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
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@
164	0.02889	0.5559	b1512	lsrR	-7.59	0.264791	265 -- 277	71 -- 84	lsr operon transcriptional repressor	_____________264____________278\n_____________\|______________\|\n5'-GCU...GCGGA______________CUAUC...AGA-3'\n______________UCGCG_UGGUUUUA\n______________\|\|:\|\|_\|\|\|:\|\|\|\|\n______________AGUGC_ACCGAAAU\n3'-CGC...UUUCA_____A________CAAUA...AAG-5'\n_____________\|______________\|\n_____________85_____________70\n	271 -- 277	71 -- 77	-14.8882 kcal/mol	6.73904 kcal/mol	0.5567 kcal/mol	264 278@LB@ \| \|@LB@5'-GCU...GCGGA CUAUC...AGA-3'@LB@ UCGCG UGGUUUUA@LB@ \|\|:\|\| \|\|\|:\|\|\|\|@LB@ AGUGC ACCGAAAU@LB@3'-CGC...UUUCA A CAAUA...AAG-5'@LB@ \| \|@LB@ 85 70@LB@@LB@@LB@Energy -7.59 kcal/mol@LB@Hybridization Energy -14.8882 kcal/mol@LB@Unfolding Energy - mRNA 6.73904 kcal/mol@LB@Unfolding Energy - sRNA 0.5567 kcal/mol@LB@@LB@Position - mRNA 265 -- 277@LB@Position - sRNA 71 -- 84@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 71 -- 77@LB@
129	0.02219	0.5385	b4034	malE	-15.67	0.010476	105 -- 137	9 -- 40	maltose transporter subunit	_____________104_______________________________138\n_____________\|_________________________________\|\n5'-AGG...GGGGC____G___AAG____AUG_________U_____AUAAA...UGG-3'\n______________GUAG_GGC___GAGG___GAAAGAGGU_GCCGU\n______________\|:\|\|_\|:\|___:\|\|\|___:\|\|\|\|\|\|\|\|_\|\|\|\|:\n______________CGUC_CUG___UUCC___UUUUCUCCA_CGGCG\n3'-CGC...UUGCC____A___AAG____CAA_______________AGGCAAAG-5'\n_____________\|_________________________________\|\n_____________41________________________________8\n	125 -- 131	14 -- 20	-33.6959 kcal/mol	8.2816 kcal/mol	9.74463 kcal/mol	104 138@LB@ \| \|@LB@5'-AGG...GGGGC G AAG AUG U AUAAA...UGG-3'@LB@ GUAG GGC GAGG GAAAGAGGU GCCGU@LB@ \|:\|\| \|:\| :\|\|\| :\|\|\|\|\|\|\|\| \|\|\|\|:@LB@ CGUC CUG UUCC UUUUCUCCA CGGCG@LB@3'-CGC...UUGCC A AAG CAA AGGCAAAG-5'@LB@ \| \|@LB@ 41 8@LB@@LB@@LB@Energy -15.67 kcal/mol@LB@Hybridization Energy -33.6959 kcal/mol@LB@Unfolding Energy - mRNA 8.2816 kcal/mol@LB@Unfolding Energy - sRNA 9.74463 kcal/mol@LB@@LB@Position - mRNA 105 -- 137@LB@Position - sRNA 9 -- 40@LB@Position Seed - mRNA 125 -- 131@LB@Position Seed - sRNA 14 -- 20@LB@
7	0.001275	0.5385	b2175	mepS	-13.85	0.022182	178 -- 188	25 -- 35	murein DD-endopeptidase space-maker hydrolase mutational suppressor of prc thermosensitivity outer membrane lipoprotein weak murein LD-carboxypeptidase	_____________177_________189\n_____________\|___________\|\n5'-CAA...UUAAG___________AAAAC...CAA-3'\n______________GACUUCAAGGG\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________CUGAAGUUCCC\n3'-CGC...CGUCA___________AAUUU...AAG-5'\n_____________\|___________\|\n_____________36__________24\n	182 -- 188	25 -- 31	-19.9152 kcal/mol	2.73903 kcal/mol	3.32958 kcal/mol	177 189@LB@ \| \|@LB@5'-CAA...UUAAG AAAAC...CAA-3'@LB@ GACUUCAAGGG@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ CUGAAGUUCCC@LB@3'-CGC...CGUCA AAUUU...AAG-5'@LB@ \| \|@LB@ 36 24@LB@@LB@@LB@Energy -13.85 kcal/mol@LB@Hybridization Energy -19.9152 kcal/mol@LB@Unfolding Energy - mRNA 2.73903 kcal/mol@LB@Unfolding Energy - sRNA 3.32958 kcal/mol@LB@@LB@Position - mRNA 178 -- 188@LB@Position - sRNA 25 -- 35@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 25 -- 31@LB@
