Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
51	0.002608	0.1727	b2299	yfcD	-9.22	0.194301	162 -- 171	49 -- 58	putative NUDIX hydrolase	_____________161________172\n_____________\|__________\|\n5'-AGA...CAAAA__________GAGCG...AGU-3'\n______________UGCGCCGUAA\n______________\|\|\|\|\|\|\|\|\|\|\n______________ACGCGGCAUU\n3'-UUU...AACCG__________UAAUA...GUG-5'\n_____________\|__________\|\n_____________59_________48\n	165 -- 171	49 -- 55	-16.7903 kcal/mol	2.6527 kcal/mol	4.92198 kcal/mol	161 172@LB@ \| \|@LB@5'-AGA...CAAAA GAGCG...AGU-3'@LB@ UGCGCCGUAA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ ACGCGGCAUU@LB@3'-UUU...AACCG UAAUA...GUG-5'@LB@ \| \|@LB@ 59 48@LB@@LB@@LB@Energy -9.22 kcal/mol@LB@Hybridization Energy -16.7903 kcal/mol@LB@Unfolding Energy - mRNA 2.6527 kcal/mol@LB@Unfolding Energy - sRNA 4.92198 kcal/mol@LB@@LB@Position - mRNA 162 -- 171@LB@Position - sRNA 49 -- 58@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 49 -- 55@LB@
91	0.004841	0.1855	b3194	mlaE	-9.16	0.198986	180 -- 189	67 -- 76	ABC transporter maintaining OM lipid asymmetry inner membrane permease protein	_____________179________190\n_____________\|__________\|\n5'-GGA...UCUUU__________UUAAG...GCA-3'\n______________UACCAGGGAG\n______________:\|\|\|\|\|\|\|\|:\n______________GUGGUCCCUU\n3'-UUU...CGGUU__________UAGAA...GUG-5'\n_____________\|__________\|\n_____________77_________66\n	183 -- 189	67 -- 73	-15.9485 kcal/mol	2.86999 kcal/mol	3.9178 kcal/mol	179 190@LB@ \| \|@LB@5'-GGA...UCUUU UUAAG...GCA-3'@LB@ UACCAGGGAG@LB@ :\|\|\|\|\|\|\|\|:@LB@ GUGGUCCCUU@LB@3'-UUU...CGGUU UAGAA...GUG-5'@LB@ \| \|@LB@ 77 66@LB@@LB@@LB@Energy -9.16 kcal/mol@LB@Hybridization Energy -15.9485 kcal/mol@LB@Unfolding Energy - mRNA 2.86999 kcal/mol@LB@Unfolding Energy - sRNA 3.9178 kcal/mol@LB@@LB@Position - mRNA 180 -- 189@LB@Position - sRNA 67 -- 76@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 67 -- 73@LB@
188	0.01115	0.2089	b4377	yjjU	-9.16	0.198952	213 -- 243	51 -- 77	putative patatin-like family phospholipase	_____________212______________________________244\n_____________\|________________________________\|\n5'-AGG...AGCGA_____UGUAACG_______AAUAU________UGUCG...GAC-3'\n______________AUACC________CUUGGU_____UGCGCCGU\n______________\|:\|\|\|________\|\|\|\|\|:_____\|\|\|\|\|\|\|\|\n______________UGUGG________GAACCG_____ACGCGGCA\n3'-UUU...GCGGU_____UCCCUUUA___________________UUUAA...GUG-5'\n_____________\|________________________________\|\n_____________78_______________________________50\n	237 -- 243	51 -- 57	-26.4777 kcal/mol	7.99131 kcal/mol	9.32737 kcal/mol	212 244@LB@ \| \|@LB@5'-AGG...AGCGA UGUAACG AAUAU UGUCG...GAC-3'@LB@ AUACC CUUGGU UGCGCCGU@LB@ \|:\|\|\| \|\|\|\|\|: \|\|\|\|\|\|\|\|@LB@ UGUGG GAACCG ACGCGGCA@LB@3'-UUU...GCGGU UCCCUUUA UUUAA...GUG-5'@LB@ \| \|@LB@ 78 50@LB@@LB@@LB@Energy -9.16 kcal/mol@LB@Hybridization Energy -26.4777 kcal/mol@LB@Unfolding Energy - mRNA 7.99131 kcal/mol@LB@Unfolding Energy - sRNA 9.32737 kcal/mol@LB@@LB@Position - mRNA 213 -- 243@LB@Position - sRNA 51 -- 77@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 51 -- 57@LB@
