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
65	0.003263	0.1727	b2584	pka	-7.67	0.359085	49 -- 62	69 -- 82	protein lysine acetyltransferase	_____________48_____________63\n_____________\|______________\|\n5'-AGG...AUGGC__G___________CGGCG...GUA-3'\n______________CG_CGAUACCGGGG\n______________\|\|_\|:\|:\|\|\|:\|\|\|\n______________GC_GUUGUGGUCCC\n3'-UUU...AUGAC__G___________UUUAG...GUG-5'\n_____________\|______________\|\n_____________83_____________68\n	56 -- 62	69 -- 75	-21.7159 kcal/mol	7.18281 kcal/mol	6.85849 kcal/mol	48 63@LB@ \| \|@LB@5'-AGG...AUGGC G CGGCG...GUA-3'@LB@ CG CGAUACCGGGG@LB@ \|\| \|:\|:\|\|\|:\|\|\|@LB@ GC GUUGUGGUCCC@LB@3'-UUU...AUGAC G UUUAG...GUG-5'@LB@ \| \|@LB@ 83 68@LB@@LB@@LB@Energy -7.67 kcal/mol@LB@Hybridization Energy -21.7159 kcal/mol@LB@Unfolding Energy - mRNA 7.18281 kcal/mol@LB@Unfolding Energy - sRNA 6.85849 kcal/mol@LB@@LB@Position - mRNA 49 -- 62@LB@Position - sRNA 69 -- 82@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 69 -- 75@LB@
31	0.001682	0.1727	b1887	cheW	-12.93	0.037697	13 -- 28	70 -- 86	purine-binding chemotaxis protein	_____________12________________29\n_____________\|_________________\|\n5'-GUG...AAUUA_________________UUGUG...UCC-3'\n______________AUUG_GUCAACACCAGG\n______________\|:\|\|_\|:\|\|\|\|\|\|\|\|\|\|\n______________UGAC_CGGUUGUGGUCC\n3'-UUU...GCUUA____G____________CUUUA...GUG-5'\n_____________\|_________________\|\n_____________87________________69\n	22 -- 28	70 -- 76	-24.746 kcal/mol	4.53921 kcal/mol	7.27772 kcal/mol	12 29@LB@ \| \|@LB@5'-GUG...AAUUA UUGUG...UCC-3'@LB@ AUUG GUCAACACCAGG@LB@ \|:\|\| \|:\|\|\|\|\|\|\|\|\|\|@LB@ UGAC CGGUUGUGGUCC@LB@3'-UUU...GCUUA G CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -12.93 kcal/mol@LB@Hybridization Energy -24.746 kcal/mol@LB@Unfolding Energy - mRNA 4.53921 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 13 -- 28@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 70 -- 76@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@
197	0.01211	0.2164	b0495	ybbA	-7.53	0.379415	88 -- 97	1 -- 10	putative ABC transporter ATPase	_____________87_________98\n_____________\|__________\|\n5'-GCC...CAGGC__________UGGCA...UCA-3'\n______________CAGGCCGCGC\n______________\|\|\|\|\|\|\|\|:\|\n______________GUCCGGCGUG\n3'-UUU...AAAAA__________-5'\n_____________\|_________\|\n_____________11________1\n	91 -- 97	1 -- 7	-21.6304 kcal/mol	8.71663 kcal/mol	5.44172 kcal/mol	87 98@LB@ \| \|@LB@5'-GCC...CAGGC UGGCA...UCA-3'@LB@ CAGGCCGCGC@LB@ \|\|\|\|\|\|\|\|:\|@LB@ GUCCGGCGUG@LB@3'-UUU...AAAAA -5'@LB@ \| \|@LB@ 11 1@LB@@LB@@LB@Energy -7.53 kcal/mol@LB@Hybridization Energy -21.6304 kcal/mol@LB@Unfolding Energy - mRNA 8.71663 kcal/mol@LB@Unfolding Energy - sRNA 5.44172 kcal/mol@LB@@LB@Position - mRNA 88 -- 97@LB@Position - sRNA 1 -- 10@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 1 -- 7@LB@
