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
89	0.004811	0.1855	b4336	yjiN	-13.14	0.034257	120 -- 134	70 -- 84	zinc-type alcohol dehydrogenase-like protein		_____________119_____________135\n_____________\|_______________\|\n5'-GGU...UCGCG_______________CAGCC...CCA-3'\n______________UGCGCCAGCAUCAGG\n______________\|\|\|\|\|\|\|:\|\|:\|\|\|\|\n______________ACGCGGUUGUGGUCC\n3'-UUU...UUAUG_______________CUUUA...GUG-5'\n_____________\|_______________\|\n_____________85______________69\n	128 -- 134	70 -- 76	-28.7852 kcal/mol	8.39668 kcal/mol	7.24859 kcal/mol	119 135@LB@ \| \|@LB@5'-GGU...UCGCG CAGCC...CCA-3'@LB@ UGCGCCAGCAUCAGG@LB@ \|\|\|\|\|\|\|:\|\|:\|\|\|\|@LB@ ACGCGGUUGUGGUCC@LB@3'-UUU...UUAUG CUUUA...GUG-5'@LB@ \| \|@LB@ 85 69@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -28.7852 kcal/mol@LB@Unfolding Energy - mRNA 8.39668 kcal/mol@LB@Unfolding Energy - sRNA 7.24859 kcal/mol@LB@@LB@Position - mRNA 120 -- 134@LB@Position - sRNA 70 -- 84@LB@Position Seed - mRNA 128 -- 134@LB@Position Seed - sRNA 70 -- 76@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@
47	0.002359	0.1727	b1520	yneE	-16.33	0.007995	225 -- 237	50 -- 62	bestrophin family putative inner membrane protein		_____________224___________238\n_____________\|_____________\|\n5'-CGU...AACAC_____________UUUUU...UCU-3'\n______________UGGCUGCGCCGUA\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________ACCGACGCGGCAU\n3'-UUU...UUAGA_____________UUAAU...GUG-5'\n_____________\|_____________\|\n_____________63____________49\n	231 -- 237	50 -- 56	-27.5123 kcal/mol	5.30923 kcal/mol	5.87004 kcal/mol	224 238@LB@ \| \|@LB@5'-CGU...AACAC UUUUU...UCU-3'@LB@ UGGCUGCGCCGUA@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ ACCGACGCGGCAU@LB@3'-UUU...UUAGA UUAAU...GUG-5'@LB@ \| \|@LB@ 63 49@LB@@LB@@LB@Energy -16.33 kcal/mol@LB@Hybridization Energy -27.5123 kcal/mol@LB@Unfolding Energy - mRNA 5.30923 kcal/mol@LB@Unfolding Energy - sRNA 5.87004 kcal/mol@LB@@LB@Position - mRNA 225 -- 237@LB@Position - sRNA 50 -- 62@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 50 -- 56@LB@
83	0.004611	0.1855	b1593	ynfK	-13.15	0.034145	276 -- 295	66 -- 83	putative dethiobiotin synthetase		_____________275__________________296\n_____________\|____________________\|\n5'-CAC...UACAA________CUC_________AACGG-3'\n______________GCGUUAGC___CCAGGGAAA\n______________\|\|\|::\|:\|___\|\|\|\|\|\|\|\|\|\n______________CGCGGUUG___GGUCCCUUU\n3'-UUU...UAUGA________U___________AGAAC...GUG-5'\n_____________\|____________________\|\n_____________84___________________65\n	289 -- 295	66 -- 72	-26.3491 kcal/mol	5.84339 kcal/mol	7.35847 kcal/mol	275 296@LB@ \| \|@LB@5'-CAC...UACAA CUC AACGG-3'@LB@ GCGUUAGC CCAGGGAAA@LB@ \|\|\|::\|:\| \|\|\|\|\|\|\|\|\|@LB@ CGCGGUUG GGUCCCUUU@LB@3'-UUU...UAUGA U AGAAC...GUG-5'@LB@ \| \|@LB@ 84 65@LB@@LB@@LB@Energy -13.15 kcal/mol@LB@Hybridization Energy -26.3491 kcal/mol@LB@Unfolding Energy - mRNA 5.84339 kcal/mol@LB@Unfolding Energy - sRNA 7.35847 kcal/mol@LB@@LB@Position - mRNA 276 -- 295@LB@Position - sRNA 66 -- 83@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 66 -- 72@LB@
148	0.008708	0.2059	b1754	ynjB	-13.35	0.031185	160 -- 171	50 -- 61	putative ABC transporter periplasmic binding protein		_____________159__________172\n_____________\|____________\|\n5'-CCG...UCAGG____________UUCCU...AAA-3'\n______________GGCUGUGCCGUA\n______________\|\|\|\|\|:\|\|\|\|\|\|\n______________CCGACGCGGCAU\n3'-UUU...UAGAA____________UUAAU...GUG-5'\n_____________\|____________\|\n_____________62___________49\n	165 -- 171	50 -- 56	-23.078 kcal/mol	3.86799 kcal/mol	5.86332 kcal/mol	159 172@LB@ \| \|@LB@5'-CCG...UCAGG UUCCU...AAA-3'@LB@ GGCUGUGCCGUA@LB@ \|\|\|\|\|:\|\|\|\|\|\|@LB@ CCGACGCGGCAU@LB@3'-UUU...UAGAA UUAAU...GUG-5'@LB@ \| \|@LB@ 62 49@LB@@LB@@LB@Energy -13.35 kcal/mol@LB@Hybridization Energy -23.078 kcal/mol@LB@Unfolding Energy - mRNA 3.86799 kcal/mol@LB@Unfolding Energy - sRNA 5.86332 kcal/mol@LB@@LB@Position - mRNA 160 -- 171@LB@Position - sRNA 50 -- 61@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 50 -- 56@LB@
