Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
11	0.0003708	0.1087	b4201	priB	-14.90	0.029310	176 -- 193	6 -- 26	primosomal protein N	_____________175___________________194\n_____________\|_____________________\|\n5'-AGG...GAAGC__________U__________AUUUC...AUC-3'\n______________UGGGGAU_UC___GAAGAGUA\n______________\|\|\|\|\|\|:_\|\|___\|\|\|:\|\|:\|\n______________ACCCCUG_AG___CUUUUCGU\n3'-UUU...GUUUU_______U__UUU________CACCG-5'\n_____________\|_____________________\|\n_____________27____________________5\n	187 -- 193	6 -- 12	-19.0189 kcal/mol	3.41067 kcal/mol	0.706421 kcal/mol	175 194@LB@ \| \|@LB@5'-AGG...GAAGC U AUUUC...AUC-3'@LB@ UGGGGAU UC GAAGAGUA@LB@ \|\|\|\|\|\|: \|\| \|\|\|:\|\|:\|@LB@ ACCCCUG AG CUUUUCGU@LB@3'-UUU...GUUUU U UUU CACCG-5'@LB@ \| \|@LB@ 27 5@LB@@LB@@LB@Energy -14.90 kcal/mol@LB@Hybridization Energy -19.0189 kcal/mol@LB@Unfolding Energy - mRNA 3.41067 kcal/mol@LB@Unfolding Energy - sRNA 0.706421 kcal/mol@LB@@LB@Position - mRNA 176 -- 193@LB@Position - sRNA 6 -- 26@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 6 -- 12@LB@
84	0.005241	0.2147	b2513	yfgM	-12.13	0.116945	176 -- 204	2 -- 26	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________175___________________________205\n_____________\|_____________________________\|\n5'-GGC...GUUAC____UUAAGG_________G_CAGC____AAAUU...UUG-3'\n______________UGGG______AAGGAGAAG_A____GUGG\n______________\|\|\|\|______\|\|:\|\|:\|\|\|_\|____\|\|\|\|\n______________ACCC______UUUCUUUUC_U____CACC\n3'-UUU...GUUUU____CUGUAG_________G_________G-5'\n_____________\|_____________________________\|\n_____________27____________________________1\n	188 -- 194	8 -- 14	-19.1762 kcal/mol	4.53021 kcal/mol	2.5184 kcal/mol	175 205@LB@ \| \|@LB@5'-GGC...GUUAC UUAAGG G CAGC AAAUU...UUG-3'@LB@ UGGG AAGGAGAAG A GUGG@LB@ \|\|\|\| \|\|:\|\|:\|\|\| \| \|\|\|\|@LB@ ACCC UUUCUUUUC U CACC@LB@3'-UUU...GUUUU CUGUAG G G-5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -12.13 kcal/mol@LB@Hybridization Energy -19.1762 kcal/mol@LB@Unfolding Energy - mRNA 4.53021 kcal/mol@LB@Unfolding Energy - sRNA 2.5184 kcal/mol@LB@@LB@Position - mRNA 176 -- 204@LB@Position - sRNA 2 -- 26@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 8 -- 14@LB@
99	0.006147	0.2179	b4477	dgoA	-14.15	0.044006	176 -- 210	1 -- 31	2-oxo-3-deoxygalactonate 6-phosphate aldolase	_____________175___________________________________211\n_____________\|_____________________________________\|\n5'-CAG...CAUUU____C___UAUAA___G_____CUCAU__________AAACU...UCG-3'\n______________CAGG_UGG_____GGA_CAUCG_______GCAGUGGC\n______________\|\|::_\|\|\|_____\|\|\|_\|\|\|\|:_______\|\|\|\|\|\|\|\|\n______________GUUU_ACC_____CCU_GUAGU_______CGUCACCG\n3'-UUU...GAGGU____U_________________UUCUUUU________-5'\n_____________\|____________________________________\|\n_____________32___________________________________1\n	204 -- 210	1 -- 7	-26.5297 kcal/mol	9.84206 kcal/mol	2.53929 kcal/mol	175 211@LB@ \| \|@LB@5'-CAG...CAUUU C UAUAA G CUCAU AAACU...UCG-3'@LB@ CAGG UGG GGA CAUCG GCAGUGGC@LB@ \|\|:: \|\|\| \|\|\| \|\|\|\|: \|\|\|\|\|\|\|\|@LB@ GUUU ACC CCU GUAGU CGUCACCG@LB@3'-UUU...GAGGU U UUCUUUU -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -14.15 kcal/mol@LB@Hybridization Energy -26.5297 kcal/mol@LB@Unfolding Energy - mRNA 9.84206 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 176 -- 210@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 1 -- 7@LB@
