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
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@
51	0.002608	0.1727	b2299	yfcD	-9.22	0.194301	162 -- 171	49 -- 58	putative NUDIX hydrolase		_____________161________172\n_____________\|__________\|\n5'-AGA...CAAAA__________GAGCG...AGU-3'\n______________UGCGCCGUAA\n______________\|\|\|\|\|\|\|\|\|\|\n______________ACGCGGCAUU\n3'-UUU...AACCG__________UAAUA...GUG-5'\n_____________\|__________\|\n_____________59_________48\n	165 -- 171	49 -- 55	-16.7903 kcal/mol	2.6527 kcal/mol	4.92198 kcal/mol	161 172@LB@ \| \|@LB@5'-AGA...CAAAA GAGCG...AGU-3'@LB@ UGCGCCGUAA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ ACGCGGCAUU@LB@3'-UUU...AACCG UAAUA...GUG-5'@LB@ \| \|@LB@ 59 48@LB@@LB@@LB@Energy -9.22 kcal/mol@LB@Hybridization Energy -16.7903 kcal/mol@LB@Unfolding Energy - mRNA 2.6527 kcal/mol@LB@Unfolding Energy - sRNA 4.92198 kcal/mol@LB@@LB@Position - mRNA 162 -- 171@LB@Position - sRNA 49 -- 58@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 49 -- 55@LB@
113	0.005997	0.1855	b1765	ydjA	-10.36	0.119141	118 -- 144	49 -- 76	putative oxidoreductase		_____________117___________________________145\n_____________\|_____________________________\|\n5'-AUU...CUUGU__G__________GC__A___________CAAAA...GUA-3'\n______________CA_CAGG__AAUU__GG_CUGUGCUGUAA\n______________\|\|_\|\|\|\|__\|\|\|:__\|\|_\|\|\|:\|\|:\|\|\|\|\n______________GU_GUCC__UUAG__CC_GACGCGGCAUU\n3'-UUU...CGGUU__G____CU____AA______________UAAUA...GUG-5'\n_____________\|_____________________________\|\n_____________77____________________________48\n	138 -- 144	49 -- 55	-28.7704 kcal/mol	9.07167 kcal/mol	9.34253 kcal/mol	117 145@LB@ \| \|@LB@5'-AUU...CUUGU G GC A CAAAA...GUA-3'@LB@ CA CAGG AAUU GG CUGUGCUGUAA@LB@ \|\| \|\|\|\| \|\|\|: \|\| \|\|\|:\|\|:\|\|\|\|@LB@ GU GUCC UUAG CC GACGCGGCAUU@LB@3'-UUU...CGGUU G CU AA UAAUA...GUG-5'@LB@ \| \|@LB@ 77 48@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -28.7704 kcal/mol@LB@Unfolding Energy - mRNA 9.07167 kcal/mol@LB@Unfolding Energy - sRNA 9.34253 kcal/mol@LB@@LB@Position - mRNA 118 -- 144@LB@Position - sRNA 49 -- 76@LB@Position Seed - mRNA 138 -- 144@LB@Position Seed - sRNA 49 -- 55@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@
23	0.001421	0.1727	b1234	rssA	-12.55	0.044848	179 -- 192	61 -- 74	putative patatin-like family phospholipase		_____________178____________193\n_____________\|______________\|\n5'-GAU...GCAUU______________CGGGA...AAA-3'\n______________CCAGGGGAAUCUUG\n______________\|\|\|\|\|\|:\|\|\|\|\|\|\|\n______________GGUCCCUUUAGAAC\n3'-UUU...GUUGU______________CGACG...GUG-5'\n_____________\|______________\|\n_____________75_____________60\n	186 -- 192	61 -- 67	-22.3239 kcal/mol	6.14875 kcal/mol	3.62869 kcal/mol	178 193@LB@ \| \|@LB@5'-GAU...GCAUU CGGGA...AAA-3'@LB@ CCAGGGGAAUCUUG@LB@ \|\|\|\|\|\|:\|\|\|\|\|\|\|@LB@ GGUCCCUUUAGAAC@LB@3'-UUU...GUUGU CGACG...GUG-5'@LB@ \| \|@LB@ 75 60@LB@@LB@@LB@Energy -12.55 kcal/mol@LB@Hybridization Energy -22.3239 kcal/mol@LB@Unfolding Energy - mRNA 6.14875 kcal/mol@LB@Unfolding Energy - sRNA 3.62869 kcal/mol@LB@@LB@Position - mRNA 179 -- 192@LB@Position - sRNA 61 -- 74@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 61 -- 67@LB@
