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
45	0.002234	0.1727	b0055	djlA	-13.22	0.033048	207 -- 250	35 -- 76	membrane-anchored DnaK co-chaperone DNA-binding protein	_____________206___________________________________________251\n_____________\|_____________________________________________\|\n5'-GAC...UGCAG_________AA____A_____GUG_______CCUUAC________CGGCG...UUG-3'\n______________UAUUGGGGA__AAUC_UUGGC___GCCGUGG_______UGAUGGG\n______________:\|:::\|\|\|\|__\|\|\|\|_\|\|\|\|\|___\|\|\|\|\|::_______\|\|\|\|\|:\|\n______________GUGGUCCCU__UUAG_AACCG___CGGCAUU_______ACUACUC\n3'-UUU...CGGUU_____________________ACG_______UAAUAAU_______AAUGU...GUG-5'\n_____________\|_____________________________________________\|\n_____________77____________________________________________34\n	244 -- 250	35 -- 41	-37.823 kcal/mol	15.2445 kcal/mol	9.3594 kcal/mol	206 251@LB@ \| \|@LB@5'-GAC...UGCAG AA A GUG CCUUAC CGGCG...UUG-3'@LB@ UAUUGGGGA AAUC UUGGC GCCGUGG UGAUGGG@LB@ :\|:::\|\|\|\| \|\|\|\| \|\|\|\|\| \|\|\|\|\|:: \|\|\|\|\|:\|@LB@ GUGGUCCCU UUAG AACCG CGGCAUU ACUACUC@LB@3'-UUU...CGGUU ACG UAAUAAU AAUGU...GUG-5'@LB@ \| \|@LB@ 77 34@LB@@LB@@LB@Energy -13.22 kcal/mol@LB@Hybridization Energy -37.823 kcal/mol@LB@Unfolding Energy - mRNA 15.2445 kcal/mol@LB@Unfolding Energy - sRNA 9.3594 kcal/mol@LB@@LB@Position - mRNA 207 -- 250@LB@Position - sRNA 35 -- 76@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 35 -- 41@LB@
101	0.005473	0.1855	b1129	phoQ	-8.66	0.244665	211 -- 219	79 -- 87	sensory histidine kinase in two-component regulatory system with PhoP	_____________210_______220\n_____________\|_________\|\n5'-AUG...AAAAU_________UUUUU...GAA-3'\n______________UACUGCGUC\n______________\|\|\|\|\|\|\|:\|\n______________AUGACGCGG\n3'-UUU...CGCUU_________UUGUG...GUG-5'\n_____________\|_________\|\n_____________88________78\n	213 -- 219	79 -- 85	-14.7172 kcal/mol	1.01485 kcal/mol	5.0453 kcal/mol	210 220@LB@ \| \|@LB@5'-AUG...AAAAU UUUUU...GAA-3'@LB@ UACUGCGUC@LB@ \|\|\|\|\|\|\|:\|@LB@ AUGACGCGG@LB@3'-UUU...CGCUU UUGUG...GUG-5'@LB@ \| \|@LB@ 88 78@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -14.7172 kcal/mol@LB@Unfolding Energy - mRNA 1.01485 kcal/mol@LB@Unfolding Energy - sRNA 5.0453 kcal/mol@LB@@LB@Position - mRNA 211 -- 219@LB@Position - sRNA 79 -- 87@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 79 -- 85@LB@
189	0.01136	0.2116	b3413	gntX	-9.78	0.152759	211 -- 235	52 -- 76	DNA catabolic protein	_____________210_______________________236\n_____________\|_________________________\|\n5'-CCC...AACAG_______AUU__GC_____A_____AAUGC...AUA-3'\n______________UACCGGG___AU__UGGCU_UGCCG\n______________:\|\|\|:\|\|___\|\|__\|\|\|\|\|_:\|\|\|\|\n______________GUGGUCC___UA__ACCGA_GCGGC\n3'-UUU...CGGUU_______CUU__GA_____C_____AUUUA...GUG-5'\n_____________\|_________________________\|\n_____________77________________________51\n	211 -- 217	70 -- 76	-26.9968 kcal/mol	7.94838 kcal/mol	9.26585 kcal/mol	210 236@LB@ \| \|@LB@5'-CCC...AACAG AUU GC A AAUGC...AUA-3'@LB@ UACCGGG AU UGGCU UGCCG@LB@ :\|\|\|:\|\| \|\| \|\|\|\|\| :\|\|\|\|@LB@ GUGGUCC UA ACCGA GCGGC@LB@3'-UUU...CGGUU CUU GA C AUUUA...GUG-5'@LB@ \| \|@LB@ 77 51@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -26.9968 kcal/mol@LB@Unfolding Energy - mRNA 7.94838 kcal/mol@LB@Unfolding Energy - sRNA 9.26585 kcal/mol@LB@@LB@Position - mRNA 211 -- 235@LB@Position - sRNA 52 -- 76@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 70 -- 76@LB@