72	0.004007	0.1953	b2175	mepS	-13.55	0.059767	177 -- 194	6 -- 23	murein DD-endopeptidase space-maker hydrolase mutational suppressor of prc thermosensitivity outer membrane lipoprotein weak murein LD-carboxypeptidase	_____________176________________195\n_____________\|__________________\|\n5'-CAA...GUUAA____U__________A__AACAA...CAA-3'\n______________GGAC_UCAAGGGAAA_CA\n______________\|\|\|\|_\|\|\|\|:\|:\|\|\|_\|\|\n______________CCUG_AGUUUCUUUU_GU\n3'-UUU...UUACC____U__________C__CACCG-5'\n_____________\|__________________\|\n_____________24_________________5\n	185 -- 191	9 -- 15	-17.1277 kcal/mol	2.97845 kcal/mol	0.599171 kcal/mol	176 195@LB@ \| \|@LB@5'-CAA...GUUAA U A AACAA...CAA-3'@LB@ GGAC UCAAGGGAAA CA@LB@ \|\|\|\| \|\|\|\|:\|:\|\|\| \|\|@LB@ CCUG AGUUUCUUUU GU@LB@3'-UUU...UUACC U C CACCG-5'@LB@ \| \|@LB@ 24 5@LB@@LB@@LB@Energy -13.55 kcal/mol@LB@Hybridization Energy -17.1277 kcal/mol@LB@Unfolding Energy - mRNA 2.97845 kcal/mol@LB@Unfolding Energy - sRNA 0.599171 kcal/mol@LB@@LB@Position - mRNA 177 -- 194@LB@Position - sRNA 6 -- 23@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 9 -- 15@LB@
54	0.00267	0.1735	b0131	panD	-12.96	0.079905	178 -- 195	5 -- 22	aspartate 1-decarboxylase	_____________177________________196\n_____________\|__________________\|\n5'-AUU...UUAAC____GGGU__________AAGUU...UUG-3'\n______________GACA____AGAAAGGUAG\n______________\|\|\|\|____\|\|\|\|\|:\|:\|\|\n______________CUGU____UCUUUUCGUC\n3'-UUU...UACCC____AGUU__________ACCG-5'\n_____________\|__________________\|\n_____________23_________________4\n	189 -- 195	5 -- 11	-16.4376 kcal/mol	1.9462 kcal/mol	1.53637 kcal/mol	177 196@LB@ \| \|@LB@5'-AUU...UUAAC GGGU AAGUU...UUG-3'@LB@ GACA AGAAAGGUAG@LB@ \|\|\|\| \|\|\|\|\|:\|:\|\|@LB@ CUGU UCUUUUCGUC@LB@3'-UUU...UACCC AGUU ACCG-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -12.96 kcal/mol@LB@Hybridization Energy -16.4376 kcal/mol@LB@Unfolding Energy - mRNA 1.9462 kcal/mol@LB@Unfolding Energy - sRNA 1.53637 kcal/mol@LB@@LB@Position - mRNA 178 -- 195@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 5 -- 11@LB@
110	0.007401	0.2348	b0784	moaD	-14.78	0.031320	178 -- 203	3 -- 25	molybdopterin synthase small subunit	_____________177________________________204\n_____________\|__________________________\|\n5'-GCA...AAGUC___U___U______U________A__AUUAA...AGC-3'\n______________GGG_GAC_UUAAGG_GGAAGCGG_UG\n______________\|\|\|_\|\|\|_\|:\|\|:\|_::\|\|\|\|:\|_\|\|\n______________CCC_CUG_AGUUUC_UUUUCGUC_AC\n3'-UUU...UUUUA_______U__________________CG-5'\n_____________\|__________________________\|\n_____________26_________________________2\n	194 -- 200	5 -- 11	-23.9822 kcal/mol	6.68375 kcal/mol	2.5166 kcal/mol	177 204@LB@ \| \|@LB@5'-GCA...AAGUC U U U A AUUAA...AGC-3'@LB@ GGG GAC UUAAGG GGAAGCGG UG@LB@ \|\|\| \|\|\| \|:\|\|:\| ::\|\|\|\|:\| \|\|@LB@ CCC CUG AGUUUC UUUUCGUC AC@LB@3'-UUU...UUUUA U CG-5'@LB@ \| \|@LB@ 26 2@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -23.9822 kcal/mol@LB@Unfolding Energy - mRNA 6.68375 kcal/mol@LB@Unfolding Energy - sRNA 2.5166 kcal/mol@LB@@LB@Position - mRNA 178 -- 203@LB@Position - sRNA 3 -- 25@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 5 -- 11@LB@
128	0.00928	0.2491	b0491	fetB	-12.70	0.090276	178 -- 195	1 -- 17	iron export ABC transporter permease; peroxide resistance protein	_____________177________________196\n_____________\|__________________\|\n5'-GCC...CAUGC________U____GAA__ACGCU...AGA-3'\n______________CGGAGAAA_GCAG___GC\n______________\|::\|\|\|\|\|_\|\|\|\|___\|\|\n______________GUUUCUUU_CGUC___CG\n3'-UUU...CUGUA________U____AC___-5'\n_____________\|_________________\|\n_____________18________________1\n	179 -- 185	10 -- 16	-17.1669 kcal/mol	3.03232 kcal/mol	1.43853 kcal/mol	177 196@LB@ \| \|@LB@5'-GCC...CAUGC U GAA ACGCU...AGA-3'@LB@ CGGAGAAA GCAG GC@LB@ \|::\|\|\|\|\| \|\|\|\| \|\|@LB@ GUUUCUUU CGUC CG@LB@3'-UUU...CUGUA U AC -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -12.70 kcal/mol@LB@Hybridization Energy -17.1669 kcal/mol@LB@Unfolding Energy - mRNA 3.03232 kcal/mol@LB@Unfolding Energy - sRNA 1.43853 kcal/mol@LB@@LB@Position - mRNA 178 -- 195@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 10 -- 16@LB@
