Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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	Additional homologs
158	0.02721	0.5559	b1724	ydiZ	-8.58	0.183444	272 -- 279	57 -- 64	uncharacterized protein		_____________271______280\n_____________\|________\|\n5'-UUU...AUUAA________AUAAU...ACG-3'\n______________CGAGUUGA\n______________\|\|\|\|\|\|\|\|\n______________GCUCAACU\n3'-CGC...AAUAA________CUUUG...AAG-5'\n_____________\|________\|\n_____________65_______56\n	273 -- 279	57 -- 63	-11.4752 kcal/mol	1.7639 kcal/mol	1.12823 kcal/mol	271 280@LB@ \| \|@LB@5'-UUU...AUUAA AUAAU...ACG-3'@LB@ CGAGUUGA@LB@ \|\|\|\|\|\|\|\|@LB@ GCUCAACU@LB@3'-CGC...AAUAA CUUUG...AAG-5'@LB@ \| \|@LB@ 65 56@LB@@LB@@LB@Energy -8.58 kcal/mol@LB@Hybridization Energy -11.4752 kcal/mol@LB@Unfolding Energy - mRNA 1.7639 kcal/mol@LB@Unfolding Energy - sRNA 1.12823 kcal/mol@LB@@LB@Position - mRNA 272 -- 279@LB@Position - sRNA 57 -- 64@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 57 -- 63@LB@
190	0.03345	0.5559	b4090	rpiB	-6.75	0.355761	259 -- 286	57 -- 78	ribose 5-phosphate isomerase B/allose 6-phosphate isomerase		_____________258__________________________287\n_____________\|____________________________\|\n5'-AAC...AAUAG____ACA________AGCG___C_____AGUGA...AAG-3'\n______________UGGC___UUUAGUUG____UGG_GUUGA\n______________\|\|\|\|___\|\|\|\|\|\|\|:____:\|:_\|\|\|\|\|\n______________ACCG___AAAUCAAU____GCU_CAACU\n3'-CGC...GUGCA_______________AA___________CUUUG...AAG-5'\n_____________\|____________________________\|\n_____________79___________________________56\n	267 -- 273	67 -- 73	-15.2709 kcal/mol	7.30632 kcal/mol	1.21856 kcal/mol	258 287@LB@ \| \|@LB@5'-AAC...AAUAG ACA AGCG C AGUGA...AAG-3'@LB@ UGGC UUUAGUUG UGG GUUGA@LB@ \|\|\|\| \|\|\|\|\|\|\|: :\|: \|\|\|\|\|@LB@ ACCG AAAUCAAU GCU CAACU@LB@3'-CGC...GUGCA AA CUUUG...AAG-5'@LB@ \| \|@LB@ 79 56@LB@@LB@@LB@Energy -6.75 kcal/mol@LB@Hybridization Energy -15.2709 kcal/mol@LB@Unfolding Energy - mRNA 7.30632 kcal/mol@LB@Unfolding Energy - sRNA 1.21856 kcal/mol@LB@@LB@Position - mRNA 259 -- 286@LB@Position - sRNA 57 -- 78@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 67 -- 73@LB@
193	0.03391	0.5559	b3642	pyrE	-10.20	0.097546	70 -- 90	57 -- 80	orotate phosphoribosyltransferase		_____________69_______________________91\n_____________\|________________________\|\n5'-CGG...AUCUU_______C___CC_______GG__AUCGA...AUU-3'\n______________GUUGGCU_UGG_____CGAG__GA\n______________\|\|\|\|\|\|\|_\|:\|_____\|\|\|\|__\|\|\n______________CAACCGA_AUC_____GCUC__CU\n3'-CGC...AAGUG_______A___AAUAA____AA__CUUUG...AAG-5'\n_____________\|________________________\|\n_____________81_______________________56\n	70 -- 76	74 -- 80	-18.9167 kcal/mol	7.49492 kcal/mol	1.21861 kcal/mol	69 91@LB@ \| \|@LB@5'-CGG...AUCUU C CC