Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
81	0.008673	0.3575	b1683	sufB	-9.84	0.294156	211 -- 257	124 -- 171	component of SufBCD Fe-S cluster assembly scaffold	_____________210_______________258\n_____________\|_________________\|\n5'-GUU...AAUCA________AAUU_____ACCCU...AGC-3'\n______________GAUAUUCA____UCACA\n______________:\|\|\|:\|\|\|____\|\|\|\|\|\n______________UUAUGAGU____AGUGU\n3'-UUU...UGUGG________C________GUACU...UAG-5'\n_____________\|_________________\|\n_____________172_______________123\n	127 -- 133	175 -- 181	-8.93573 kcal/mol	1.46068 kcal/mol	0.409577 kcal/mol	210 258@LB@ \| \|@LB@5'-GUU...AAUCA AAUU ACCCU...AGC-3'@LB@ GAUAUUCA UCACA@LB@ :\|\|\|:\|\|\| \|\|\|\|\|@LB@ UUAUGAGU AGUGU@LB@3'-UUU...UGUGG C GUACU...UAG-5'@LB@ \| \|@LB@ 172 123@LB@@LB@@LB@Energy -9.84 kcal/mol@LB@Hybridization Energy -8.93573 kcal/mol@LB@Unfolding Energy - mRNA 1.46068 kcal/mol@LB@Unfolding Energy - sRNA 0.409577 kcal/mol@LB@@LB@Position - mRNA 211 -- 257@LB@Position - sRNA 124 -- 171@LB@Position Seed - mRNA 127 -- 133@LB@Position Seed - sRNA 175 -- 181@LB@
82	0.008839	0.3575	b3680	yidL	-8.33	0.532337	91 -- 113	142 -- 164	AraC family putative transcriptional regulator	_____________90________________114\n_____________\|_________________\|\n5'-AAC...UGCGU________GCAG_____UUCUU...UGA-3'\n______________CGGGUCAG____UCAGA\n______________\|::\|\|\|\|:____\|\|\|\|\|\n______________GUUCAGUU____AGUCU\n3'-UUU...CGUCC________GAA______UAACG...UAG-5'\n_____________\|_________________\|\n_____________165_______________141\n	97 -- 103	151 -- 157	-14.3717 kcal/mol	4.36777 kcal/mol	4.37859 kcal/mol	90 114@LB@ \| \|@LB@5'-AAC...UGCGU GCAG UUCUU...UGA-3'@LB@ CGGGUCAG UCAGA@LB@ \|::\|\|\|\|: \|\|\|\|\|@LB@ GUUCAGUU AGUCU@LB@3'-UUU...CGUCC GAA UAACG...UAG-5'@LB@ \| \|@LB@ 165 141@LB@@LB@@LB@Energy -8.33 kcal/mol@LB@Hybridization Energy -14.3717 kcal/mol@LB@Unfolding Energy - mRNA 4.36777 kcal/mol@LB@Unfolding Energy - sRNA 4.37859 kcal/mol@LB@@LB@Position - mRNA 91 -- 113@LB@Position - sRNA 142 -- 164@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 151 -- 157@LB@
83	0.008941	0.3575	b3343	tusB	-13.46	0.055944	1 -- 14	190 -- 203	mnm(5)-s(2)U34-tRNA synthesis 2-thiolation protein	______________1_____________15\n______________\|_____________\|\n___________5'-_______C______ACAUU...GCG-3'\n______________GCUGGCG_GUGAUU\n______________\|\|\|\|\|\|\|_\|\|\|\|\|\|\n______________CGACCGC_CACUAA\n3'-UUU...UUAGA_______C______AAUGU...UAG-5'\n_____________\|______________\|\n_____________204____________189\n	1 -- 7	197 -- 203	-22.3351 kcal/mol	4.22102 kcal/mol	9.06745 kcal/mol	1 15@LB@ \| \|@LB@ 5'- C ACAUU...GCG-3'@LB@ GCUGGCG GUGAUU@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ CGACCGC CACUAA@LB@3'-UUU...UUAGA C AAUGU...UAG-5'@LB@ \| \|@LB@ 204 189@LB@@LB@@LB@Energy -13.46 kcal/mol@LB@Hybridization Energy -22.3351 kcal/mol@LB@Unfolding Energy - mRNA 4.22102 kcal/mol@LB@Unfolding Energy - sRNA 9.06745 kcal/mol@LB@@LB@Position - mRNA 1 -- 14@LB@Position - sRNA 190 -- 203@LB@Position Seed - mRNA 1 -- 7@LB@Position Seed - sRNA 197 -- 203@LB@