5	0.0009313	0.5385	b3829	metE	-12.51	0.038445	233 -- 242	75 -- 84	5-methyltetrahydropteroyltriglutamate- homocysteine S-methyltransferase	_____________232________243\n_____________\|__________\|\n5'-GAG...UUCCC__________CUGCG...GUG-3'\n______________UCGCGUUGGC\n______________\|\|:\|\|\|\|\|\|\|\n______________AGUGCAACCG\n3'-CGC...UUUCA__________AAAUC...AAG-5'\n_____________\|__________\|\n_____________85_________74\n	236 -- 242	75 -- 81	-17.7887 kcal/mol	4.77726 kcal/mol	0.505918 kcal/mol	232 243@LB@ \| \|@LB@5'-GAG...UUCCC CUGCG...GUG-3'@LB@ UCGCGUUGGC@LB@ \|\|:\|\|\|\|\|\|\|@LB@ AGUGCAACCG@LB@3'-CGC...UUUCA AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -12.51 kcal/mol@LB@Hybridization Energy -17.7887 kcal/mol@LB@Unfolding Energy - mRNA 4.77726 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 233 -- 242@LB@Position - sRNA 75 -- 84@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 75 -- 81@LB@
83	0.01501	0.5385	b2114	metG	-6.55	0.379655	47 -- 64	63 -- 79	methionyl-tRNA synthetase	_____________46_________________65\n_____________\|__________________\|\n5'-AUU...GUGAU_____CUG__A_______UUCAU...AUG-3'\n______________UUGGC___GG_UUGUUCG\n______________\|\|\|\|\|___:\|_\|\|:\|\|\|\|\n______________AACCG___UC_AAUAAGC\n3'-CGC...AGUGC_____AAA__________UCAAC...AAG-5'\n_____________\|__________________\|\n_____________80_________________62\n	58 -- 64	63 -- 69	-14.0866 kcal/mol	6.80006 kcal/mol	0.735636 kcal/mol	46 65@LB@ \| \|@LB@5'-AUU...GUGAU CUG A UUCAU...AUG-3'@LB@ UUGGC GG UUGUUCG@LB@ \|\|\|\|\| :\| \|\|:\|\|\|\|@LB@ AACCG UC AAUAAGC@LB@3'-CGC...AGUGC AAA UCAAC...AAG-5'@LB@ \| \|@LB@ 80 62@LB@@LB@@LB@Energy -6.55 kcal/mol@LB@Hybridization Energy -14.0866 kcal/mol@LB@Unfolding Energy - mRNA 6.80006 kcal/mol@LB@Unfolding Energy - sRNA 0.735636 kcal/mol@LB@@LB@Position - mRNA 47 -- 64@LB@Position - sRNA 63 -- 79@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 63 -- 69@LB@
124	0.02124	0.5385	b0198	metI	-9.85	0.112177	270 -- 285	71 -- 87	DL-methionine transporter subunit	_____________269_______________286\n_____________\|_________________\|\n5'-UCA...UAUCC_____UU__________UGAUU...CGG-3'\n______________GGUUU___UUGGCUUUG\n______________:\|\|\|:___\|\|\|\|\|\|\|\|:\n______________UCAAG___AACCGAAAU\n3'-CGC...CGUUU_____UGC_________CAAUA...AAG-5'\n_____________\|_________________\|\n_____________88________________70\n	279 -- 285	71 -- 77	-13.0228 kcal/mol	2.60961 kcal/mol	0.562376 kcal/mol	269 286@LB@ \| \|@LB@5'-UCA...UAUCC UU UGAUU...CGG-3'@LB@ GGUUU UUGGCUUUG@LB@ :\|\|\|: \|\|\|\|\|\|\|\|:@LB@ UCAAG AACCGAAAU@LB@3'-CGC...CGUUU UGC CAAUA...AAG-5'@LB@ \| \|@LB@ 88 70@LB@@LB@@LB@Energy -9.85 kcal/mol@LB@Hybridization Energy -13.0228 kcal/mol@LB@Unfolding Energy - mRNA 2.60961 kcal/mol@LB@Unfolding Energy - sRNA 0.562376 kcal/mol@LB@@LB@Position - mRNA 270 -- 285@LB@Position - sRNA 71 -- 87@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 71 -- 77@LB@
