Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
3	8.668e-05	0.08442	b3892	fdoI	-15.80	0.018551	255 -- 278	1 -- 22	formate dehydrogenase-O cytochrome b556 subunit	_____________254_________________279\n_____________\|___________________\|\n5'-CCA...UGGAU____G___UC_________CUGGC...UGG-3'\n______________CACC_CCU__UGCUUCAUC\n______________\|\|\|\|_\|\|\|__\|\|\|\|\|\|\|\|\|\n______________GUGG_GGA__ACGAAGUAG\n3'-UUU...ACCCC____G______________-5'\n_____________\|__________________\|\n_____________23_________________1\n	272 -- 278	1 -- 7	-24.2792 kcal/mol	4.44512 kcal/mol	7.16879 kcal/mol	254 279@LB@ \| \|@LB@5'-CCA...UGGAU G UC CUGGC...UGG-3'@LB@ CACC CCU UGCUUCAUC@LB@ \|\|\|\| \|\|\| \|\|\|\|\|\|\|\|\|@LB@ GUGG GGA ACGAAGUAG@LB@3'-UUU...ACCCC G -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -15.80 kcal/mol@LB@Hybridization Energy -24.2792 kcal/mol@LB@Unfolding Energy - mRNA 4.44512 kcal/mol@LB@Unfolding Energy - sRNA 7.16879 kcal/mol@LB@@LB@Position - mRNA 255 -- 278@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 1 -- 7@LB@
46	0.004081	0.2985	b2466	ypfG	-10.37	0.233995	256 -- 280	68 -- 95	DUF1176 family protein	_____________255_____281\n_____________\|_______\|\n5'-AAA...CAAAC_______UUAAU...UCA-3'\n______________GUCACAU\n______________\|\|\|\|\|\|:\n______________CAGUGUG\n3'-UUU...UGAGU_______UACUA...UAG-5'\n_____________\|_______\|\n_____________96______67\n	57 -- 63	168 -- 174	-9.42181 kcal/mol	2.13246 kcal/mol	0.260649 kcal/mol	255 281@LB@ \| \|@LB@5'-AAA...CAAAC UUAAU...UCA-3'@LB@ GUCACAU@LB@ \|\|\|\|\|\|:@LB@ CAGUGUG@LB@3'-UUU...UGAGU UACUA...UAG-5'@LB@ \| \|@LB@ 96 67@LB@@LB@@LB@Energy -10.37 kcal/mol@LB@Hybridization Energy -9.42181 kcal/mol@LB@Unfolding Energy - mRNA 2.13246 kcal/mol@LB@Unfolding Energy - sRNA 0.260649 kcal/mol@LB@@LB@Position - mRNA 256 -- 280@LB@Position - sRNA 68 -- 95@LB@Position Seed - mRNA 57 -- 63@LB@Position Seed - sRNA 168 -- 174@LB@
59	0.005693	0.3247	b1959	yedA	-9.74	0.306961	258 -- 278	1 -- 22	amino acid exporter for phenylalanine threonine	_____________257_______279\n_____________\|_________\|\n5'-UCA...UGAUA_________CAGGU...GCU-3'\n______________CUUGCUUCA\n______________\|\|\|\|\|\|\|\|\|\n______________GAACGAAGU\n3'-UUU...UGGGG_________AG-5'\n_____________\|_________\|\n_____________23________0\n	90 -- 96	3 -- 9	-13.1616 kcal/mol	3.16944 kcal/mol	1.03153 kcal/mol	257 279@LB@ \| \|@LB@5'-UCA...UGAUA CAGGU...GCU-3'@LB@ CUUGCUUCA@LB@ \|\|\|\|\|\|\|\|\|@LB@ GAACGAAGU@LB@3'-UUU...UGGGG AG-5'@LB@ \| \|@LB@ 23 0@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -13.1616 kcal/mol@LB@Unfolding Energy - mRNA 3.16944 kcal/mol@LB@Unfolding Energy - sRNA 1.03153 kcal/mol@LB@@LB@Position - mRNA 258 -- 278@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 90 -- 96@LB@Position Seed - sRNA 3 -- 9@LB@
124	0.0136	0.3575	b4065	yjcE	-10.85	0.188871	258 -- 289	125 -- 174	putative cation/proton antiporter	_____________257___________290\n_____________\|_____________\|\n5'-UAU...UGGUC_____U_______CCUUU...UGC-3'\n______________ACUCG_GUCAUGC\n______________\|\|\|\|:_\|\|\|\|::\|\n______________UGAGU_CAGUGUG\n3'-UUU...GGUUA_____________UACUA...UAG-5'\n_____________\|_____________\|\n_____________175___________124\n	267 -- 273	168 -- 174	-13.2629 kcal/mol	3.88311 kcal/mol	0.283892 kcal/mol	257 290@LB@ \| \|@LB@5'-UAU...UGGUC U CCUUU...UGC-3'@LB@ ACUCG GUCAUGC@LB@ \|\|\|\|: \|\|\|\|::\|@LB@ UGAGU CAGUGUG@LB@3'-UUU...GGUUA UACUA...UAG-5'@LB@ \| \|@LB@ 175 124@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -13.2629 kcal/mol@LB@Unfolding Energy - mRNA 3.88311 kcal/mol@LB@Unfolding Energy - sRNA 0.283892 kcal/mol@LB@@LB@Position - mRNA 258 -- 289@LB@Position - sRNA 125 -- 174@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 168 -- 174@LB@
