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
127	0.007097	0.1961	b4065	yjcE	-10.62	0.105957	81 -- 91	51 -- 62	putative cation/proton antiporter	_____________80___________92\n_____________\|____________\|\n5'-UAU...GGCAA____________UUUUA...UGC-3'\n______________UGGCUGC_CCGU\n______________\|\|\|\|\|\|\|_\|\|\|\|\n______________ACCGACG_GGCA\n3'-UUU...UUAGA_______C____UUUAA...GUG-5'\n_____________\|____________\|\n_____________63___________50\n	81 -- 87	56 -- 62	-18.8543 kcal/mol	3.34811 kcal/mol	4.8826 kcal/mol	80 92@LB@ \| \|@LB@5'-UAU...GGCAA UUUUA...UGC-3'@LB@ UGGCUGC CCGU@LB@ \|\|\|\|\|\|\| \|\|\|\|@LB@ ACCGACG GGCA@LB@3'-UUU...UUAGA C UUUAA...GUG-5'@LB@ \| \|@LB@ 63 50@LB@@LB@@LB@Energy -10.62 kcal/mol@LB@Hybridization Energy -18.8543 kcal/mol@LB@Unfolding Energy - mRNA 3.34811 kcal/mol@LB@Unfolding Energy - sRNA 4.8826 kcal/mol@LB@@LB@Position - mRNA 81 -- 91@LB@Position - sRNA 51 -- 62@LB@Position Seed - mRNA 81 -- 87@LB@Position Seed - sRNA 56 -- 62@LB@
60	0.003031	0.1727	b3432	glgB	-10.57	0.108575	114 -- 123	51 -- 60	1 4-alpha-glucan branching enzyme	_____________113________124\n_____________\|__________\|\n5'-CAU...AGAGU__________UCAGG...GAC-3'\n______________GCUGCGCCGU\n______________\|\|\|\|\|\|\|\|\|\|\n______________CGACGCGGCA\n3'-UUU...AGAAC__________UUUAA...GUG-5'\n_____________\|__________\|\n_____________61_________50\n	117 -- 123	51 -- 57	-20.705 kcal/mol	5.26394 kcal/mol	4.87294 kcal/mol	113 124@LB@ \| \|@LB@5'-CAU...AGAGU UCAGG...GAC-3'@LB@ GCUGCGCCGU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CGACGCGGCA@LB@3'-UUU...AGAAC UUUAA...GUG-5'@LB@ \| \|@LB@ 61 50@LB@@LB@@LB@Energy -10.57 kcal/mol@LB@Hybridization Energy -20.705 kcal/mol@LB@Unfolding Energy - mRNA 5.26394 kcal/mol@LB@Unfolding Energy - sRNA 4.87294 kcal/mol@LB@@LB@Position - mRNA 114 -- 123@LB@Position - sRNA 51 -- 60@LB@Position Seed - mRNA 117 -- 123@LB@Position Seed - sRNA 51 -- 57@LB@
124	0.006738	0.1913	b2533	suhB	-10.44	0.114821	158 -- 166	51 -- 59	inositol monophosphatase	_____________157_______167\n_____________\|_________\|\n5'-UUG...AUACU_________UUUCC...AGA-3'\n______________CUGCGCCGU\n______________\|\|\|\|\|\|\|\|\|\n______________GACGCGGCA\n3'-UUU...GAACC_________UUUAA...GUG-5'\n_____________\|_________\|\n_____________60________50\n	160 -- 166	51 -- 57	-17.2912 kcal/mol	2.02049 kcal/mol	4.83013 kcal/mol	157 167@LB@ \| \|@LB@5'-UUG...AUACU UUUCC...AGA-3'@LB@ CUGCGCCGU@LB@ \|\|\|\|\|\|\|\|\|@LB@ GACGCGGCA@LB@3'-UUU...GAACC UUUAA...GUG-5'@LB@ \| \|@LB@ 60 50@LB@@LB@@LB@Energy -10.44 kcal/mol@LB@Hybridization Energy -17.2912 kcal/mol@LB@Unfolding Energy - mRNA 2.02049 kcal/mol@LB@Unfolding Energy - sRNA 4.83013 kcal/mol@LB@@LB@Position - mRNA 158 -- 166@LB@Position - sRNA 51 -- 59@LB@Position Seed - mRNA 160 -- 166@LB@Position Seed - sRNA 51 -- 57@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@
