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
125	0.009022	0.2491	b0658	ybeX	-16.01	0.015431	14 -- 34	5 -- 21	putative ion transport	_____________13____________________35\n_____________\|_____________________\|\n5'-UUA...CGAUC__________UGAC_______AAGAA...ACC-3'\n______________ACAUCGAAGA____GAAGCAG\n______________\|\|\|\|\|:\|\|\|\|____:\|\|\|\|\|\|\n______________UGUAGUUUCU____UUUCGUC\n3'-UUU...ACCCC_____________________ACCG-5'\n_____________\|_____________________\|\n_____________22____________________4\n	28 -- 34	5 -- 11	-20.2475 kcal/mol	2.73159 kcal/mol	1.5073 kcal/mol	13 35@LB@ \| \|@LB@5'-UUA...CGAUC UGAC AAGAA...ACC-3'@LB@ ACAUCGAAGA GAAGCAG@LB@ \|\|\|\|\|:\|\|\|\| :\|\|\|\|\|\|@LB@ UGUAGUUUCU UUUCGUC@LB@3'-UUU...ACCCC ACCG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -16.01 kcal/mol@LB@Hybridization Energy -20.2475 kcal/mol@LB@Unfolding Energy - mRNA 2.73159 kcal/mol@LB@Unfolding Energy - sRNA 1.5073 kcal/mol@LB@@LB@Position - mRNA 14 -- 34@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 5 -- 11@LB@
127	0.009277	0.2491	b2781	mazG	-12.70	0.090074	53 -- 69	8 -- 24	nucleoside triphosphate pyrophosphohydrolase	_____________52________________70\n_____________\|_________________\|\n5'-UGA...CAAGA__A___A__________AACAG...CGC-3'\n______________GG_GCA_CGAAGAAAGG\n______________\|\|_:\|\|_\|:\|\|\|\|\|\|:\|\n______________CC_UGU_GUUUCUUUUC\n3'-UUU...UUUAC__C___A__________GUCACCG-5'\n_____________\|_________________\|\n_____________25________________7\n	63 -- 69	8 -- 14	-16.258 kcal/mol	2.86814 kcal/mol	0.688982 kcal/mol	52 70@LB@ \| \|@LB@5'-UGA...CAAGA A A AACAG...CGC-3'@LB@ GG GCA CGAAGAAAGG@LB@ \|\| :\|\| \|:\|\|\|\|\|\|:\|@LB@ CC UGU GUUUCUUUUC@LB@3'-UUU...UUUAC C A GUCACCG-5'@LB@ \| \|@LB@ 25 7@LB@@LB@@LB@Energy -12.70 kcal/mol@LB@Hybridization Energy -16.258 kcal/mol@LB@Unfolding Energy - mRNA 2.86814 kcal/mol@LB@Unfolding Energy - sRNA 0.688982 kcal/mol@LB@@LB@Position - mRNA 53 -- 69@LB@Position - sRNA 8 -- 24@LB@Position Seed - mRNA 63 -- 69@LB@Position Seed - sRNA 8 -- 14@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@
129	0.009293	0.2491	b0428	cyoE	-12.51	0.098557	18 -- 26	1 -- 9	protoheme IX farnesyltransferase	_____________17________27\n_____________\|_________\|\n5'-GGA...GCAAU_________ACAGG...GCA-3'\n______________GGCAGUGGU\n______________:\|\|\|\|\|\|\|:\n______________UCGUCACCG\n3'-UUU...UCUUU_________-5'\n_____________\|________\|\n_____________10_______1\n	20 -- 26	1 -- 7	-15.8954 kcal/mol	2.13019 kcal/mol	1.2588 kcal/mol	17 27@LB@ \| \|@LB@5'-GGA...GCAAU ACAGG...GCA-3'@LB@ GGCAGUGGU@LB@ :\|\|\|\|\|\|\|:@LB@ UCGUCACCG@LB@3'-UUU...UCUUU -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -12.51 kcal/mol@LB@Hybridization Energy -15.8954 kcal/mol@LB@Unfolding Energy - mRNA 2.13019 kcal/mol@LB@Unfolding Energy - sRNA 1.2588 kcal/mol@LB@@LB@Position - mRNA 18 -- 26@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 1 -- 7@LB@
