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
92	0.01569	0.5385	b1246	oppD	-11.32	0.062179	266 -- 290	69 -- 90	oligopeptide ABC transporter ATPase	_____________265_______________________291\n_____________\|_________________________\|\n5'-AGC...AACGU_____A_______GUCAC_______ACCCC...ACG-3'\n______________GAAAG_UUUGCGU_____CUUUAGU\n______________:\|\|\|\|_\|\|::\|\|\|_____\|\|\|\|\|\|\|\n______________UUUUC_AAGUGCA_____GAAAUCA\n3'-CGC...AGGCG_____________ACC_________AUAAG...AAG-5'\n_____________\|_________________________\|\n_____________91________________________68\n	284 -- 290	69 -- 75	-14.6652 kcal/mol	2.76867 kcal/mol	0.572281 kcal/mol	265 291@LB@ \| \|@LB@5'-AGC...AACGU A GUCAC ACCCC...ACG-3'@LB@ GAAAG UUUGCGU CUUUAGU@LB@ :\|\|\|\| \|\|::\|\|\| \|\|\|\|\|\|\|@LB@ UUUUC AAGUGCA GAAAUCA@LB@3'-CGC...AGGCG ACC AUAAG...AAG-5'@LB@ \| \|@LB@ 91 68@LB@@LB@@LB@Energy -11.32 kcal/mol@LB@Hybridization Energy -14.6652 kcal/mol@LB@Unfolding Energy - mRNA 2.76867 kcal/mol@LB@Unfolding Energy - sRNA 0.572281 kcal/mol@LB@@LB@Position - mRNA 266 -- 290@LB@Position - sRNA 69 -- 90@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 69 -- 75@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@
33	0.006009	0.5385	b1264	trpE	-12.63	0.036478	39 -- 48	79 -- 88	component I of anthranilate synthase	_____________38_________49\n_____________\|__________\|\n5'-UGU...UACGC__________AAAAA...CGG-3'\n______________AAGUUCACGU\n______________\|\|\|\|\|\|\|\|\|\|\n______________UUCAAGUGCA\n3'-CGC...GCGUU__________ACCGA...AAG-5'\n_____________\|__________\|\n_____________89_________78\n	42 -- 48	79 -- 85	-13.8612 kcal/mol	0.721964 kcal/mol	0.505265 kcal/mol	38 49@LB@ \| \|@LB@5'-UGU...UACGC AAAAA...CGG-3'@LB@ AAGUUCACGU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UUCAAGUGCA@LB@3'-CGC...GCGUU ACCGA...AAG-5'@LB@ \| \|@LB@ 89 78@LB@@LB@@LB@Energy -12.63 kcal/mol@LB@Hybridization Energy -13.8612 kcal/mol@LB@Unfolding Energy - mRNA 0.721964 kcal/mol@LB@Unfolding Energy - sRNA 0.505265 kcal/mol@LB@@LB@Position - mRNA 39 -- 48@LB@Position - sRNA 79 -- 88@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 79 -- 85@LB@
59	0.01163	0.5385	b1279	yciS	-7.12	0.313424	44 -- 60	74 -- 90	DUF1049 family inner membrane protein function unknown	_____________43________________61\n_____________\|_________________\|\n5'-ACC...AACAA_______A___C_____GAUUU...UGU-3'\n______________GAAAGUU_ACG_UGGUU\n______________:\|\|\|\|\|\|_\|\|\|_\|\|\|:\|\n______________UUUUCAA_UGC_ACCGA\n3'-CGC...AGGCG_______G___A_____AAUCA...AAG-5'\n_____________\|_________________\|\n_____________91________________73\n	44 -- 50	84 -- 90	-13.3715 kcal/mol	5.7376 kcal/mol	0.517587 kcal/mol	43 61@LB@ \| \|@LB@5'-ACC...AACAA A C GAUUU...UGU-3'@LB@ GAAAGUU ACG UGGUU@LB@ :\|\|\|\|\|\| \|\|\| \|\|\|:\|@LB@ UUUUCAA UGC ACCGA@LB@3'-CGC...AGGCG G A AAUCA...AAG-5'@LB@ \| \|@LB@ 91 73@LB@@LB@@LB@Energy -7.12 kcal/mol@LB@Hybridization Energy -13.3715 kcal/mol@LB@Unfolding Energy - mRNA 5.7376 kcal/mol@LB@Unfolding Energy - sRNA 0.517587 kcal/mol@LB@@LB@Position - mRNA 44 -- 60@LB@Position - sRNA 74 -- 90@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 84 -- 90@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@
