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
120	0.01222	0.3104	b0916	ycaQ	-9.32	0.156865	225 -- 243	1 -- 17	DUF1006 family protein with C-terminal wHTH domain	_____________224_________________244\n_____________\|___________________\|\n5'-UGG...CCCUU__U_________AAUC___ACCUU...AUA-3'\n______________GC_GAUGCGCGU____UUC\n______________:\|_:\|\|\|\|\|\|\|\|____\|\|\|\n______________UG_UUACGCGCA____AAG\n3'-UUU...ACUAU__U_________GA_____-5'\n_____________\|__________________\|\n_____________18_________________1\n	230 -- 236	6 -- 12	-16.5738 kcal/mol	6.00902 kcal/mol	1.23994 kcal/mol	224 244@LB@ \| \|@LB@5'-UGG...CCCUU U AAUC ACCUU...AUA-3'@LB@ GC GAUGCGCGU UUC@LB@ :\| :\|\|\|\|\|\|\|\| \|\|\|@LB@ UG UUACGCGCA AAG@LB@3'-UUU...ACUAU U GA -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -16.5738 kcal/mol@LB@Unfolding Energy - mRNA 6.00902 kcal/mol@LB@Unfolding Energy - sRNA 1.23994 kcal/mol@LB@@LB@Position - mRNA 225 -- 243@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 6 -- 12@LB@
137	0.01327	0.3104	b3858	yihD	-10.36	0.105347	5 -- 11	5 -- 11	DUF1040 protein YihD	_____________4_______12\n_____________\|_______\|\n_______5'-AUAA_______AGCGA...CGA-3'\n______________GCGCGUC\n______________\|\|\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	5 -- 11	5 -- 11	-14.974 kcal/mol	3.50324 kcal/mol	1.11145 kcal/mol	4 12@LB@ \| \|@LB@ 5'-AUAA AGCGA...CGA-3'@LB@ GCGCGUC@LB@ \|\|\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -14.974 kcal/mol@LB@Unfolding Energy - mRNA 3.50324 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 5 -- 11@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 5 -- 11@LB@
113	0.01159	0.3104	b1279	yciS	-9.20	0.164515	90 -- 101	6 -- 18	DUF1049 family inner membrane protein function unknown	_____________89____________102\n_____________\|_____________\|\n5'-ACC...UCAUC_____________GGAUG...UGU-3'\n______________AAC_AAUGCGUGU\n______________\|\|\|_\|\|\|\|\|\|:\|\|\n______________UUG_UUACGCGCA\n3'-UUU...UACUA___U_________GAAAG-5'\n_____________\|_____________\|\n_____________19____________5\n	95 -- 101	6 -- 12	-13.4585 kcal/mol	3.04139 kcal/mol	1.21878 kcal/mol	89 102@LB@ \| \|@LB@5'-ACC...UCAUC GGAUG...UGU-3'@LB@ AAC AAUGCGUGU@LB@ \|\|\| \|\|\|\|\|\|:\|\|@LB@ UUG UUACGCGCA@LB@3'-UUU...UACUA U GAAAG-5'@LB@ \| \|@LB@ 19 5@LB@@LB@@LB@Energy -9.20 kcal/mol@LB@Hybridization Energy -13.4585 kcal/mol@LB@Unfolding Energy - mRNA 3.04139 kcal/mol@LB@Unfolding Energy - sRNA 1.21878 kcal/mol@LB@@LB@Position - mRNA 90 -- 101@LB@Position - sRNA 6 -- 18@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 6 -- 12@LB@
106	0.0109	0.3104	b2510	yfgJ	-10.53	0.098521	243 -- 261	5 -- 21	DUF1407 family protein	_____________242_________________262\n_____________\|___________________\|\n5'-UAA...AUCAG________CC_________GCCGA...UUU-3'\n______________GAUAACGG__AUGCGCGUU\n______________\|\|\|\|\|\|::__\|\|\|\|\|\|\|\|:\n______________CUAUUGUU__UACGCGCAG\n3'-UUU...UACUA___________________AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	255 -- 261	5 -- 11	-20.9599 kcal/mol	9.18032 kcal/mol	1.24955 kcal/mol	242 262@LB@ \| \|@LB@5'-UAA...AUCAG CC GCCGA...UUU-3'@LB@ GAUAACGG AUGCGCGUU@LB@ \|\|\|\|\|\|:: \|\|\|\|\|\|\|\|:@LB@ CUAUUGUU UACGCGCAG@LB@3'-UUU...UACUA AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -10.53 kcal/mol@LB@Hybridization Energy -20.9599 kcal/mol@LB@Unfolding Energy - mRNA 9.18032 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 243 -- 261@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 5 -- 11@LB@
