Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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	Additional homologs
183	0.01807	0.3104	b1508	hipB	-7.23	0.331427	238 -- 247	10 -- 19	antitoxin of HipAB toxin-antitoxin system	b1299 b1434	_____________237________248\n_____________\|__________\|\n5'-AUG...GCAAU__________AAUGA...AAA-3'\n______________UGGCGAAUGC\n______________\|::\|:\|\|\|\|\|\n______________AUUGUUUACG\n3'-UUU...CUACU__________CGCAG...AAG-5'\n_____________\|__________\|\n_____________20_________9\n	241 -- 247	10 -- 16	-11.7956 kcal/mol	3.36082 kcal/mol	1.20833 kcal/mol	237 248@LB@ \| \|@LB@5'-AUG...GCAAU AAUGA...AAA-3'@LB@ UGGCGAAUGC@LB@ \|::\|:\|\|\|\|\|@LB@ AUUGUUUACG@LB@3'-UUU...CUACU CGCAG...AAG-5'@LB@ \| \|@LB@ 20 9@LB@@LB@@LB@Energy -7.23 kcal/mol@LB@Hybridization Energy -11.7956 kcal/mol@LB@Unfolding Energy - mRNA 3.36082 kcal/mol@LB@Unfolding Energy - sRNA 1.20833 kcal/mol@LB@@LB@Position - mRNA 238 -- 247@LB@Position - sRNA 10 -- 19@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 10 -- 16@LB@
171	0.01687	0.3104	b1512	lsrR	-11.43	0.068975	231 -- 262	7 -- 31	lsr operon transcriptional repressor	b4295	_____________230______________________________263\n_____________\|________________________________\|\n5'-GCU...CAGAA______AUGUG___A__AG_______C_____GAUCG...AGA-3'\n______________CAGGGA_____UGA_GA__AACAGGU_GCGCG\n______________\|\|\|\|\|\|_____\|\|\|_\|\|__\|\|\|\|::\|_\|\|\|\|\|\n______________GUCCCU_____ACU_CU__UUGUUUA_CGCGC\n3'-UUU...CUUAA______________A__A______________AGAAAG-5'\n_____________\|________________________________\|\n_____________32_______________________________6\n	250 -- 256	12 -- 18	-27.0439 kcal/mol	7.86672 kcal/mol	7.75103 kcal/mol	230 263@LB@ \| \|@LB@5'-GCU...CAGAA AUGUG A AG C GAUCG...AGA-3'@LB@ CAGGGA UGA GA AACAGGU GCGCG@LB@ \|\|\|\|\|\| \|\|\| \|\| \|\|\|\|::\| \|\|\|\|\|@LB@ GUCCCU ACU CU UUGUUUA CGCGC@LB@3'-UUU...CUUAA A A AGAAAG-5'@LB@ \| \|@LB@ 32 6@LB@@LB@@LB@Energy -11.43 kcal/mol@LB@Hybridization Energy -27.0439 kcal/mol@LB@Unfolding Energy - mRNA 7.86672 kcal/mol@LB@Unfolding Energy - sRNA 7.75103 kcal/mol@LB@@LB@Position - mRNA 231 -- 262@LB@Position - sRNA 7 -- 31@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 12 -- 18@LB@
163	0.0151	0.3104	b1517	lsrF	-8.60	0.205199	166 -- 179	8 -- 21	putative autoinducer-2 (AI-2) aldolase		_____________165____________180\n_____________\|______________\|\n5'-AAA...AAUAC___UU_U_______AUUAC...AUU-3'\n______________GAU__C_GAUGUGC\n______________\|\|\|__\|_:\|\|\|:\|\|\n______________CUA__G_UUACGCG\n3'-UUU...UACUA___UU_U_______CAGAAAG-5'\n_____________\|______________\|\n_____________22_____________7\n	173 -- 179	8 -- 14	-12.6785 kcal/mol	2.84069 kcal/mol	1.23638 kcal/mol	165 180@LB@ \| \|@LB@5'-AAA...AAUAC UU U AUUAC...AUU-3'@LB@ GAU C GAUGUGC@LB@ \|\|\| \| :\|\|\|:\|\|@LB@ CUA G UUACGCG@LB@3'-UUU...UACUA UU U CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -12.6785 kcal/mol@LB@Unfolding Energy - mRNA 2.84069 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 166 -- 179@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 8 -- 14@LB@