46	0.009803	0.5385	b1418	cybB	-9.32	0.138160	281 -- 295	73 -- 89	cytochrome b561	_____________280_______________296\n_____________\|_________________\|\n5'-AAC...GCAAU_________________CUUCC-3'\n______________GGAGUUU_CG_UGGUUU\n______________::\|\|\|\|:_\|\|_\|\|\|:\|\|\n______________UUUCAAG_GC_ACCGAA\n3'-CGC...GGCGU_______U__A______AUCAA...AAG-5'\n_____________\|_________________\|\n_____________90________________72\n	281 -- 287	83 -- 89	-12.2046 kcal/mol	2.36714 kcal/mol	0.517627 kcal/mol	280 296@LB@ \| \|@LB@5'-AAC...GCAAU CUUCC-3'@LB@ GGAGUUU CG UGGUUU@LB@ ::\|\|\|\|: \|\| \|\|\|:\|\|@LB@ UUUCAAG GC ACCGAA@LB@3'-CGC...GGCGU U A AUCAA...AAG-5'@LB@ \| \|@LB@ 90 72@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -12.2046 kcal/mol@LB@Unfolding Energy - mRNA 2.36714 kcal/mol@LB@Unfolding Energy - sRNA 0.517627 kcal/mol@LB@@LB@Position - mRNA 281 -- 295@LB@Position - sRNA 73 -- 89@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 83 -- 89@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@
160	0.02795	0.5559	b1475	fdnH	-7.98	0.230122	69 -- 80	24 -- 35	formate dehydrogenase-N Fe-S (beta) subunit nitrate-inducible	_____________68___________81\n_____________\|____________\|\n5'-CGC...ACUGG____________GUCGC...UUA-3'\n______________GGCUUUGAGGGU\n______________\|:\|\|\|::\|\|\|\|\|\n______________CUGAAGUUCCCA\n3'-CGC...CGUCA____________AUUUU...AAG-5'\n_____________\|____________\|\n_____________36___________23\n	74 -- 80	24 -- 30	-17.8377 kcal/mol	6.53052 kcal/mol	3.32971 kcal/mol	68 81@LB@ \| \|@LB@5'-CGC...ACUGG GUCGC...UUA-3'@LB@ GGCUUUGAGGGU@LB@ \|:\|\|\|::\|\|\|\|\|@LB@ CUGAAGUUCCCA@LB@3'-CGC...CGUCA AUUUU...AAG-5'@LB@ \| \|@LB@ 36 23@LB@@LB@@LB@Energy -7.98 kcal/mol@LB@Hybridization Energy -17.8377 kcal/mol@LB@Unfolding Energy - mRNA 6.53052 kcal/mol@LB@Unfolding Energy - sRNA 3.32971 kcal/mol@LB@@LB@Position - mRNA 69 -- 80@LB@Position - sRNA 24 -- 35@LB@Position Seed - mRNA 74 -- 80@LB@Position Seed - sRNA 24 -- 30@LB@
107	0.01867	0.5385	b1478	adhP	-13.80	0.022588	200 -- 222	62 -- 83	ethanol-active dehydrogenase/acetaldehyde-active reductase	_____________199_____________________223\n_____________\|_______________________\|\n5'-GCA...GGAAC____AA____GC_______A___AGGAU...GUU-3'\n______________UAUG__GGCU__AGUUGUU_CGA\n______________:\|:\|__\|\|\|\|__\|\|\|\|:\|\|_\|\|\|\n______________GUGC__CCGA__UCAAUAA_GCU\n3'-CGC...UUCAA____AA____AA___________CAACU...AAG-5'\n_____________\|_______________________\|\n_____________84______________________61\n	212 -- 218	65 -- 71	-18.0685 kcal/mol	2.64248 kcal/mol	1.62352 kcal/mol	199 223@LB@ \| \|@LB@5'-GCA...GGAAC AA GC A AGGAU...GUU-3'@LB@ UAUG GGCU AGUUGUU CGA@LB@ :\|:\| \|\|\|\| \|\|\|\|:\|\| \|\|\|@LB@ GUGC CCGA UCAAUAA GCU@LB@3'-CGC...UUCAA AA AA CAACU...AAG-5'@LB@ \| \|@LB@ 84 61@LB@@LB@@LB@Energy -13.80 kcal/mol@LB@Hybridization Energy -18.0685 kcal/mol@LB@Unfolding Energy - mRNA 2.64248 kcal/mol@LB@Unfolding Energy - sRNA 1.62352 kcal/mol@LB@@LB@Position - mRNA 200 -- 222@LB@Position - sRNA 62 -- 83@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 65 -- 71@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@

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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