Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
171	0.01957	0.3668	b2498	upp	-5.84	0.210430	244 -- 265	42 -- 61	uracil phosphoribosyltransferase	_____________243____________________266\n_____________\|______________________\|\n5'-GGC...CAAGC_______GA___G_________UAUCA...CCG-3'\n______________UGGGACU__UGC_UGAGCAAGA\n______________\|\|::\|\|\|__\|\|\|_\|:\|\|\|\|\|\|\|\n______________ACUUUGA__ACG_AUUCGUUCU\n3'-UUU...GCCCU____________A_________UCGUG...CAA-5'\n_____________\|______________________\|\n_____________62_____________________41\n	259 -- 265	42 -- 48	-21.1169 kcal/mol	8.03919 kcal/mol	7.23689 kcal/mol	243 266@LB@ \| \|@LB@5'-GGC...CAAGC GA G UAUCA...CCG-3'@LB@ UGGGACU UGC UGAGCAAGA@LB@ \|\|::\|\|\| \|\|\| \|:\|\|\|\|\|\|\|@LB@ ACUUUGA ACG AUUCGUUCU@LB@3'-UUU...GCCCU A UCGUG...CAA-5'@LB@ \| \|@LB@ 62 41@LB@@LB@@LB@Energy -5.84 kcal/mol@LB@Hybridization Energy -21.1169 kcal/mol@LB@Unfolding Energy - mRNA 8.03919 kcal/mol@LB@Unfolding Energy - sRNA 7.23689 kcal/mol@LB@@LB@Position - mRNA 244 -- 265@LB@Position - sRNA 42 -- 61@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 42 -- 48@LB@
172	0.01959	0.3668	b0336	codB	-6.02	0.190787	88 -- 108	28 -- 40	cytosine transporter	_____________87____________________109\n_____________\|_____________________\|\n5'-CCA...UUUUU_____CAUUCAUA________AUAUU...UUU-3'\n______________GCACU________UAAAAAAU\n______________\|\|\|\|\|________\|\|\|\|\|\|\|\|\n______________CGUGA________AUUUUUUA\n3'-UUU...UUCUU_____________________AGCAA...CAA-5'\n_____________\|_____________________\|\n_____________41____________________27\n	102 -- 108	28 -- 34	-8.50412 kcal/mol	0.843154 kcal/mol	1.63611 kcal/mol	87 109@LB@ \| \|@LB@5'-CCA...UUUUU CAUUCAUA AUAUU...UUU-3'@LB@ GCACU UAAAAAAU@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ CGUGA AUUUUUUA@LB@3'-UUU...UUCUU AGCAA...CAA-5'@LB@ \| \|@LB@ 41 27@LB@@LB@@LB@Energy -6.02 kcal/mol@LB@Hybridization Energy -8.50412 kcal/mol@LB@Unfolding Energy - mRNA 0.843154 kcal/mol@LB@Unfolding Energy - sRNA 1.63611 kcal/mol@LB@@LB@Position - mRNA 88 -- 108@LB@Position - sRNA 28 -- 40@LB@Position Seed - mRNA 102 -- 108@LB@Position Seed - sRNA 28 -- 34@LB@
173	0.01972	0.3669	b3426	glpD	-5.91	0.203159	207 -- 224	3 -- 20	sn-glycerol-3-phosphate dehydrogenase aerobic FAD/NAD(P)-binding	_____________206_________________225\n_____________\|___________________\|\n5'-AAC...UGGAA____A_________U____AUAGG...AGG-3'\n______________ACCA__AGAUCUGA_UGUG\n______________\|\|\|\|__\|:\|\|\|\|\|\|_\|\|\|\|\n______________UGGU__UUUAGACU_ACAC\n3'-UUU...CAAUG____CC_____________AA-5'\n_____________\|___________________\|\n_____________21__________________2\n	