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
187	0.01374	0.2529	b1344	ttcA	-15.51	0.020761	46 -- 73	1 -- 29	tRNA s(2)C32 thioltransferase iron sulfur cluster protein	_____________45_____________________________74\n_____________\|______________________________\|\n5'-GCU...CAGCC____________G___CUGC_____A____GUAUG...UCA-3'\n______________AAAUGGGG_CAU_AAA_____GCAG_UGGU\n______________\|\|\|\|\|\|\|\|_\|\|\|_\|\|\|_____\|\|\|\|_\|\|\|:\n______________UUUACCCC_GUA_UUU_____CGUC_ACCG\n3'-UUU...GGUGU________U___G___CUUUU_________-5'\n_____________\|_____________________________\|\n_____________30____________________________1\n	47 -- 53	22 -- 28	-26.0543 kcal/mol	8.02666 kcal/mol	2.51907 kcal/mol	45 74@LB@ \| \|@LB@5'-GCU...CAGCC G CUGC A GUAUG...UCA-3'@LB@ AAAUGGGG CAU AAA GCAG UGGU@LB@ \|\|\|\|\|\|\|\| \|\|\| \|\|\| \|\|\|\| \|\|\|:@LB@ UUUACCCC GUA UUU CGUC ACCG@LB@3'-UUU...GGUGU U G CUUUU -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -15.51 kcal/mol@LB@Hybridization Energy -26.0543 kcal/mol@LB@Unfolding Energy - mRNA 8.02666 kcal/mol@LB@Unfolding Energy - sRNA 2.51907 kcal/mol@LB@@LB@Position - mRNA 46 -- 73@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 22 -- 28@LB@
32	0.001499	0.1635	b0661	miaB	-12.88	0.082685	213 -- 250	6 -- 36	tRNA-i(6)A37 methylthiotransferase	_____________212____________________________________251\n_____________\|______________________________________\|\n5'-CGC...AAAAA_______UU_AAACC_____C_______U___C_____CGAUU...AAC-3'\n______________CUCCAUA__A_____UGGGG_UGUCAGA_GAA_GAGUA\n______________\|\|\|\|\|:\|__\|_____\|\|\|\|\|_::\|\|\|:\|_\|\|\|_:\|\|:\|\n______________GAGGUGU__U_____ACCCC_GUAGUUU_CUU_UUCGU\n3'-UUU...UACCC_______UU___________U_________________CACCG-5'\n_____________\|______________________________________\|\n_____________37_____________________________________5\n	234 -- 240	14 -- 20	-26.1374 kcal/mol	6.57825 kcal/mol	6.67617 kcal/mol	212 251@LB@ \| \|@LB@5'-CGC...AAAAA UU AAACC C U C CGAUU...AAC-3'@LB@ CUCCAUA A UGGGG UGUCAGA GAA GAGUA@LB@ \|\|\|\|\|:\| \| \|\|\|\|\| ::\|\|\|:\| \|\|\| :\|\|:\|@LB@ GAGGUGU U ACCCC GUAGUUU CUU UUCGU@LB@3'-UUU...UACCC UU U CACCG-5'@LB@ \| \|@LB@ 37 5@LB@@LB@@LB@Energy -12.88 kcal/mol@LB@Hybridization Energy -26.1374 kcal/mol@LB@Unfolding Energy - mRNA 6.57825 kcal/mol@LB@Unfolding Energy - sRNA 6.67617 kcal/mol@LB@@LB@Position - mRNA 213 -- 250@LB@Position - sRNA 6 -- 36@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 14 -- 20@LB@
107	0.007146	0.2343	b0085	murE	-14.50	0.036427	193 -- 205	1 -- 25	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:meso- diaminopimelate ligase	_____________192_______________________206\n_____________\|_________________________\|\n5'-UGC...GGCGA_________________________AGAUC...CGG-3'\n______________GGGGACA____________GGUGGC\n______________\|\|\|\|\|\|\|____________:\|\|\|\|\|\n______________CCCCUGU____________UCACCG\n3'-UUU...UUUUA_______AGUUUCUUUUCG______-5'\n_____________\|________________________\|\n_____________26_______________________1\n	193 -- 199	19 -- 25	-21.3886 kcal/mol	4.36682 kcal/mol	2.51748 kcal/mol	192 206@LB@ \| \|@LB@5'-UGC...GGCGA AGAUC...CGG-3'@LB@ GGGGACA GGUGGC@LB@ \|\|\|\|\|\|\| :\|\|\|\|\|@LB@ CCCCUGU UCACCG@LB@3'-UUU...UUUUA AGUUUCUUUUCG -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -14.50 kcal/mol@LB@Hybridization Energy -21.3886 kcal/mol@LB@Unfolding Energy - mRNA 4.36682 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 193 -- 205@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 19 -- 25@LB@