191	0.01171	0.2159	b4221	tamB	-9.06	0.207346	81 -- 101	52 -- 76	translocation and assembly module for autotransporter export inner membrane subunit	_____________80_________________________102\n_____________\|__________________________\|\n5'-ACC...ACCGG__________________G_______GGAAU...AUC-3'\n______________UACCGGGG___UC__GGC_UGCGCUG\n______________:\|\|\|:\|\|\|___\|\|__\|\|\|_\|\|\|\|\|:\|\n______________GUGGUCCC___AG__CCG_ACGCGGC\n3'-UUU...CGGUU________UUU__AA___________AUUUA...GUG-5'\n_____________\|__________________________\|\n_____________77_________________________51\n	95 -- 101	52 -- 58	-29.4253 kcal/mol	11.0996 kcal/mol	9.26585 kcal/mol	80 102@LB@ \| \|@LB@5'-ACC...ACCGG G GGAAU...AUC-3'@LB@ UACCGGGG UC GGC UGCGCUG@LB@ :\|\|\|:\|\|\| \|\| \|\|\| \|\|\|\|\|:\|@LB@ GUGGUCCC AG CCG ACGCGGC@LB@3'-UUU...CGGUU UUU AA AUUUA...GUG-5'@LB@ \| \|@LB@ 77 51@LB@@LB@@LB@Energy -9.06 kcal/mol@LB@Hybridization Energy -29.4253 kcal/mol@LB@Unfolding Energy - mRNA 11.0996 kcal/mol@LB@Unfolding Energy - sRNA 9.26585 kcal/mol@LB@@LB@Position - mRNA 81 -- 101@LB@Position - sRNA 52 -- 76@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 52 -- 58@LB@
92	0.004911	0.1855	b3732	atpD	-9.01	0.211333	117 -- 128	1 -- 11	F1 sector of membrane-bound ATP synthase beta subunit	_____________116__________129\n_____________\|____________\|\n5'-GGC...GCUCG_______A____UACUC...AAA-3'\n______________UCAGGCC_GCAU\n______________\|\|\|\|\|\|\|_\|\|\|:\n______________AGUCCGG_CGUG\n3'-UUU...CAAAA____________-5'\n_____________\|___________\|\n_____________12__________1\n	117 -- 123	5 -- 11	-17.8068 kcal/mol	3.15312 kcal/mol	5.60325 kcal/mol	116 129@LB@ \| \|@LB@5'-GGC...GCUCG A UACUC...AAA-3'@LB@ UCAGGCC GCAU@LB@ \|\|\|\|\|\|\| \|\|\|:@LB@ AGUCCGG CGUG@LB@3'-UUU...CAAAA -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -17.8068 kcal/mol@LB@Unfolding Energy - mRNA 3.15312 kcal/mol@LB@Unfolding Energy - sRNA 5.60325 kcal/mol@LB@@LB@Position - mRNA 117 -- 128@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 117 -- 123@LB@Position Seed - sRNA 5 -- 11@LB@