175	0.01031	0.2074	b1834	yebT	-10.32	0.121003	270 -- 282	51 -- 62	MCE domain protein	_____________269___________283\n_____________\|_____________\|\n5'-UCU...CUUUC_______U_____UCAUC...UUG-3'\n______________UGGCUGC_GCCGU\n______________\|\|\|\|\|\|\|_\|\|\|\|\|\n______________ACCGACG_CGGCA\n3'-UUU...UUAGA_____________UUUAA...GUG-5'\n_____________\|_____________\|\n_____________63____________50\n	270 -- 276	56 -- 62	-21.4836 kcal/mol	6.28034 kcal/mol	4.8826 kcal/mol	269 283@LB@ \| \|@LB@5'-UCU...CUUUC U UCAUC...UUG-3'@LB@ UGGCUGC GCCGU@LB@ \|\|\|\|\|\|\| \|\|\|\|\|@LB@ ACCGACG CGGCA@LB@3'-UUU...UUAGA UUUAA...GUG-5'@LB@ \| \|@LB@ 63 50@LB@@LB@@LB@Energy -10.32 kcal/mol@LB@Hybridization Energy -21.4836 kcal/mol@LB@Unfolding Energy - mRNA 6.28034 kcal/mol@LB@Unfolding Energy - sRNA 4.8826 kcal/mol@LB@@LB@Position - mRNA 270 -- 282@LB@Position - sRNA 51 -- 62@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 56 -- 62@LB@
104	0.005642	0.1855	b1476	fdnI	-8.74	0.236866	280 -- 291	51 -- 62	formate dehydrogenase-N cytochrome B556 (gamma) subunit nitrate-inducible	_____________279__________292\n_____________\|____________\|\n5'-CGU...CUUCC____G_______CCGGG...UUU-3'\n______________UGGU_GCGCUGU\n______________\|\|\|:_\|\|\|\|:\|\|\n______________ACCG_CGCGGCA\n3'-UUU...UUAGA____A_______UUUAA...GUG-5'\n_____________\|____________\|\n_____________63___________50\n	285 -- 291	51 -- 57	-16.7644 kcal/mol	3.14516 kcal/mol	4.8826 kcal/mol	279 292@LB@ \| \|@LB@5'-CGU...CUUCC G CCGGG...UUU-3'@LB@ UGGU GCGCUGU@LB@ \|\|\|: \|\|\|\|:\|\|@LB@ ACCG CGCGGCA@LB@3'-UUU...UUAGA A UUUAA...GUG-5'@LB@ \| \|@LB@ 63 50@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -16.7644 kcal/mol@LB@Unfolding Energy - mRNA 3.14516 kcal/mol@LB@Unfolding Energy - sRNA 4.8826 kcal/mol@LB@@LB@Position - mRNA 280 -- 291@LB@Position - sRNA 51 -- 62@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 51 -- 57@LB@
172	0.0102	0.2071	b1383	ydbL	-9.96	0.141752	21 -- 31	52 -- 62	DUF1318 family protein	_____________20__________32\n_____________\|___________\|\n5'-AAA...UUUAC___________ACGUC...UAG-3'\n______________UGGCUGCGUUG\n______________\|\|\|\|\|\|\|\|::\|\n______________ACCGACGCGGC\n3'-UUU...UUAGA___________AUUUA...GUG-5'\n_____________\|___________\|\n_____________63__________51\n	25 -- 31	52 -- 58	-19.6889 kcal/mol	4.85225 