213 -- 219	7 -- 13	-16.1802 kcal/mol	2.74973 kcal/mol	7.52321 kcal/mol	206 225@LB@ \| \|@LB@5'-AAC...UGGAA A U AUAGG...AGG-3'@LB@ ACCA AGAUCUGA UGUG@LB@ \|\|\|\| \|:\|\|\|\|\|\| \|\|\|\|@LB@ UGGU UUUAGACU ACAC@LB@3'-UUU...CAAUG CC AA-5'@LB@ \| \|@LB@ 21 2@LB@@LB@@LB@Energy -5.91 kcal/mol@LB@Hybridization Energy -16.1802 kcal/mol@LB@Unfolding Energy - mRNA 2.74973 kcal/mol@LB@Unfolding Energy - sRNA 7.52321 kcal/mol@LB@@LB@Position - mRNA 207 -- 224@LB@Position - sRNA 3 -- 20@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 7 -- 13@LB@
174	0.01992	0.3669	b1098	tmk	-8.25	0.051647	183 -- 196	29 -- 42	thymidylate kinase	_____________182____________197\n_____________\|______________\|\n5'-UAA...UCUGA______________AAAAA...GCG-3'\n______________AAGUGCUUAAGGAA\n______________\|\|\|::\|\|\|\|\|::\|\|\n______________UUCGUGAAUUUUUU\n3'-UUU...CGUUC______________AAGCA...CAA-5'\n_____________\|______________\|\n_____________43_____________28\n	190 -- 196	29 -- 35	-11.8447 kcal/mol	1.97362 kcal/mol	1.62369 kcal/mol	182 197@LB@ \| \|@LB@5'-UAA...UCUGA AAAAA...GCG-3'@LB@ AAGUGCUUAAGGAA@LB@ \|\|\|::\|\|\|\|\|::\|\|@LB@ UUCGUGAAUUUUUU@LB@3'-UUU...CGUUC AAGCA...CAA-5'@LB@ \| \|@LB@ 43 28@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -11.8447 kcal/mol@LB@Unfolding Energy - mRNA 1.97362 kcal/mol@LB@Unfolding Energy - sRNA 1.62369 kcal/mol@LB@@LB@Position - mRNA 183 -- 196@LB@Position - sRNA 29 -- 42@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 29 -- 35@LB@
175	0.01993	0.3669	b0183	rnhB	-5.94	0.199165	195 -- 215	23 -- 41	ribonuclease HII degrades RNA of DNA-RNA hybrids	_____________194___________________216\n_____________\|_____________________\|\n5'-AAU...GAGUU_____AA___UC_________UAUCC...UCC-3'\n______________AGCAC__UGA__GAAUUUGUU\n______________\|\|\|\|\|__\|:\|__:\|\|\|\|:\|\|\|\n______________UCGUG__AUU__UUUAAGCAA\n3'-UUU...GUUCU_____A____U__________UGUGG...CAA-5'\n_____________\|_____________________\|\n_____________42____________________22\n	209 -- 215	23 -- 29	-11.3649 kcal/mol	3.77136 kcal/mol	1.64896 kcal/mol	194 216@LB@ \| \|@LB@5'-AAU...GAGUU AA UC UAUCC...UCC-3'@LB@ AGCAC UGA GAAUUUGUU@LB@ \|\|\|\|\| \|:\| :\|\|\|\|:\|\|\|@LB@ UCGUG AUU UUUAAGCAA@LB@3'-UUU...GUUCU A U UGUGG...CAA-5'@LB@ \| \|@LB@ 42 22@LB@@LB@@LB@Energy -5.94 kcal/mol@LB@Hybridization Energy -11.3649 kcal/mol@LB@Unfolding Energy - mRNA 3.77136 kcal/mol@LB@Unfolding Energy - sRNA 1.64896 kcal/mol@LB@@LB@Position - mRNA 195 -- 215@LB@Position - sRNA 23 -- 41@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 23 -- 29@LB@
