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
77	0.007102	0.3087	b0832	gsiD	-8.78	0.192254	77 -- 85	7 -- 15	glutathione ABC transporter permease	_____________76________86\n_____________\|_________\|\n5'-UUG...CGUAG_________AUUAC...GAU-3'\n______________AAAUGCGUG\n______________\|\|\|\|\|\|\|:\|\n______________UUUACGCGC\n3'-UUU...UAUUG_________AGAAAG-5'\n_____________\|_________\|\n_____________16________6\n	79 -- 85	7 -- 13	-12.0627 kcal/mol	2.10506 kcal/mol	1.17837 kcal/mol	76 86@LB@ \| \|@LB@5'-UUG...CGUAG AUUAC...GAU-3'@LB@ AAAUGCGUG@LB@ \|\|\|\|\|\|\|:\|@LB@ UUUACGCGC@LB@3'-UUU...UAUUG AGAAAG-5'@LB@ \| \|@LB@ 16 6@LB@@LB@@LB@Energy -8.78 kcal/mol@LB@Hybridization Energy -12.0627 kcal/mol@LB@Unfolding Energy - mRNA 2.10506 kcal/mol@LB@Unfolding Energy - sRNA 1.17837 kcal/mol@LB@@LB@Position - mRNA 77 -- 85@LB@Position - sRNA 7 -- 15@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 7 -- 13@LB@
63	0.0059	0.3087	b3834	ubiJ	-8.76	0.193647	289 -- 295	4 -- 10	aerobic ubiquinone synthesis protein SCP2 family protein	_____________288_____296\n_____________\|_______\|\n5'-GCU...CCGCU_______GCUGG-3'\n______________CGCGUCU\n______________\|\|\|\|\|\|\|\n______________GCGCAGA\n3'-UUU...UUUAC_______AAG-5'\n_____________\|_______\|\n_____________11______3\n	289 -- 295	4 -- 10	-11.2085 kcal/mol	1.2993 kcal/mol	1.14958 kcal/mol	288 296@LB@ \| \|@LB@5'-GCU...CCGCU GCUGG-3'@LB@ CGCGUCU@LB@ \|\|\|\|\|\|\|@LB@ GCGCAGA@LB@3'-UUU...UUUAC AAG-5'@LB@ \| \|@LB@ 11 3@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -11.2085 kcal/mol@LB@Unfolding Energy - mRNA 1.2993 kcal/mol@LB@Unfolding Energy - sRNA 1.14958 kcal/mol@LB@@LB@Position - mRNA 289 -- 295@LB@Position - sRNA 4 -- 10@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 4 -- 10@LB@
168	0.01645	0.3104	b3720	bglH	-8.64	0.202347	15 -- 28	9 -- 22	carbohydrate-specific outer membrane porin cryptic	_____________14_____________29\n_____________\|______________\|\n5'-AUU...GAUCG_________UG___AAGGA...GCC-3'\n______________UGAUGAUAA__GCG\n______________\|\|\|\|:\|:\|\|__\|\|\|\n______________ACUAUUGUU__CGC\n3'-UUU...CUACU_________UA___GCAGAAAG-5'\n_____________\|______________\|\n_____________23_____________8\n	17 -- 23	14 -- 20	-13.7208 kcal/mol	3.8428 kcal/mol	1.23827 kcal/mol	14 29@LB@ \| \|@LB@5'-AUU...GAUCG UG AAGGA...GCC-3'@LB@ UGAUGAUAA GCG@LB@ \|\|\|\|:\|:\|\| \|\|\|@LB@ ACUAUUGUU CGC@LB@3'-UUU...CUACU UA GCAGAAAG-5'@LB@ \| \|@LB@ 23 8@LB@@LB@@LB@Energy -8.64 kcal/mol@LB@Hybridization Energy -13.7208 kcal/mol@LB@Unfolding Energy - mRNA 3.8428 kcal/mol@LB@Unfolding Energy - sRNA 1.23827 kcal/mol@LB@@LB@Position - mRNA 15 -- 28@LB@Position - sRNA 9 -- 22@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 14 -- 20@LB@