175	0.03099	0.5559	b2149	mglA	-9.34	0.136967	92 -- 105	70 -- 84	methyl-galactoside ABC transporter ATPase	_____________91______________106\n_____________\|_______________\|\n5'-CGA...GUACC__________G____AUAAA...AUU-3'\n______________UUAUGUUGGC__UAG\n______________\|:\|:\|\|\|\|\|\|__\|\|\|\n______________AGUGCAACCG__AUC\n3'-CGC...UUUCA__________AA___AAUAA...AAG-5'\n_____________\|_______________\|\n_____________85______________69\n	95 -- 101	75 -- 81	-15.5186 kcal/mol	5.61316 kcal/mol	0.563314 kcal/mol	91 106@LB@ \| \|@LB@5'-CGA...GUACC G AUAAA...AUU-3'@LB@ UUAUGUUGGC UAG@LB@ \|:\|:\|\|\|\|\|\| \|\|\|@LB@ AGUGCAACCG AUC@LB@3'-CGC...UUUCA AA AAUAA...AAG-5'@LB@ \| \|@LB@ 85 69@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -15.5186 kcal/mol@LB@Unfolding Energy - mRNA 5.61316 kcal/mol@LB@Unfolding Energy - sRNA 0.563314 kcal/mol@LB@@LB@Position - mRNA 92 -- 105@LB@Position - sRNA 70 -- 84@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 75 -- 81@LB@
138	0.02324	0.5385	b1826	mgrB	-8.64	0.179438	205 -- 238	60 -- 90	regulatory peptide for PhoPQ feedback inhibition	_____________204__________________________________239\n_____________\|____________________________________\|\n5'-UAC...AGUGA___________A___G_CGUUC__________U___GUUGG...AAU-3'\n______________AAAAGUUU_CG_UGG_U_____UGGUUGU_CG_GGU\n______________\|\|\|\|\|\|\|:_\|\|_\|\|\|_\|_____\|:\|\|\|:\|_\|\|_:\|\|\n______________UUUUCAAG_GC_ACC_A_____AUCAAUA_GC_UCA\n3'-CGC...AGGCG________U__A___G_A___________A______ACUCU...AAG-5'\n_____________\|____________________________________\|\n_____________91___________________________________59\n	226 -- 232	66 -- 72	-16.3224 kcal/mol	5.97183 kcal/mol	1.70935 kcal/mol	204 239@LB@ \| \|@LB@5'-UAC...AGUGA A G CGUUC U GUUGG...AAU-3'@LB@ AAAAGUUU CG UGG U UGGUUGU CG GGU@LB@ \|\|\|\|\|\|\|: \|\| \|\|\| \| \|:\|\|\|:\| \|\| :\|\|@LB@ UUUUCAAG GC ACC A AUCAAUA GC UCA@LB@3'-CGC...AGGCG U A G A A ACUCU...AAG-5'@LB@ \| \|@LB@ 91 59@LB@@LB@@LB@Energy -8.64 kcal/mol@LB@Hybridization Energy -16.3224 kcal/mol@LB@Unfolding Energy - mRNA 5.97183 kcal/mol@LB@Unfolding Energy - sRNA 1.70935 kcal/mol@LB@@LB@Position - mRNA 205 -- 238@LB@Position - sRNA 60 -- 90@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 66 -- 72@LB@
50	0.0104	0.5385	b0661	miaB	-10.15	0.099644	35 -- 45	74 -- 85	tRNA-i(6)A37 methylthiotransferase	_____________34___________46\n_____________\|____________\|\n5'-CGC...GCAAU____________GAUUU...AAC-3'\n______________UUC_CGUUGGUU\n______________\|\|\|_\|\|\|\|\|\|:\|\n______________AAG_GCAACCGA\n3'-CGC...UUUUC___U________AAUCA...AAG-5'\n_____________\|____________\|\n_____________86___________73\n	39 -- 45	74 -- 80	-13.4892 kcal/mol	2.82751 kcal/mol	0.512001 kcal/mol	34 46@LB@ \| \|@LB@5'-CGC...GCAAU GAUUU...AAC-3'@LB@ UUC CGUUGGUU@LB@ \|\|\| \|\|\|\|\|\|:\|@LB@ AAG GCAACCGA@LB@3'-CGC...UUUUC U AAUCA...AAG-5'@LB@ \| \|@LB@ 86 73@LB@@LB@@LB@Energy -10.15 kcal/mol@LB@Hybridization Energy -13.4892 kcal/mol@LB@Unfolding Energy - mRNA 2.82751 kcal/mol@LB@Unfolding Energy - sRNA 0.512001 kcal/mol@LB@@LB@Position - mRNA 35 -- 45@LB@Position - sRNA 74 -- 85@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 74 -- 80@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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