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
121	0.02058	0.5385	b0796	ybiH	-9.41	0.133616	217 -- 230	24 -- 36	DUF1956 domain-containing tetR family putative transcriptional regulator	_____________216____________231\n_____________\|______________\|\n5'-CGG...UGCCA____AA________GAACA...CCA-3'\n______________UGAC__UCAAGGGU\n______________\|\|\|\|__\|\|\|\|\|\|\|\|\n______________ACUG__AGUUCCCA\n3'-CGC...CCGUC____A_________AUUUU...AAG-5'\n_____________\|______________\|\n_____________37_____________23\n	224 -- 230	24 -- 30	-15.9856 kcal/mol	3.24975 kcal/mol	3.33025 kcal/mol	216 231@LB@ \| \|@LB@5'-CGG...UGCCA AA GAACA...CCA-3'@LB@ UGAC UCAAGGGU@LB@ \|\|\|\| \|\|\|\|\|\|\|\|@LB@ ACUG AGUUCCCA@LB@3'-CGC...CCGUC A AUUUU...AAG-5'@LB@ \| \|@LB@ 37 23@LB@@LB@@LB@Energy -9.41 kcal/mol@LB@Hybridization Energy -15.9856 kcal/mol@LB@Unfolding Energy - mRNA 3.24975 kcal/mol@LB@Unfolding Energy - sRNA 3.33025 kcal/mol@LB@@LB@Position - mRNA 217 -- 230@LB@Position - sRNA 24 -- 36@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 24 -- 30@LB@
18	0.003137	0.5385	b1824	yobF	-13.30	0.027752	169 -- 188	14 -- 35	DUF2527 family heat-induced protein	_____________168____________________189\n_____________\|______________________\|\n5'-GCC...UAACA________________C_____ACAGU...UGU-3'\n______________GAUUUC__GGGUUAAA_GAGGU\n______________\|\|:\|\|\|__\|\|\|\|\|\|\|\|_\|\|\|\|\|\n______________CUGAAG__CCCAAUUU_CUCCA\n3'-CGC...CGUCA______UU________U_____CGGCG...AAG-5'\n_____________\|______________________\|\n_____________36_____________________13\n	176 -- 182	20 -- 26	-23.4961 kcal/mol	6.86312 kcal/mol	3.33183 kcal/mol	168 189@LB@ \| \|@LB@5'-GCC...UAACA C ACAGU...UGU-3'@LB@ GAUUUC GGGUUAAA GAGGU@LB@ \|\|:\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ CUGAAG CCCAAUUU CUCCA@LB@3'-CGC...CGUCA UU U CGGCG...AAG-5'@LB@ \| \|@LB@ 36 13@LB@@LB@@LB@Energy -13.30 kcal/mol@LB@Hybridization Energy -23.4961 kcal/mol@LB@Unfolding Energy - mRNA 6.86312 kcal/mol@LB@Unfolding Energy - sRNA 3.33183 kcal/mol@LB@@LB@Position - mRNA 169 -- 188@LB@Position - sRNA 14 -- 35@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 20 -- 26@LB@
11	0.002269	0.5385	b1205	ychH	-11.36	0.061344	181 -- 195	75 -- 90	DUF2583 family putative inner membrane protein	_____________180______________196\n_____________\|________________\|\n5'-CAA...ACCCA___________GA___GACAU...UAC-3'\n______________GAAAGUUC_CG__GGU\n______________:\|\|\|\|\|\|\|_\|\|__\|\|:\n______________UUUUCAAG_GC__CCG\n3'-CGC...AGGCG________U__AA___AAAUC...AAG-5'\n_____________\|________________\|\n_____________91_______________74\n	182 -- 188	83 -- 89	-14.0006 kcal/mol	2.12575 kcal/mol	0.517251 kcal/mol	180 196@LB@ \| \|@LB@5'-CAA...ACCCA GA GACAU...UAC-3'@LB@ GAAAGUUC CG GGU@LB@ :\|\|\|\|\|\|\| \|\| \|\|:@LB@ UUUUCAAG GC CCG@LB@3'-CGC...AGGCG U AA AAAUC...AAG-5'@LB@ \| \|@LB@ 91 74@LB@@LB@@LB@Energy -11.36 kcal/mol@LB@Hybridization Energy -14.0006 kcal/mol@LB@Unfolding Energy - mRNA 2.12575 kcal/mol@LB@Unfolding Energy - sRNA 0.517251 kcal/mol@LB@@LB@Position - mRNA 181 -- 195@LB@Position - sRNA 75 -- 90@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 83 -- 89@LB@