188	0.01115	0.2089	b4377	yjjU	-9.16	0.198952	213 -- 243	51 -- 77	putative patatin-like family phospholipase		_____________212______________________________244\n_____________\|________________________________\|\n5'-AGG...AGCGA_____UGUAACG_______AAUAU________UGUCG...GAC-3'\n______________AUACC________CUUGGU_____UGCGCCGU\n______________\|:\|\|\|________\|\|\|\|\|:_____\|\|\|\|\|\|\|\|\n______________UGUGG________GAACCG_____ACGCGGCA\n3'-UUU...GCGGU_____UCCCUUUA___________________UUUAA...GUG-5'\n_____________\|________________________________\|\n_____________78_______________________________50\n	237 -- 243	51 -- 57	-26.4777 kcal/mol	7.99131 kcal/mol	9.32737 kcal/mol	212 244@LB@ \| \|@LB@5'-AGG...AGCGA UGUAACG AAUAU UGUCG...GAC-3'@LB@ AUACC CUUGGU UGCGCCGU@LB@ \|:\|\|\| \|\|\|\|\|: \|\|\|\|\|\|\|\|@LB@ UGUGG GAACCG ACGCGGCA@LB@3'-UUU...GCGGU UCCCUUUA UUUAA...GUG-5'@LB@ \| \|@LB@ 78 50@LB@@LB@@LB@Energy -9.16 kcal/mol@LB@Hybridization Energy -26.4777 kcal/mol@LB@Unfolding Energy - mRNA 7.99131 kcal/mol@LB@Unfolding Energy - sRNA 9.32737 kcal/mol@LB@@LB@Position - mRNA 213 -- 243@LB@Position - sRNA 51 -- 77@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 51 -- 57@LB@
34	0.001871	0.1727	b4485	ytfR	-15.36	0.012458	204 -- 227	64 -- 86	putative sugar ABC transporter ATPase		_____________203_______________________228\n_____________\|_________________________\|\n5'-CCU...CCAUG__GAC__A_________________CUCCG...GCC-3'\n______________AC___CG_CCAACACCA_GGAGAUC\n______________\|\|___\|\|_\|\|\|\|\|\|\|\|\|_\|\|\|:\|\|\|\n______________UG___GC_GGUUGUGGU_CCUUUAG\n3'-UUU...GCUUA__AC_____________C_______AACCG...GUG-5'\n_____________\|_________________________\|\n_____________87________________________63\n	221 -- 227	64 -- 70	-26.9267 kcal/mol	4.18191 kcal/mol	7.38435 kcal/mol	203 228@LB@ \| \|@LB@5'-CCU...CCAUG GAC A CUCCG...GCC-3'@LB@ AC CG CCAACACCA GGAGAUC@LB@ \|\| \|\| \|\|\|\|\|\|\|\|\| \|\|\|:\|\|\|@LB@ UG GC GGUUGUGGU CCUUUAG@LB@3'-UUU...GCUUA AC C AACCG...GUG-5'@LB@ \| \|@LB@ 87 63@LB@@LB@@LB@Energy -15.36 kcal/mol@LB@Hybridization Energy -26.9267 kcal/mol@LB@Unfolding Energy - mRNA 4.18191 kcal/mol@LB@Unfolding Energy - sRNA 7.38435 kcal/mol@LB@@LB@Position - mRNA 204 -- 227@LB@Position - sRNA 64 -- 86@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 64 -- 70@LB@