84	0.009006	0.3575	b1924	fliD	-8.51	0.498321	24 -- 43	139 -- 158	flagellar filament capping protein	_____________23_____________44\n_____________\|______________\|\n5'-CGU...UAAAA____C_________UUUUU...UUU-3'\n______________CAAC_UUUAGAAUU\n______________\|\|\|\|_\|\|:\|\|\|\|\|\|\n______________GUUG_AAGUCUUAA\n3'-UUU...GUUCA____A_________CGCCA...UAG-5'\n_____________\|______________\|\n_____________159____________138\n	37 -- 43	139 -- 145	-11.0468 kcal/mol	1.39956 kcal/mol	1.83266 kcal/mol	23 44@LB@ \| \|@LB@5'-CGU...UAAAA C UUUUU...UUU-3'@LB@ CAAC UUUAGAAUU@LB@ \|\|\|\| \|\|:\|\|\|\|\|\|@LB@ GUUG AAGUCUUAA@LB@3'-UUU...GUUCA A CGCCA...UAG-5'@LB@ \| \|@LB@ 159 138@LB@@LB@@LB@Energy -8.51 kcal/mol@LB@Hybridization Energy -11.0468 kcal/mol@LB@Unfolding Energy - mRNA 1.39956 kcal/mol@LB@Unfolding Energy - sRNA 1.83266 kcal/mol@LB@@LB@Position - mRNA 24 -- 43@LB@Position - sRNA 139 -- 158@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 139 -- 145@LB@
85	0.009065	0.3575	b3155	yhbQ	-10.34	0.236900	54 -- 88	123 -- 160	GIY-YIG nuclease superfamily protein	_____________53______________________89\n_____________\|_______________________\|\n5'-UUU...GAUCC_____G__GACAAUAA_______ACCGG...GCG-3'\n______________GUACC_CC________GCUUUAU\n______________\|:\|\|\|_\|\|________\|\|\|\|:\|\|\n______________CGUGG_GG________CGAAGUA\n3'-UUU...UACCC_____G__AA_____________G-5'\n_____________\|_______________________\|\n_____________161_____________________122\n	245 -- 251	2 -- 8	-16.2438 kcal/mol	1.2562 kcal/mol	7.2187 kcal/mol	53 89@LB@ \| \|@LB@5'-UUU...GAUCC G GACAAUAA ACCGG...GCG-3'@LB@ GUACC CC GCUUUAU@LB@ \|:\|\|\| \|\| \|\|\|\|:\|\|@LB@ CGUGG GG CGAAGUA@LB@3'-UUU...UACCC G AA G-5'@LB@ \| \|@LB@ 161 122@LB@@LB@@LB@Energy -10.34 kcal/mol@LB@Hybridization Energy -16.2438 kcal/mol@LB@Unfolding Energy - mRNA 1.2562 kcal/mol@LB@Unfolding Energy - sRNA 7.2187 kcal/mol@LB@@LB@Position - mRNA 54 -- 88@LB@Position - sRNA 123 -- 160@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 2 -- 8@LB@
86	0.009326	0.3575	b0899	ycaM	-11.50	0.140486	23 -- 68	127 -- 173	putative transporter	_____________22_______________________________________________________69\n_____________\|________________________________________________________\|\n5'-AGC...GAACU____GUU______UC_____UUUUUU___UCUU__A__U__C____U_________AAUUU...AUG-3'\n______________UACU___UCACAC____UGC______GUU____CU_UC_GA_UUGC__UUAUUCCA\n______________\|\|\|\|___\|\|\|\|\|\|____\|\|\|______\|\|:____\|\|_\|\|_\|\|_\|\|\|\|__\|:\|\|:\|\|\|\n______________AUGA___AGUGUG____ACG______CAG____GA_AG_CU_AACG__AGUAGGGU\n3'-UUU...UGGUU____GUC______UACU___UCCGUU___UU____A__U__U____CC________GACGU...UAG-5'\n_____________\|________________________________________________________\|\n_____________174______________________________________________________126\n	62 -- 68	127 -- 133	-29.7478 kcal/mol	2.56458 kcal/mol	15.6497 kcal/mol	22 69@LB@ \| \|@LB@5'-AGC...GAACU GUU UC UUUUUU UCUU A U C U AAUUU...AUG-3'@LB@ UACU UCACAC UGC GUU CU UC GA UUGC UUAUUCCA@LB@ \|\|\|\| \|\|\|\|\|\| \|\|\| \|\|: \|\| \|\| \|\| \|\|\|\| \|:\|\|:\|\|\|@LB@ AUGA AGUGUG ACG CAG GA AG CU AACG AGUAGGGU@LB@3'-UUU...UGGUU GUC UACU UCCGUU UU A U U CC GACGU...UAG-5'@LB@ \| \|@LB@ 174 126@LB@@LB@@LB@Energy -11.50 kcal/mol@LB@Hybridization Energy -29.7478 kcal/mol@LB@Unfolding Energy - mRNA 2.56458 kcal/mol@LB@Unfolding Energy - sRNA 15.6497 kcal/mol@LB@@LB@Position - mRNA 23 -- 68@LB@Position - sRNA 127 -- 173@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 127 -- 133@LB@