47	0.004619	0.3205	b4142	groS	-15.85	0.018169	259 -- 271	196 -- 208	Cpn10 chaperonin GroES small subunit of GroESL	_____________258_______________________________272\n_____________\|_________________________________\|\n5'-UGA...AACUA_____________CAUCGUUCUG__________UGCAG...CUA-3'\n______________AAUCUGCUGGCGG__________ACCG__GCUC\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|__________\|\|\|:__:\|\|\|\n______________UUAGACGACCGCC__________UGGU__UGAG\n3'-UUU...CCAUA_____________CACUAAAAUG____UA____UCAGU...UAG-5'\n_____________\|_________________________________\|\n_____________209_______________________________195\n	265 -- 271	196 -- 202	-33.1058 kcal/mol	10.148 kcal/mol	14.8106 kcal/mol	258 272@LB@ \| \|@LB@5'-UGA...AACUA CAUCGUUCUG UGCAG...CUA-3'@LB@ AAUCUGCUGGCGG ACCG GCUC@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|: :\|\|\|@LB@ UUAGACGACCGCC UGGU UGAG@LB@3'-UUU...CCAUA CACUAAAAUG UA UCAGU...UAG-5'@LB@ \| \|@LB@ 209 195@LB@@LB@@LB@Energy -15.85 kcal/mol@LB@Hybridization Energy -33.1058 kcal/mol@LB@Unfolding Energy - mRNA 10.148 kcal/mol@LB@Unfolding Energy - sRNA 14.8106 kcal/mol@LB@@LB@Position - mRNA 259 -- 271@LB@Position - sRNA 196 -- 208@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 196 -- 202@LB@
103	0.0111	0.3575	b2821	ptrA	-11.45	0.143539	261 -- 295	141 -- 175	protease III	_____________260_______________________________________296\n_____________\|_________________________________________\|\n5'-GCU...GCACC___A_____G______AA____AU_______CGA_______AACCA-3'\n______________CUU_AGUCA_GCA_GA__CGGG__GG_CAGC___UUCAGGA\n______________\|\|:_\|\|\|\|\|_:\|\|_\|\|__\|:\|\|__:\|_\|\|:\|___\|\|\|\|\|:\|\n______________GAG_UCAGU_UGU_CU__GUCC__UC_GUUG___AAGUCUU\n3'-UUU...GUUAU_________G___A__AC____GU__A____A_________AACGC...UAG-5'\n_____________\|_________________________________________\|\n_____________176_______________________________________140\n	289 -- 295	141 -- 147	-30.7779 kcal/mol	8.8583 kcal/mol	8.83168 kcal/mol	260 296@LB@ \| \|@LB@5'-GCU...GCACC A G AA AU CGA AACCA-3'@LB@ CUU AGUCA GCA GA CGGG GG CAGC UUCAGGA@LB@ \|\|: \|\|\|\|\| :\|\| \|\| \|:\|\| :\| \|\|:\| \|\|\|\|\|:\|@LB@ GAG UCAGU UGU CU GUCC UC GUUG AAGUCUU@LB@3'-UUU...GUUAU G A AC GU A A AACGC...UAG-5'@LB@ \| \|@LB@ 176 140@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -30.7779 kcal/mol@LB@Unfolding Energy - mRNA 8.8583 kcal/mol@LB@Unfolding Energy - sRNA 8.83168 kcal/mol@LB@@LB@Position - mRNA 261 -- 295@LB@Position - sRNA 141 -- 175@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 141 -- 147@LB@
73	0.007584	0.3458	b0059	rapA	-13.35	0.058963	263 -- 277	46 -- 60	RNA polymerase remodeling/recycling factor ATPase; RNA polymerase-associated ATP-dependent RNA translocase	_____________262_____________278\n_____________\|_______________\|\n5'-GCU...GGAAC_______________UGCGC...UUU-3'\n______________CGUUGUCGCGGUGGA\n______________\|\|:\|\|\|\|\|\|\|\|\|::\|\n______________GCGACAGCGCCAUUU\n3'-UUU...UUGAA_______________UAUCA...UAG-5'\n_____________\|_______________\|\n_____________61______________45\n	269 -- 275	48 -- 54	-26.0749 kcal/mol	7.19742 kcal/mol	6.07408 kcal/mol	262 278@LB@ \| \|@LB@5'-GCU...GGAAC UGCGC...UUU-3'@LB@ CGUUGUCGCGGUGGA@LB@ \|\|:\|\|\|\|\|\|\|\|\|::\|@LB@ GCGACAGCGCCAUUU@LB@3'-UUU...UUGAA UAUCA...UAG-5'@LB@ \| \|@LB@ 61 45@LB@@LB@@LB@Energy -13.35 kcal/mol@LB@Hybridization Energy -26.0749 kcal/mol@LB@Unfolding Energy - mRNA 7.19742 kcal/mol@LB@Unfolding Energy - sRNA 6.07408 kcal/mol@LB@@LB@Position - mRNA 263 -- 277@LB@Position - sRNA 46 -- 60@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 48 -- 54@LB@