130	0.009344	0.2491	b2840	ygeA	-9.74	0.301486	266 -- 295	2 -- 29	Asp/Glu_racemase family protein	_____________265____________________________296\n_____________\|______________________________\|\n5'-AAA...UUGAU_____AA_________C__C___UU_____GCUUC-3'\n______________AAAUG__GGCAUUAAA_AG_GGC__GGUGG\n______________\|\|\|\|\|__\|:\|\|\|:\|\|\|_\|:_:\|\|__:\|\|\|\|\n______________UUUAC__CUGUAGUUU_UU_UCG__UCACC\n3'-UUU...GGUGU_____CC_________C__U__________G-5'\n_____________\|______________________________\|\n_____________30_____________________________1\n	275 -- 281	14 -- 20	-20.8158 kcal/mol	8.56062 kcal/mol	2.51906 kcal/mol	265 296@LB@ \| \|@LB@5'-AAA...UUGAU AA C C UU GCUUC-3'@LB@ AAAUG GGCAUUAAA AG GGC GGUGG@LB@ \|\|\|\|\| \|:\|\|\|:\|\|\| \|: :\|\| :\|\|\|\|@LB@ UUUAC CUGUAGUUU UU UCG UCACC@LB@3'-UUU...GGUGU CC C U G-5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -20.8158 kcal/mol@LB@Unfolding Energy - mRNA 8.56062 kcal/mol@LB@Unfolding Energy - sRNA 2.51906 kcal/mol@LB@@LB@Position - mRNA 266 -- 295@LB@Position - sRNA 2 -- 29@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 14 -- 20@LB@
131	0.009354	0.2491	b4478	dgoD	-14.24	0.041949	180 -- 199	1 -- 22	D-galactonate dehydratase	_____________179____________________200\n_____________\|______________________\|\n5'-AAA...GUUAA_____AUC______________AAUGA...UGA-3'\n______________GGCGU____GAGAGGCAGUG_C\n______________\|:\|:\|____\|\|:\|:\|\|\|\|\|\|_\|\n______________CUGUA____CUUUUCGUCAC_G\n3'-UUU...UACCC_____GUUU___________C_-5'\n_____________\|_____________________\|\n_____________23____________________1\n	192 -- 198	3 -- 9	-21.1696 kcal/mol	5.38995 kcal/mol	1.54023 kcal/mol	179 200@LB@ \| \|@LB@5'-AAA...GUUAA AUC AAUGA...UGA-3'@LB@ GGCGU GAGAGGCAGUG C@LB@ \|:\|:\| \|\|:\|:\|\|\|\|\|\| \|@LB@ CUGUA CUUUUCGUCAC G@LB@3'-UUU...UACCC GUUU C -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -14.24 kcal/mol@LB@Hybridization Energy -21.1696 kcal/mol@LB@Unfolding Energy - mRNA 5.38995 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 180 -- 199@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 3 -- 9@LB@
132	0.00937	0.2491	b1120	cobB	-12.17	0.114836	175 -- 191	3 -- 18	deacetylase of acs and cheY chemotaxis regulator	_____________174_______________192\n_____________\|_________________\|\n5'-CGC...UUUUU_______U_________CCGGA...AUC-3'\n______________UCAGAGA_AAAGUGGUG\n______________\|\|\|:\|\|\|_\|\|\|\|::\|\|\|\n______________AGUUUCU_UUUCGUCAC\n3'-UUU...CCUGU_________________CG-5'\n_____________\|_________________\|\n_____________19________________2\n	185 -- 191	3 -- 9	-17.0979 kcal/mol	3.47557 kcal/mol	1.45388 kcal/mol	174 192@LB@ \| \|@LB@5'-CGC...UUUUU U CCGGA...AUC-3'@LB@ UCAGAGA AAAGUGGUG@LB@ \|\|\|:\|\|\| \|\|\|\|::\|\|\|@LB@ AGUUUCU UUUCGUCAC@LB@3'-UUU...CCUGU CG-5'@LB@ \| \|@LB@ 19 2@LB@@LB@@LB@Energy -12.17 kcal/mol@LB@Hybridization Energy -17.0979 kcal/mol@LB@Unfolding Energy - mRNA 3.47557 kcal/mol@LB@Unfolding Energy - sRNA 1.45388 kcal/mol@LB@@LB@Position - mRNA 175 -- 191@LB@Position - sRNA 3 -- 18@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 3 -- 9@LB@
