Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
187	0.01114	0.2089	b0801	ybiC	-12.72	0.041489	266 -- 279	27 -- 40	putative dehydrogenase	b0517	_____________265____________280\n_____________\|______________\|\n5'-GCU...CGUCA_______A______AACAA...UUG-3'\n______________GAUGGGU_GCGAGG\n______________\|\|\|\|:\|\|_:\|:\|\|\|\n______________CUACUCA_UGUUCC\n3'-UUU...UAAUA_______A______CGUGU...GUG-5'\n_____________\|______________\|\n_____________41_____________26\n	266 -- 272	34 -- 40	-18.8068 kcal/mol	3.48138 kcal/mol	2.60767 kcal/mol	265 280@LB@ \| \|@LB@5'-GCU...CGUCA A AACAA...UUG-3'@LB@ GAUGGGU GCGAGG@LB@ \|\|\|\|:\|\| :\|:\|\|\|@LB@ CUACUCA UGUUCC@LB@3'-UUU...UAAUA A CGUGU...GUG-5'@LB@ \| \|@LB@ 41 26@LB@@LB@@LB@Energy -12.72 kcal/mol@LB@Hybridization Energy -18.8068 kcal/mol@LB@Unfolding Energy - mRNA 3.48138 kcal/mol@LB@Unfolding Energy - sRNA 2.60767 kcal/mol@LB@@LB@Position - mRNA 266 -- 279@LB@Position - sRNA 27 -- 40@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 34 -- 40@LB@
108	0.005783	0.1855	b3951	pflD	-15.90	0.009733	233 -- 258	63 -- 86	putative glycine radical domain-containing pyruvate formate-lyase	b0823	_____________232________________________259\n_____________\|__________________________\|\n5'-GAU...ACUGC_____UU_________C_U_______CGCUG...AAA-3'\n______________ACUGU__GCCAAUACC_G_GAAAUCU\n______________\|\|\|\|:__\|\|\|\|\|:\|\|\|_\|_\|\|\|\|\|\|\|\n______________UGACG__CGGUUGUGG_C_CUUUAGA\n3'-UUU...GCUUA________________U_C_______ACCGA...GUG-5'\n_____________\|__________________________\|\n_____________87_________________________62\n	252 -- 258	63 -- 69	-27.9307 kcal/mol	4.64309 kcal/mol	7.38602 kcal/mol	232 259@LB@ \| \|@LB@5'-GAU...ACUGC UU C U CGCUG...AAA-3'@LB@ ACUGU GCCAAUACC G GAAAUCU@LB@ \|\|\|\|: \|\|\|\|\|:\|\|\| \| \|\|\|\|\|\|\|@LB@ UGACG CGGUUGUGG C CUUUAGA@LB@3'-UUU...GCUUA U C ACCGA...GUG-5'@LB@ \| \|@LB@ 87 62@LB@@LB@@LB@Energy -15.90 kcal/mol@LB@Hybridization Energy -27.9307 kcal/mol@LB@Unfolding Energy - mRNA 4.64309 kcal/mol@LB@Unfolding Energy - sRNA 7.38602 kcal/mol@LB@@LB@Position - mRNA 233 -- 258@LB@Position - sRNA 63 -- 86@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 63 -- 69@LB@
161	0.009429	0.2062	b1372	stfR	-7.17	0.431291	283 -- 297	69 -- 83	Rac prophage; putative tail fiber protein	b1547	_____________282_____________298\n_____________\|_______________\|\n5'-CAC...AAAAC__AA________C__UGG-3'\n______________GU__CAGCACCA_GG\n______________\|:__\|\|:\|\|\|\|\|_\|\|\n______________CG__GUUGUGGU_CC\n3'-UUU...UAUGA__CG________C__UUUAG...GUG-5'\n_____________\|_______________\|\n_____________84______________68\n	288 -- 294	72 -- 78	-17.3245 kcal/mol	2.81769 kcal/mol	7.33837 kcal/mol	282 298@LB@ \| \|@LB@5'-CAC...AAAAC AA C UGG-3'@LB@ GU CAGCACCA GG@LB@ \|: \|\|:\|\|\|\|\| \|\|@LB@ CG GUUGUGGU CC@LB@3'-UUU...UAUGA CG C UUUAG...GUG-5'@LB@ \| \|@LB@ 84 68@LB@@LB@@LB@Energy -7.17 kcal/mol@LB@Hybridization Energy -17.3245 kcal/mol@LB@Unfolding Energy - mRNA 2.81769 kcal/mol@LB@Unfolding Energy - sRNA 7.33837 kcal/mol@LB@@LB@Position - mRNA 283 -- 297@LB@Position - sRNA 69 -- 83@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 72 -- 78@LB@