176	0.02022	0.37	b0495	ybbA	-5.55	0.244939	212 -- 247	24 -- 59	putative ABC transporter ATPase	_____________211___________________________________248\n_____________\|_____________________________________\|\n5'-GCC...GCGGA____A_____G____UCAUCAU___________C___CGGUC...UCA-3'\n______________AAAC_UUGUU_AAGU________CUUAAGAAGU_CGU\n______________\|\|\|\|_\|\|\|:\|_\|\|\|:________\|\|\|\|\|:\|\|:\|_\|\|\|\n______________UUUG_AACGA_UUCG________GAAUUUUUUA_GCA\n3'-UUU...CCUAC__________A____UUCUUCGU__________A___AUGUG...CAA-5'\n_____________\|_____________________________________\|\n_____________60____________________________________23\n	235 -- 241	30 -- 36	-18.4731 kcal/mol	6.64875 kcal/mol	6.27609 kcal/mol	211 248@LB@ \| \|@LB@5'-GCC...GCGGA A G UCAUCAU C CGGUC...UCA-3'@LB@ AAAC UUGUU AAGU CUUAAGAAGU CGU@LB@ \|\|\|\| \|\|\|:\| \|\|\|: \|\|\|\|\|:\|\|:\| \|\|\|@LB@ UUUG AACGA UUCG GAAUUUUUUA GCA@LB@3'-UUU...CCUAC A UUCUUCGU A AUGUG...CAA-5'@LB@ \| \|@LB@ 60 23@LB@@LB@@LB@Energy -5.55 kcal/mol@LB@Hybridization Energy -18.4731 kcal/mol@LB@Unfolding Energy - mRNA 6.64875 kcal/mol@LB@Unfolding Energy - sRNA 6.27609 kcal/mol@LB@@LB@Position - mRNA 212 -- 247@LB@Position - sRNA 24 -- 59@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 30 -- 36@LB@
177	0.02045	0.3721	b3148	yraN	-6.85	0.120614	263 -- 276	37 -- 54	UPF0102 family protein	_____________262________________277\n_____________\|__________________\|\n5'-GGU...GGCGA__________________AAGCG...GCA-3'\n______________UGC____GUGGGAAGCAC\n______________\|\|\|____\|:::\|\|\|\|\|\|\|\n______________ACG____CGUUCUUCGUG\n3'-UUU...UUUGA___AAUU___________AAUUU...CAA-5'\n_____________\|__________________\|\n_____________55_________________36\n	270 -- 276	37 -- 43	-17.1481 kcal/mol	4.14332 kcal/mol	6.1584 kcal/mol	262 277@LB@ \| \|@LB@5'-GGU...GGCGA AAGCG...GCA-3'@LB@ UGC GUGGGAAGCAC@LB@ \|\|\| \|:::\|\|\|\|\|\|\|@LB@ ACG CGUUCUUCGUG@LB@3'-UUU...UUUGA AAUU AAUUU...CAA-5'@LB@ \| \|@LB@ 55 36@LB@@LB@@LB@Energy -6.85 kcal/mol@LB@Hybridization Energy -17.1481 kcal/mol@LB@Unfolding Energy - mRNA 4.14332 kcal/mol@LB@Unfolding Energy - sRNA 6.1584 kcal/mol@LB@@LB@Position - mRNA 263 -- 276@LB@Position - sRNA 37 -- 54@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 37 -- 43@LB@
178	0.02074	0.3753	b4324	uxuR	-9.92	0.017203	196 -- 210	8 -- 22	fructuronate-inducible hexuronate regulon transcriptional repressor; autorepressor	_____________195_____________211\n_____________\|_______________\|\n5'-UAC...ACACA______U________CCACC...UGC-3'\n______________ACACCA_GAAAUCUG\n______________\|\|\|\|\|\|_\|\|\|\|\|\|\|\|\n______________UGUGGU_CUUUAGAC\n3'-UUU...AGCAA______C________UACACAA-5'\n_____________\|_______________\|\n_____________23______________7\n	