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
92	0.009361	0.3104	b3652	recG	-7.88	0.265686	265 -- 278	7 -- 20	ATP-dependent DNA helicase	_____________264_____________279\n_____________\|_______________\|\n5'-CAA...ACUUA________C______AAAAU...UGC-3'\n______________GUAACAAA_UG_GCG\n______________:\|\|\|\|\|\|\|_\|\|_\|\|\|\n______________UAUUGUUU_AC_CGC\n3'-UUU...ACUAC___________G___AGAAAG-5'\n_____________\|_______________\|\n_____________21______________6\n	266 -- 272	13 -- 19	-11.4583 kcal/mol	2.34189 kcal/mol	1.23906 kcal/mol	264 279@LB@ \| \|@LB@5'-CAA...ACUUA C AAAAU...UGC-3'@LB@ GUAACAAA UG GCG@LB@ :\|\|\|\|\|\|\| \|\| \|\|\|@LB@ UAUUGUUU AC CGC@LB@3'-UUU...ACUAC G AGAAAG-5'@LB@ \| \|@LB@ 21 6@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -11.4583 kcal/mol@LB@Unfolding Energy - mRNA 2.34189 kcal/mol@LB@Unfolding Energy - sRNA 1.23906 kcal/mol@LB@@LB@Position - mRNA 265 -- 278@LB@Position - sRNA 7 -- 20@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 13 -- 19@LB@
108	0.01118	0.3104	b2565	recO	-9.71	0.135448	294 -- 300	5 -- 11	gap repair protein	_____________293____300\n_____________\|______\|\n5'-GAA...GGCGC_______-3'\n______________GUGCGUC\n______________\|:\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	294 -- 300	5 -- 11	-11.8762 kcal/mol	1.05403 kcal/mol	1.11145 kcal/mol	293 300@LB@ \| \|@LB@5'-GAA...GGCGC -3'@LB@ GUGCGUC@LB@ \|:\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -9.71 kcal/mol@LB@Hybridization Energy -11.8762 kcal/mol@LB@Unfolding Energy - mRNA 1.05403 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 294 -- 300@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 5 -- 11@LB@
93	0.009444	0.3104	b3822	recQ	-7.42	0.310549	176 -- 212	9 -- 45	ATP-dependent DNA helicase	_____________175____________________________________213\n_____________\|______________________________________\|\n5'-CGC...CUGUU________A__CAA__________AU______CAG___GAAGU...UUA-3'\n______________UUUAUUUC_GG___UC_GGGGUGA__GUGGCG___GCG\n______________\|\|:\|\|:\|\|_\|:___\|\|_\|\|\|:\|\|\|__:\|::\|:___\|\|\|\n______________AAGUAGAG_CU___AG_CCCUACU__UAUUGU___CGC\n3'-UUU...UUUUA________A__UA___U_______AC______UUA___GCAGAAAG-5'\n_____________\|______________________________________\|\n_____________46_____________________________________8\n	192 -- 198	23 -- 29	-25.6556 kcal/mol	8.78202 kcal/mol	9.45193 kcal/mol	175 213@LB@ \| \|@LB@5'-CGC...CUGUU A CAA AU CAG GAAGU...UUA-3'@LB@ UUUAUUUC GG UC GGGGUGA GUGGCG GCG@LB@ \|\|:\|\|:\|\| \|: \|\| \|\|\|:\|\|\| :\|::\|: \|\|\|@LB@ AAGUAGAG CU AG CCCUACU UAUUGU CGC@LB@3'-UUU...UUUUA A UA U AC UUA GCAGAAAG-5'@LB@ \| \|@LB@ 46 8@LB@@LB@@LB@Energy -7.42 kcal/mol@LB@Hybridization Energy -25.6556 kcal/mol@LB@Unfolding Energy - mRNA 8.78202 kcal/mol@LB@Unfolding Energy - sRNA 9.45193 kcal/mol@LB@@LB@Position - mRNA 176 -- 212@LB@Position - sRNA 9 -- 45@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 23 -- 29@LB@
194	0.0191	0.3104	b2698	recX	-10.17	0.113250	93 -- 107	8 -- 22	regulatory protein for RecA	_____________92______________108\n_____________\|_______________\|\n5'-AAA...GUAGA__________G____AGCAG...GAC-3'\n______________UGAUAGCGAA_GCGU\n______________\|\|\|\|\|:\|:\|\|_\|\|\|:\n______________ACUAUUGUUU_CGCG\n3'-UUU...CUACU__________A____CAGAAAG-5'\n_____________\|_______________\|\n_____________23______________7\n	96 -- 102	13 -- 19	-16.2974 kcal/mol	4.88496 kcal/mol	1.23838 kcal/mol	92 108@LB@ \| \|@LB@5'-AAA...GUAGA G AGCAG...GAC-3'@LB@ UGAUAGCGAA GCGU@LB@ \|\|\|\|\|:\|:\|\| \|\|\|:@LB@ ACUAUUGUUU CGCG@LB@3'-UUU...CUACU A CAGAAAG-5'@LB@ \| \|@LB@ 23 7@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -16.2974 kcal/mol@LB@Unfolding Energy - mRNA 4.88496 kcal/mol@LB@Unfolding Energy - sRNA 1.23838 kcal/mol@LB@@LB@Position - mRNA 93 -- 107@LB@Position - sRNA 8 -- 22@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 13 -- 19@LB@
