Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
67	0.01414	0.6177	b0474	adk	-7.17	0.151538	186 -- 198	39 -- 51	adenylate kinase	_____________185___________199\n_____________\|_____________\|\n5'-ACC...AUUUU_______U_____CAAUG...AUA-3'\n______________AAGGGGA_UUUCG\n______________\|\|\|:\|\|\|_\|\|\|\|:\n______________UUCUCCU_AAAGU\n3'-UUU...GCAGU_______U_____AAAAA...ACA-5'\n_____________\|_____________\|\n_____________52____________38\n	186 -- 192	45 -- 51	-12.5937 kcal/mol	4.3836 kcal/mol	1.04441 kcal/mol	185 199@LB@ \| \|@LB@5'-ACC...AUUUU U CAAUG...AUA-3'@LB@ AAGGGGA UUUCG@LB@ \|\|\|:\|\|\| \|\|\|\|:@LB@ UUCUCCU AAAGU@LB@3'-UUU...GCAGU U AAAAA...ACA-5'@LB@ \| \|@LB@ 52 38@LB@@LB@@LB@Energy -7.17 kcal/mol@LB@Hybridization Energy -12.5937 kcal/mol@LB@Unfolding Energy - mRNA 4.3836 kcal/mol@LB@Unfolding Energy - sRNA 1.04441 kcal/mol@LB@@LB@Position - mRNA 186 -- 198@LB@Position - sRNA 39 -- 51@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 45 -- 51@LB@
170	0.03452	0.6177	b0792	ybhR	-7.08	0.157577	208 -- 236	47 -- 69	putative ABC transporter permease	_____________207____________________________237\n_____________\|______________________________\|\n5'-CAG...GUUUC______UA___ACGUUAA____________UUGCA...AGG-3'\n______________AUCGCU__UGG_______UCCG_CAAAGAG\n______________\|\|\|\|\|\|__\|\|\|_______:\|\|\|_\|\|\|\|\|\|\|\n______________UAGCGA__ACC_______GGGC_GUUUCUC\n3'-UUU...GGUUA______UA______________A_______CUUAA...ACA-5'\n_____________\|______________________________\|\n_____________70_____________________________46\n	230 -- 236	47 -- 53	-23.2437 kcal/mol	4.95079 kcal/mol	11.2154 kcal/mol	207 237@LB@ \| \|@LB@5'-CAG...GUUUC UA ACGUUAA UUGCA...AGG-3'@LB@ AUCGCU UGG UCCG CAAAGAG@LB@ \|\|\|\|\|\| \|\|\| :\|\|\| \|\|\|\|\|\|\|@LB@ UAGCGA ACC GGGC GUUUCUC@LB@3'-UUU...GGUUA UA A CUUAA...ACA-5'@LB@ \| \|@LB@ 70 46@LB@@LB@@LB@Energy -7.08 kcal/mol@LB@Hybridization Energy -23.2437 kcal/mol@LB@Unfolding Energy - mRNA 4.95079 kcal/mol@LB@Unfolding Energy - sRNA 11.2154 kcal/mol@LB@@LB@Position - mRNA 208 -- 236@LB@Position - sRNA 47 -- 69@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 47 -- 53@LB@
68	0.01422	0.6177	b3826	yigL	-7.04	0.159921	44 -- 50	49 -- 55	pyridoxal phosphate phosphatase	_____________43______51\n_____________\|_______\|\n5'-GCA...AUCCU_______GAGGA...CGC-3'\n______________GUCGAAG\n______________\|\|\|:\|\|\|\n______________CAGUUUC\n3'-UUU...CCGGG_______UCCUU...ACA-5'\n_____________\|_______\|\n_____________56______48\n	44 -- 50	49 -- 55	-7.68974 kcal/mol	0.331193 kcal/mol	0.314364 kcal/mol	43 51@LB@ \| \|@LB@5'-GCA...AUCCU GAGGA...CGC-3'@LB@ GUCGAAG@LB@ \|\|\|:\|\|\|@LB@ CAGUUUC@LB@3'-UUU...CCGGG UCCUU...ACA-5'@LB@ \| \|@LB@ 56 48@LB@@LB@@LB@Energy -7.04 kcal/mol@LB@Hybridization Energy -7.68974 kcal/mol@LB@Unfolding Energy - mRNA 0.331193 kcal/mol@LB@Unfolding Energy - sRNA 0.314364 kcal/mol@LB@@LB@Position - mRNA 44 -- 50@LB@Position - sRNA 49 -- 55@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 49 -- 55@LB@