71	0.003482	0.1727	b4046	zur	-8.96	0.216158	254 -- 300	53 -- 94	transcriptional repressor Zn(II)-binding	_____________253__________________________________________________300\n_____________\|____________________________________________________\|\n5'-UAA...UGCGC__A___U___________UGACCCCAC______U___________________-3'\n______________GC_GCG_AAUG_UGCGCC_________AGCGCC__GGAAGU____GUUGCGCC\n______________\|\|_\|\|\|_\|\|\|:_\|\|\|\|\|\|_________\|:\|:\|\|__\|\|\|\|:\|____\|:\|\|\|\|\|\|\n______________CG_CGC_UUAU_ACGCGG_________UUGUGG__CCUUUA____CGACGCGG\n3'-UUU...CCCCA___________G_____________________UC______GAAC________CAUUU...GUG-5'\n_____________\|_____________________________________________________\|\n_____________95____________________________________________________52\n	294 -- 300	53 -- 59	-43.5981 kcal/mol	17.5702 kcal/mol	17.0684 kcal/mol	253 300@LB@ \| \|@LB@5'-UAA...UGCGC A U UGACCCCAC U -3'@LB@ GC GCG AAUG UGCGCC AGCGCC GGAAGU GUUGCGCC@LB@ \|\| \|\|\| \|\|\|: \|\|\|\|\|\| \|:\|:\|\| \|\|\|\|:\| \|:\|\|\|\|\|\|@LB@ CG CGC UUAU ACGCGG UUGUGG CCUUUA CGACGCGG@LB@3'-UUU...CCCCA G UC GAAC CAUUU...GUG-5'@LB@ \| \|@LB@ 95 52@LB@@LB@@LB@Energy -8.96 kcal/mol@LB@Hybridization Energy -43.5981 kcal/mol@LB@Unfolding Energy - mRNA 17.5702 kcal/mol@LB@Unfolding Energy - sRNA 17.0684 kcal/mol@LB@@LB@Position - mRNA 254 -- 300@LB@Position - sRNA 53 -- 94@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 53 -- 59@LB@
26	0.001553	0.1727	b0853	ybjN	-8.94	0.217650	161 -- 169	52 -- 60	negative regulator of motility; multicopy suppressor of coaA(Ts)	_____________160_______170\n_____________\|_________\|\n5'-CGC...CGUAA_________GUCUU...AUC-3'\n______________GCUGUGCCG\n______________\|\|\|\|:\|\|\|\|\n______________CGACGCGGC\n3'-UUU...AGAAC_________AUUUA...GUG-5'\n_____________\|_________\|\n_____________61________51\n	163 -- 169	52 -- 58	-18.9448 kcal/mol	5.13325 kcal/mol	4.86882 kcal/mol	160 170@LB@ \| \|@LB@5'-CGC...CGUAA GUCUU...AUC-3'@LB@ GCUGUGCCG@LB@ \|\|\|\|:\|\|\|\|@LB@ CGACGCGGC@LB@3'-UUU...AGAAC AUUUA...GUG-5'@LB@ \| \|@LB@ 61 51@LB@@LB@@LB@Energy -8.94 kcal/mol@LB@Hybridization Energy -18.9448 kcal/mol@LB@Unfolding Energy - mRNA 5.13325 kcal/mol@LB@Unfolding Energy - sRNA 4.86882 kcal/mol@LB@@LB@Position - mRNA 161 -- 169@LB@Position - sRNA 52 -- 60@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 52 -- 58@LB@
55	0.002731	0.1727	b2480	bcp	-8.89	0.222722	156 -- 187	28 -- 56	peroxiredoxin; thiol peroxidase thioredoxin-dependent	_____________155_________________________________188\n_____________\|___________________________________\|\n5'-GAG...AUUAA______C_______CCCAAC_______________AUGGA...UUC-3'\n______________CGUCGU_AAUUAUU______AUGAUGA___ACAGG\n______________\|\|:\|\|\|_\|\|\|\|\|\|\|______\|\|\|\|\|\|\|___\|\|\|:\|\n______________GCGGCA_UUAAUAA______UACUACU___UGUUC\n3'-UUU...CCGAC______U____________________CAA_____CCGUG...GUG-5'\n_____________\|___________________________________\|\n_____________57__________________________________27\n	176 -- 182	36 -- 42	-21.7802 kcal/mol	6.3273 kcal/mol	6.56571 