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
61	0.01179	0.5385	b3748	rbsD	-10.58	0.083988	129 -- 141	72 -- 84	D-ribose pyranase	_____________128___________142\n_____________\|_____________\|\n5'-GGU...UAACG_____A_______CCCAA...UCC-3'\n______________UCACG_UGGUUUU\n______________\|\|\|\|\|_\|\|\|:\|\|\|\n______________AGUGC_ACCGAAA\n3'-CGC...UUUCA_____A_______UCAAU...AAG-5'\n_____________\|_____________\|\n_____________85____________71\n	135 -- 141	72 -- 78	-14.1499 kcal/mol	3.06287 kcal/mol	0.509125 kcal/mol	128 142@LB@ \| \|@LB@5'-GGU...UAACG A CCCAA...UCC-3'@LB@ UCACG UGGUUUU@LB@ \|\|\|\|\| \|\|\|:\|\|\|@LB@ AGUGC ACCGAAA@LB@3'-CGC...UUUCA A UCAAU...AAG-5'@LB@ \| \|@LB@ 85 71@LB@@LB@@LB@Energy -10.58 kcal/mol@LB@Hybridization Energy -14.1499 kcal/mol@LB@Unfolding Energy - mRNA 3.06287 kcal/mol@LB@Unfolding Energy - sRNA 0.509125 kcal/mol@LB@@LB@Position - mRNA 129 -- 141@LB@Position - sRNA 72 -- 84@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 72 -- 78@LB@
62	0.01254	0.5385	b0027	lspA	-10.68	0.080768	51 -- 66	75 -- 90	prolipoprotein signal peptidase (signal peptidase II)	_____________50________________67\n_____________\|_________________\|\n5'-UAU...GGGCU______________A__AAAGC...ACU-3'\n______________GAAAG_UCGCGUUG_GU\n______________:\|\|\|\|_\|\|:\|\|\|\|\|_\|:\n______________UUUUC_AGUGCAAC_CG\n3'-CGC...AGGCG_____A___________AAAUC...AAG-5'\n_____________\|_________________\|\n_____________91________________74\n	57 -- 63	77 -- 83	-15.4073 kcal/mol	4.21469 kcal/mol	0.517251 kcal/mol	50 67@LB@ \| \|@LB@5'-UAU...GGGCU A AAAGC...ACU-3'@LB@ GAAAG UCGCGUUG GU@LB@ :\|\|\|\| \|\|:\|\|\|\|\| \|:@LB@ UUUUC AGUGCAAC CG@LB@3'-CGC...AGGCG A AAAUC...AAG-5'@LB@ \| \|@LB@ 91 74@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -15.4073 kcal/mol@LB@Unfolding Energy - mRNA 4.21469 kcal/mol@LB@Unfolding Energy - sRNA 0.517251 kcal/mol@LB@@LB@Position - mRNA 51 -- 66@LB@Position - sRNA 75 -- 90@LB@Position Seed - mRNA 57 -- 63@LB@Position Seed - sRNA 77 -- 83@LB@
63	0.01271	0.5385	b3306	rpsH	-10.49	0.086924	89 -- 100	56 -- 67	30S ribosomal subunit protein S8	_____________88___________101\n_____________\|____________\|\n5'-AGC...CGGAA____________CCGUA...AAG-3'\n______________GUUCGGGUUGAG\n______________:\|\|\|\|:\|\|\|\|\|\|\n______________UAAGCUCAACUC\n3'-CGC...AUCAA____________UUUGA...AAG-5'\n_____________\|____________\|\n_____________68___________55\n	94 -- 100	56 -- 62	-16.8063 kcal/mol	4.74141 kcal/mol	1.57281 kcal/mol	88 101@LB@ \| \|@LB@5'-AGC...CGGAA CCGUA...AAG-3'@LB@ GUUCGGGUUGAG@LB@ :\|\|\|\|:\|\|\|\|\|\|@LB@ UAAGCUCAACUC@LB@3'-CGC...AUCAA UUUGA...AAG-5'@LB@ \| \|@LB@ 68 55@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -16.8063 kcal/mol@LB@Unfolding Energy - mRNA 4.74141 kcal/mol@LB@Unfolding Energy - sRNA 1.57281 kcal/mol@LB@@LB@Position - mRNA 89 -- 100@LB@Position - sRNA 56 -- 67@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 56 -- 62@LB@