96	0.01055	0.3575	b1953	yodD	-11.39	0.147949	264 -- 273	196 -- 205	uncharacterized protein	_____________263_____274\n_____________\|_______\|\n5'-CCA...UUCAC_______GUUUU...AAG-3'\n______________CUUCAUC\n______________\|\|\|\|\|\|\|\n______________GAAGUAG\n3'-UUU...GGAAC_______-5'\n_____________\|______\|\n_____________206____196\n	33 -- 39	1 -- 7	-8.82286 kcal/mol	0.690587 kcal/mol	0.701705 kcal/mol	263 274@LB@ \| \|@LB@5'-CCA...UUCAC GUUUU...AAG-3'@LB@ CUUCAUC@LB@ \|\|\|\|\|\|\|@LB@ GAAGUAG@LB@3'-UUU...GGAAC -5'@LB@ \| \|@LB@ 206 196@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -8.82286 kcal/mol@LB@Unfolding Energy - mRNA 0.690587 kcal/mol@LB@Unfolding Energy - sRNA 0.701705 kcal/mol@LB@@LB@Position - mRNA 264 -- 273@LB@Position - sRNA 196 -- 205@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 1 -- 7@LB@
170	0.01941	0.3812	b3911	cpxA	-13.13	0.065341	265 -- 299	168 -- 204	sensory histidine kinase in two-component regulatory system with CpxR	_____________264______300\n_____________\|________\|\n5'-UAU...GUUUC________GAUAG...GCC-3'\n______________UGCUUCAU\n______________\|\|\|\|\|\|\|\|\n______________ACGAAGUA\n3'-UUU...GGGGA________G-5'\n_____________\|________\|\n_____________205______167\n	196 -- 202	2 -- 8	-10.3801 kcal/mol	3.0426 kcal/mol	0.709873 kcal/mol	264 300@LB@ \| \|@LB@5'-UAU...GUUUC GAUAG...GCC-3'@LB@ UGCUUCAU@LB@ \|\|\|\|\|\|\|\|@LB@ ACGAAGUA@LB@3'-UUU...GGGGA G-5'@LB@ \| \|@LB@ 205 167@LB@@LB@@LB@Energy -13.13 kcal/mol@LB@Hybridization Energy -10.3801 kcal/mol@LB@Unfolding Energy - mRNA 3.0426 kcal/mol@LB@Unfolding Energy - sRNA 0.709873 kcal/mol@LB@@LB@Position - mRNA 265 -- 299@LB@Position - sRNA 168 -- 204@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 2 -- 8@LB@
58	0.005664	0.3247	b1878	flhE	-13.77	0.048330	266 -- 286	140 -- 162	proton seal during flagellar secretion	_____________265_____________________287\n_____________\|_______________________\|\n5'-CGU...AUGUG__________AGUGUA_______UACGC...AUC-3'\n______________GCAGGCAAGU________GGAAU\n______________\|\|\|\|\|\|\|\|\|\|________:\|\|\|\|\n______________CGUCCGUUCA________UCUUA\n3'-UUU...UACUA__________GUUGAAAG_____ACGCC...UAG-5'\n_____________\|_______________________\|\n_____________163_____________________139\n	269 -- 275	153 -- 159	-20.7539 kcal/mol	2.26514 kcal/mol	7.696 kcal/mol	265 287@LB@ \| \|@LB@5'-CGU...AUGUG AGUGUA UACGC...AUC-3'@LB@ GCAGGCAAGU GGAAU@LB@ \|\|\|\|\|\|\|\|\|\| :\|\|\|\|@LB@ CGUCCGUUCA UCUUA@LB@3'-UUU...UACUA GUUGAAAG ACGCC...UAG-5'@LB@ \| \|@LB@ 163 139@LB@@LB@@LB@Energy -13.77 kcal/mol@LB@Hybridization Energy -20.7539 kcal/mol@LB@Unfolding Energy - mRNA 2.26514 kcal/mol@LB@Unfolding Energy - sRNA 7.696 kcal/mol@LB@@LB@Position - mRNA 266 -- 286@LB@Position - sRNA 140 -- 162@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 153 -- 159@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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