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
9	0.0003241	0.1198	b1110	ycfJ	-9.50	0.172514	224 -- 251	52 -- 76	uncharacterized protein	_____________223__________________________252\n_____________\|____________________________\|\n5'-ACU...GCGGG_______AUU__U___GCA_________GGCGU...AAU-3'\n______________UAUCGGG___GG_GUC___GCUGCGCUG\n______________:\|:\|:\|\|___\|:_:\|\|___\|\|\|\|\|\|\|:\|\n______________GUGGUCC___CU_UAG___CGACGCGGC\n3'-UUU...CGGUU____________U___AAC_________AUUUA...GUG-5'\n_____________\|____________________________\|\n_____________77___________________________51\n	245 -- 251	52 -- 58	-26.6822 kcal/mol	7.91875 kcal/mol	9.26585 kcal/mol	223 252@LB@ \| \|@LB@5'-ACU...GCGGG AUU U GCA GGCGU...AAU-3'@LB@ UAUCGGG GG GUC GCUGCGCUG@LB@ :\|:\|:\|\| \|: :\|\| \|\|\|\|\|\|\|:\|@LB@ GUGGUCC CU UAG CGACGCGGC@LB@3'-UUU...CGGUU U AAC AUUUA...GUG-5'@LB@ \| \|@LB@ 77 51@LB@@LB@@LB@Energy -9.50 kcal/mol@LB@Hybridization Energy -26.6822 kcal/mol@LB@Unfolding Energy - mRNA 7.91875 kcal/mol@LB@Unfolding Energy - sRNA 9.26585 kcal/mol@LB@@LB@Position - mRNA 224 -- 251@LB@Position - sRNA 52 -- 76@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 52 -- 58@LB@
7	0.0001601	0.08054	b1864	yebC	-15.40	0.012230	213 -- 249	54 -- 89	UPF0082 family protein	_____________212_____________________________________250\n_____________\|_______________________________________\|\n5'-CGU...GUCAU____AA__G___________AC_____GUAAA_______AGGAU...UAA-3'\n______________AGUA__UG_GCCAACACCAG____AUC_____GCUGCGC\n______________\|:\|\|__\|\|_\|\|\|\|\|\|\|\|\|\|\|____\|\|\|_____\|\|\|\|\|\|\|\n______________UUAU__AC_CGGUUGUGGUC____UAG_____CGACGCG\n3'-UUU...CGCGC____G___G___________CCUU___AAC_________GCAUU...GUG-5'\n_____________\|_______________________________________\|\n_____________90______________________________________53\n	243 -- 249	54 -- 60	-38.8431 kcal/mol	7.10336 kcal/mol	16.3388 kcal/mol	212 250@LB@ \| \|@LB@5'-CGU...GUCAU AA G AC GUAAA AGGAU...UAA-3'@LB@ AGUA UG GCCAACACCAG AUC GCUGCGC@LB@ \|:\|\| \|\| \|\|\|\|\|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ UUAU AC CGGUUGUGGUC UAG CGACGCG@LB@3'-UUU...CGCGC G G CCUU AAC GCAUU...GUG-5'@LB@ \| \|@LB@ 90 53@LB@@LB@@LB@Energy -15.40 kcal/mol@LB@Hybridization Energy -38.8431 kcal/mol@LB@Unfolding Energy - mRNA 7.10336 kcal/mol@LB@Unfolding Energy - sRNA 16.3388 kcal/mol@LB@@LB@Position - mRNA 213 -- 249@LB@Position - sRNA 54 -- 89@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 54 -- 60@LB@
13	0.0004745	0.1198	b1688	ydiK	-12.82	0.039628	213 -- 226	68 -- 82	UPF0118 family inner membrane protein	_____________212_____________227\n_____________\|_______________\|\n5'-AUG...AUGUU_______________UGUCG...CCU-3'\n______________CGUCAGC_CCAGGGA\n______________\|\|:\|\|:\|_\|\|\|\|\|\|\|\n______________GCGGUUG_GGUCCCU\n3'-UUU...AUGAC_______U_______UUAGA...GUG-5'\n_____________\|_______________\|\n_____________83______________67\n	220 -- 226	68 -- 74	-23.7232 kcal/mol	