87	0.009479	0.3575	b1192	ldcA	-9.25	0.375459	184 -- 216	125 -- 154	murein tetrapeptide carboxypeptidase; LD-carboxypeptidase A	_____________183_______________217\n_____________\|_________________\|\n5'-UGC...AGCAC__CG_____________UCCAG...UCA-3'\n______________GC__CGCUG_CGUGGUA\n______________:\|__\|\|\|\|\|_\|\|:\|\|\|\|\n______________UG__GCGAC_GCGCCAU\n3'-UUU...CGUGU__AA_____A_______UUUAU...UAG-5'\n_____________\|_________________\|\n_____________155_______________124\n	261 -- 267	48 -- 54	-20.6657 kcal/mol	8.36057 kcal/mol	6.14531 kcal/mol	183 217@LB@ \| \|@LB@5'-UGC...AGCAC CG UCCAG...UCA-3'@LB@ GC CGCUG CGUGGUA@LB@ :\| \|\|\|\|\| \|\|:\|\|\|\|@LB@ UG GCGAC GCGCCAU@LB@3'-UUU...CGUGU AA A UUUAU...UAG-5'@LB@ \| \|@LB@ 155 124@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -20.6657 kcal/mol@LB@Unfolding Energy - mRNA 8.36057 kcal/mol@LB@Unfolding Energy - sRNA 6.14531 kcal/mol@LB@@LB@Position - mRNA 184 -- 216@LB@Position - sRNA 125 -- 154@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 48 -- 54@LB@
88	0.009956	0.3575	b2672	ygaM	-12.38	0.093122	193 -- 231	56 -- 92	putative membrane-anchored DUF883 family ribosome-binding protein	_____________192______232\n_____________\|________\|\n5'-AAC...UGAAC________AGAAA...AGU-3'\n______________CUCAGUUA\n______________\|\|\|\|\|\|:\|\n______________GAGUCAGU\n3'-UUU...GUUAU________GUGUA...UAG-5'\n_____________\|________\|\n_____________93_______55\n	142 -- 148	171 -- 177	-10.1878 kcal/mol	1.87036 kcal/mol	0.207782 kcal/mol	192 232@LB@ \| \|@LB@5'-AAC...UGAAC AGAAA...AGU-3'@LB@ CUCAGUUA@LB@ \|\|\|\|\|\|:\|@LB@ GAGUCAGU@LB@3'-UUU...GUUAU GUGUA...UAG-5'@LB@ \| \|@LB@ 93 55@LB@@LB@@LB@Energy -12.38 kcal/mol@LB@Hybridization Energy -10.1878 kcal/mol@LB@Unfolding Energy - mRNA 1.87036 kcal/mol@LB@Unfolding Energy - sRNA 0.207782 kcal/mol@LB@@LB@Position - mRNA 193 -- 231@LB@Position - sRNA 56 -- 92@LB@Position Seed - mRNA 142 -- 148@LB@Position Seed - sRNA 171 -- 177@LB@
89	0.009985	0.3575	b0477	gsk	-9.51	0.338446	88 -- 115	123 -- 150	inosine/guanosine kinase	_____________87_____________116\n_____________\|______________\|\n5'-UUU...UCGCC_________AC___CCGUA...CUG-3'\n______________GCUCAGUUA__CAC\n______________:\|\|\|\|\|\|:\|__\|\|\|\n______________UGAGUCAGU__GUG\n3'-UUU...GGUUA______________UACUA...UAG-5'\n_____________\|______________\|\n_____________151____________122\n	175 -- 181	171 -- 177	-13.3754 kcal/mol	2.68541 kcal/mol	0.283892 kcal/mol	87 116@LB@ \| \|@LB@5'-UUU...UCGCC AC CCGUA...CUG-3'@LB@ GCUCAGUUA CAC@LB@ :\|\|\|\|\|\|:\| \|\|\|@LB@ UGAGUCAGU GUG@LB@3'-UUU...GGUUA UACUA...UAG-5'@LB@ \| \|@LB@ 151 122@LB@@LB@@LB@Energy -9.51 kcal/mol@LB@Hybridization Energy -13.3754 kcal/mol@LB@Unfolding Energy - mRNA 2.68541 kcal/mol@LB@Unfolding Energy - sRNA 0.283892 kcal/mol@LB@@LB@Position - mRNA 88 -- 115@LB@Position - sRNA 123 -- 150@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 171 -- 177@LB@
90	0.01008	0.3575	b3994	thiC	-11.53	0.138483	145 -- 158	1 -- 14	phosphomethylpyrimidine synthase	_____________144_________159\n_____________\|___________\|\n5'-AUG...CGUCU___________CGUCG...UUU-3'\n______________CUUGCUUCAUC\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________GAACGAAGUAG\n3'-UUU...UGGGG___________-5'\n_____________\|__________\|\n_____________15_________1\n	152 -- 158	1 -- 7	-17.5294 kcal/mol	1.22878 kcal/mol	1.03329 kcal/mol	144 159@LB@ \| \|@LB@5'-AUG...CGUCU CGUCG...UUU-3'@LB@ CUUGCUUCAUC@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ GAACGAAGUAG@LB@3'-UUU...UGGGG -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -11.53 kcal/mol@LB@Hybridization Energy -17.5294 kcal/mol@LB@Unfolding Energy - mRNA 1.22878 kcal/mol@LB@Unfolding Energy - sRNA 1.03329 kcal/mol@LB@@LB@Position - mRNA 145 -- 158@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 1 -- 7@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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