175	0.01275	0.2504	b3057	bacA	-10.43	0.234919	238 -- 261	5 -- 26	undecaprenyl pyrophosphate phosphatase	_____________237______________________262\n_____________\|________________________\|\n5'-UUC...AAUAU____U_UG_________UU_A___AAUUU...UUG-3'\n______________UGGG_G__GUCGAAGGA__G_CAG\n______________\|\|\|\|_\|__:\|\|:\|\|\|:\|__\|_\|\|\|\n______________ACCC_C__UAGUUUCUU__C_GUC\n3'-UUU...GUUUU______UG_________UU_____ACCG-5'\n_____________\|________________________\|\n_____________27_______________________4\n	248 -- 254	11 -- 17	-20.3624 kcal/mol	7.43347 kcal/mol	2.50108 kcal/mol	237 262@LB@ \| \|@LB@5'-UUC...AAUAU U UG UU A AAUUU...UUG-3'@LB@ UGGG G GUCGAAGGA G CAG@LB@ \|\|\|\| \| :\|\|:\|\|\|:\| \| \|\|\|@LB@ ACCC C UAGUUUCUU C GUC@LB@3'-UUU...GUUUU UG UU ACCG-5'@LB@ \| \|@LB@ 27 4@LB@@LB@@LB@Energy -10.43 kcal/mol@LB@Hybridization Energy -20.3624 kcal/mol@LB@Unfolding Energy - mRNA 7.43347 kcal/mol@LB@Unfolding Energy - sRNA 2.50108 kcal/mol@LB@@LB@Position - mRNA 238 -- 261@LB@Position - sRNA 5 -- 26@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 11 -- 17@LB@
85	0.0054	0.2147	b4461	yfjD	-16.56	0.010978	60 -- 89	2 -- 27	UPF0053 family inner membrane protein	_____________59______________________________90\n_____________\|_______________________________\|\n5'-GAA...CUGCU___________AUCAU______U________ACGCC...UCA-3'\n______________GUGGGGACAUU_____GAAGGA_GGC_GUGG\n______________:\|\|\|\|\|\|\|\|\|:_____:\|\|\|:\|_:\|\|_\|\|\|\|\n______________UACCCCUGUAG_____UUUCUU_UCG_CACC\n3'-UUU...UGUUU______________________U___U____G-5'\n_____________\|_______________________________\|\n_____________28______________________________1\n	64 -- 70	17 -- 23	-31.7913 kcal/mol	12.7137 kcal/mol	2.51866 kcal/mol	59 90@LB@ \| \|@LB@5'-GAA...CUGCU AUCAU U ACGCC...UCA-3'@LB@ GUGGGGACAUU GAAGGA GGC GUGG@LB@ :\|\|\|\|\|\|\|\|\|: :\|\|\|:\| :\|\| \|\|\|\|@LB@ UACCCCUGUAG UUUCUU UCG CACC@LB@3'-UUU...UGUUU U U G-5'@LB@ \| \|@LB@ 28 1@LB@@LB@@LB@Energy -16.56 kcal/mol@LB@Hybridization Energy -31.7913 kcal/mol@LB@Unfolding Energy - mRNA 12.7137 kcal/mol@LB@Unfolding Energy - sRNA 2.51866 kcal/mol@LB@@LB@Position - mRNA 60 -- 89@LB@Position - sRNA 2 -- 27@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 17 -- 23@LB@
7	0.0001218	0.05555	b1811	yoaH	-21.30	0.000256	259 -- 293	1 -- 35	UPF0181 family protein	_____________258__________________________________294\n_____________\|____________________________________\|\n5'-ACG...GCGGA____G___C__AU____________U______C___CAGGCAA-3'\n______________UCCA_GAA_UG__GGCA_CAAGGGA_GAGCAG_GGC\n______________\|\|\|\|_:\|\|_\|\|__\|:\|\|_\|\|\|:\|:\|_:\|\|\|\|\|_\|\|\|\n______________AGGU_UUU_AC__CUGU_GUUUCUU_UUCGUC_CCG\n3'-UUU...ACCCG____G___U__CC____A______________A___-5'\n_____________\|___________________________________\|\n_____________36__________________________________1\n	276 -- 282	11 -- 17	-33.9537 kcal/mol	7.61738 kcal/mol	5.03645 kcal/mol	258 294@LB@ \| \|@LB@5'-ACG...GCGGA G C AU U C CAGGCAA-3'@LB@ UCCA GAA UG GGCA CAAGGGA GAGCAG GGC@LB@ \|\|\|\| :\|\| \|\| \|:\|\| \|\|\|:\|:\| :\|\|\|\|\| \|\|\|@LB@ AGGU UUU AC CUGU GUUUCUU UUCGUC CCG@LB@3'-UUU...ACCCG G U CC A A -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -21.30 kcal/mol@LB@Hybridization Energy -33.9537 kcal/mol@LB@Unfolding Energy - mRNA 7.61738 kcal/mol@LB@Unfolding Energy - sRNA 5.03645 kcal/mol@LB@@LB@Position - mRNA 259 -- 293@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 11 -- 17@LB@