58	0.002925	0.1727	b0427	yajR	-11.14	0.084219	218 -- 238	54 -- 78	putative transporter		_____________217________________________239\n_____________\|__________________________\|\n5'-CGU...AAAAU_________U________________GACCU...CGG-3'\n______________GACGCCAGG_GAGA____GGC_GCGC\n______________:\|\|:\|\|\|\|\|_\|\|:\|____\|\|\|_\|\|\|\|\n______________UUGUGGUCC_CUUU____CCG_CGCG\n3'-UUU...CGCGG______________AGAA___A____GCAUU...GUG-5'\n_____________\|__________________________\|\n_____________79_________________________53\n	220 -- 226	70 -- 76	-28.7218 kcal/mol	8.65047 kcal/mol	8.92888 kcal/mol	217 239@LB@ \| \|@LB@5'-CGU...AAAAU U GACCU...CGG-3'@LB@ GACGCCAGG GAGA GGC GCGC@LB@ :\|\|:\|\|\|\|\| \|\|:\| \|\|\| \|\|\|\|@LB@ UUGUGGUCC CUUU CCG CGCG@LB@3'-UUU...CGCGG AGAA A GCAUU...GUG-5'@LB@ \| \|@LB@ 79 53@LB@@LB@@LB@Energy -11.14 kcal/mol@LB@Hybridization Energy -28.7218 kcal/mol@LB@Unfolding Energy - mRNA 8.65047 kcal/mol@LB@Unfolding Energy - sRNA 8.92888 kcal/mol@LB@@LB@Position - mRNA 218 -- 238@LB@Position - sRNA 54 -- 78@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 70 -- 76@LB@
196	0.01202	0.2159	b1729	ydjN	-13.87	0.024594	143 -- 155	72 -- 84	putative transporter		_____________142___________156\n_____________\|_____________\|\n5'-CAU...AAUCU_____________UGACU...UGC-3'\n______________UGCGCCAACACUA\n______________\|\|\|\|\|\|\|\|\|\|\|:\|\n______________ACGCGGUUGUGGU\n3'-UUU...UUAUG_____________CCCUU...GUG-5'\n_____________\|_____________\|\n_____________85____________71\n	149 -- 155	72 -- 78	-23.7045 kcal/mol	2.6326 kcal/mol	7.20328 kcal/mol	142 156@LB@ \| \|@LB@5'-CAU...AAUCU UGACU...UGC-3'@LB@ UGCGCCAACACUA@LB@ \|\|\|\|\|\|\|\|\|\|\|:\|@LB@ ACGCGGUUGUGGU@LB@3'-UUU...UUAUG CCCUU...GUG-5'@LB@ \| \|@LB@ 85 71@LB@@LB@@LB@Energy -13.87 kcal/mol@LB@Hybridization Energy -23.7045 kcal/mol@LB@Unfolding Energy - mRNA 2.6326 kcal/mol@LB@Unfolding Energy - sRNA 7.20328 kcal/mol@LB@@LB@Position - mRNA 143 -- 155@LB@Position - sRNA 72 -- 84@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 72 -- 78@LB@
130	0.007275	0.1966	b1638	pdxH	-11.04	0.087983	237 -- 249	47 -- 59	pyridoxine 5'-phosphate oxidase		_____________236___________250\n_____________\|_____________\|\n5'-UCU...CGCAU_____________ACACC...CCC-3'\n______________CUGCGCCGUGAAU\n______________\|\|\|\|\|\|\|\|\|:\|\|\|\n______________GACGCGGCAUUUA\n3'-UUU...GAACC_____________AUAAU...GUG-5'\n_____________\|_____________\|\n_____________60____________46\n	243 -- 249	47 -- 53	-22.1181 kcal/mol	4.88729 kcal/mol	6.18672 kcal/mol	236 250@LB@ \| \|@LB@5'-UCU...CGCAU ACACC...CCC-3'@LB@ CUGCGCCGUGAAU@LB@ \|\|\|\|\|\|\|\|\|:\|\|\|@LB@ GACGCGGCAUUUA@LB@3'-UUU...GAACC AUAAU...GUG-5'@LB@ \| \|@LB@ 60 46@LB@@LB@@LB@Energy -11.04 kcal/mol@LB@Hybridization Energy -22.1181 kcal/mol@LB@Unfolding Energy - mRNA 4.88729 kcal/mol@LB@Unfolding Energy - sRNA 6.18672 kcal/mol@LB@@LB@Position - mRNA 237 -- 249@LB@Position - sRNA 47 -- 59@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 47 -- 53@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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