177	0.01288	0.2504	b3455	livG	-10.61	0.218983	178 -- 198	5 -- 24	branched-chain amino acid ABC transporter ATPase	_____________177___________________199\n_____________\|_____________________\|\n5'-AUG...AAAAC__C___GCG____________GCAUG...UCG-3'\n______________GG_GCA___AAAGGAGAGCAG\n______________\|\|_:\|\|___\|\|\|\|:\|:\|\|\|\|\|\n______________CC_UGU___UUUCUUUUCGUC\n3'-UUU...UUUAC__C___AG_____________ACCG-5'\n_____________\|_____________________\|\n_____________25____________________4\n	192 -- 198	5 -- 11	-19.5574 kcal/mol	6.51739 kcal/mol	2.42705 kcal/mol	177 199@LB@ \| \|@LB@5'-AUG...AAAAC C GCG GCAUG...UCG-3'@LB@ GG GCA AAAGGAGAGCAG@LB@ \|\| :\|\| \|\|\|\|:\|:\|\|\|\|\|@LB@ CC UGU UUUCUUUUCGUC@LB@3'-UUU...UUUAC C AG ACCG-5'@LB@ \| \|@LB@ 25 4@LB@@LB@@LB@Energy -10.61 kcal/mol@LB@Hybridization Energy -19.5574 kcal/mol@LB@Unfolding Energy - mRNA 6.51739 kcal/mol@LB@Unfolding Energy - sRNA 2.42705 kcal/mol@LB@@LB@Position - mRNA 178 -- 198@LB@Position - sRNA 5 -- 24@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 5 -- 11@LB@
124	0.008958	0.2491	b0124	gcd	-13.85	0.051383	179 -- 193	48 -- 62	glucose dehydrogenase	_____________178_____________194\n_____________\|_______________\|\n5'-UAA...AUUAA_______________UCUCU...GGC-3'\n______________UGAAUUGAAAUGGUG\n______________\|\|\|\|::\|\|\|\|\|\|\|:\|\n______________ACUUGGCUUUACCGC\n3'-UUU...UUGGA_______________CCCAA...CCG-5'\n_____________\|_______________\|\n_____________63______________47\n	187 -- 193	48 -- 54	-20.4838 kcal/mol	2.67361 kcal/mol	3.96136 kcal/mol	178 194@LB@ \| \|@LB@5'-UAA...AUUAA UCUCU...GGC-3'@LB@ UGAAUUGAAAUGGUG@LB@ \|\|\|\|::\|\|\|\|\|\|\|:\|@LB@ ACUUGGCUUUACCGC@LB@3'-UUU...UUGGA CCCAA...CCG-5'@LB@ \| \|@LB@ 63 47@LB@@LB@@LB@Energy -13.85 kcal/mol@LB@Hybridization Energy -20.4838 kcal/mol@LB@Unfolding Energy - mRNA 2.67361 kcal/mol@LB@Unfolding Energy - sRNA 3.96136 kcal/mol@LB@@LB@Position - mRNA 179 -- 193@LB@Position - sRNA 48 -- 62@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 48 -- 54@LB@
4	1.99e-05	0.01653	b4255	rraB	-17.36	0.006479	180 -- 205	1 -- 23	protein inhibitor of RNase E	_____________179________________________206\n_____________\|__________________________\|\n5'-GAG...CGGCA_________GA____U____CA____AAACC...CCA-3'\n______________GGACAUUAA__GGAA_GAGC__UGGC\n______________\|\|\|\|\|\|:\|\|__:\|\|\|_:\|\|\|__\|\|\|\|\n______________CCUGUAGUU__UCUU_UUCG__ACCG\n3'-UUU...UUACC____________________UC____-5'\n_____________\|_________________________\|\n_____________24________________________1\n	182 -- 188	15 -- 21	-24.3176 kcal/mol	5.37332 kcal/mol	1.57928 kcal/mol	179 206@LB@ \| \|@LB@5'-GAG...CGGCA GA U CA AAACC...CCA-3'@LB@ GGACAUUAA GGAA GAGC UGGC@LB@ \|\|\|\|\|\|:\|\| :\|\|\| :\|\|\| \|\|\|\|@LB@ CCUGUAGUU UCUU UUCG ACCG@LB@3'-UUU...UUACC UC -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -17.36 kcal/mol@LB@Hybridization Energy -24.3176 kcal/mol@LB@Unfolding Energy - mRNA 5.37332 kcal/mol@LB@Unfolding Energy - sRNA 1.57928 kcal/mol@LB@@LB@Position - mRNA 180 -- 205@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 15 -- 21@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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