89	0.009028	0.3104	b0529	folD	-8.62	0.203566	239 -- 251	4 -- 17	bifunctional 5 10-methylene-tetrahydrofolate dehydrogenase/ 5 10-methylene-tetrahydrofolate cyclohydrolase	_____________238____________252\n_____________\|______________\|\n5'-CAA...GCGCA______________GAAGU...CAC-3'\n______________GCAGGUGCGC_UCU\n______________:\|\|::\|\|\|\|\|_\|\|\|\n______________UGUUUACGCG_AGA\n3'-UUU...ACUAU__________C___AAG-5'\n_____________\|______________\|\n_____________18_____________3\n	242 -- 248	8 -- 14	-17.587 kcal/mol	7.73476 kcal/mol	1.22888 kcal/mol	238 252@LB@ \| \|@LB@5'-CAA...GCGCA GAAGU...CAC-3'@LB@ GCAGGUGCGC UCU@LB@ :\|\|::\|\|\|\|\| \|\|\|@LB@ UGUUUACGCG AGA@LB@3'-UUU...ACUAU C AAG-5'@LB@ \| \|@LB@ 18 3@LB@@LB@@LB@Energy -8.62 kcal/mol@LB@Hybridization Energy -17.587 kcal/mol@LB@Unfolding Energy - mRNA 7.73476 kcal/mol@LB@Unfolding Energy - sRNA 1.22888 kcal/mol@LB@@LB@Position - mRNA 239 -- 251@LB@Position - sRNA 4 -- 17@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 8 -- 14@LB@
114	0.01161	0.3104	b3392	hofP	-8.60	0.204995	138 -- 147	1 -- 11	DNA catabolic protein	_____________137_________148\n_____________\|___________\|\n5'-ACU...CGUGA___________GUUAA...GCG-3'\n______________GC_CGUUUUUC\n______________\|\|_\|\|\|:\|\|\|\|\n______________CG_GCAGAAAG\n3'-UUU...GUUUA__C________-5'\n_____________\|__________\|\n_____________12_________1\n	141 -- 147	1 -- 7	-12.6405 kcal/mol	2.86562 kcal/mol	1.17076 kcal/mol	137 148@LB@ \| \|@LB@5'-ACU...CGUGA GUUAA...GCG-3'@LB@ GC CGUUUUUC@LB@ \|\| \|\|\|:\|\|\|\|@LB@ CG GCAGAAAG@LB@3'-UUU...GUUUA C -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -12.6405 kcal/mol@LB@Unfolding Energy - mRNA 2.86562 kcal/mol@LB@Unfolding Energy - sRNA 1.17076 kcal/mol@LB@@LB@Position - mRNA 138 -- 147@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 1 -- 7@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@
133	0.01287	0.3104	b3179	rlmE	-8.60	0.205247	24 -- 43	1 -- 17	23S rRNA U2552 2'-O-ribose methyltransferase SAM-dependent	_____________23___________________44\n_____________\|____________________\|\n5'-GCC...CUUGA__________CAGAC_____AGGUG...CCC-3'\n______________GCGGAUGUGC_____CUUUC\n______________:\|::\|\|\|:\|\|_____\|\|\|\|\|\n______________UGUUUACGCG_____GAAAG\n3'-UUU...ACUAU__________CA________-5'\n_____________\|___________________\|\n_____________18__________________1\n	27 -- 33	8 -- 14	-16.3409 kcal/mol	6.50016 kcal/mol	1.23994 kcal/mol	23 44@LB@ \| \|@LB@5'-GCC...CUUGA CAGAC AGGUG...CCC-3'@LB@ GCGGAUGUGC CUUUC@LB@ :\|::\|\|\|:\|\| \|\|\|\|\|@LB@ UGUUUACGCG GAAAG@LB@3'-UUU...ACUAU CA -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -16.3409 kcal/mol@LB@Unfolding Energy - mRNA 6.50016 kcal/mol@LB@Unfolding Energy - sRNA 1.23994 kcal/mol@LB@@LB@Position - mRNA 24 -- 43@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 8 -- 14@LB@