40	0.007925	0.6129	b1109	ndh	-7.04	0.160101	187 -- 195	46 -- 54	respiratory NADH dehydrogenase 2/cupric reductase	_____________186_______196\n_____________\|_________\|\n5'-UGU...UAAAU_________UCACG...AAG-3'\n______________UUAAGGGGG\n______________\|:\|\|:\|:\|\|\n______________AGUUUCUCC\n3'-UUU...CGGGC_________UUAAA...ACA-5'\n_____________\|_________\|\n_____________55________45\n	189 -- 195	46 -- 52	-9.48398 kcal/mol	1.51964 kcal/mol	0.922697 kcal/mol	186 196@LB@ \| \|@LB@5'-UGU...UAAAU UCACG...AAG-3'@LB@ UUAAGGGGG@LB@ \|:\|\|:\|:\|\|@LB@ AGUUUCUCC@LB@3'-UUU...CGGGC UUAAA...ACA-5'@LB@ \| \|@LB@ 55 45@LB@@LB@@LB@Energy -7.04 kcal/mol@LB@Hybridization Energy -9.48398 kcal/mol@LB@Unfolding Energy - mRNA 1.51964 kcal/mol@LB@Unfolding Energy - sRNA 0.922697 kcal/mol@LB@@LB@Position - mRNA 187 -- 195@LB@Position - sRNA 46 -- 54@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 46 -- 52@LB@
38	0.007716	0.6129	b0480	ushA	-6.97	0.165152	186 -- 197	45 -- 55	bifunctional UDP-sugar hydrolase/5'-nucleotidase	_____________185__________198\n_____________\|____________\|\n5'-AGG...AUCAG_________A__AGUAU...AAA-3'\n______________GUCAGGGAG_GA\n______________\|\|\|\|::\|\|\|_\|\|\n______________CAGUUUCUC_CU\n3'-UUU...CCGGG____________UAAAG...ACA-5'\n_____________\|____________\|\n_____________56___________44\n	188 -- 194	47 -- 53	-13.3467 kcal/mol	5.44454 kcal/mol	0.930875 kcal/mol	185 198@LB@ \| \|@LB@5'-AGG...AUCAG A AGUAU...AAA-3'@LB@ GUCAGGGAG GA@LB@ \|\|\|\|::\|\|\| \|\|@LB@ CAGUUUCUC CU@LB@3'-UUU...CCGGG UAAAG...ACA-5'@LB@ \| \|@LB@ 56 44@LB@@LB@@LB@Energy -6.97 kcal/mol@LB@Hybridization Energy -13.3467 kcal/mol@LB@Unfolding Energy - mRNA 5.44454 kcal/mol@LB@Unfolding Energy - sRNA 0.930875 kcal/mol@LB@@LB@Position - mRNA 186 -- 197@LB@Position - sRNA 45 -- 55@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 47 -- 53@LB@
194	0.04051	0.6177	b0814	ompX	-6.96	0.165642	107 -- 118	50 -- 61	outer membrane protein X	_____________106__________119\n_____________\|____________\|\n5'-CUG...UGAAA____________CAUCA...CAC-3'\n______________UGGCCCGUUAGA\n______________\|\|\|\|\|\|\|\|:\|:\|\n______________ACCGGGCAGUUU\n3'-UUU...CGAUA____________CUCCU...ACA-5'\n_____________\|____________\|\n_____________62___________49\n	111 -- 117	51 -- 57	-20.1081 kcal/mol	2.98628 kcal/mol	10.1573 kcal/mol	106 119@LB@ \| \|@LB@5'-CUG...UGAAA CAUCA...CAC-3'@LB@ UGGCCCGUUAGA@LB@ \|\|\|\|\|\|\|\|:\|:\|@LB@ ACCGGGCAGUUU@LB@3'-UUU...CGAUA CUCCU...ACA-5'@LB@ \| \|@LB@ 62 49@LB@@LB@@LB@Energy -6.96 kcal/mol@LB@Hybridization Energy -20.1081 kcal/mol@LB@Unfolding Energy - mRNA 2.98628 kcal/mol@LB@Unfolding Energy - sRNA 10.1573 kcal/mol@LB@@LB@Position - mRNA 107 -- 118@LB@Position - sRNA 50 -- 61@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 51 -- 57@LB@
153	0.03061	0.6177	b4060	yjcB	-6.94	0.167417	88 -- 108	29 -- 50	putative inner membrane protein	_____________87_____________________109\n_____________\|______________________\|\n5'-AUA...CAAAC____U____________G____CUGCA...GGU-3'\n______________AGAG__GUUUCAUUUUU_UGUU\n______________\|\|\|\|__:\|\|\|\|\|\|\|\|\|\|_\|:\|\|\n______________UCUC__UAAAGUAAAAA_AUAA\n3'-UUU...CAGUU____CU___________A____UAAUA...ACA-5'\n_____________\|______________________\|\n_____________51_____________________28\n	97 -- 103	34 -- 40	-13.8913 kcal/mol	5.87088 kcal/mol	1.08007 kcal/mol	87 109@LB@ \| \|@LB@5'-AUA...CAAAC U G CUGCA...GGU-3'@LB@ AGAG GUUUCAUUUUU UGUU@LB@ \|\|\|\| :\|\|\|\|\|\|\|\|\|\| \|:\|\|@LB@ UCUC UAAAGUAAAAA AUAA@LB@3'-UUU...CAGUU CU A UAAUA...ACA-5'@LB@ \| \|@LB@ 51 28@LB@@LB@@LB@Energy -6.94 kcal/mol@LB@Hybridization Energy -13.8913 kcal/mol@LB@Unfolding Energy - mRNA 5.87088 kcal/mol@LB@Unfolding Energy - sRNA 1.08007 kcal/mol@LB@@LB@Position - mRNA 88 -- 108@LB@Position - sRNA 29 -- 50@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 34 -- 40@LB@
