Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
137	0.0102	0.2504	b0957	ompA	-10.25	0.250752	198 -- 232	1 -- 30	outer membrane protein A (3a;II*;G;d)	_____________197_________________________________233\n_____________\|___________________________________\|\n5'-CUU...CGCAA______AAAAA____GCUAUCGC__UU________ACUGG...AAC-3'\n______________AAAAUG_____GACA________GA__GCAGUGGC\n______________\|\|\|\|\|\|_____\|\|\|\|________:\|__\|\|\|\|\|\|\|\|\n______________UUUUAC_____CUGU________UU__CGUCACCG\n3'-UUU...AGGUG______CC_______AGUUUC____UU________-5'\n_____________\|__________________________________\|\n_____________31_________________________________1\n	226 -- 232	1 -- 7	-21.624 kcal/mol	8.85247 kcal/mol	2.51911 kcal/mol	197 233@LB@ \| \|@LB@5'-CUU...CGCAA AAAAA GCUAUCGC UU ACUGG...AAC-3'@LB@ AAAAUG GACA GA GCAGUGGC@LB@ \|\|\|\|\|\| \|\|\|\| :\| \|\|\|\|\|\|\|\|@LB@ UUUUAC CUGU UU CGUCACCG@LB@3'-UUU...AGGUG CC AGUUUC UU -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -10.25 kcal/mol@LB@Hybridization Energy -21.624 kcal/mol@LB@Unfolding Energy - mRNA 8.85247 kcal/mol@LB@Unfolding Energy - sRNA 2.51911 kcal/mol@LB@@LB@Position - mRNA 198 -- 232@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 1 -- 7@LB@
140	0.01029	0.2504	b3247	rng	-10.20	0.255190	49 -- 63	1 -- 14	ribonuclease G	_____________48______________64\n_____________\|_______________\|\n5'-GUU...CCGUU___U_______GU__AUACG...CGC-3'\n______________AGA_AAAGCAG__GC\n______________\|\|\|_\|\|\|\|\|\|\|__\|\|\n______________UCU_UUUCGUC__CG\n3'-UUU...UAGUU___________AC__-5'\n_____________\|______________\|\n_____________15_____________1\n	53 -- 59	5 -- 11	-13.7724 kcal/mol	2.22711 kcal/mol	1.34059 kcal/mol	48 64@LB@ \| \|@LB@5'-GUU...CCGUU U GU AUACG...CGC-3'@LB@ AGA AAAGCAG GC@LB@ \|\|\| \|\|\|\|\|\|\| \|\|@LB@ UCU UUUCGUC CG@LB@3'-UUU...UAGUU AC -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -13.7724 kcal/mol@LB@Unfolding Energy - mRNA 2.22711 kcal/mol@LB@Unfolding Energy - sRNA 1.34059 kcal/mol@LB@@LB@Position - mRNA 49 -- 63@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 5 -- 11@LB@
190	0.01401	0.2529	b2478	dapA	-10.08	0.266807	73 -- 98	6 -- 25	dihydrodipicolinate synthase	_____________72_________________________99\n_____________\|__________________________\|\n5'-GGC...UUUAA____UGA____UUCUU__________UAAAA...CCA-3'\n______________GGGG___GUUG_____AAGGAAAGCA\n______________\|\|\|\|___:\|::_____\|\|\|:\|\|\|\|\|\|\n______________CCCC___UAGU_____UUCUUUUCGU\n3'-UUU...UUUUA____UG____________________CACCG-5'\n_____________\|__________________________\|\n_____________26_________________________5\n	92 -- 98	6 -- 12	-17.2074 kcal/mol	