203 -- 209	9 -- 15	-19.4171 kcal/mol	1.94047 kcal/mol	7.56026 kcal/mol	195 211@LB@ \| \|@LB@5'-UAC...ACACA U CCACC...UGC-3'@LB@ ACACCA GAAAUCUG@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UGUGGU CUUUAGAC@LB@3'-UUU...AGCAA C UACACAA-5'@LB@ \| \|@LB@ 23 7@LB@@LB@@LB@Energy -9.92 kcal/mol@LB@Hybridization Energy -19.4171 kcal/mol@LB@Unfolding Energy - mRNA 1.94047 kcal/mol@LB@Unfolding Energy - sRNA 7.56026 kcal/mol@LB@@LB@Position - mRNA 196 -- 210@LB@Position - sRNA 8 -- 22@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 9 -- 15@LB@
179	0.02107	0.3768	b3226	nanR	-7.22	0.096643	281 -- 296	26 -- 41	sialic acid-inducible nan operon repressor	_____________280______________297\n_____________\|________________\|\n5'-AUU...CCGCU_____G_______C__UCCG-3'\n______________GGCGC_UAAAAAA_UC\n______________:\|\|:\|_\|\|\|\|\|\|\|_\|\|\n______________UCGUG_AUUUUUU_AG\n3'-UUU...GUUCU_____A_______A__CAAUG...CAA-5'\n_____________\|________________\|\n_____________42_______________25\n	287 -- 293	29 -- 35	-11.6683 kcal/mol	2.7952 kcal/mol	1.64829 kcal/mol	280 297@LB@ \| \|@LB@5'-AUU...CCGCU G C UCCG-3'@LB@ GGCGC UAAAAAA UC@LB@ :\|\|:\| \|\|\|\|\|\|\| \|\|@LB@ UCGUG AUUUUUU AG@LB@3'-UUU...GUUCU A A CAAUG...CAA-5'@LB@ \| \|@LB@ 42 25@LB@@LB@@LB@Energy -7.22 kcal/mol@LB@Hybridization Energy -11.6683 kcal/mol@LB@Unfolding Energy - mRNA 2.7952 kcal/mol@LB@Unfolding Energy - sRNA 1.64829 kcal/mol@LB@@LB@Position - mRNA 281 -- 296@LB@Position - sRNA 26 -- 41@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 29 -- 35@LB@
180	0.02111	0.3768	b2753	iap	-4.77	0.357003	164 -- 179	25 -- 40	aminopeptidase in alkaline phosphatase isozyme conversion	_____________163______________180\n_____________\|________________\|\n5'-UAG...CUAUG___G_A__________CAUGG...CUA-3'\n______________GCG_U_AAAAAAUUUG\n______________\|\|:_\|_\|\|\|\|\|\|\|\|:\|\n______________CGU_A_UUUUUUAAGC\n3'-UUU...UUCUU___G_A__________AAUGU...CAA-5'\n_____________\|________________\|\n_____________41_______________24\n	170 -- 176	28 -- 34	-8.71545 kcal/mol	2.29678 kcal/mol	1.64821 kcal/mol	163 180@LB@ \| \|@LB@5'-UAG...CUAUG G A CAUGG...CUA-3'@LB@ GCG U AAAAAAUUUG@LB@ \|\|: \| \|\|\|\|\|\|\|\|:\|@LB@ CGU A UUUUUUAAGC@LB@3'-UUU...UUCUU G A AAUGU...CAA-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -4.77 kcal/mol@LB@Hybridization Energy -8.71545 kcal/mol@LB@Unfolding Energy - mRNA 2.29678 kcal/mol@LB@Unfolding Energy - sRNA 1.64821 kcal/mol@LB@@LB@Position - mRNA 164 -- 179@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 28 -- 34@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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