117	0.006292	0.1893	b1769	ydjE	-12.05	0.056060	116 -- 139	36 -- 59	putative MFS sugar transporter membrane protein	b1775	_____________115______________________140\n_____________\|________________________\|\n5'-AUU...UGUUC_______U____A__AA_______UAAAG...UAA-3'\n______________CUGCGCC_UGAA_UA__AUGAUGA\n______________\|\|\|\|\|\|\|_\|:\|\|_\|\|__\|\|\|\|\|\|\|\n______________GACGCGG_AUUU_AU__UACUACU\n3'-UUU...GAACC_______C____A__AA_______CAAUG...GUG-5'\n_____________\|________________________\|\n_____________60_______________________35\n	133 -- 139	36 -- 42	-22.8542 kcal/mol	3.06151 kcal/mol	7.74108 kcal/mol	115 140@LB@ \| \|@LB@5'-AUU...UGUUC U A AA UAAAG...UAA-3'@LB@ CUGCGCC UGAA UA AUGAUGA@LB@ \|\|\|\|\|\|\| \|:\|\| \|\| \|\|\|\|\|\|\|@LB@ GACGCGG AUUU AU UACUACU@LB@3'-UUU...GAACC C A AA CAAUG...GUG-5'@LB@ \| \|@LB@ 60 35@LB@@LB@@LB@Energy -12.05 kcal/mol@LB@Hybridization Energy -22.8542 kcal/mol@LB@Unfolding Energy - mRNA 3.06151 kcal/mol@LB@Unfolding Energy - sRNA 7.74108 kcal/mol@LB@@LB@Position - mRNA 116 -- 139@LB@Position - sRNA 36 -- 59@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 36 -- 42@LB@
97	0.005188	0.1855	b3060	ttdR	-16.80	0.006462	125 -- 147	67 -- 90	transcriptional activator of ttdABT	b1799	_____________124______________________148\n_____________\|________________________\|\n5'-UCC...AGAAU________________G_______UGGCA...CGC-3'\n______________GAAUAUUGCGCCAG_A_CAGGGAA\n______________\|\|\|\|\|:\|\|\|\|\|\|\|:_\|_\|\|\|\|\|\|\|\n______________CUUAUGACGCGGUU_U_GUCCCUU\n3'-UUU...ACGCG______________G_G_______UAGAA...GUG-5'\n_____________\|________________________\|\n_____________91_______________________66\n	141 -- 147	67 -- 73	-34.0784 kcal/mol	7.10756 kcal/mol	10.1694 kcal/mol	124 148@LB@ \| \|@LB@5'-UCC...AGAAU G UGGCA...CGC-3'@LB@ GAAUAUUGCGCCAG A CAGGGAA@LB@ \|\|\|\|\|:\|\|\|\|\|\|\|: \| \|\|\|\|\|\|\|@LB@ CUUAUGACGCGGUU U GUCCCUU@LB@3'-UUU...ACGCG G G UAGAA...GUG-5'@LB@ \| \|@LB@ 91 66@LB@@LB@@LB@Energy -16.80 kcal/mol@LB@Hybridization Energy -34.0784 kcal/mol@LB@Unfolding Energy - mRNA 7.10756 kcal/mol@LB@Unfolding Energy - sRNA 10.1694 kcal/mol@LB@@LB@Position - mRNA 125 -- 147@LB@Position - sRNA 67 -- 90@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 67 -- 73@LB@