181	0.01793	0.3104	b1594	mlc	-11.10	0.078496	11 -- 37	1 -- 18	glucosamine anaerobic growth regulon transcriptional repressor; autorepressor		_____________10__________________________38\n_____________\|___________________________\|\n5'-AAA...UCAUG______GUCCGGC_______AA_____GUAUU...GUA-3'\n______________AACAAA_______UGCGCGU__CUUUC\n______________\|\|\|\|\|\|_______\|\|\|\|\|\|\|__\|\|\|\|\|\n______________UUGUUU_______ACGCGCA__GAAAG\n3'-UUU...UACUA___________________________-5'\n_____________\|__________________________\|\n_____________19_________________________1\n	24 -- 30	6 -- 12	-16.8416 kcal/mol	4.49753 kcal/mol	1.24077 kcal/mol	10 38@LB@ \| \|@LB@5'-AAA...UCAUG GUCCGGC AA GUAUU...GUA-3'@LB@ AACAAA UGCGCGU CUUUC@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ UUGUUU ACGCGCA GAAAG@LB@3'-UUU...UACUA -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -11.10 kcal/mol@LB@Hybridization Energy -16.8416 kcal/mol@LB@Unfolding Energy - mRNA 4.49753 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 11 -- 37@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 6 -- 12@LB@
55	0.005043	0.3024	b1625	cnu	-10.91	0.084723	38 -- 57	1 -- 21	nucleoid-associated oriC-binding protein; H-NS and StpA stabilizing factor		_____________37____________________58\n_____________\|_____________________\|\n5'-UUU...UCAGG_________________AC__UUUUC...AUC-3'\n______________GAUAGUAAA_GCGCGUU__UC\n______________\|\|\|\|::\|\|\|_\|\|\|\|\|\|:__\|\|\n______________CUAUUGUUU_CGCGCAG__AG\n3'-UUU...UACUA_________A_______AA__-5'\n_____________\|____________________\|\n_____________22___________________1\n	47 -- 53	5 -- 11	-17.9355 kcal/mol	5.76636 kcal/mol	1.25763 kcal/mol	37 58@LB@ \| \|@LB@5'-UUU...UCAGG AC UUUUC...AUC-3'@LB@ GAUAGUAAA GCGCGUU UC@LB@ \|\|\|\|::\|\|\| \|\|\|\|\|\|: \|\|@LB@ CUAUUGUUU CGCGCAG AG@LB@3'-UUU...UACUA A AA -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -10.91 kcal/mol@LB@Hybridization Energy -17.9355 kcal/mol@LB@Unfolding Energy - mRNA 5.76636 kcal/mol@LB@Unfolding Energy - sRNA 1.25763 kcal/mol@LB@@LB@Position - mRNA 38 -- 57@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 5 -- 11@LB@
42	0.002847	0.2296	b1638	pdxH	-9.07	0.172497	29 -- 35	5 -- 11	pyridoxine 5'-phosphate oxidase		_____________28______36\n_____________\|_______\|\n5'-UCU...CUGGC_______ACACU...CCC-3'\n______________GCGCGUU\n______________\|\|\|\|\|\|:\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	29 -- 35	5 -- 11	-12.2635 kcal/mol	2.08033 kcal/mol	1.11145 kcal/mol	28 36@LB@ \| \|@LB@5'-UCU...CUGGC ACACU...CCC-3'@LB@ GCGCGUU@LB@ \|\|\|\|\|\|:@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -9.07 kcal/mol@LB@Hybridization Energy -12.2635 kcal/mol@LB@Unfolding Energy - mRNA 2.08033 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 29 -- 35@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 29 -- 35@LB@Position Seed - sRNA 5 -- 11@LB@
26	0.001545	0.1943	b1678	ldtE	-10.42	0.102915	208 -- 217	2 -- 11	murein L D-transpeptidase		_____________207________218\n_____________\|__________\|\n5'-UCU...GAAAC__________GCUUA...GCC-3'\n______________GCGCGUCUUU\n______________\|\|\|\|\|\|\|\|\|\|\n______________CGCGCAGAAA\n3'-UUU...GUUUA__________G-5'\n_____________\|__________\|\n_____________12_________1\n	211 -- 217	2 -- 8	-16.5846 kcal/mol	4.99595 kcal/mol	1.16977 kcal/mol	207 218@LB@ \| \|@LB@5'-UCU...GAAAC GCUUA...GCC-3'@LB@ GCGCGUCUUU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CGCGCAGAAA@LB@3'-UUU...GUUUA G-5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -10.42 kcal/mol@LB@Hybridization Energy -16.5846 kcal/mol@LB@Unfolding Energy - mRNA 4.99595 kcal/mol@LB@Unfolding Energy - sRNA 1.16977 kcal/mol@LB@@LB@Position - mRNA 208 -- 217@LB@Position - sRNA 2 -- 11@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 2 -- 8@LB@