58	0.00518	0.3024	b4068	yjcH	-12.19	0.050580	228 -- 240	8 -- 21	DUF485 family inner membrane protein	_____________227____________241\n_____________\|______________\|\n5'-ACC...GGAUA__A___________AUUUC...UGC-3'\n______________GA_GAC_AAUGCGC\n______________\|\|_:\|\|_\|\|\|\|\|\|\|\n______________CU_UUG_UUACGCG\n3'-UUU...UACUA__A___U_______CAGAAAG-5'\n_____________\|______________\|\n_____________22_____________7\n	234 -- 240	8 -- 14	-14.481 kcal/mol	1.05266 kcal/mol	1.23638 kcal/mol	227 241@LB@ \| \|@LB@5'-ACC...GGAUA A AUUUC...UGC-3'@LB@ GA GAC AAUGCGC@LB@ \|\| :\|\| \|\|\|\|\|\|\|@LB@ CU UUG UUACGCG@LB@3'-UUU...UACUA A U CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -12.19 kcal/mol@LB@Hybridization Energy -14.481 kcal/mol@LB@Unfolding Energy - mRNA 1.05266 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 228 -- 240@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 8 -- 14@LB@
143	0.01362	0.3104	b3284	smg	-7.50	0.302399	64 -- 82	5 -- 21	DUF494 family putative periplasmic protein	_____________63__________________83\n_____________\|___________________\|\n5'-UUC...GAUGA_______CC__U__A____GUCGC...CAG-3'\n______________GGUAACA__UG_UG_CGUC\n______________\|:\|\|\|\|\|__\|\|_:\|_\|\|\|\|\n______________CUAUUGU__AC_GC_GCAG\n3'-UUU...UACUA_______UU__________AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	64 -- 70	15 -- 21	-13.2614 kcal/mol	4.51132 kcal/mol	1.24955 kcal/mol	63 83@LB@ \| \|@LB@5'-UUC...GAUGA CC U A GUCGC...CAG-3'@LB@ GGUAACA UG UG CGUC@LB@ \|:\|\|\|\|\| \|\| :\| \|\|\|\|@LB@ CUAUUGU AC GC GCAG@LB@3'-UUU...UACUA UU AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -7.50 kcal/mol@LB@Hybridization Energy -13.2614 kcal/mol@LB@Unfolding Energy - mRNA 4.51132 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 64 -- 82@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 15 -- 21@LB@
73	0.006809	0.3087	b4146	epmB	-12.79	0.039583	278 -- 298	1 -- 22	EF-P-Lys34 lysylation protein; weak lysine 2 3-aminomutase	_____________277____________________299\n_____________\|______________________\|\n5'-UUC...GAUCC______ACUUC___________GA-3'\n______________UGAUGA______UGCGUCUUUU\n______________\|\|\|\|:\|______:\|\|\|\|\|\|\|\|:\n______________ACUAUU______GCGCAGAAAG\n3'-UUU...CUACU______GUUUAC__________-5'\n_____________\|_____________________\|\n_____________23____________________1\n	292 -- 298	1 -- 7	-16.8007 kcal/mol	2.75078 kcal/mol	1.25963 kcal/mol	277 299@LB@ \| \|@LB@5'-UUC...GAUCC ACUUC GA-3'@LB@ UGAUGA UGCGUCUUUU@LB@ \|\|\|\|:\| :\|\|\|\|\|\|\|\|:@LB@ ACUAUU GCGCAGAAAG@LB@3'-UUU...CUACU GUUUAC -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -12.79 kcal/mol@LB@Hybridization Energy -16.8007 kcal/mol@LB@Unfolding Energy - mRNA 2.75078 kcal/mol@LB@Unfolding Energy - sRNA 1.25963 kcal/mol@LB@@LB@Position - mRNA 278 -- 298@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 1 -- 7@LB@