3.92329 kcal/mol	6.98098 kcal/mol	212 227@LB@ \| \|@LB@5'-AUG...AUGUU UGUCG...CCU-3'@LB@ CGUCAGC CCAGGGA@LB@ \|\|:\|\|:\| \|\|\|\|\|\|\|@LB@ GCGGUUG GGUCCCU@LB@3'-UUU...AUGAC U UUAGA...GUG-5'@LB@ \| \|@LB@ 83 67@LB@@LB@@LB@Energy -12.82 kcal/mol@LB@Hybridization Energy -23.7232 kcal/mol@LB@Unfolding Energy - mRNA 3.92329 kcal/mol@LB@Unfolding Energy - sRNA 6.98098 kcal/mol@LB@@LB@Position - mRNA 213 -- 226@LB@Position - sRNA 68 -- 82@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 68 -- 74@LB@
112	0.005982	0.1855	b1820	yobD	-7.30	0.411799	229 -- 243	1 -- 14	UPF0266 family inner membrane protein	_____________228_____________244\n_____________\|_______________\|\n5'-ACC...GAUUC______UC_______UCCUG...CCC-3'\n______________UUUUCA__GCCGCAC\n______________\|\|\|\|\|\|__\|\|\|\|\|\|\|\n______________AAAAGU__CGGCGUG\n3'-UUU...UGACA______C________-5'\n_____________\|______________\|\n_____________15_____________1\n	237 -- 243	1 -- 7	-17.9899 kcal/mol	4.95197 kcal/mol	5.72803 kcal/mol	228 244@LB@ \| \|@LB@5'-ACC...GAUUC UC UCCUG...CCC-3'@LB@ UUUUCA GCCGCAC@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ AAAAGU CGGCGUG@LB@3'-UUU...UGACA C -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -7.30 kcal/mol@LB@Hybridization Energy -17.9899 kcal/mol@LB@Unfolding Energy - mRNA 4.95197 kcal/mol@LB@Unfolding Energy - sRNA 5.72803 kcal/mol@LB@@LB@Position - mRNA 229 -- 243@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 1 -- 7@LB@
5	5.466e-05	0.03849	b0713	ybgL	-10.83	0.096857	234 -- 242	53 -- 61	UPF0271 family protein	_____________233_______243\n_____________\|_________\|\n5'-GCC...GCGAA_________AGCGA...AUG-3'\n______________GGCUGCGCC\n______________\|\|\|\|\|\|\|\|\|\n______________CCGACGCGG\n3'-UUU...UAGAA_________CAUUU...GUG-5'\n_____________\|_________\|\n_____________62________52\n	236 -- 242	53 -- 59	-22.2033 kcal/mol	6.50503 kcal/mol	4.87107 kcal/mol	233 243@LB@ \| \|@LB@5'-GCC...GCGAA AGCGA...AUG-3'@LB@ GGCUGCGCC@LB@ \|\|\|\|\|\|\|\|\|@LB@ CCGACGCGG@LB@3'-UUU...UAGAA CAUUU...GUG-5'@LB@ \| \|@LB@ 62 52@LB@@LB@@LB@Energy -10.83 kcal/mol@LB@Hybridization Energy -22.2033 kcal/mol@LB@Unfolding Energy - mRNA 6.50503 kcal/mol@LB@Unfolding Energy - sRNA 4.87107 kcal/mol@LB@@LB@Position - mRNA 234 -- 242@LB@Position - sRNA 53 -- 61@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 53 -- 59@LB@
11	0.0004411	0.1198	b3154	yhbP	-10.16	0.129625	138 -- 186	18 -- 75	UPF0306 family protein	_____________137_________________________________________________________187\n_____________\|___________________________________________________________\|\n5'-AAA...AAGAA_______U____AUC_U________CAU______________GU_____CC________AAAAG...UUU-3'\n______________ACCAGGG__GUC___G_CUGCGUCG___GUUA________AG___CAGG__CACAGUAU\n______________\|\|\|\|\|\|\|__:\|\|___\|_\|\|\|\|\|:\|\|___:\|\|\|________\|\|___\|\|:\|__\|\|\|\|\|:\|:\n______________UGGUCCC__UAG___C_GACGCGGC___UAAU________UC___GUUC__GUGUCGUG\n3'-UUU...GGUUG_______UU___AAC__________AUU____AAUACUAC__AAU____CC________ACAAA...GUG-5'\n_____________\|___________________________________________________________\|\n_____________76__________________________________________________________17\n	