43	0.003009	0.2325	b3429	glgA	-8.59	0.206361	152 -- 163	7 -- 22	glycogen synthase	_____________151______________164\n_____________\|________________\|\n5'-GUA...CGUGC________________AAAUG...ACG-3'\n______________UGGUAAC____GCGCG\n______________\|\|:\|\|\|\|____\|\|\|\|\|\n______________ACUAUUG____CGCGC\n3'-UUU...CUACU_______UUUA_____AGAAAG-5'\n_____________\|________________\|\n_____________23_______________6\n	152 -- 158	16 -- 22	-13.429 kcal/mol	3.59934 kcal/mol	1.24379 kcal/mol	151 164@LB@ \| \|@LB@5'-GUA...CGUGC AAAUG...ACG-3'@LB@ UGGUAAC GCGCG@LB@ \|\|:\|\|\|\| \|\|\|\|\|@LB@ ACUAUUG CGCGC@LB@3'-UUU...CUACU UUUA AGAAAG-5'@LB@ \| \|@LB@ 23 6@LB@@LB@@LB@Energy -8.59 kcal/mol@LB@Hybridization Energy -13.429 kcal/mol@LB@Unfolding Energy - mRNA 3.59934 kcal/mol@LB@Unfolding Energy - sRNA 1.24379 kcal/mol@LB@@LB@Position - mRNA 152 -- 163@LB@Position - sRNA 7 -- 22@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 16 -- 22@LB@
197	0.01929	0.3104	b2185	rplY	-8.58	0.206984	8 -- 20	7 -- 19	50S ribosomal subunit protein L25	_____________7_____________21\n_____________\|_____________\|\n____5'-CCAGUAC_____________AAAAA...GCA-3'\n______________UGGCAGGUGCGUG\n______________\|::\|\|::\|\|\|\|:\|\n______________AUUGUUUACGCGC\n3'-UUU...CUACU_____________AGAAAG-5'\n_____________\|_____________\|\n_____________20____________6\n	14 -- 20	7 -- 13	-17.3397 kcal/mol	7.54262 kcal/mol	1.21943 kcal/mol	7 21@LB@ \| \|@LB@ 5'-CCAGUAC AAAAA...GCA-3'@LB@ UGGCAGGUGCGUG@LB@ \|::\|\|::\|\|\|\|:\|@LB@ AUUGUUUACGCGC@LB@3'-UUU...CUACU AGAAAG-5'@LB@ \| \|@LB@ 20 6@LB@@LB@@LB@Energy -8.58 kcal/mol@LB@Hybridization Energy -17.3397 kcal/mol@LB@Unfolding Energy - mRNA 7.54262 kcal/mol@LB@Unfolding Energy - sRNA 1.21943 kcal/mol@LB@@LB@Position - mRNA 8 -- 20@LB@Position - sRNA 7 -- 19@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 7 -- 13@LB@
122	0.01233	0.3104	b3599	mtlA	-8.56	0.208645	247 -- 281	4 -- 32	mannitol-specific PTS enzyme: IIA IIB and IIC components	_____________246_________________________________282\n_____________\|___________________________________\|\n5'-GAU...UUUCC____CAAC_________C_____AUCG________AUCGC...UCA-3'\n______________UCAG____AUGGUGAUG_CAAAU____GCGCGUUU\n______________\|\|\|\|____\|\|\|:\|\|\|\|:_\|\|\|\|\|____\|\|\|\|\|\|:\|\n______________AGUC____UACUACUAU_GUUUA____CGCGCAGA\n3'-UUU...ACUUA____CC___________U_________________AAG-5'\n_____________\|___________________________________\|\n_____________33__________________________________3\n	275 -- 281	4 -- 10	-27.4972 kcal/mol	11.1013 kcal/mol	7.84022 kcal/mol	246 282@LB@ \| \|@LB@5'-GAU...UUUCC CAAC C AUCG AUCGC...UCA-3'@LB@ UCAG AUGGUGAUG CAAAU GCGCGUUU@LB@ \|\|\|\| \|\|\|:\|\|\|\|: \|\|\|\|\| \|\|\|\|\|\|:\|@LB@ AGUC UACUACUAU GUUUA CGCGCAGA@LB@3'-UUU...ACUUA CC U AAG-5'@LB@ \| \|@LB@ 33 3@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -27.4972 kcal/mol@LB@Unfolding Energy - mRNA 11.1013 kcal/mol@LB@Unfolding Energy - sRNA 7.84022 kcal/mol@LB@@LB@Position - mRNA 247 -- 281@LB@Position - sRNA 4 -- 32@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 4 -- 10@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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