22	0.001393	0.1727	b0794	ybhF	-14.07	0.022426	148 -- 164	67 -- 84	putative ABC transporter ATPase	_____________147________________165\n_____________\|__________________\|\n5'-UAC...GAUGA__________________UGCCA...GUU-3'\n______________UGCGUU_ACGCCAGGGAA\n______________\|\|\|\|::_\|\|:\|\|\|\|\|\|\|\|\n______________ACGCGG_UGUGGUCCCUU\n3'-UUU...UUAUG______U___________UAGAA...GUG-5'\n_____________\|__________________\|\n_____________85_________________66\n	158 -- 164	67 -- 73	-27.705 kcal/mol	6.27905 kcal/mol	7.35473 kcal/mol	147 165@LB@ \| \|@LB@5'-UAC...GAUGA UGCCA...GUU-3'@LB@ UGCGUU ACGCCAGGGAA@LB@ \|\|\|\|:: \|\|:\|\|\|\|\|\|\|\|@LB@ ACGCGG UGUGGUCCCUU@LB@3'-UUU...UUAUG U UAGAA...GUG-5'@LB@ \| \|@LB@ 85 66@LB@@LB@@LB@Energy -14.07 kcal/mol@LB@Hybridization Energy -27.705 kcal/mol@LB@Unfolding Energy - mRNA 6.27905 kcal/mol@LB@Unfolding Energy - sRNA 7.35473 kcal/mol@LB@@LB@Position - mRNA 148 -- 164@LB@Position - sRNA 67 -- 84@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 67 -- 73@LB@
148	0.008708	0.2059	b1754	ynjB	-13.35	0.031185	160 -- 171	50 -- 61	putative ABC transporter periplasmic binding protein	_____________159__________172\n_____________\|____________\|\n5'-CCG...UCAGG____________UUCCU...AAA-3'\n______________GGCUGUGCCGUA\n______________\|\|\|\|\|:\|\|\|\|\|\|\n______________CCGACGCGGCAU\n3'-UUU...UAGAA____________UUAAU...GUG-5'\n_____________\|____________\|\n_____________62___________49\n	165 -- 171	50 -- 56	-23.078 kcal/mol	3.86799 kcal/mol	5.86332 kcal/mol	159 172@LB@ \| \|@LB@5'-CCG...UCAGG UUCCU...AAA-3'@LB@ GGCUGUGCCGUA@LB@ \|\|\|\|\|:\|\|\|\|\|\|@LB@ CCGACGCGGCAU@LB@3'-UUU...UAGAA UUAAU...GUG-5'@LB@ \| \|@LB@ 62 49@LB@@LB@@LB@Energy -13.35 kcal/mol@LB@Hybridization Energy -23.078 kcal/mol@LB@Unfolding Energy - mRNA 3.86799 kcal/mol@LB@Unfolding Energy - sRNA 5.86332 kcal/mol@LB@@LB@Position - mRNA 160 -- 171@LB@Position - sRNA 50 -- 61@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 50 -- 56@LB@
199	0.0124	0.2193	b0128	yadH	-9.95	0.142385	61 -- 79	68 -- 88	putative ABC transporter permease	_____________60____________________80\n_____________\|_____________________\|\n5'-UUA...UUGAA_________G___________UCAAC...UCA-3'\n______________GUGCUGCGU_AGCA__GGGGA\n______________:\|:\|\|\|\|\|:_\|:\|\|__:\|\|\|\|\n______________UAUGACGCG_UUGU__UCCCU\n3'-UUU...GCGCU_________G____GG_____UUAGA...GUG-5'\n_____________\|_____________________\|\n_____________89____________________67\n	61 -- 67	82 -- 88	-26.4707 kcal/mol	9.14335 kcal/mol	7.38144 kcal/mol	60 80@LB@ \| \|@LB@5'-UUA...UUGAA