GG AUCGA...AUU-3'@LB@ GUUGGCU UGG CGAG GA@LB@ \|\|\|\|\|\|\| \|:\| \|\|\|\| \|\|@LB@ CAACCGA AUC GCUC CU@LB@3'-CGC...AAGUG A AAUAA AA CUUUG...AAG-5'@LB@ \| \|@LB@ 81 56@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -18.9167 kcal/mol@LB@Unfolding Energy - mRNA 7.49492 kcal/mol@LB@Unfolding Energy - sRNA 1.21861 kcal/mol@LB@@LB@Position - mRNA 70 -- 90@LB@Position - sRNA 57 -- 80@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 74 -- 80@LB@
198	0.03475	0.5559	b1249	clsA	-8.08	0.221640	216 -- 230	57 -- 82	cardiolipin synthase 1		_____________215________________________231\n_____________\|__________________________\|\n5'-GUC...UUUAU__________________________UUGGC...CAG-3'\n______________ACGUUGGU___________GAGUUGG\n______________\|\|\|\|\|\|\|:___________\|\|\|\|\|\|:\n______________UGCAACCG___________CUCAACU\n3'-CGC...UCAAG________AAAUCAAUAAG_______CUUUG...AAG-5'\n_____________\|__________________________\|\n_____________83_________________________56\n	224 -- 230	57 -- 63	-16.5635 kcal/mol	7.18735 kcal/mol	1.29708 kcal/mol	215 231@LB@ \| \|@LB@5'-GUC...UUUAU UUGGC...CAG-3'@LB@ ACGUUGGU GAGUUGG@LB@ \|\|\|\|\|\|\|: \|\|\|\|\|\|:@LB@ UGCAACCG CUCAACU@LB@3'-CGC...UCAAG AAAUCAAUAAG CUUUG...AAG-5'@LB@ \| \|@LB@ 83 56@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -16.5635 kcal/mol@LB@Unfolding Energy - mRNA 7.18735 kcal/mol@LB@Unfolding Energy - sRNA 1.29708 kcal/mol@LB@@LB@Position - mRNA 216 -- 230@LB@Position - sRNA 57 -- 82@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 57 -- 63@LB@
6	0.001078	0.5385	b0849	grxA	-11.19	0.065759	209 -- 232	58 -- 81	glutaredoxin 1 redox coenzyme for ribonucleotide reductase (RNR1a)		_____________208______________________233\n_____________\|________________________\|\n5'-AGU...CAAAC____AU_______C__________CCCUU...AUC-3'\n______________CGUU__UUUUGGU_GUUCGGGUUG\n______________\|\|\|\|__:\|\|\|:\|\|_:\|\|\|\|:\|\|\|\|\n______________GCAA__GAAAUCA_UAAGCUCAAC\n3'-CGC...CAAGU____CC_______A__________UCUUU...AAG-5'\n_____________\|________________________\|\n_____________82_______________________57\n	226 -- 232	58 -- 64	-21.2762 kcal/mol	8.79419 kcal/mol	1.29619 kcal/mol	208 233@LB@ \| \|@LB@5'-AGU...CAAAC AU C CCCUU...AUC-3'@LB@ CGUU UUUUGGU GUUCGGGUUG@LB@ \|\|\|\| :\|\|\|:\|\| :\|\|\|\|:\|\|\|\|@LB@ GCAA GAAAUCA UAAGCUCAAC@LB@3'-CGC...CAAGU CC A UCUUU...AAG-5'@LB@ \| \|@LB@ 82 57@LB@@LB@@LB@Energy -11.19 kcal/mol@LB@Hybridization Energy -21.2762 kcal/mol@LB@Unfolding Energy - mRNA 8.79419 kcal/mol@LB@Unfolding Energy - sRNA 1.29619 kcal/mol@LB@@LB@Position - mRNA 209 -- 232@LB@Position - sRNA 58 -- 81@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 58 -- 64@LB@