133	0.009634	0.2504	b2551	glyA	-13.83	0.051752	272 -- 286	6 -- 21	serine hydroxymethyltransferase	_____________271______________287\n_____________\|________________\|\n5'-CAA...AAAGU________________CAUCG...UCG-3'\n______________ACGUC_AGGAAGAGCA\n______________\|\|:\|\|_\|:\|\|\|:\|\|\|\|\n______________UGUAG_UUCUUUUCGU\n3'-UUU...ACCCC_____U__________CACCG-5'\n_____________\|________________\|\n_____________22_______________5\n	280 -- 286	6 -- 12	-16.7043 kcal/mol	2.28484 kcal/mol	0.584589 kcal/mol	271 287@LB@ \| \|@LB@5'-CAA...AAAGU CAUCG...UCG-3'@LB@ ACGUC AGGAAGAGCA@LB@ \|\|:\|\| \|:\|\|\|:\|\|\|\|@LB@ UGUAG UUCUUUUCGU@LB@3'-UUU...ACCCC U CACCG-5'@LB@ \| \|@LB@ 22 5@LB@@LB@@LB@Energy -13.83 kcal/mol@LB@Hybridization Energy -16.7043 kcal/mol@LB@Unfolding Energy - mRNA 2.28484 kcal/mol@LB@Unfolding Energy - sRNA 0.584589 kcal/mol@LB@@LB@Position - mRNA 272 -- 286@LB@Position - sRNA 6 -- 21@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 6 -- 12@LB@
134	0.009704	0.2504	b1444	patD	-10.55	0.224369	279 -- 297	10 -- 25	gamma-aminobutyraldehyde dehydrogenase	_____________278_________________298\n_____________\|___________________\|\n5'-UCG...CAACG_________UUACU_____UUG-3'\n______________GGGGACGUU_____GGAAA\n______________\|\|\|\|\|\|:\|:_____:\|\|\|\|\n______________CCCCUGUAG_____UCUUU\n3'-UUU...UUUUA_________UU________UCGUC...CCG-5'\n_____________\|___________________\|\n_____________26__________________9\n	281 -- 287	17 -- 23	-18.1658 kcal/mol	6.94606 kcal/mol	0.670388 kcal/mol	278 298@LB@ \| \|@LB@5'-UCG...CAACG UUACU UUG-3'@LB@ GGGGACGUU GGAAA@LB@ \|\|\|\|\|\|:\|: :\|\|\|\|@LB@ CCCCUGUAG UCUUU@LB@3'-UUU...UUUUA UU UCGUC...CCG-5'@LB@ \| \|@LB@ 26 9@LB@@LB@@LB@Energy -10.55 kcal/mol@LB@Hybridization Energy -18.1658 kcal/mol@LB@Unfolding Energy - mRNA 6.94606 kcal/mol@LB@Unfolding Energy - sRNA 0.670388 kcal/mol@LB@@LB@Position - mRNA 279 -- 297@LB@Position - sRNA 10 -- 25@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 17 -- 23@LB@
135	0.009724	0.2504	b1387	paaZ	-12.57	0.095542	174 -- 198	5 -- 30	oxepin-CoA hydrolase and 3-oxo-5 6-dehydrosuberyl-CoA semialdehyde dehydrogenase	_____________173_________________________199\n_____________\|___________________________\|\n5'-UAA...CAACA______U_AA_____U___________CGAUG...AAG-3'\n______________GAAAUG_G__ACAUC___GGAGAGUAG\n______________:\|\|\|\|\|_\|__\|\|\|\|\|___\|:\|:\|\|:\|\|\n______________UUUUAC_C__UGUAG___CUUUUCGUC\n3'-UUU...AGGUG________CC_____UUU_________ACCG-5'\n_____________\|___________________________\|\n_____________31__________________________4\n	192 -- 198	5 -- 11	-19.0129 kcal/mol	3.93627 kcal/mol	2.50278 kcal/mol	173 199@LB@ \| \|@LB@5'-UAA...CAACA U AA U CGAUG...AAG-3'@LB@ GAAAUG G ACAUC GGAGAGUAG@LB@ :\|\|\|\|\| \| \|\|\|\|\| \|:\|:\|\|:\|\|@LB@ UUUUAC C UGUAG CUUUUCGUC@LB@3'-UUU...AGGUG CC UUU ACCG-5'@LB@ \| \|@LB@ 31 4@LB@@LB@@LB@Energy -12.57 kcal/mol@LB@Hybridization Energy -19.0129 kcal/mol@LB@Unfolding Energy - mRNA 3.93627 kcal/mol@LB@Unfolding Energy - sRNA 2.50278 kcal/mol@LB@@LB@Position - mRNA 174 -- 198@LB@Position - sRNA 5 -- 30@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 5 -- 11@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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usability assessment

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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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