6.41889 kcal/mol	0.70636 kcal/mol	72 99@LB@ \| \|@LB@5'-GGC...UUUAA UGA UUCUU UAAAA...CCA-3'@LB@ GGGG GUUG AAGGAAAGCA@LB@ \|\|\|\| :\|:: \|\|\|:\|\|\|\|\|\|@LB@ CCCC UAGU UUCUUUUCGU@LB@3'-UUU...UUUUA UG CACCG-5'@LB@ \| \|@LB@ 26 5@LB@@LB@@LB@Energy -10.08 kcal/mol@LB@Hybridization Energy -17.2074 kcal/mol@LB@Unfolding Energy - mRNA 6.41889 kcal/mol@LB@Unfolding Energy - sRNA 0.70636 kcal/mol@LB@@LB@Position - mRNA 73 -- 98@LB@Position - sRNA 6 -- 25@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 6 -- 12@LB@
168	0.01219	0.2504	b1830	prc	-10.01	0.273454	1 -- 12	6 -- 17	carboxy-terminal protease for penicillin-binding protein 3	______________1___________13\n______________\|___________\|\n___________5'-_______C____CACCC...CGG-3'\n______________CGAAGAA_AGCA\n______________\|:\|\|\|\|\|_\|\|\|\|\n______________GUUUCUU_UCGU\n3'-UUU...CUGUA_______U____CACCG-5'\n_____________\|____________\|\n_____________18___________5\n	1 -- 7	11 -- 17	-11.3077 kcal/mol	0.751361 kcal/mol	0.542636 kcal/mol	1 13@LB@ \| \|@LB@ 5'- C CACCC...CGG-3'@LB@ CGAAGAA AGCA@LB@ \|:\|\|\|\|\| \|\|\|\|@LB@ GUUUCUU UCGU@LB@3'-UUU...CUGUA U CACCG-5'@LB@ \| \|@LB@ 18 5@LB@@LB@@LB@Energy -10.01 kcal/mol@LB@Hybridization Energy -11.3077 kcal/mol@LB@Unfolding Energy - mRNA 0.751361 kcal/mol@LB@Unfolding Energy - sRNA 0.542636 kcal/mol@LB@@LB@Position - mRNA 1 -- 12@LB@Position - sRNA 6 -- 17@LB@Position Seed - mRNA 1 -- 7@LB@Position Seed - sRNA 11 -- 17@LB@
27	0.001238	0.1512	b4045	yjbJ	-9.99	0.275707	259 -- 267	19 -- 28	stress-induced protein UPF0337 family	_____________258________268\n_____________\|__________\|\n5'-CGU...AGAGC__________AACUG...AAG-3'\n______________AAUGGGG_CA\n______________\|\|\|\|\|\|\|_\|\|\n______________UUACCCC_GU\n3'-UUU...GUGUU_______U__AGUUU...CCG-5'\n_____________\|__________\|\n_____________29_________18\n	259 -- 265	22 -- 28	-11.8839 kcal/mol	1.24365 kcal/mol	0.649553 kcal/mol	258 268@LB@ \| \|@LB@5'-CGU...AGAGC AACUG...AAG-3'@LB@ AAUGGGG CA@LB@ \|\|\|\|\|\|\| \|\|@LB@ UUACCCC GU@LB@3'-UUU...GUGUU U AGUUU...CCG-5'@LB@ \| \|@LB@ 29 18@LB@@LB@@LB@Energy -9.99 kcal/mol@LB@Hybridization Energy -11.8839 kcal/mol@LB@Unfolding Energy - mRNA 1.24365 kcal/mol@LB@Unfolding Energy - sRNA 0.649553 kcal/mol@LB@@LB@Position - mRNA 259 -- 267@LB@Position - sRNA 19 -- 28@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 22 -- 28@LB@