155 -- 161	52 -- 58	-41.8924 kcal/mol	11.5669 kcal/mol	20.1571 kcal/mol	137 187@LB@ \| \|@LB@5'-AAA...AAGAA U AUC U CAU GU CC AAAAG...UUU-3'@LB@ ACCAGGG GUC G CUGCGUCG GUUA AG CAGG CACAGUAU@LB@ \|\|\|\|\|\|\| :\|\| \| \|\|\|\|\|:\|\| :\|\|\| \|\| \|\|:\| \|\|\|\|\|:\|:@LB@ UGGUCCC UAG C GACGCGGC UAAU UC GUUC GUGUCGUG@LB@3'-UUU...GGUUG UU AAC AUU AAUACUAC AAU CC ACAAA...GUG-5'@LB@ \| \|@LB@ 76 17@LB@@LB@@LB@Energy -10.16 kcal/mol@LB@Hybridization Energy -41.8924 kcal/mol@LB@Unfolding Energy - mRNA 11.5669 kcal/mol@LB@Unfolding Energy - sRNA 20.1571 kcal/mol@LB@@LB@Position - mRNA 138 -- 186@LB@Position - sRNA 18 -- 75@LB@Position Seed - mRNA 155 -- 161@LB@Position Seed - sRNA 52 -- 58@LB@
183	0.011	0.2089	b0906	ycaP	-11.77	0.063722	48 -- 74	48 -- 75	UPF0702 family putative inner membrane protein	_____________47___________________________75\n_____________\|____________________________\|\n5'-AGU...UCUUU________UAAA___U_______A____AAUCA...UCU-3'\n______________GCCGGGGA_____UG_UUGCGUC_UGAA\n______________:\|\|:\|\|\|\|_____\|\|_:\|\|\|\|:\|_\|:\|\|\n______________UGGUCCCU_____AC_GACGCGG_AUUU\n3'-UUU...GGUUG________UUAGA__C_______C____AAUAA...GUG-5'\n_____________\|____________________________\|\n_____________76___________________________47\n	63 -- 69	53 -- 59	-25.8143 kcal/mol	5.22968 kcal/mol	8.81811 kcal/mol	47 75@LB@ \| \|@LB@5'-AGU...UCUUU UAAA U A AAUCA...UCU-3'@LB@ GCCGGGGA UG UUGCGUC UGAA@LB@ :\|\|:\|\|\|\| \|\| :\|\|\|\|:\| \|:\|\|@LB@ UGGUCCCU AC GACGCGG AUUU@LB@3'-UUU...GGUUG UUAGA C C AAUAA...GUG-5'@LB@ \| \|@LB@ 76 47@LB@@LB@@LB@Energy -11.77 kcal/mol@LB@Hybridization Energy -25.8143 kcal/mol@LB@Unfolding Energy - mRNA 5.22968 kcal/mol@LB@Unfolding Energy - sRNA 8.81811 kcal/mol@LB@@LB@Position - mRNA 48 -- 74@LB@Position - sRNA 48 -- 75@LB@Position Seed - mRNA 63 -- 69@LB@Position Seed - sRNA 53 -- 59@LB@
15	0.000767	0.1666	b2497	uraA	-16.56	0.007223	161 -- 232	28 -- 90	uracil permease	_____________160_________________________________________________________________________233\n_____________\|___________________________________________________________________________\|\n5'-AGC...UUUUU_____AA_____UAU_____AUAAUA___A___U___A__AU_AC________C_____CGG_______GA____ACCGC...UCC-3'\n______________GAGUA__GCGCC___AACAC______CAG_GGA_AAU_CU__G__GCGCCGUG___UAU___GGUGAGU___AAG\n______________\|\|:\|\|__\|\|\|\|\|___\|\|\|\|\|______\|\|\|_\|\|\|_\|\|\|_\|\|__\|__\|\|\|\|\|\|\|:___\|\|\|___\|:\|\|\|\|\|___\|\|\|\n______________CUUAU__CGCGG___UUGUG______GUC_CCU_UUA_GA__C__CGCGGCAU___AUA___CUACUCA___UUC\n3'-UUU...ACGCG_____GA_________________________________AC_GA________UUA___AUA_______AUG___CCGUG...GUG-5'\n_____________\|___________________________________________________________________________\|\n_____________91__________________________________________________________________________27\n	