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
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@
192	0.01187	0.2159	b2600	tyrA	-9.34	0.184498	136 -- 155	70 -- 86	fused chorismate mutase T/prephenate dehydrogenase	_____________135__________________156\n_____________\|____________________\|\n5'-UCG...GCCUU_______G__AUU_______AUCUG...UGG-3'\n______________GCUGCGU_AA___CAUCAGG\n______________:\|\|\|\|\|:_\|\|___\|\|:\|\|\|\|\n______________UGACGCG_UU___GUGGUCC\n3'-UUU...GCUUA_______G____________CUUUA...GUG-5'\n_____________\|____________________\|\n_____________87___________________69\n	149 -- 155	70 -- 76	-22.0981 kcal/mol	5.48162 kcal/mol	7.27772 kcal/mol	135 156@LB@ \| \|@LB@5'-UCG...GCCUU G AUU AUCUG...UGG-3'@LB@ GCUGCGU AA CAUCAGG@LB@ :\|\|\|\|\|: \|\| \|\|:\|\|\|\|@LB@ UGACGCG UU GUGGUCC@LB@3'-UUU...GCUUA G CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -22.0981 kcal/mol@LB@Unfolding Energy - mRNA 5.48162 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 136 -- 155@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 70 -- 76@LB@
193	0.01192	0.2159	b2453	eutG	-10.04	0.136932	27 -- 40	17 -- 30	ethanol dehydrogenase involved in ethanolamine utilization; aldehyde reductase	_____________26_____________41\n_____________\|______________\|\n5'-GGC...UAUUG_______G______ACUGA...GUC-3'\n______________AAGGGCA_GGCAUU\n______________\|\|\|\|\|\|\|_:\|\|\|:\|\n______________UUCCCGU_UCGUGA\n3'-UUU...CAAUG_______G______CAAAA...GUG-5'\n_____________\|______________\|\n_____________31_____________16\n	27 -- 33	24 -- 30	-21.9245 kcal/mol	3.17394 kcal/mol	8.71417 kcal/mol	26 41@LB@ \| \|@LB@5'-GGC...UAUUG G ACUGA...GUC-3'@LB@ AAGGGCA GGCAUU@LB@ \|\|\|\|\|\|\| :\|\|\|:\|@LB@ UUCCCGU UCGUGA@LB@3'-UUU...CAAUG G CAAAA...GUG-5'@LB@ \| \|@LB@ 31 16@LB@@LB@@LB@Energy -10.04 kcal/mol@LB@Hybridization Energy -21.9245 kcal/mol@LB@Unfolding Energy - mRNA 3.17394 kcal/mol@LB@Unfolding Energy - sRNA 8.71417 kcal/mol@LB@@LB@Position - mRNA 27 -- 40@LB@Position - sRNA 17 -- 30@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 24 -- 30@LB@
194	0.01194	0.2159	b3454	livF	-10.01	0.138607	25 -- 47	72 -- 86	branched-chain amino acid ABC transporter ATPase	_____________24______________________48\n_____________\|_______________________\|\n5'-AGA...GCCGA_______AAUCAUCA________CUAUC...UUG-3'\n______________ACUGCGC________CAACACCA\n______________\|\|\|\|\|\|\|________\|\|\|\|\|\|\|\|\n______________UGACGCG________GUUGUGGU\n3'-UUU...GCUUA_______________________CCCUU...GUG-5'\n_____________\|_______________________\|\n_____________87______________________71\n	41 -- 47	72 -- 78	-22.1496 kcal/mol	4.90616 kcal/mol	7.23529 kcal/mol	24 48@LB@ \| \|@LB@5'-AGA...GCCGA AAUCAUCA CUAUC...UUG-3'@LB@ ACUGCGC CAACACCA@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UGACGCG GUUGUGGU@LB@3'-UUU...GCUUA CCCUU...GUG-5'@LB@ \| \|@LB@ 87 71@LB@@LB@@LB@Energy -10.01 kcal/mol@LB@Hybridization Energy -22.1496 kcal/mol@LB@Unfolding Energy - mRNA 4.90616 kcal/mol@LB@Unfolding Energy - sRNA 7.23529 kcal/mol@LB@@LB@Position - mRNA 25 -- 47@LB@Position - sRNA 72 -- 86@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 72 -- 78@LB@
195	0.01197	0.2159	b0738	tolR	-7.83	0.338188	180 -- 193	26 -- 40	membrane spanning protein in TolA-TolQ-TolR complex	_____________179_____________194\n_____________\|_______________\|\n5'-UGG...UUAGC______CA_______GUAAG...UGG-3'\n______________GA_GAG__ACAAGGG\n______________\|\|_\|\|\|__\|\|\|\|\|\|\|\n______________CU_CUC__UGUUCCC\n3'-UUU...UAAUA__A___AA_______GUGUC...GUG-5'\n_____________\|_______________\|\n_____________41______________25\n	187 -- 193	26 -- 32	-14.5104 kcal/mol	3.98616 kcal/mol	2.69022 kcal/mol	179 194@LB@ \| \|@LB@5'-UGG...UUAGC CA GUAAG...UGG-3'@LB@ GA GAG ACAAGGG@LB@ \|\| \|\|\| \|\|\|\|\|\|\|@LB@ CU CUC UGUUCCC@LB@3'-UUU...UAAUA A AA GUGUC...GUG-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -7.83 kcal/mol@LB@Hybridization Energy -14.5104 kcal/mol@LB@Unfolding Energy - mRNA 3.98616 kcal/mol@LB@Unfolding Energy - sRNA 2.69022 kcal/mol@LB@@LB@Position - mRNA 180 -- 193@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 26 -- 32@LB@
