GGCGA...AAG-5'@LB@ \| \|@LB@ 35 12@LB@@LB@@LB@Energy -9.10 kcal/mol@LB@Hybridization Energy -19.7427 kcal/mol@LB@Unfolding Energy - mRNA 7.311 kcal/mol@LB@Unfolding Energy - sRNA 3.33198 kcal/mol@LB@@LB@Position - mRNA 222 -- 240@LB@Position - sRNA 13 -- 34@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 13 -- 19@LB@
117	0.01966	0.5385	b1203	ychF	-10.24	0.095997	26 -- 41	73 -- 87	catalase inhibitor protein; ATPase K+-dependent ribosome-associated	_____________25_______________42\n_____________\|________________\|\n5'-GAA...AAUGU_______A_A______GACCA...CAU-3'\n______________GGUUUAC_G_UGGCUU\n______________:\|\|\|:\|\|_\|_\|\|\|\|\|\|\n______________UCAAGUG_C_ACCGAA\n3'-CGC...CGUUU_________A______AUCAA...AAG-5'\n_____________\|________________\|\n_____________88_______________72\n	26 -- 32	81 -- 87	-15.1856 kcal/mol	4.42747 kcal/mol	0.51474 kcal/mol	25 42@LB@ \| \|@LB@5'-GAA...AAUGU A A GACCA...CAU-3'@LB@ GGUUUAC G UGGCUU@LB@ :\|\|\|:\|\| \| \|\|\|\|\|\|@LB@ UCAAGUG C ACCGAA@LB@3'-CGC...CGUUU A AUCAA...AAG-5'@LB@ \| \|@LB@ 88 72@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -15.1856 kcal/mol@LB@Unfolding Energy - mRNA 4.42747 kcal/mol@LB@Unfolding Energy - sRNA 0.51474 kcal/mol@LB@@LB@Position - mRNA 26 -- 41@LB@Position - sRNA 73 -- 87@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 81 -- 87@LB@
118	0.01985	0.5385	b2318	truA	-10.16	0.099312	131 -- 143	70 -- 82	tRNA pseudouridine(38-40) synthase	_____________130___________144\n_____________\|_____________\|\n5'-GUG...CGAUA_____C_______CGGCG...GCA-3'\n______________ACGUU_GCUUUGG\n______________\|\|\|\|\|_\|\|\|\|\|:\|\n______________UGCAA_CGAAAUC\n3'-CGC...UCAAG_____C_______AAUAA...AAG-5'\n_____________\|_____________\|\n_____________83____________69\n	137 -- 143	70 -- 76	-13.1761 kcal/mol	2.62838 kcal/mol	0.389672 kcal/mol	130 144@LB@ \| \|@LB@5'-GUG...CGAUA C CGGCG...GCA-3'@LB@ ACGUU GCUUUGG@LB@ \|\|\|\|\| \|\|\|\|\|:\|@LB@ UGCAA CGAAAUC@LB@3'-CGC...UCAAG C AAUAA...AAG-5'@LB@ \| \|@LB@ 83 69@LB@@LB@@LB@Energy -10.16 kcal/mol@LB@Hybridization Energy -13.1761 kcal/mol@LB@Unfolding Energy - mRNA 2.62838 kcal/mol@LB@Unfolding Energy - sRNA 0.389672 kcal/mol@LB@@LB@Position - mRNA 131 -- 143@LB@Position - sRNA 70 -- 82@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 70 -- 76@LB@
119	0.02023	0.5385	b3579	yiaO	-11.14	0.066893	104 -- 124	64 -- 84	2 3-diketo-L-gulonate-binding periplasmic protein	_____________103_____________________125\n_____________\|_______________________\|\n5'-ACU...UUCCC______CC_______________AUUAU...AAA-3'\n______________UUACGU__UGGUUUUA__UAUUC\n______________\|:\|\|\|\|__\|\|\|:\|\|\|\|__\|\|\|\|\|\n______________AGUGCA__ACCGAAAU__AUAAG\n3'-CGC...UUUCA________________CA_____CUCAA...AAG-5'\n_____________\|_______________________\|\n_____________85______________________63\n	113 -- 119	71 -- 77	-15.3214 kcal/mol	3.60448 kcal/mol	0.573392 kcal/mol	103 125@LB@ \| \|@LB@5'-ACU...UUCCC CC AUUAU...AAA-3'@LB@ UUACGU UGGUUUUA UAUUC@LB@ \|:\|\|\|\| \|\|\|:\|\|\|\| \|\|\|\|\|@LB@ AGUGCA ACCGAAAU AUAAG@LB@3'-CGC...UUUCA CA CUCAA...AAG-5'@LB@ \| \|@LB@ 85 63@LB@@LB@@LB@Energy -11.14 kcal/mol@LB@Hybridization Energy -15.3214 kcal/mol@LB@Unfolding Energy - mRNA 3.60448 kcal/mol@LB@Unfolding Energy - sRNA 0.573392 kcal/mol@LB@@LB@Position - mRNA 104 -- 124@LB@Position - sRNA 64 -- 84@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 71 -- 77@LB@
120	0.02045	0.5385	b0979	cbdB	-12.05	0.046235	177 -- 194	16 -- 34	cytochrome bd-II oxidase subunit II	_____________176_________________195\n_____________\|___________________\|\n5'-AUA...ACGCA__AA_______________AAAAU...GCU-3'\n______________GC__CAGGGG_UAAAGGAG\n______________:\|__\|\|:\|\|\|_\|\|\|\|:\|\|\|\n______________UG__GUUCCC_AUUUUCUC\n3'-CGC...GUCAC__AA______A________CACGG...AAG-5'\n_____________\|___________________\|\n_____________35__________________15\n	188 -- 194	16 -- 22	-18.7902 kcal/mol	3.40633 kcal/mol	3.33043 kcal/mol	176 195@LB@ \| \|@LB@5'-AUA...ACGCA AA AAAAU...GCU-3'@LB@ GC CAGGGG UAAAGGAG@LB@ :\| \|\|:\|\|\| \|\|\|\|:\|\|\|@LB@ UG GUUCCC AUUUUCUC@LB@3'-CGC...GUCAC AA A CACGG...AAG-5'@LB@ \| \|@LB@ 35 15@LB@@LB@@LB@Energy -12.05 kcal/mol@LB@Hybridization Energy -18.7902 kcal/mol@LB@Unfolding Energy - mRNA 3.40633 kcal/mol@LB@Unfolding Energy - sRNA 3.33043 kcal/mol@LB@@LB@Position - mRNA 177 -- 194@LB@Position - sRNA 16 -- 34@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 16 -- 22@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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