G UCAAC...UCA-3'@LB@ GUGCUGCGU AGCA GGGGA@LB@ :\|:\|\|\|\|\|: \|:\|\| :\|\|\|\|@LB@ UAUGACGCG UUGU UCCCU@LB@3'-UUU...GCGCU G GG UUAGA...GUG-5'@LB@ \| \|@LB@ 89 67@LB@@LB@@LB@Energy -9.95 kcal/mol@LB@Hybridization Energy -26.4707 kcal/mol@LB@Unfolding Energy - mRNA 9.14335 kcal/mol@LB@Unfolding Energy - sRNA 7.38144 kcal/mol@LB@@LB@Position - mRNA 61 -- 79@LB@Position - sRNA 68 -- 88@LB@Position Seed - mRNA 61 -- 67@LB@Position Seed - sRNA 82 -- 88@LB@
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@
85	0.004761	0.1855	b2077	iceT	-11.46	0.073016	53 -- 74	64 -- 86	putative citrate/iron-citrate/zinc-citrate efflux transporter	_____________52______________________75\n_____________\|_______________________\|\n5'-CGG...UCGGA______G_______CU_______ACCAU...UUC-3'\n______________GCUGCG_CAAC_CC__GGGGAUC\n______________:\|\|\|\|\|_\|\|\|\|_\|\|__\|\|::\|\|\|\n______________UGACGC_GUUG_GG__CCUUUAG\n3'-UUU...GCUUA______G____U__UC_______AACCG...GUG-5'\n_____________\|_______________________\|\n_____________87______________________63\n	68 -- 74	64 -- 70	-29.0378 kcal/mol	10.1908 kcal/mol	7.38435 kcal/mol	52 75@LB@ \| \|@LB@5'-CGG...UCGGA G CU ACCAU...UUC-3'@LB@ GCUGCG CAAC CC GGGGAUC@LB@ :\|\|\|\|\| \|\|\|\| \|\| \|\|::\|\|\|@LB@ UGACGC GUUG GG CCUUUAG@LB@3'-UUU...GCUUA G U UC AACCG...GUG-5'@LB@ \| \|@LB@ 87 63@LB@@LB@@LB@Energy -11.46 kcal/mol@LB@Hybridization Energy -29.0378 kcal/mol@LB@Unfolding Energy - mRNA 10.1908 kcal/mol@LB@Unfolding Energy - sRNA 7.38435 kcal/mol@LB@@LB@Position - mRNA 53 -- 74@LB@Position - sRNA 64 -- 86@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 64 -- 70@LB@
121	0.006643	0.1913	b1813	nudL	-11.92	0.059353	114 -- 132	70 -- 86	putative CoA pyrophosphohydrolase weak 3-phosphohydroxypyruvate phosphatase	_____________113_________________133\n_____________\|___________________\|\n5'-CCU...GUGGA____U________G_____AAGAA...CUG-3'\n______________AUUG_CGCCGAUA_CCAGG\n______________\|:\|\|_\|\|\|\|:\|:\|_\|\|\|\|\|\n______________UGAC_GCGGUUGU_GGUCC\n3'-UUU...GCUUA___________________CUUUA...GUG-5'\n_____________\|___________________\|\n_____________87__________________69\n	120 -- 126	75 -- 81	-24.7024 kcal/mol	5.50013 kcal/mol	7.27772 kcal/mol	113 133@LB@ \| \|@LB@5'-CCU...GUGGA U G AAGAA...CUG-3'@LB@ AUUG CGCCGAUA CCAGG@LB@ \|:\|\| \|\|\|\|:\|:\| \|\|\|\|\|@LB@ UGAC GCGGUUGU GGUCC@LB@3'-UUU...GCUUA CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -24.7024 kcal/mol@LB@Unfolding Energy - mRNA 5.50013 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 114 -- 132@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 75 -- 81@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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