17	0.003067	0.5385	b1628	rsxB	-11.62	0.055094	175 -- 198	58 -- 77	SoxR iron-sulfur cluster reduction factor component; putative iron-sulfur protein		_____________174______________________199\n_____________\|________________________\|\n5'-CAC...UUAUG_________G_____GUGA_____UAAUG...ACG-3'\n______________GGCUUUAGU_GUUUG____AGUUG\n______________\|\|\|\|\|\|\|\|\|_:\|\|:\|____\|\|\|\|\|\n______________CCGAAAUCA_UAAGC____UCAAC\n3'-CGC...UGCAA_________A______________UCUUU...AAG-5'\n_____________\|________________________\|\n_____________78_______________________57\n	177 -- 183	69 -- 75	-20.3316 kcal/mol	7.50919 kcal/mol	1.19974 kcal/mol	174 199@LB@ \| \|@LB@5'-CAC...UUAUG G GUGA UAAUG...ACG-3'@LB@ GGCUUUAGU GUUUG AGUUG@LB@ \|\|\|\|\|\|\|\|\| :\|\|:\| \|\|\|\|\|@LB@ CCGAAAUCA UAAGC UCAAC@LB@3'-CGC...UGCAA A UCUUU...AAG-5'@LB@ \| \|@LB@ 78 57@LB@@LB@@LB@Energy -11.62 kcal/mol@LB@Hybridization Energy -20.3316 kcal/mol@LB@Unfolding Energy - mRNA 7.50919 kcal/mol@LB@Unfolding Energy - sRNA 1.19974 kcal/mol@LB@@LB@Position - mRNA 175 -- 198@LB@Position - sRNA 58 -- 77@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 69 -- 75@LB@
123	0.02095	0.5385	b2562	yfhL	-10.74	0.078719	174 -- 195	59 -- 77	putative 4Fe-4S cluster-containing protein		_____________173____________________196\n_____________\|______________________\|\n5'-AGC...CGCCC_____GU_______UGA_____UCCUU...UUA-3'\n______________GGUUU__GUUGUUU___GAGUU\n______________\|\|:\|\|__\|\|\|:\|\|:___\|\|\|\|\|\n______________CCGAA__CAAUAAG___CUCAA\n3'-CGC...UGCAA_____AU_______________CUCUU...AAG-5'\n_____________\|______________________\|\n_____________78_____________________58\n	181 -- 187	64 -- 70	-15.8972 kcal/mol	4.34594 kcal/mol	0.811926 kcal/mol	173 196@LB@ \| \|@LB@5'-AGC...CGCCC GU UGA UCCUU...UUA-3'@LB@ GGUUU GUUGUUU GAGUU@LB@ \|\|:\|\| \|\|\|:\|\|: \|\|\|\|\|@LB@ CCGAA CAAUAAG CUCAA@LB@3'-CGC...UGCAA AU CUCUU...AAG-5'@LB@ \| \|@LB@ 78 58@LB@@LB@@LB@Energy -10.74 kcal/mol@LB@Hybridization Energy -15.8972 kcal/mol@LB@Unfolding Energy - mRNA 4.34594 kcal/mol@LB@Unfolding Energy - sRNA 0.811926 kcal/mol@LB@@LB@Position - mRNA 174 -- 195@LB@Position - sRNA 59 -- 77@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 64 -- 70@LB@
128	0.02183	0.5385	b0874	ybjE	-9.13	0.148469	198 -- 230	59 -- 85	putative transporter		_____________197_______________________________231\n_____________\|_________________________________\|\n5'-GGG...GGGUU________UUCUG____GUUAAUC____U____CCCCU...UAA-3'\n______________UUCAUGUU_____GGCU_______AUUC_GGUU\n______________\|\|\|\|:\|\|\|_____\|\|\|\|_______\|\|\|\|_:\|\|\|\n______________AAGUGCAA_____CCGA_______UAAG_UCAA\n3'-CGC...UUUUC_________________AAUCAA_____C____CUCUU...AAG-5'\n_____________\|_________________________________\|\n_____________86________________________________58\n	199 -- 205	78 -- 84	-15.801 kcal/mol	4.95896 kcal/mol	1.70749 kcal/mol	197 231@LB@ \| \|@LB@5'-GGG...GGGUU