64	0.01278	0.5385	b1718	infC	-10.82	0.076139	1 -- 9	71 -- 79	translation initiation factor IF-3	______________1________10\n______________\|________\|\n___________5'-_________AAAUC...AGC-3'\n______________UUGGCUUUA\n______________\|\|\|\|\|\|\|\|\|\n______________AACCGAAAU\n3'-CGC...AGUGC_________CAAUA...AAG-5'\n_____________\|_________\|\n_____________80________70\n	3 -- 9	71 -- 77	-11.2516 kcal/mol	0.206511 kcal/mol	0.222833 kcal/mol	1 10@LB@ \| \|@LB@ 5'- AAAUC...AGC-3'@LB@ UUGGCUUUA@LB@ \|\|\|\|\|\|\|\|\|@LB@ AACCGAAAU@LB@3'-CGC...AGUGC CAAUA...AAG-5'@LB@ \| \|@LB@ 80 70@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -11.2516 kcal/mol@LB@Unfolding Energy - mRNA 0.206511 kcal/mol@LB@Unfolding Energy - sRNA 0.222833 kcal/mol@LB@@LB@Position - mRNA 1 -- 9@LB@Position - sRNA 71 -- 79@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 71 -- 77@LB@
65	0.01282	0.5385	b0589	fepG	-12.08	0.045738	8 -- 17	74 -- 83	iron-enterobactin ABC transporter permease	_____________7__________18\n_____________\|__________\|\n____5'-CAUAUGG__________GGUGG...CGC-3'\n______________CGCGUUGGCU\n______________\|:\|\|\|\|\|\|\|\|\n______________GUGCAACCGA\n3'-CGC...UUCAA__________AAUCA...AAG-5'\n_____________\|__________\|\n_____________84_________73\n	11 -- 17	74 -- 80	-17.1529 kcal/mol	4.57841 kcal/mol	0.494551 kcal/mol	7 18@LB@ \| \|@LB@ 5'-CAUAUGG GGUGG...CGC-3'@LB@ CGCGUUGGCU@LB@ \|:\|\|\|\|\|\|\|\|@LB@ GUGCAACCGA@LB@3'-CGC...UUCAA AAUCA...AAG-5'@LB@ \| \|@LB@ 84 73@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -17.1529 kcal/mol@LB@Unfolding Energy - mRNA 4.57841 kcal/mol@LB@Unfolding Energy - sRNA 0.494551 kcal/mol@LB@@LB@Position - mRNA 8 -- 17@LB@Position - sRNA 74 -- 83@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 74 -- 80@LB@
66	0.01284	0.5385	b1645	ydhK	-10.57	0.084210	155 -- 164	75 -- 84	putative efflux protein (PET) component of YdhJK efflux pump	_____________154________165\n_____________\|__________\|\n5'-CAG...CGAUG__________GUCGG...UGG-3'\n______________UCACGUUGGU\n______________\|\|\|\|\|\|\|\|\|:\n______________AGUGCAACCG\n3'-CGC...UUUCA__________AAAUC...AAG-5'\n_____________\|__________\|\n_____________85_________74\n	158 -- 164	75 -- 81	-15.7281 kcal/mol	4.6508 kcal/mol	0.505918 kcal/mol	154 165@LB@ \| \|@LB@5'-CAG...CGAUG GUCGG...UGG-3'@LB@ UCACGUUGGU@LB@ \|\|\|\|\|\|\|\|\|:@LB@ AGUGCAACCG@LB@3'-CGC...UUUCA AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -10.57 kcal/mol@LB@Hybridization Energy -15.7281 kcal/mol@LB@Unfolding Energy - mRNA 4.6508 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 155 -- 164@LB@Position - sRNA 75 -- 84@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 75 -- 81@LB@
67	0.01284	0.5385	b1294	sapA	-9.42	0.132690	25 -- 48	61 -- 86	antimicrobial peptide transport ABC transporter periplasmic binding protein	_____________24_________________________49\n_____________\|__________________________\|\n5'-UAC...AAGUU________GA___A_______A____AAAUC...ACA-3'\n______________GUUC_UGU__GUU_UAGUUAU__GAG\n______________\|\|\|\|_:\|\|__\|:\|_\|\|\|\|\|\|\|__\|\|\|\n______________CAAG_GCA__CGA_AUCAAUA__CUC\n3'-CGC...GUUUU____U___AC___A_______AG___AACUC...AAG-5'\n_____________\|__________________________\|\n_____________87_________________________60\n	38 -- 44	66 -- 72	-17.3513 kcal/mol	6.21881 kcal/mol	1.70915 kcal/mol	24 49@LB@ \| \|@LB@5'-UAC...AAGUU GA A A AAAUC...ACA-3'@LB@ GUUC UGU GUU UAGUUAU GAG@LB@ \|\|\|\| :\|\| \|:\| \|\|\|\|\|\|\| \|\|\|@LB@ CAAG GCA CGA AUCAAUA CUC@LB@3'-CGC...GUUUU U AC A AG AACUC...AAG-5'@LB@ \| \|@LB@ 87 60@LB@@LB@@LB@Energy -9.42 kcal/mol@LB@Hybridization Energy -17.3513 kcal/mol@LB@Unfolding Energy - mRNA 6.21881 kcal/mol@LB@Unfolding Energy - sRNA 1.70915 kcal/mol@LB@@LB@Position - mRNA 25 -- 48@LB@Position - sRNA 61 -- 86@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 66 -- 72@LB@