197	0.0142	0.2529	b2295	yfbV	-14.79	0.031139	250 -- 276	1 -- 25	UPF0208 family inner membrane protein	_____________249_________________________277\n_____________\|___________________________\|\n5'-AUG...UCGCC_______G__UUACUC____AC_____CGCUG...CGG-3'\n______________GGGGACA_CA______AAAG__GUGGC\n______________\|\|\|\|\|\|\|_\|\|______\|\|\|\|__\|\|\|\|\|\n______________CCCCUGU_GU______UUUC__CACCG\n3'-UUU...UUUUA_______A__UUCU______GU_____-5'\n_____________\|__________________________\|\n_____________26_________________________1\n	250 -- 256	19 -- 25	-25.4481 kcal/mol	8.13822 kcal/mol	2.51748 kcal/mol	249 277@LB@ \| \|@LB@5'-AUG...UCGCC G UUACUC AC CGCUG...CGG-3'@LB@ GGGGACA CA AAAG GUGGC@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\| \|\|\|\|\|@LB@ CCCCUGU GU UUUC CACCG@LB@3'-UUU...UUUUA A UUCU GU -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -14.79 kcal/mol@LB@Hybridization Energy -25.4481 kcal/mol@LB@Unfolding Energy - mRNA 8.13822 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 250 -- 276@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 19 -- 25@LB@
170	0.01232	0.2504	b2580	ung	-11.45	0.156876	183 -- 205	1 -- 22	uracil-DNA-glycosylase	_____________182______________________206\n_____________\|________________________\|\n5'-UCU...UUGAA_______C________G__A____UAACG...CCG-3'\n______________GAU_UCG_AGGAGAGC_AG_UGGC\n______________\|\|:_\|\|:_\|\|:\|:\|\|\|_\|\|_\|\|\|\|\n______________CUG_AGU_UCUUUUCG_UC_ACCG\n3'-UUU...UACCC___U___U________________-5'\n_____________\|_______________________\|\n_____________23______________________1\n	191 -- 197	7 -- 13	-20.4372 kcal/mol	7.45123 kcal/mol	1.54023 kcal/mol	182 206@LB@ \| \|@LB@5'-UCU...UUGAA C G A UAACG...CCG-3'@LB@ GAU UCG AGGAGAGC AG UGGC@LB@ \|\|: \|\|: \|\|:\|:\|\|\| \|\| \|\|\|\|@LB@ CUG AGU UCUUUUCG UC ACCG@LB@3'-UUU...UACCC U U -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -20.4372 kcal/mol@LB@Unfolding Energy - mRNA 7.45123 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 183 -- 205@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 7 -- 13@LB@
178	0.01293	0.2504	b4258	valS	-13.78	0.053235	248 -- 266	1 -- 21	valyl-tRNA synthetase	_____________247___________________267\n_____________\|_____________________\|\n5'-AUC...UACGA_____U_______________UACUU...AAA-3'\n______________GCA_C_GGGAAAAGCAG_GGC\n______________:\|\|_\|_::\|\|\|\|\|\|\|\|\|_\|\|\|\n______________UGU_G_UUCUUUUCGUC_CCG\n3'-UUU...ACCCC___A_U___________A___-5'\n_____________\|____________________\|\n_____________22___________________1\n	257 -- 263	5 -- 11	-22.196 kcal/mol	6.90555 kcal/mol	1.51103 kcal/mol	247 267@LB@ \| \|@LB@5'-AUC...UACGA U UACUU...AAA-3'@LB@ GCA C GGGAAAAGCAG GGC@LB@ :\|\| \| ::\|\|\|\|\|\|\|\|\| \|\|\|@LB@ UGU G UUCUUUUCGUC CCG@LB@3'-UUU...ACCCC A U A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -13.78 kcal/mol@LB@Hybridization Energy -22.196 kcal/mol@LB@Unfolding Energy - mRNA 6.90555 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 248 -- 266@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 5 -- 11@LB@
42	0.002133	0.1648	b0968	yccX	-12.44	0.101807	184 -- 198	5 -- 23	weak acylphosphatase	_____________183_________________199\n_____________\|___________________\|\n5'-GGC...AUUAA___________________CAAUG...CCG-3'\n______________GGAUA____AGGAGAGCAG\n______________\|\|\|:\|____\|\|:\|:\|\|\|\|\|\n______________CCUGU____UCUUUUCGUC\n3'-UUU...UUACC_____AGUU__________ACCG-5'\n_____________\|___________________\|\n_____________24__________________4\n	192 -- 198	5 -- 11	-17.1825 kcal/mol	3.17176 kcal/mol	1.57523 kcal/mol	183 199@LB@ \| \|@LB@5'-GGC...AUUAA CAAUG...CCG-3'@LB@ GGAUA AGGAGAGCAG@LB@ \|\|\|:\| \|\|:\|:\|\|\|\|\|@LB@ CCUGU UCUUUUCGUC@LB@3'-UUU...UUACC AGUU ACCG-5'@LB@ \| \|@LB@ 24 4@LB@@LB@@LB@Energy -12.44 kcal/mol@LB@Hybridization Energy -17.1825 kcal/mol@LB@Unfolding Energy - mRNA 3.17176 kcal/mol@LB@Unfolding Energy - sRNA 1.57523 kcal/mol@LB@@LB@Position - mRNA 184 -- 198@LB@Position - sRNA 5 -- 23@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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