196	0.01202	0.2159	b1729	ydjN	-13.87	0.024594	143 -- 155	72 -- 84	putative transporter	_____________142___________156\n_____________\|_____________\|\n5'-CAU...AAUCU_____________UGACU...UGC-3'\n______________UGCGCCAACACUA\n______________\|\|\|\|\|\|\|\|\|\|\|:\|\n______________ACGCGGUUGUGGU\n3'-UUU...UUAUG_____________CCCUU...GUG-5'\n_____________\|_____________\|\n_____________85____________71\n	149 -- 155	72 -- 78	-23.7045 kcal/mol	2.6326 kcal/mol	7.20328 kcal/mol	142 156@LB@ \| \|@LB@5'-CAU...AAUCU UGACU...UGC-3'@LB@ UGCGCCAACACUA@LB@ \|\|\|\|\|\|\|\|\|\|\|:\|@LB@ ACGCGGUUGUGGU@LB@3'-UUU...UUAUG CCCUU...GUG-5'@LB@ \| \|@LB@ 85 71@LB@@LB@@LB@Energy -13.87 kcal/mol@LB@Hybridization Energy -23.7045 kcal/mol@LB@Unfolding Energy - mRNA 2.6326 kcal/mol@LB@Unfolding Energy - sRNA 7.20328 kcal/mol@LB@@LB@Position - mRNA 143 -- 155@LB@Position - sRNA 72 -- 84@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 72 -- 78@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@
198	0.01217	0.2164	b1236	galU	-11.62	0.068156	187 -- 208	56 -- 74	glucose-1-phosphate uridylyltransferase	_____________186____________________209\n_____________\|______________________\|\n5'-CAA...ACAGU_____A______AAA_______CAUUA...UGC-3'\n______________CCAGG_GAAUUU___UGGCUGC\n______________\|\|\|\|\|_:\|\|\|:\|___\|\|\|\|\|\|\|\n______________GGUCC_UUUAGA___ACCGACG\n3'-UUU...GUUGU_____C________________CGGCA...GUG-5'\n_____________\|______________________\|\n_____________75_____________________55\n	202 -- 208	56 -- 62	-24.2568 kcal/mol	4.50323 kcal/mol	8.13729 kcal/mol	186 209@LB@ \| \|@LB@5'-CAA...ACAGU A AAA CAUUA...UGC-3'@LB@ CCAGG GAAUUU UGGCUGC@LB@ \|\|\|\|\| :\|\|\|:\| \|\|\|\|\|\|\|@LB@ GGUCC UUUAGA ACCGACG@LB@3'-UUU...GUUGU C CGGCA...GUG-5'@LB@ \| \|@LB@ 75 55@LB@@LB@@LB@Energy -11.62 kcal/mol@LB@Hybridization Energy -24.2568 kcal/mol@LB@Unfolding Energy - mRNA 4.50323 kcal/mol@LB@Unfolding Energy - sRNA 8.13729 kcal/mol@LB@@LB@Position - mRNA 187 -- 208@LB@Position - sRNA 56 -- 74@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 56 -- 62@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@
200	0.01246	0.2193	b0425	panE	-12.07	0.055655	285 -- 293	54 -- 62	2-dehydropantoate reductase NADPH-specific	_____________284_______294\n_____________\|_________\|\n5'-AUC...AGGGC_________GUACCGC-3'\n______________UGGCUGCGC\n______________\|\|\|\|\|\|\|\|\|\n______________ACCGACGCG\n3'-UUU...UUAGA_________GCAUU...GUG-5'\n_____________\|_________\|\n_____________63________53\n	287 -- 293	54 -- 60	-19.0333 kcal/mol	2.09185 kcal/mol	4.8739 kcal/mol	284 294@LB@ \| \|@LB@5'-AUC...AGGGC GUACCGC-3'@LB@ UGGCUGCGC@LB@ \|\|\|\|\|\|\|\|\|@LB@ ACCGACGCG@LB@3'-UUU...UUAGA GCAUU...GUG-5'@LB@ \| \|@LB@ 63 53@LB@@LB@@LB@Energy -12.07 kcal/mol@LB@Hybridization Energy -19.0333 kcal/mol@LB@Unfolding Energy - mRNA 2.09185 kcal/mol@LB@Unfolding Energy - sRNA 4.8739 kcal/mol@LB@@LB@Position - mRNA 285 -- 293@LB@Position - sRNA 54 -- 62@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 54 -- 60@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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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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