122	0.02068	0.5385	b4529	ydbJ	-12.93	0.032363	174 -- 233	8 -- 79	DUF333 family putative lipoprotein	_____________173_______________________________________________________________________234\n_____________\|_________________________________________________________________________\|\n5'-GCA...GUCGU_______GAA________UCA______GAAAA__U___A____C____________________U________UUAUU...GUU-3'\n______________UUGGCUU_________GA___GAGGAA_____GA_GCG_GCAG_G_UUUU__GGGU____AGGG_GUGCCGCU\n______________\|\|\|\|\|\|\|_________\|\|___\|\|\|:\|\|_____\|\|_:\|\|_\|\|\|\|_\|_:\|\|:__\|\|\|\|____\|\|:\|_\|\|\|\|\|\|\|\|\n______________AACCGAA_________CU___CUCUUU_____CU_UGC_CGUC_C_GAAG__CCCA____UCUC_CACGGCGA\n3'-CGC...AGUGC_______AUCAAUAAG__CAA______GAGAG__U___C____A_U____UU____AUUU_____________GGCAAAG-5'\n_____________\|_________________________________________________________________________\|\n_____________80________________________________________________________________________7\n	227 -- 233	8 -- 14	-51.0346 kcal/mol	16.597 kcal/mol	21.5113 kcal/mol	173 234@LB@ \| \|@LB@5'-GCA...GUCGU GAA UCA GAAAA U A C U UUAUU...GUU-3'@LB@ UUGGCUU GA GAGGAA GA GCG GCAG G UUUU GGGU AGGG GUGCCGCU@LB@ \|\|\|\|\|\|\| \|\| \|\|\|:\|\| \|\| :\|\| \|\|\|\| \| :\|\|: \|\|\|\| \|\|:\| \|\|\|\|\|\|\|\|@LB@ AACCGAA CU CUCUUU CU UGC CGUC C GAAG CCCA UCUC CACGGCGA@LB@3'-CGC...AGUGC AUCAAUAAG CAA GAGAG U C A U UU AUUU GGCAAAG-5'@LB@ \| \|@LB@ 80 7@LB@@LB@@LB@Energy -12.93 kcal/mol@LB@Hybridization Energy -51.0346 kcal/mol@LB@Unfolding Energy - mRNA 16.597 kcal/mol@LB@Unfolding Energy - sRNA 21.5113 kcal/mol@LB@@LB@Position - mRNA 174 -- 233@LB@Position - sRNA 8 -- 79@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 8 -- 14@LB@
157	0.02703	0.5559	b3221	yhcH	-9.14	0.148013	119 -- 127	77 -- 85	DUF386 family protein cupin superfamily	_____________118_______128\n_____________\|_________\|\n5'-AUC...GGCAU_________AUUUA...AAG-3'\n______________UUCAUGUUG\n______________\|\|\|\|:\|\|\|\|\n______________AAGUGCAAC\n3'-CGC...UUUUC_________CGAAA...AAG-5'\n_____________\|_________\|\n_____________86________76\n	121 -- 127	77 -- 83	-10.7393 kcal/mol	1.16925 kcal/mol	0.427568 kcal/mol	118 128@LB@ \| \|@LB@5'-AUC...GGCAU AUUUA...AAG-3'@LB@ UUCAUGUUG@LB@ \|\|\|\|:\|\|\|\|@LB@ AAGUGCAAC@LB@3'-CGC...UUUUC CGAAA...AAG-5'@LB@ \| \|@LB@ 86 76@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -10.7393 kcal/mol@LB@Unfolding Energy - mRNA 1.16925 kcal/mol@LB@Unfolding Energy - sRNA 0.427568 kcal/mol@LB@@LB@Position - mRNA 119 -- 127@LB@Position - sRNA 77 -- 85@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 77 -- 83@LB@
80	0.01445	0.5385	b4257	yjgN	-10.51	0.086376	202 -- 215	65 -- 78	DUF898 family inner membrane protein	_____________201____________216\n_____________\|______________\|\n5'-UUA...UUUUA_____CA_______AAUGA...UGU-3'\n______________UGGCU__AGUUAUU\n______________\|\|\|\|\|__\|\|\|\|\|\|\|\n______________ACCGA__UCAAUAA\n3'-CGC...GUGCA_____AA_______GCUCA...AAG-5'\n_____________\|______________\|\n_____________79_____________64\n	209 -- 215	65 -- 71	-13.5706 kcal/mol	2.80573 kcal/mol	0.256929 kcal/mol	201 216@LB@ \| \|@LB@5'-UUA...UUUUA CA AAUGA...UGU-3'@LB@ UGGCU AGUUAUU@LB@ \|\|\|\|\| \|\|\|\|\|\|\|@LB@ ACCGA UCAAUAA@LB@3'-CGC...GUGCA AA GCUCA...AAG-5'@LB@ \| \|@LB@ 79 64@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -13.5706 kcal/mol@LB@Unfolding Energy - mRNA 2.80573 kcal/mol@LB@Unfolding Energy - sRNA 0.256929 kcal/mol@LB@@LB@Position - mRNA 202 -- 215@LB@Position - sRNA 65 -- 78@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 65 -- 71@LB@