147	0.02922	0.6177	b3836	tatA	-6.91	0.169904	186 -- 195	44 -- 53	TatABCE protein translocation system subunit	_____________185________196\n_____________\|__________\|\n5'-CUA...UCUAC__C_______CAUGU...GUG-3'\n______________CA_AGAGGAA\n______________\|\|_\|\|\|\|\|\|\|\n______________GU_UCUCCUU\n3'-UUU...GGGCA__U_______AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	189 -- 195	44 -- 50	-10.6779 kcal/mol	2.84312 kcal/mol	0.927997 kcal/mol	185 196@LB@ \| \|@LB@5'-CUA...UCUAC C CAUGU...GUG-3'@LB@ CA AGAGGAA@LB@ \|\| \|\|\|\|\|\|\|@LB@ GU UCUCCUU@LB@3'-UUU...GGGCA U AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -6.91 kcal/mol@LB@Hybridization Energy -10.6779 kcal/mol@LB@Unfolding Energy - mRNA 2.84312 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 186 -- 195@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
53	0.01077	0.6177	b3429	glgA	-6.74	0.182373	105 -- 111	44 -- 50	glycogen synthase	_____________104_____112\n_____________\|_______\|\n5'-GUA...AACGC_______GAUGC...ACG-3'\n______________AGAGGAA\n______________\|\|\|\|\|\|\|\n______________UCUCCUU\n3'-UUU...CAGUU_______AAAGU...ACA-5'\n_____________\|_______\|\n_____________51______43\n	105 -- 111	44 -- 50	-9.00959 kcal/mol	1.43957 kcal/mol	0.825028 kcal/mol	104 112@LB@ \| \|@LB@5'-GUA...AACGC GAUGC...ACG-3'@LB@ AGAGGAA@LB@ \|\|\|\|\|\|\|@LB@ UCUCCUU@LB@3'-UUU...CAGUU AAAGU...ACA-5'@LB@ \| \|@LB@ 51 43@LB@@LB@@LB@Energy -6.74 kcal/mol@LB@Hybridization Energy -9.00959 kcal/mol@LB@Unfolding Energy - mRNA 1.43957 kcal/mol@LB@Unfolding Energy - sRNA 0.825028 kcal/mol@LB@@LB@Position - mRNA 105 -- 111@LB@Position - sRNA 44 -- 50@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 44 -- 50@LB@
152	0.03059	0.6177	b2609	rpsP	-6.70	0.186060	187 -- 203	23 -- 53	30S ribosomal subunit protein S16	_____________186______________________________204\n_____________\|________________________________\|\n5'-UCA...AUUCA__C_____________________________GUAAC...UCG-3'\n______________CA_AAGAGGA_______________UGUUAUG\n______________\|\|_\|\|\|\|\|\|\|_______________\|:\|\|\|\|\|\n______________GU_UUCUCCU_______________AUAAUAC\n3'-UUU...GGGCA__________UAAAGUAAAAAAAUA_______GGCAG...ACA-5'\n_____________\|________________________________\|\n_____________54_______________________________22\n	197 -- 203	23 -- 29	-10.7305 kcal/mol	2.84664 kcal/mol	1.18482 kcal/mol	186 204@LB@ \| \|@LB@5'-UCA...AUUCA C GUAAC...UCG-3'@LB@ CA AAGAGGA UGUUAUG@LB@ \|\| \|\|\|\|\|\|\| \|:\|\|\|\|\|@LB@ GU UUCUCCU AUAAUAC@LB@3'-UUU...GGGCA UAAAGUAAAAAAAUA GGCAG...ACA-5'@LB@ \| \|@LB@ 54 22@LB@@LB@@LB@Energy -6.70 kcal/mol@LB@Hybridization Energy -10.7305 kcal/mol@LB@Unfolding Energy - mRNA 2.84664 kcal/mol@LB@Unfolding Energy - sRNA 1.18482 kcal/mol@LB@@LB@Position - mRNA 187 -- 203@LB@Position - sRNA 23 -- 53@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 23 -- 29@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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