125	0.006795	0.1914	b3003	yghA	-11.52	0.071261	264 -- 274	70 -- 80	putative oxidoreductase	b2902	_____________263_________275\n_____________\|___________\|\n5'-AAC...AACAA___________CAUCC...UAC-3'\n______________CCGACGCCAGG\n______________\|\|:\|\|:\|\|\|\|\|\n______________GGUUGUGGUCC\n3'-UUU...GACGC___________CUUUA...GUG-5'\n_____________\|___________\|\n_____________81__________69\n	268 -- 274	70 -- 76	-20.3781 kcal/mol	2.1599 kcal/mol	6.70146 kcal/mol	263 275@LB@ \| \|@LB@5'-AAC...AACAA CAUCC...UAC-3'@LB@ CCGACGCCAGG@LB@ \|\|:\|\|:\|\|\|\|\|@LB@ GGUUGUGGUCC@LB@3'-UUU...GACGC CUUUA...GUG-5'@LB@ \| \|@LB@ 81 69@LB@@LB@@LB@Energy -11.52 kcal/mol@LB@Hybridization Energy -20.3781 kcal/mol@LB@Unfolding Energy - mRNA 2.1599 kcal/mol@LB@Unfolding Energy - sRNA 6.70146 kcal/mol@LB@@LB@Position - mRNA 264 -- 274@LB@Position - sRNA 70 -- 80@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 70 -- 76@LB@
160	0.009416	0.2062	b2095	gatZ	-8.10	0.305092	155 -- 170	18 -- 33	D-tagatose 1 6-bisphosphate aldolase 2 subunit	b3132	_____________154______________171\n_____________\|________________\|\n5'-AAU...GUGGC__________G_____AACGC...UUG-3'\n______________UGCGAGGGCA_GGCAU\n______________\|:\|:\|\|\|\|\|\|_:\|\|\|:\n______________AUGUUCCCGU_UCGUG\n3'-UUU...ACUCA__________G_____ACAAA...GUG-5'\n_____________\|________________\|\n_____________34_______________17\n	158 -- 164	24 -- 30	-26.3287 kcal/mol	9.40457 kcal/mol	8.82204 kcal/mol	154 171@LB@ \| \|@LB@5'-AAU...GUGGC G AACGC...UUG-3'@LB@ UGCGAGGGCA GGCAU@LB@ \|:\|:\|\|\|\|\|\| :\|\|\|:@LB@ AUGUUCCCGU UCGUG@LB@3'-UUU...ACUCA G ACAAA...GUG-5'@LB@ \| \|@LB@ 34 17@LB@@LB@@LB@Energy -8.10 kcal/mol@LB@Hybridization Energy -26.3287 kcal/mol@LB@Unfolding Energy - mRNA 9.40457 kcal/mol@LB@Unfolding Energy - sRNA 8.82204 kcal/mol@LB@@LB@Position - mRNA 155 -- 170@LB@Position - sRNA 18 -- 33@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 24 -- 30@LB@
59	0.002989	0.1727	b2713	hydN	-12.16	0.053402	276 -- 298	54 -- 76	formate dehydrogenase-H [4Fe-4S] ferredoxin subunit	b3573	_____________275______________________299\n_____________\|________________________\|\n5'-CUU...UUUCU_______A_____A___A______AU-3'\n______________CAUCAGG_AAAUC__GG_CUGUGC\n______________\|\|:\|\|\|\|_\|\|\|\|\|__\|\|_\|\|\|:\|\|\n______________GUGGUCC_UUUAG__CC_GACGCG\n3'-UUU...CGGUU_______C_____AA_________GCAUU...GUG-5'\n_____________\|________________________\|\n_____________77_______________________53\n	276 -- 282	70 -- 76	-25.5609 kcal/mol	4.47784 kcal/mol	8.92391 kcal/mol	275 299@LB@ \| \|@LB@5'-CUU...UUUCU A A A AU-3'@LB@ CAUCAGG AAAUC GG CUGUGC@LB@ \|\|:\|\|\|\| \|\|\|\|\| \|\| \|\|\|:\|\|@LB@ GUGGUCC UUUAG CC GACGCG@LB@3'-UUU...CGGUU C AA GCAUU...GUG-5'@LB@ \| \|@LB@ 77 53@LB@@LB@@LB@Energy -12.16 kcal/mol@LB@Hybridization Energy -25.5609 kcal/mol@LB@Unfolding Energy - mRNA 4.47784 kcal/mol@LB@Unfolding Energy - sRNA 8.92391 kcal/mol@LB@@LB@Position - mRNA 276 -- 298@LB@Position - sRNA 54 -- 76@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 70 -- 76@LB@