221 -- 227	34 -- 40	-48.784 kcal/mol	15.1604 kcal/mol	17.0677 kcal/mol	160 233@LB@ \| \|@LB@5'-AGC...UUUUU AA UAU AUAAUA A U A AU AC C CGG GA ACCGC...UCC-3'@LB@ GAGUA GCGCC AACAC CAG GGA AAU CU G GCGCCGUG UAU GGUGAGU AAG@LB@ \|\|:\|\| \|\|\|\|\| \|\|\|\|\| \|\|\| \|\|\| \|\|\| \|\| \| \|\|\|\|\|\|\|: \|\|\| \|:\|\|\|\|\| \|\|\|@LB@ CUUAU CGCGG UUGUG GUC CCU UUA GA C CGCGGCAU AUA CUACUCA UUC@LB@3'-UUU...ACGCG GA AC GA UUA AUA AUG CCGUG...GUG-5'@LB@ \| \|@LB@ 91 27@LB@@LB@@LB@Energy -16.56 kcal/mol@LB@Hybridization Energy -48.784 kcal/mol@LB@Unfolding Energy - mRNA 15.1604 kcal/mol@LB@Unfolding Energy - sRNA 17.0677 kcal/mol@LB@@LB@Position - mRNA 161 -- 232@LB@Position - sRNA 28 -- 90@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 34 -- 40@LB@
44	0.002208	0.1727	b1859	znuB	-7.63	0.365449	19 -- 38	72 -- 88	zinc ABC transporter permease	_____________18___________________39\n_____________\|____________________\|\n5'-AUG...AUGAA__________UGAAU_____CAUUU...AUU-3'\n______________GUGCUGUGCC_____CACCA\n______________:\|:\|\|\|:\|\|\|_____\|\|\|\|\|\n______________UAUGACGCGG_____GUGGU\n3'-UUU...GCGCU__________UU________CCCUU...GUG-5'\n_____________\|____________________\|\n_____________89___________________71\n	22 -- 28	79 -- 85	-22.3137 kcal/mol	7.44481 kcal/mol	7.24148 kcal/mol	18 39@LB@ \| \|@LB@5'-AUG...AUGAA UGAAU CAUUU...AUU-3'@LB@ GUGCUGUGCC CACCA@LB@ :\|:\|\|\|:\|\|\| \|\|\|\|\|@LB@ UAUGACGCGG GUGGU@LB@3'-UUU...GCGCU UU CCCUU...GUG-5'@LB@ \| \|@LB@ 89 71@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -22.3137 kcal/mol@LB@Unfolding Energy - mRNA 7.44481 kcal/mol@LB@Unfolding Energy - sRNA 7.24148 kcal/mol@LB@@LB@Position - mRNA 19 -- 38@LB@Position - sRNA 72 -- 88@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 79 -- 85@LB@
89	0.004811	0.1855	b4336	yjiN	-13.14	0.034257	120 -- 134	70 -- 84	zinc-type alcohol dehydrogenase-like protein	_____________119_____________135\n_____________\|_______________\|\n5'-GGU...UCGCG_______________CAGCC...CCA-3'\n______________UGCGCCAGCAUCAGG\n______________\|\|\|\|\|\|\|:\|\|:\|\|\|\|\n______________ACGCGGUUGUGGUCC\n3'-UUU...UUAUG_______________CUUUA...GUG-5'\n_____________\|_______________\|\n_____________85______________69\n	128 -- 134	70 -- 76	-28.7852 kcal/mol	8.39668 kcal/mol	7.24859 kcal/mol	119 135@LB@ \| \|@LB@5'-GGU...UCGCG CAGCC...CCA-3'@LB@ UGCGCCAGCAUCAGG@LB@ \|\|\|\|\|\|\|:\|\|:\|\|\|\|@LB@ ACGCGGUUGUGGUCC@LB@3'-UUU...UUAUG CUUUA...GUG-5'@LB@ \| \|@LB@ 85 69@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -28.7852 kcal/mol@LB@Unfolding Energy - mRNA 8.39668 kcal/mol@LB@Unfolding Energy - sRNA 7.24859 kcal/mol@LB@@LB@Position - mRNA 120 -- 134@LB@Position - sRNA 70 -- 84@LB@Position Seed - mRNA 128 -- 134@LB@Position Seed - sRNA 70 -- 76@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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