UUCUG GUUAAUC U CCCCU...UAA-3'@LB@ UUCAUGUU GGCU AUUC GGUU@LB@ \|\|\|\|:\|\|\| \|\|\|\| \|\|\|\| :\|\|\|@LB@ AAGUGCAA CCGA UAAG UCAA@LB@3'-CGC...UUUUC AAUCAA C CUCUU...AAG-5'@LB@ \| \|@LB@ 86 58@LB@@LB@@LB@Energy -9.13 kcal/mol@LB@Hybridization Energy -15.801 kcal/mol@LB@Unfolding Energy - mRNA 4.95896 kcal/mol@LB@Unfolding Energy - sRNA 1.70749 kcal/mol@LB@@LB@Position - mRNA 198 -- 230@LB@Position - sRNA 59 -- 85@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 78 -- 84@LB@
135	0.02294	0.5385	b4254	argI	-11.70	0.053356	4 -- 33	59 -- 85	ornithine carbamoyltransferase 1	b0273	_____________3______________________________34\n_____________\|______________________________\|\n________5'-UUC______C__UU___CC________C_____UGCCA...AUA-3'\n______________UUCACG_UG__CUU__AGUUGUUC_GGGUU\n______________\|\|\|\|\|\|_\|\|__\|\|\|__\|\|\|\|:\|\|\|_\|:\|\|\|\n______________AAGUGC_AC__GAA__UCAAUAAG_CUCAA\n3'-CGC...UUUUC______A__C____A_______________CUCUU...AAG-5'\n_____________\|______________________________\|\n_____________86_____________________________58\n	21 -- 27	64 -- 70	-19.7051 kcal/mol	6.29613 kcal/mol	1.70749 kcal/mol	3 34@LB@ \| \|@LB@ 5'-UUC C UU CC C UGCCA...AUA-3'@LB@ UUCACG UG CUU AGUUGUUC GGGUU@LB@ \|\|\|\|\|\| \|\| \|\|\| \|\|\|\|:\|\|\| \|:\|\|\|@LB@ AAGUGC AC GAA UCAAUAAG CUCAA@LB@3'-CGC...UUUUC A C A CUCUU...AAG-5'@LB@ \| \|@LB@ 86 58@LB@@LB@@LB@Energy -11.70 kcal/mol@LB@Hybridization Energy -19.7051 kcal/mol@LB@Unfolding Energy - mRNA 6.29613 kcal/mol@LB@Unfolding Energy - sRNA 1.70749 kcal/mol@LB@@LB@Position - mRNA 4 -- 33@LB@Position - sRNA 59 -- 85@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 64 -- 70@LB@
13	0.002299	0.5385	b3663	yicN	-11.49	0.058154	241 -- 256	60 -- 78	DUF1198 family protein		_____________240_________________257\n_____________\|___________________\|\n5'-CUU...GUUUG___________________GCUGA...AUC-3'\n______________UGGU__UGGUU_UUCGGGU\n______________\|\|\|:__\|:\|\|\|_\|\|\|\|:\|\|\n______________ACCG__AUCAA_AAGCUCA\n3'-CGC...GUGCA____AA_____U_______ACUCU...AAG-5'\n_____________\|___________________\|\n_____________79__________________59\n	250 -- 256	60 -- 66	-15.2298 kcal/mol	2.94333 kcal/mol	0.797083 kcal/mol	240 257@LB@ \| \|@LB@5'-CUU...GUUUG GCUGA...AUC-3'@LB@ UGGU UGGUU UUCGGGU@LB@ \|\|\|: \|:\|\|\| \|\|\|\|:\|\|@LB@ ACCG AUCAA AAGCUCA@LB@3'-CGC...GUGCA AA U ACUCU...AAG-5'@LB@ \| \|@LB@ 79 59@LB@@LB@@LB@Energy -11.49 kcal/mol@LB@Hybridization Energy -15.2298 kcal/mol@LB@Unfolding Energy - mRNA 2.94333 kcal/mol@LB@Unfolding Energy - sRNA 0.797083 kcal/mol@LB@@LB@Position - mRNA 241 -- 256@LB@Position - sRNA 60 -- 78@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 60 -- 66@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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