132	0.007501	0.1993	b1947	fliO	-6.89	0.474041	212 -- 250	53 -- 93	flagellar biosynthesis protein	_____________211_____________________________________________251\n_____________\|_______________________________________________\|\n5'-AUG...AACCA______________AAUCUUCC_______UU________________ACUGC...UCG-3'\n______________CGC___UACUGUGC________GCGCCGG_____UCU__GCUGCGCC\n______________\|\|\|___\|\|\|\|\|:\|\|________:\|:\|\|:\|_____\|\|\|__\|\|\|\|\|\|\|\|\n______________GCG___AUGACGCG________UGUGGUC_____AGA__CGACGCGG\n3'-UUU...CCCAC___CUU________GU_____________CCUUU___AC________CAUUU...GUG-5'\n_____________\|_______________________________________________\|\n_____________94______________________________________________52\n	244 -- 250	53 -- 59	-40.0502 kcal/mol	16.0889 kcal/mol	17.0683 kcal/mol	211 251@LB@ \| \|@LB@5'-AUG...AACCA AAUCUUCC UU ACUGC...UCG-3'@LB@ CGC UACUGUGC GCGCCGG UCU GCUGCGCC@LB@ \|\|\| \|\|\|\|\|:\|\| :\|:\|\|:\| \|\|\| \|\|\|\|\|\|\|\|@LB@ GCG AUGACGCG UGUGGUC AGA CGACGCGG@LB@3'-UUU...CCCAC CUU GU CCUUU AC CAUUU...GUG-5'@LB@ \| \|@LB@ 94 52@LB@@LB@@LB@Energy -6.89 kcal/mol@LB@Hybridization Energy -40.0502 kcal/mol@LB@Unfolding Energy - mRNA 16.0889 kcal/mol@LB@Unfolding Energy - sRNA 17.0683 kcal/mol@LB@@LB@Position - mRNA 212 -- 250@LB@Position - sRNA 53 -- 93@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 53 -- 59@LB@
7	0.0001601	0.08054	b1864	yebC	-15.40	0.012230	213 -- 249	54 -- 89	UPF0082 family protein	_____________212_____________________________________250\n_____________\|_______________________________________\|\n5'-CGU...GUCAU____AA__G___________AC_____GUAAA_______AGGAU...UAA-3'\n______________AGUA__UG_GCCAACACCAG____AUC_____GCUGCGC\n______________\|:\|\|__\|\|_\|\|\|\|\|\|\|\|\|\|\|____\|\|\|_____\|\|\|\|\|\|\|\n______________UUAU__AC_CGGUUGUGGUC____UAG_____CGACGCG\n3'-UUU...CGCGC____G___G___________CCUU___AAC_________GCAUU...GUG-5'\n_____________\|_______________________________________\|\n_____________90______________________________________53\n	243 -- 249	54 -- 60	-38.8431 kcal/mol	7.10336 kcal/mol	16.3388 kcal/mol	212 250@LB@ \| \|@LB@5'-CGU...GUCAU AA G AC GUAAA AGGAU...UAA-3'@LB@ AGUA UG GCCAACACCAG AUC GCUGCGC@LB@ \|:\|\| \|\| \|\|\|\|\|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ UUAU AC CGGUUGUGGUC UAG CGACGCG@LB@3'-UUU...CGCGC G G CCUU AAC GCAUU...GUG-5'@LB@ \| \|@LB@ 90 53@LB@@LB@@LB@Energy -15.40 kcal/mol@LB@Hybridization Energy -38.8431 kcal/mol@LB@Unfolding Energy - mRNA 7.10336 kcal/mol@LB@Unfolding Energy - sRNA 16.3388 kcal/mol@LB@@LB@Position - mRNA 213 -- 249@LB@Position - sRNA 54 -- 89@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 54 -- 60@LB@
13	0.0004745	0.1198	b1688	ydiK	-12.82	0.039628	213 -- 226	68 -- 82	UPF0118 family inner membrane protein	_____________212_____________227\n_____________\|_______________\|\n5'-AUG...AUGUU_______________UGUCG...CCU-3'\n______________CGUCAGC_CCAGGGA\n______________\|\|:\|\|:\|_\|\|\|\|\|\|\|\n______________GCGGUUG_GGUCCCU\n3'-UUU...AUGAC_______U_______UUAGA...GUG-5'\n_____________\|_______________\|\n_____________83______________67\n	220 -- 226	68 -- 74	-23.7232 kcal/mol	3.92329 kcal/mol	6.98098 kcal/mol	212 227@LB@ \| \|@LB@5'-AUG...AUGUU UGUCG...CCU-3'@LB@ CGUCAGC CCAGGGA@LB@ \|\|:\|\|:\| \|\|\|\|\|\|\|@LB@ GCGGUUG GGUCCCU@LB@3'-UUU...AUGAC U UUAGA...GUG-5'@LB@ \| \|@LB@ 83 67@LB@@LB@@LB@Energy -12.82 kcal/mol@LB@Hybridization Energy -23.7232 kcal/mol@LB@Unfolding Energy - mRNA 3.92329 kcal/mol@LB@Unfolding Energy - sRNA 6.98098 kcal/mol@LB@@LB@Position - mRNA 213 -- 226@LB@Position - sRNA 68 -- 82@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 68 -- 74@LB@