120	0.006631	0.1913	b0825	fsaA	-14.24	0.020734	15 -- 76	31 -- 86	fructose-6-phosphate aldolase 1	b3946	_____________14_____________________________________________________________77\n_____________\|______________________________________________________________\|\n5'-CUU...AUACG__C____G__________CC___A___G_CGAGUA______AAU____AAAAUCAU______CUCUC...CCG-3'\n______________AC_GUGC_GAUACCGGGG__AUC_UGG_U______GCGCUG___AUUG________AGUUGC\n______________\|\|_\|:\|\|_:\|:\|\|\|:\|\|\|__\|\|\|_\|\|\|_\|______\|\|\|\|:\|___\|\|\|:________\|\|\|\|:\|\n______________UG_CGCG_UUGUGGUCCC__UAG_ACC_A______CGCGGC___UAAU________UCAAUG\n3'-UUU...GCUUA__A____G__________UU___A___G_____________AUU____AAUACUAC______UUCCC...GUG-5'\n_____________\|______________________________________________________________\|\n_____________87_____________________________________________________________30\n	26 -- 32	69 -- 75	-46.4097 kcal/mol	15.1018 kcal/mol	17.0646 kcal/mol	14 77@LB@ \| \|@LB@5'-CUU...AUACG C G CC A G CGAGUA AAU AAAAUCAU CUCUC...CCG-3'@LB@ AC GUGC GAUACCGGGG AUC UGG U GCGCUG AUUG AGUUGC@LB@ \|\| \|:\|\| :\|:\|\|\|:\|\|\| \|\|\| \|\|\| \| \|\|\|\|:\| \|\|\|: \|\|\|\|:\|@LB@ UG CGCG UUGUGGUCCC UAG ACC A CGCGGC UAAU UCAAUG@LB@3'-UUU...GCUUA A G UU A G AUU AAUACUAC UUCCC...GUG-5'@LB@ \| \|@LB@ 87 30@LB@@LB@@LB@Energy -14.24 kcal/mol@LB@Hybridization Energy -46.4097 kcal/mol@LB@Unfolding Energy - mRNA 15.1018 kcal/mol@LB@Unfolding Energy - sRNA 17.0646 kcal/mol@LB@@LB@Position - mRNA 15 -- 76@LB@Position - sRNA 31 -- 86@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 69 -- 75@LB@
169	0.01004	0.2071	b2384	ypdE	-12.38	0.048278	93 -- 137	31 -- 75	aminopeptidase	b4305 b3898	_____________92______________________________________________138\n_____________\|_______________________________________________\|\n5'-AUU...UAUUU_______C__GGG____G_____AUCG___A_______C________CCCGC...UGC-3'\n______________GCCAGGG_AA____GGC_UGCGC____AAG_UGUUGUG_UG_GUUAC\n______________:\|\|\|\|\|\|_\|\|____\|\|\|_\|\|\|\|\|____\|\|:_\|:\|\|:\|\|_\|\|_\|\|\|\|\|\n______________UGGUCCC_UU____CCG_ACGCG____UUU_AUAAUAC_AC_CAAUG\n3'-UUU...GGUUG_______U__AGAA_________GCA____A_______U__U_____UUCCC...GUG-5'\n_____________\|_______________________________________________\|\n_____________76______________________________________________30\n	93 -- 99	69 -- 75	-40.1479 kcal/mol	18.4667 kcal/mol	9.29858 kcal/mol	92 138@LB@ \| \|@LB@5'-AUU...UAUUU C GGG G AUCG A C CCCGC...UGC-3'@LB@ GCCAGGG AA GGC UGCGC AAG UGUUGUG UG GUUAC@LB@ :\|\|\|\|\|\| \|\| \|\|\| \|\|\|\|\| \|\|: \|:\|\|:\|\| \|\| \|\|\|\|\|@LB@ UGGUCCC UU CCG ACGCG UUU AUAAUAC AC CAAUG@LB@3'-UUU...GGUUG U AGAA GCA A U U UUCCC...GUG-5'@LB@ \| \|@LB@ 76 30@LB@@LB@@LB@Energy -12.38 kcal/mol@LB@Hybridization Energy -40.1479 kcal/mol@LB@Unfolding Energy - mRNA 18.4667 kcal/mol@LB@Unfolding Energy - sRNA 9.29858 kcal/mol@LB@@LB@Position - mRNA 93 -- 137@LB@Position - sRNA 31 -- 75@LB@Position Seed - mRNA 93 -- 99@LB@Position Seed - sRNA 69 -- 75@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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service.

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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