74	0.006875	0.3087	b2474	tmcA	-10.30	0.108021	196 -- 222	5 -- 31	elongator methionine tRNA (ac4C34) acetyltransferase	_____________195____________________________223\n_____________\|______________________________\|\n5'-GAU...CGGGG_________C___AC____________U__ACACA...UUG-3'\n______________CAGGGAUGG_UGA__UGAC___UGCGC_UC\n______________\|\|\|\|\|\|\|\|:_\|\|\|__\|:\|\|___\|\|\|\|\|_\|\|\n______________GUCCCUACU_ACU__AUUG___ACGCG_AG\n3'-UUU...CUUAA___________________UUU_____C__AAAG-5'\n_____________\|______________________________\|\n_____________32_____________________________4\n	198 -- 204	23 -- 29	-27.934 kcal/mol	9.88036 kcal/mol	7.7585 kcal/mol	195 223@LB@ \| \|@LB@5'-GAU...CGGGG C AC U ACACA...UUG-3'@LB@ CAGGGAUGG UGA UGAC UGCGC UC@LB@ \|\|\|\|\|\|\|\|: \|\|\| \|:\|\| \|\|\|\|\| \|\|@LB@ GUCCCUACU ACU AUUG ACGCG AG@LB@3'-UUU...CUUAA UUU C AAAG-5'@LB@ \| \|@LB@ 32 4@LB@@LB@@LB@Energy -10.30 kcal/mol@LB@Hybridization Energy -27.934 kcal/mol@LB@Unfolding Energy - mRNA 9.88036 kcal/mol@LB@Unfolding Energy - sRNA 7.7585 kcal/mol@LB@@LB@Position - mRNA 196 -- 222@LB@Position - sRNA 5 -- 31@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 23 -- 29@LB@
24	0.001508	0.1943	b0150	fhuA	-11.07	0.079438	192 -- 210	5 -- 21	ferrichrome outer membrane transporter	_____________191_________________211\n_____________\|___________________\|\n5'-GGA...UCAGA____UAC___UG_______CCAAA...CAG-3'\n______________GAUA___CAA__GCGCGUU\n______________\|\|\|\|___\|\|\|__\|\|\|\|\|\|:\n______________CUAU___GUU__CGCGCAG\n3'-UUU...UACUA____U_____UA_______AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	204 -- 210	5 -- 11	-17.2518 kcal/mol	4.92886 kcal/mol	1.24955 kcal/mol	191 211@LB@ \| \|@LB@5'-GGA...UCAGA UAC UG CCAAA...CAG-3'@LB@ GAUA CAA GCGCGUU@LB@ \|\|\|\| \|\|\| \|\|\|\|\|\|:@LB@ CUAU GUU CGCGCAG@LB@3'-UUU...UACUA U UA AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -11.07 kcal/mol@LB@Hybridization Energy -17.2518 kcal/mol@LB@Unfolding Energy - mRNA 4.92886 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 192 -- 210@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 5 -- 11@LB@
45	0.00309	0.2325	b0584	fepA	-13.78	0.026215	91 -- 106	1 -- 17	ferrienterobactin outer membrane transporter	_____________90________________107\n_____________\|_________________\|\n5'-GAA...CAACU___C_____________AGGAU...ACG-3'\n______________GCA__UGCGUGUCUUUC\n______________:\|\|__\|\|\|\|:\|\|\|\|\|\|\|\n______________UGU__ACGCGCAGAAAG\n3'-UUU...ACUAU___UU____________-5'\n_____________\|________________\|\n_____________18_______________1\n	100 -- 106	1 -- 7	-21.1338 kcal/mol	6.10916 kcal/mol	1.23994 kcal/mol	90 107@LB@ \| \|@LB@5'-GAA...CAACU C AGGAU...ACG-3'@LB@ GCA UGCGUGUCUUUC@LB@ :\|\| \|\|\|\|:\|\|\|\|\|\|\|@LB@ UGU ACGCGCAGAAAG@LB@3'-UUU...ACUAU UU -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -13.78 kcal/mol@LB@Hybridization Energy -21.1338 kcal/mol@LB@Unfolding Energy - mRNA 6.10916 kcal/mol@LB@Unfolding Energy - sRNA 1.23994 kcal/mol@LB@@LB@Position - mRNA 91 -- 106@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 1 -- 7@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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