155	0.009115	0.2059	b1531	marA	-9.94	0.142609	213 -- 231	72 -- 89	multiple antibiotic resistance transcriptional regulator	_____________212_________________232\n_____________\|___________________\|\n5'-AAG...GACGC_______A_____U_____UUCAU...AGC-3'\n______________AAUACUG_CGCUA_UACCA\n______________\|\|\|\|\|\|\|_\|\|\|:\|_:\|\|\|\|\n______________UUAUGAC_GCGGU_GUGGU\n3'-UUU...CGCGC_____________U_____CCCUU...GUG-5'\n_____________\|___________________\|\n_____________90__________________71\n	213 -- 219	83 -- 89	-21.2611 kcal/mol	3.54366 kcal/mol	7.77515 kcal/mol	212 232@LB@ \| \|@LB@5'-AAG...GACGC A U UUCAU...AGC-3'@LB@ AAUACUG CGCUA UACCA@LB@ \|\|\|\|\|\|\| \|\|\|:\| :\|\|\|\|@LB@ UUAUGAC GCGGU GUGGU@LB@3'-UUU...CGCGC U CCCUU...GUG-5'@LB@ \| \|@LB@ 90 71@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -21.2611 kcal/mol@LB@Unfolding Energy - mRNA 3.54366 kcal/mol@LB@Unfolding Energy - sRNA 7.77515 kcal/mol@LB@@LB@Position - mRNA 213 -- 231@LB@Position - sRNA 72 -- 89@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 83 -- 89@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@
72	0.00375	0.1804	b0386	proC	-10.69	0.102749	216 -- 233	53 -- 70	pyrroline-5-carboxylate reductase NAD(P)-binding	_____________215________________234\n_____________\|__________________\|\n5'-CAU...AAAUC__UUUUA_________G_AAUAU...GGG-3'\n______________GG_____UUGGCUGCG_C\n______________\|\|_____\|\|\|\|\|\|\|\|\|_\|\n______________CC_____AACCGACGC_G\n3'-UUU...UGGUC__UUUAG_________G_CAUUU...GUG-5'\n_____________\|__________________\|\n_____________71_________________52\n	225 -- 231	55 -- 61	-21.889 kcal/mol	4.36146 kcal/mol	6.83419 kcal/mol	215 234@LB@ \| \|@LB@5'-CAU...AAAUC UUUUA G AAUAU...GGG-3'@LB@ GG UUGGCUGCG C@LB@ \|\| \|\|\|\|\|\|\|\|\| \|@LB@ CC AACCGACGC G@LB@3'-UUU...UGGUC UUUAG G CAUUU...GUG-5'@LB@ \| \|@LB@ 71 52@LB@@LB@@LB@Energy -10.69 kcal/mol@LB@Hybridization Energy -21.889 kcal/mol@LB@Unfolding Energy - mRNA 4.36146 kcal/mol@LB@Unfolding Energy - sRNA 6.83419 kcal/mol@LB@@LB@Position - mRNA 216 -- 233@LB@Position - sRNA 53 -- 70@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 55 -- 61@LB@
90	0.004828	0.1855	b2149	mglA	-7.32	0.409352	216 -- 239	61 -- 86	methyl-galactoside ABC transporter ATPase	_____________215________________________240\n_____________\|__________________________\|\n5'-CGA...CAACG___C____CU__________UA____UUGGA...AUU-3'\n______________ACU_CGUC____CCGGGGAA__CUUG\n______________\|\|\|_\|\|:\|____\|\|:\|\|\|\|\|__\|\|\|\|\n______________UGA_GCGG____GGUCCCUU__GAAC\n3'-UUU...GCUUA___C____UUGU________UA____CGACG...GUG-5'\n_____________\|__________________________\|\n_____________87_________________________60\n	227 -- 233	67 -- 73	-23.5814 kcal/mol	8.829 kcal/mol	7.43637 kcal/mol	215 240@LB@ \| \|@LB@5'-CGA...CAACG C CU UA UUGGA...AUU-3'@LB@ ACU CGUC CCGGGGAA CUUG@LB@ \|\|\| \|\|:\| \|\|:\|\|\|\|\| \|\|\|\|@LB@ UGA GCGG GGUCCCUU GAAC@LB@3'-UUU...GCUUA C UUGU UA CGACG...GUG-5'@LB@ \| \|@LB@ 87 60@LB@@LB@@LB@Energy -7.32 kcal/mol@LB@Hybridization Energy -23.5814 kcal/mol@LB@Unfolding Energy - mRNA 8.829 kcal/mol@LB@Unfolding Energy - sRNA 7.43637 kcal/mol@LB@@LB@Position - mRNA 216 -- 239@LB@Position - sRNA 61 -- 86@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 67 -- 73@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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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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