149	0.01422	0.3104	b0415	ribE	-7.20	0.333957	258 -- 265	4 -- 11	riboflavin synthase beta chain	_____________257______266\n_____________\|________\|\n5'-CGG...CCAUC________CAACA...GUG-3'\n______________GCGCGUUU\n______________\|\|\|\|\|\|:\|\n______________CGCGCAGA\n3'-UUU...GUUUA________AAG-5'\n_____________\|________\|\n_____________12_______3\n	259 -- 265	4 -- 10	-13.1965 kcal/mol	4.83677 kcal/mol	1.15639 kcal/mol	257 266@LB@ \| \|@LB@5'-CGG...CCAUC CAACA...GUG-3'@LB@ GCGCGUUU@LB@ \|\|\|\|\|\|:\|@LB@ CGCGCAGA@LB@3'-UUU...GUUUA AAG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -7.20 kcal/mol@LB@Hybridization Energy -13.1965 kcal/mol@LB@Unfolding Energy - mRNA 4.83677 kcal/mol@LB@Unfolding Energy - sRNA 1.15639 kcal/mol@LB@@LB@Position - mRNA 258 -- 265@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 4 -- 10@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@
10	0.0002413	0.08171	b2594	rluD	-15.70	0.011720	48 -- 64	5 -- 21	23S rRNA pseudouridine(1911 1915 1917) synthase	_____________47________________65\n_____________\|_________________\|\n5'-CCC...CACCA____UUUC_________AUGAC...GUU-3'\n______________GAUA____AUGCGCGUC\n______________\|\|\|\|____\|\|\|\|\|\|\|\|\|\n______________CUAU____UACGCGCAG\n3'-UUU...UACUA____UGUU_________AAAG-5'\n_____________\|_________________\|\n_____________22________________4\n	58 -- 64	5 -- 11	-19.7285 kcal/mol	2.7828 kcal/mol	1.24955 kcal/mol	47 65@LB@ \| \|@LB@5'-CCC...CACCA UUUC AUGAC...GUU-3'@LB@ GAUA AUGCGCGUC@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ CUAU UACGCGCAG@LB@3'-UUU...UACUA UGUU AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -15.70 kcal/mol@LB@Hybridization Energy -19.7285 kcal/mol@LB@Unfolding Energy - mRNA 2.7828 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 48 -- 64@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 5 -- 11@LB@
144	0.01383	0.3104	b1135	rluE	-11.03	0.080673	174 -- 189	5 -- 20	23S rRNA pseudouridine(2457) synthase	_____________173______________190\n_____________\|________________\|\n5'-UGU...CCGUC____A___________AUUAG...AAC-3'\n______________AUGA_AGAUGCGCGUU\n______________\|\|:\|_\|:\|\|\|\|\|\|\|\|:\n______________UAUU_UUUACGCGCAG\n3'-UUU...ACUAC____G___________AAAG-5'\n_____________\|________________\|\n_____________21_______________4\n	183 -- 189	5 -- 11	-17.9797 kcal/mol	5.69694 kcal/mol	1.24804 kcal/mol	173 190@LB@ \| \|@LB@5'-UGU...CCGUC A AUUAG...AAC-3'@LB@ AUGA AGAUGCGCGUU@LB@ \|\|:\| \|:\|\|\|\|\|\|\|\|:@LB@ UAUU UUUACGCGCAG@LB@3'-UUU...ACUAC G AAAG-5'@LB@ \| \|@LB@ 21 4@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -17.9797 kcal/mol@LB@Unfolding Energy - mRNA 5.69694 kcal/mol@LB@Unfolding Energy - sRNA 1.24804 kcal/mol@LB@@LB@Position - mRNA 174 -- 189@LB@Position - sRNA 5 -- 20@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 5 -- 11@LB@
70	0.006501	0.3087	b3301	rplO	-9.96	0.122936	194 -- 206	8 -- 20	50S ribosomal subunit protein L15	_____________193___________207\n_____________\|_____________\|\n5'-UUC...GAGGA____G________UUAAA...GUG-3'\n______________GUAA_AGAUGCGU\n______________:\|\|\|_\|:\|\|\|\|\|:\n______________UAUU_UUUACGCG\n3'-UUU...ACUAC____G________CAGAAAG-5'\n_____________\|_____________\|\n_____________21____________7\n	200 -- 206	8 -- 14	-13.6668 kcal/mol	2.47062 kcal/mol	1.23367 kcal/mol	193 207@LB@ \| \|@LB@5'-UUC...GAGGA G UUAAA...GUG-3'@LB@ GUAA AGAUGCGU@LB@ :\|\|\| \|:\|\|\|\|\|:@LB@ UAUU UUUACGCG@LB@3'-UUU...ACUAC G CAGAAAG-5'@LB@ \| \|@LB@ 21 7@LB@@LB@@LB@Energy -9.96 kcal/mol@LB@Hybridization Energy -13.6668 kcal/mol@LB@Unfolding Energy - mRNA 2.47062 kcal/mol@LB@Unfolding Energy - sRNA 1.23367 kcal/mol@LB@@LB@Position - mRNA 194 -- 206@LB@Position - sRNA 8 -- 20@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 8 -- 14@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@

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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