112	0.005982	0.1855	b1820	yobD	-7.30	0.411799	229 -- 243	1 -- 14	UPF0266 family inner membrane protein		_____________228_____________244\n_____________\|_______________\|\n5'-ACC...GAUUC______UC_______UCCUG...CCC-3'\n______________UUUUCA__GCCGCAC\n______________\|\|\|\|\|\|__\|\|\|\|\|\|\|\n______________AAAAGU__CGGCGUG\n3'-UUU...UGACA______C________-5'\n_____________\|______________\|\n_____________15_____________1\n	237 -- 243	1 -- 7	-17.9899 kcal/mol	4.95197 kcal/mol	5.72803 kcal/mol	228 244@LB@ \| \|@LB@5'-ACC...GAUUC UC UCCUG...CCC-3'@LB@ UUUUCA GCCGCAC@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ AAAAGU CGGCGUG@LB@3'-UUU...UGACA C -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -7.30 kcal/mol@LB@Hybridization Energy -17.9899 kcal/mol@LB@Unfolding Energy - mRNA 4.95197 kcal/mol@LB@Unfolding Energy - sRNA 5.72803 kcal/mol@LB@@LB@Position - mRNA 229 -- 243@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 1 -- 7@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@
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@
44	0.002208	0.1727	b1859	znuB	-7.63	0.365449	19 -- 38	72 -- 88	zinc ABC transporter permease		_____________18___________________39\n_____________\|____________________\|\n5'-AUG...AUGAA__________UGAAU_____CAUUU...AUU-3'\n______________GUGCUGUGCC_____CACCA\n______________:\|:\|\|\|:\|\|\|_____\|\|\|\|\|\n______________UAUGACGCGG_____GUGGU\n3'-UUU...GCGCU__________UU________CCCUU...GUG-5'\n_____________\|____________________\|\n_____________89___________________71\n	22 -- 28	79 -- 85	-22.3137 kcal/mol	7.44481 kcal/mol	7.24148 kcal/mol	18 39@LB@ \| \|@LB@5'-AUG...AUGAA UGAAU CAUUU...AUU-3'@LB@ GUGCUGUGCC CACCA@LB@ :\|:\|\|\|:\|\|\| \|\|\|\|\|@LB@ UAUGACGCGG GUGGU@LB@3'-UUU...GCGCU UU CCCUU...GUG-5'@LB@ \| \|@LB@ 89 71@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -22.3137 kcal/mol@LB@Unfolding Energy - mRNA 7.44481 kcal/mol@LB@Unfolding Energy - sRNA 7.24148 kcal/mol@LB@@LB@Position - mRNA 19 -- 38@LB@Position - sRNA 72 -- 88@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 79 -- 85@LB@
71	0.003482	0.1727	b4046	zur	-8.96	0.216158	254 -- 300	53 -- 94	transcriptional repressor Zn(II)-binding		_____________253__________________________________________________300\n_____________\|____________________________________________________\|\n5'-UAA...UGCGC__A___U___________UGACCCCAC______U___________________-3'\n______________GC_GCG_AAUG_UGCGCC_________AGCGCC__GGAAGU____GUUGCGCC\n______________\|\|_\|\|\|_\|\|\|:_\|\|\|\|\|\|_________\|:\|:\|\|__\|\|\|\|:\|____\|:\|\|\|\|\|\|\n______________CG_CGC_UUAU_ACGCGG_________UUGUGG__CCUUUA____CGACGCGG\n3'-UUU...CCCCA___________G_____________________UC______GAAC________CAUUU...GUG-5'\n_____________\|_____________________________________________________\|\n_____________95____________________________________________________52\n	294 -- 300	53 -- 59	-43.5981 kcal/mol	17.5702 kcal/mol	17.0684 kcal/mol	253 300@LB@ \| \|@LB@5'-UAA...UGCGC A U UGACCCCAC U -3'@LB@ GC GCG AAUG UGCGCC AGCGCC GGAAGU GUUGCGCC@LB@ \|\| \|\|\| \|\|\|: \|\|\|\|\|\| \|:\|:\|\| \|\|\|\|:\| \|:\|\|\|\|\|\|@LB@ CG CGC UUAU ACGCGG UUGUGG CCUUUA CGACGCGG@LB@3'-UUU...CCCCA G UC GAAC CAUUU...GUG-5'@LB@ \| \|@LB@ 95 52@LB@@LB@@LB@Energy -8.96 kcal/mol@LB@Hybridization Energy -43.5981 kcal/mol@LB@Unfolding Energy - mRNA 17.5702 kcal/mol@LB@Unfolding Energy - sRNA 17.0684 kcal/mol@LB@@LB@Position - mRNA 254 -- 300@LB@Position - sRNA 53 -- 94@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 53 -- 59@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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