68	0.013	0.5385	b2823	ppdC	-12.74	0.034901	243 -- 262	69 -- 89	putative prepilin peptidase-dependent protein	_____________242___________________263\n_____________\|_____________________\|\n5'-ACG...UGCCG_____A_________GA____GUUGA...UCC-3'\n______________GAGGU__AUGUUGGC__UGGU\n______________:\|:\|\|__\|:\|\|\|\|\|\|__\|:\|\|\n______________UUUCA__UGCAACCG__AUCA\n3'-CGC...GGCGU_____AG________AA____AUAAG...AAG-5'\n_____________\|_____________________\|\n_____________90____________________68\n	250 -- 256	75 -- 81	-18.5568 kcal/mol	5.24273 kcal/mol	0.572143 kcal/mol	242 263@LB@ \| \|@LB@5'-ACG...UGCCG A GA GUUGA...UCC-3'@LB@ GAGGU AUGUUGGC UGGU@LB@ :\|:\|\| \|:\|\|\|\|\|\| \|:\|\|@LB@ UUUCA UGCAACCG AUCA@LB@3'-CGC...GGCGU AG AA AUAAG...AAG-5'@LB@ \| \|@LB@ 90 68@LB@@LB@@LB@Energy -12.74 kcal/mol@LB@Hybridization Energy -18.5568 kcal/mol@LB@Unfolding Energy - mRNA 5.24273 kcal/mol@LB@Unfolding Energy - sRNA 0.572143 kcal/mol@LB@@LB@Position - mRNA 243 -- 262@LB@Position - sRNA 69 -- 89@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 75 -- 81@LB@
69	0.01301	0.5385	b0174	ispU	-11.35	0.061456	97 -- 106	71 -- 80	undecaprenyl pyrophosphate synthase	_____________96_________107\n_____________\|__________\|\n5'-CGU...AAGUA__________UAAGG...AAA-3'\n______________GUUGGCUUUA\n______________\|\|\|\|\|\|\|\|\|\|\n______________CAACCGAAAU\n3'-CGC...AAGUG__________CAAUA...AAG-5'\n_____________\|__________\|\n_____________81_________70\n	100 -- 106	71 -- 77	-14.3232 kcal/mol	2.73321 kcal/mol	0.236872 kcal/mol	96 107@LB@ \| \|@LB@5'-CGU...AAGUA UAAGG...AAA-3'@LB@ GUUGGCUUUA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CAACCGAAAU@LB@3'-CGC...AAGUG CAAUA...AAG-5'@LB@ \| \|@LB@ 81 70@LB@@LB@@LB@Energy -11.35 kcal/mol@LB@Hybridization Energy -14.3232 kcal/mol@LB@Unfolding Energy - mRNA 2.73321 kcal/mol@LB@Unfolding Energy - sRNA 0.236872 kcal/mol@LB@@LB@Position - mRNA 97 -- 106@LB@Position - sRNA 71 -- 80@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 71 -- 77@LB@
70	0.01301	0.5385	b1424	opgD	-12.13	0.044753	222 -- 240	70 -- 90	OPG biosynthetic periplasmic protein	_____________221___________________241\n_____________\|_____________________\|\n5'-AAU...UUAUU_________A_______A___CCGCC...CAG-3'\n______________AAAGGUUCA___UGGCU_UGG\n______________\|\|\|:\|\|\|\|\|___\|\|\|\|\|_\|:\|\n______________UUUUCAAGU___ACCGA_AUC\n3'-CGC...AGGCG_________GCA_____A___AAUAA...AAG-5'\n_____________\|_____________________\|\n_____________91____________________69\n	224 -- 230	82 -- 88	-16.4191 kcal/mol	3.71348 kcal/mol	0.572228 kcal/mol	221 241@LB@ \| \|@LB@5'-AAU...UUAUU A A CCGCC...CAG-3'@LB@ AAAGGUUCA UGGCU UGG@LB@ \|\|\|:\|\|\|\|\| \|\|\|\|\| \|:\|@LB@ UUUUCAAGU ACCGA AUC@LB@3'-CGC...AGGCG GCA A AAUAA...AAG-5'@LB@ \| \|@LB@ 91 69@LB@@LB@@LB@Energy -12.13 kcal/mol@LB@Hybridization Energy -16.4191 kcal/mol@LB@Unfolding Energy - mRNA 3.71348 kcal/mol@LB@Unfolding Energy - sRNA 0.572228 kcal/mol@LB@@LB@Position - mRNA 222 -- 240@LB@Position - sRNA 70 -- 90@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 82 -- 88@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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