143	0.02402	0.5467	b4029	yjbH	-10.20	0.097639	107 -- 117	75 -- 85	DUF940 family extracellular polysaccharide protein	_____________106_________118\n_____________\|___________\|\n5'-GCG...CAUUA___________CUCGC...AUU-3'\n______________UUUAUGUUGGC\n______________\|\|:\|:\|\|\|\|\|\|\n______________AAGUGCAACCG\n3'-CGC...UUUUC___________AAAUC...AAG-5'\n_____________\|___________\|\n_____________86__________74\n	111 -- 117	75 -- 81	-14.6823 kcal/mol	3.97178 kcal/mol	0.509769 kcal/mol	106 118@LB@ \| \|@LB@5'-GCG...CAUUA CUCGC...AUU-3'@LB@ UUUAUGUUGGC@LB@ \|\|:\|:\|\|\|\|\|\|@LB@ AAGUGCAACCG@LB@3'-CGC...UUUUC AAAUC...AAG-5'@LB@ \| \|@LB@ 86 74@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -14.6823 kcal/mol@LB@Unfolding Energy - mRNA 3.97178 kcal/mol@LB@Unfolding Energy - sRNA 0.509769 kcal/mol@LB@@LB@Position - mRNA 107 -- 117@LB@Position - sRNA 75 -- 85@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 75 -- 81@LB@
179	0.03159	0.5559	b0790	ybhP	-12.03	0.046743	250 -- 264	71 -- 85	endo/exonuclease/phosphatase family protein	_____________249_____________265\n_____________\|_______________\|\n5'-AGU...CAAUA_____AAA_______CCGCG...UUC-3'\n______________UUCAC___GGCUUUA\n______________\|\|\|\|\|___\|\|\|\|\|\|\|\n______________AAGUG___CCGAAAU\n3'-CGC...UUUUC_____CAA_______CAAUA...AAG-5'\n_____________\|_______________\|\n_____________86______________70\n	258 -- 264	71 -- 77	-13.6298 kcal/mol	1.04243 kcal/mol	0.560731 kcal/mol	249 265@LB@ \| \|@LB@5'-AGU...CAAUA AAA CCGCG...UUC-3'@LB@ UUCAC GGCUUUA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|@LB@ AAGUG CCGAAAU@LB@3'-CGC...UUUUC CAA CAAUA...AAG-5'@LB@ \| \|@LB@ 86 70@LB@@LB@@LB@Energy -12.03 kcal/mol@LB@Hybridization Energy -13.6298 kcal/mol@LB@Unfolding Energy - mRNA 1.04243 kcal/mol@LB@Unfolding Energy - sRNA 0.560731 kcal/mol@LB@@LB@Position - mRNA 250 -- 264@LB@Position - sRNA 71 -- 85@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 71 -- 77@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@
60	0.01169	0.5385	b2441	eutB	-14.17	0.019414	238 -- 261	12 -- 34	ethanolamine ammonia-lyase large subunit heavy chain	_____________237______________________262\n_____________\|________________________\|\n5'-CUG...AUAUC_G_______AUG____________UGGCU...UGG-3'\n______________A_UUUAAGG___UAAAAGAGGUGC\n______________\|_\|\|:\|\|\|\|___\|\|\|\|\|\|\|\|\|\|\|\|\n______________U_AAGUUCC___AUUUUCUCCACG\n3'-CGC...GUCAC_G_______CA_____________GCGAG...AAG-5'\n_____________\|________________________\|\n_____________35_______________________11\n	255 -- 261	12 -- 18	-24.3693 kcal/mol	4.39141 kcal/mol	5.80707 kcal/mol	237 262@LB@ \| \|@LB@5'-CUG...AUAUC G AUG UGGCU...UGG-3'@LB@ A UUUAAGG UAAAAGAGGUGC@LB@ \| \|\|:\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|@LB@ U AAGUUCC AUUUUCUCCACG@LB@3'-CGC...GUCAC G CA GCGAG...AAG-5'@LB@ \| \|@LB@ 35 11@LB@@LB@@LB@Energy -14.17 kcal/mol@LB@Hybridization Energy -24.3693 kcal/mol@LB@Unfolding Energy - mRNA 4.39141 kcal/mol@LB@Unfolding Energy - sRNA 5.80707 kcal/mol@LB@@LB@Position - mRNA 238 -- 261@LB@Position - sRNA 12 -- 34@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 12 -- 18@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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