161	0.01501	0.3104	b1709	btuD	-8.32	0.227073	129 -- 137	1 -- 9	vitamin B12 ABC transporter ATPase		_____________128_______138\n_____________\|_________\|\n5'-GCA...AUCCA_________CCCGG...GGC-3'\n______________GCGUUUUUC\n______________\|\|\|\|:\|\|\|\|\n______________CGCAGAAAG\n3'-UUU...UUACG_________-5'\n_____________\|________\|\n_____________10_______1\n	131 -- 137	1 -- 7	-11.771 kcal/mol	2.3321 kcal/mol	1.11751 kcal/mol	128 138@LB@ \| \|@LB@5'-GCA...AUCCA CCCGG...GGC-3'@LB@ GCGUUUUUC@LB@ \|\|\|\|:\|\|\|\|@LB@ CGCAGAAAG@LB@3'-UUU...UUACG -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.32 kcal/mol@LB@Hybridization Energy -11.771 kcal/mol@LB@Unfolding Energy - mRNA 2.3321 kcal/mol@LB@Unfolding Energy - sRNA 1.11751 kcal/mol@LB@@LB@Position - mRNA 129 -- 137@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 131 -- 137@LB@Position Seed - sRNA 1 -- 7@LB@
104	0.01032	0.3104	b1714	pheS	-13.82	0.025875	273 -- 287	5 -- 21	phenylalanine tRNA synthetase alpha subunit		_____________272_______________288\n_____________\|_________________\|\n5'-UUG...CGUUA_________________GAAUA...GUA-3'\n______________GAUAAU__GUGCGCGUC\n______________\|\|\|\|\|:__:\|\|\|\|\|\|\|\|\n______________CUAUUG__UACGCGCAG\n3'-UUU...UACUA______UU_________AAAG-5'\n_____________\|_________________\|\n_____________22________________4\n	281 -- 287	5 -- 11	-20.2911 kcal/mol	5.22554 kcal/mol	1.24955 kcal/mol	272 288@LB@ \| \|@LB@5'-UUG...CGUUA GAAUA...GUA-3'@LB@ GAUAAU GUGCGCGUC@LB@ \|\|\|\|\|: :\|\|\|\|\|\|\|\|@LB@ CUAUUG UACGCGCAG@LB@3'-UUU...UACUA UU AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -13.82 kcal/mol@LB@Hybridization Energy -20.2911 kcal/mol@LB@Unfolding Energy - mRNA 5.22554 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 273 -- 287@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 5 -- 11@LB@
110	0.01118	0.3104	b1726	yniB	-10.98	0.082506	169 -- 185	3 -- 23	putative inner membrane protein		_____________168___________________186\n_____________\|_____________________\|\n5'-AAG...ACUAA_____________________AAUCA...UGA-3'\n______________GUGA_AACGA___CGCGUCUU\n______________:\|\|\|_\|\|\|:\|___\|\|\|\|\|\|\|\|\n______________UACU_UUGUU___GCGCAGAA\n3'-UUU...CCUAC____A_____UAC________AG-5'\n_____________\|_____________________\|\n_____________24____________________2\n	179 -- 185	3 -- 9	-16.6558 kcal/mol	3.14383 kcal/mol	2.53367 kcal/mol	168 186@LB@ \| \|@LB@5'-AAG...ACUAA AAUCA...UGA-3'@LB@ GUGA AACGA CGCGUCUU@LB@ :\|\|\| \|\|\|:\| \|\|\|\|\|\|\|\|@LB@ UACU UUGUU GCGCAGAA@LB@3'-UUU...CCUAC A UAC AG-5'@LB@ \| \|@LB@ 24 2@LB@@LB@@LB@Energy -10.98 kcal/mol@LB@Hybridization Energy -16.6558 kcal/mol@LB@Unfolding Energy - mRNA 3.14383 kcal/mol@LB@Unfolding Energy - sRNA 2.53367 kcal/mol@LB@@LB@Position - mRNA 169 -- 185@LB@Position - sRNA 3 -- 23@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 3 -- 9@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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