kcal/mol	4.8804 kcal/mol	20 32@LB@ \| \|@LB@5'-AAA...UUUAC ACGUC...UAG-3'@LB@ UGGCUGCGUUG@LB@ \|\|\|\|\|\|\|\|::\|@LB@ ACCGACGCGGC@LB@3'-UUU...UUAGA AUUUA...GUG-5'@LB@ \| \|@LB@ 63 51@LB@@LB@@LB@Energy -9.96 kcal/mol@LB@Hybridization Energy -19.6889 kcal/mol@LB@Unfolding Energy - mRNA 4.85225 kcal/mol@LB@Unfolding Energy - sRNA 4.8804 kcal/mol@LB@@LB@Position - mRNA 21 -- 31@LB@Position - sRNA 52 -- 62@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 52 -- 58@LB@
170	0.01004	0.2071	b3887	dtd	-7.24	0.420466	57 -- 66	52 -- 62	D-tyr-tRNA(Tyr) deacylase	_____________56__________67\n_____________\|___________\|\n5'-GGA...AUUUA___________GCGGU...UCG-3'\n______________UGG_UGUGCUG\n______________\|\|\|_\|\|:\|\|:\|\n______________ACC_ACGCGGC\n3'-UUU...UUAGA___G_______AUUUA...GUG-5'\n_____________\|___________\|\n_____________63__________51\n	60 -- 66	52 -- 58	-13.8062 kcal/mol	1.68508 kcal/mol	4.8804 kcal/mol	56 67@LB@ \| \|@LB@5'-GGA...AUUUA GCGGU...UCG-3'@LB@ UGG UGUGCUG@LB@ \|\|\| \|\|:\|\|:\|@LB@ ACC ACGCGGC@LB@3'-UUU...UUAGA G AUUUA...GUG-5'@LB@ \| \|@LB@ 63 51@LB@@LB@@LB@Energy -7.24 kcal/mol@LB@Hybridization Energy -13.8062 kcal/mol@LB@Unfolding Energy - mRNA 1.68508 kcal/mol@LB@Unfolding Energy - sRNA 4.8804 kcal/mol@LB@@LB@Position - mRNA 57 -- 66@LB@Position - sRNA 52 -- 62@LB@Position Seed - mRNA 60 -- 66@LB@Position Seed - sRNA 52 -- 58@LB@
49	0.00252	0.1727	b3452	ugpA	-14.40	0.019328	59 -- 78	52 -- 70	sn-glycerol-3-phosphate ABC transporter permease	_____________58___________________79\n_____________\|____________________\|\n5'-GAG...AGCGU_______AGUU_________CUUUG...CGG-3'\n______________GGAAAUC____GCUGCGCCG\n______________\|\|\|\|\|\|\|____\|\|\|\|\|\|\|\|\|\n______________CCUUUAG____CGACGCGGC\n3'-UUU...UGGUC_______AAC__________AUUUA...GUG-5'\n_____________\|____________________\|\n_____________71___________________51\n	72 -- 78	52 -- 58	-27.9409 kcal/mol	6.69662 kcal/mol	6.84683 kcal/mol	58 79@LB@ \| \|@LB@5'-GAG...AGCGU AGUU CUUUG...CGG-3'@LB@ GGAAAUC GCUGCGCCG@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ CCUUUAG CGACGCGGC@LB@3'-UUU...UGGUC AAC AUUUA...GUG-5'@LB@ \| \|@LB@ 71 51@LB@@LB@@LB@Energy -14.40 kcal/mol@LB@Hybridization Energy -27.9409 kcal/mol@LB@Unfolding Energy - mRNA 6.69662 kcal/mol@LB@Unfolding Energy - sRNA 6.84683 kcal/mol@LB@@LB@Position - mRNA 59 -- 78@LB@Position - sRNA 52 -- 70@LB@Position Seed - mRNA 72 -- 78@LB@Position Seed - sRNA 52 -- 58@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@

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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