kcal/mol	155 188@LB@ \| \|@LB@5'-GAG...AUUAA C CCCAAC AUGGA...UUC-3'@LB@ CGUCGU AAUUAUU AUGAUGA ACAGG@LB@ \|\|:\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|:\|@LB@ GCGGCA UUAAUAA UACUACU UGUUC@LB@3'-UUU...CCGAC U CAA CCGUG...GUG-5'@LB@ \| \|@LB@ 57 27@LB@@LB@@LB@Energy -8.89 kcal/mol@LB@Hybridization Energy -21.7802 kcal/mol@LB@Unfolding Energy - mRNA 6.3273 kcal/mol@LB@Unfolding Energy - sRNA 6.56571 kcal/mol@LB@@LB@Position - mRNA 156 -- 187@LB@Position - sRNA 28 -- 56@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 36 -- 42@LB@
146	0.008611	0.2059	b3750	rbsC	-8.88	0.223197	137 -- 159	56 -- 77	D-ribose ABC transporter permease	_____________136_______________________160\n_____________\|_________________________\|\n5'-GAU...AGGCC_____________G_UAA_______CGCUG...UCU-3'\n______________AC_CCA_GGAAGU_U___UGGCUGC\n______________\|\|_\|\|\|_\|\|\|\|:\|_\|___\|\|\|\|\|\|\|\n______________UG_GGU_CCUUUA_A___ACCGACG\n3'-UUU...GCGGU__U___C______G___________CGGCA...GUG-5'\n_____________\|_________________________\|\n_____________78________________________55\n	153 -- 159	56 -- 62	-22.4095 kcal/mol	5.11916 kcal/mol	8.4081 kcal/mol	136 160@LB@ \| \|@LB@5'-GAU...AGGCC G UAA CGCUG...UCU-3'@LB@ AC CCA GGAAGU U UGGCUGC@LB@ \|\| \|\|\| \|\|\|\|:\| \| \|\|\|\|\|\|\|@LB@ UG GGU CCUUUA A ACCGACG@LB@3'-UUU...GCGGU U C G CGGCA...GUG-5'@LB@ \| \|@LB@ 78 55@LB@@LB@@LB@Energy -8.88 kcal/mol@LB@Hybridization Energy -22.4095 kcal/mol@LB@Unfolding Energy - mRNA 5.11916 kcal/mol@LB@Unfolding Energy - sRNA 8.4081 kcal/mol@LB@@LB@Position - mRNA 137 -- 159@LB@Position - sRNA 56 -- 77@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 56 -- 62@LB@
163	0.009572	0.2068	b4126	yjdI	-8.84	0.226749	182 -- 194	26 -- 41	putative 4Fe-4S mono-cluster protein	_____________181______________195\n_____________\|________________\|\n5'-UAG...CAUAC_______A________AAGGU...GCG-3'\n______________UGAUGAG____GAGGG\n______________\|\|\|\|\|\|\|____:\|\|\|\|\n______________ACUACUC____UUCCC\n3'-UUU...AUAAU_______AAUG_____GUGUC...GUG-5'\n_____________\|________________\|\n_____________42_______________25\n	182 -- 188	35 -- 41	-13.4129 kcal/mol	1.87738 kcal/mol	2.69216 kcal/mol	181 195@LB@ \| \|@LB@5'-UAG...CAUAC A AAGGU...GCG-3'@LB@ UGAUGAG GAGGG@LB@ \|\|\|\|\|\|\| :\|\|\|\|@LB@ ACUACUC UUCCC@LB@3'-UUU...AUAAU AAUG GUGUC...GUG-5'@LB@ \| \|@LB@ 42 25@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -13.4129 kcal/mol@LB@Unfolding Energy - mRNA 1.87738 kcal/mol@LB@Unfolding Energy - sRNA 2.69216 kcal/mol@LB@@LB@Position - mRNA 182 -- 194@LB@Position - sRNA 26 -- 41@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 35 -- 41@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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