10	0.0003274	0.1087	b1020	phoH	-9.93	0.281763	74 -- 85	48 -- 59	ATP-binding protein; putative PhoH family P-loop ATPase	_____________73___________86\n_____________\|____________\|\n5'-AAU...AUGUC____________UUUUA...AAC-3'\n______________ACUGAAAUGGUG\n______________\|\|:\|\|\|\|\|\|\|:\|\n______________UGGCUUUACCGC\n3'-UUU...GAACU____________CCCAA...CCG-5'\n_____________\|____________\|\n_____________60___________47\n	79 -- 85	48 -- 54	-17.134 kcal/mol	3.24305 kcal/mol	3.96136 kcal/mol	73 86@LB@ \| \|@LB@5'-AAU...AUGUC UUUUA...AAC-3'@LB@ ACUGAAAUGGUG@LB@ \|\|:\|\|\|\|\|\|\|:\|@LB@ UGGCUUUACCGC@LB@3'-UUU...GAACU CCCAA...CCG-5'@LB@ \| \|@LB@ 60 47@LB@@LB@@LB@Energy -9.93 kcal/mol@LB@Hybridization Energy -17.134 kcal/mol@LB@Unfolding Energy - mRNA 3.24305 kcal/mol@LB@Unfolding Energy - sRNA 3.96136 kcal/mol@LB@@LB@Position - mRNA 74 -- 85@LB@Position - sRNA 48 -- 59@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 48 -- 54@LB@
41	0.002071	0.1648	b0992	yccM	-9.88	0.287125	161 -- 167	1 -- 7	putative 4Fe-4S membrane protein	_____________160_____168\n_____________\|_______\|\n5'-AUC...UAGAA_______AUUUG...AAG-3'\n______________UAGUGGC\n______________:\|\|\|\|\|\|\n______________GUCACCG\n3'-UUU...UUUUC_______-5'\n_____________\|______\|\n_____________8______1\n	161 -- 167	1 -- 7	-11.7646 kcal/mol	0.660682 kcal/mol	1.22779 kcal/mol	160 168@LB@ \| \|@LB@5'-AUC...UAGAA AUUUG...AAG-3'@LB@ UAGUGGC@LB@ :\|\|\|\|\|\|@LB@ GUCACCG@LB@3'-UUU...UUUUC -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -11.7646 kcal/mol@LB@Unfolding Energy - mRNA 0.660682 kcal/mol@LB@Unfolding Energy - sRNA 1.22779 kcal/mol@LB@@LB@Position - mRNA 161 -- 167@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 1 -- 7@LB@
90	0.005632	0.2147	b1234	rssA	-9.83	0.291555	191 -- 222	1 -- 26	putative patatin-like family phospholipase	_____________190_______________________________223\n_____________\|_________________________________\|\n5'-GAU...AAUCU__C____AUAAU_______AUAAAAA_______UGGCG...AAA-3'\n______________UG_GGGA_____GAGAAAG_______UAG_GGC\n______________\|\|_\|\|\|\|_____:\|\|\|\|\|:_______:\|\|_\|\|\|\n______________AC_CCCU_____UUCUUUU_______GUC_CCG\n3'-UUU...GUUUU_______GUAGU_______C_________A___-5'\n_____________\|________________________________\|\n_____________27_______________________________1\n	203 -- 209	9 -- 15	-16.1024 kcal/mol	3.75149 kcal/mol	2.51842 kcal/mol	190 223@LB@ \| \|@LB@5'-GAU...AAUCU C AUAAU AUAAAAA UGGCG...AAA-3'@LB@ UG GGGA GAGAAAG UAG GGC@LB@ \|\| \|\|\|\| :\|\|\|\|\|: :\|\| \|\|\|@LB@ AC CCCU UUCUUUU GUC CCG@LB@3'-UUU...GUUUU GUAGU C A -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -9.83 kcal/mol@LB@Hybridization Energy -16.1024 kcal/mol@LB@Unfolding Energy - mRNA 3.75149 kcal/mol@LB@Unfolding Energy - sRNA 2.51842 kcal/mol@LB@@LB@Position - mRNA 191 -- 222@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 9 -- 15@LB@
171	0.01235	0.2504	b1092	fabD	-9.75	0.300248	258 -- 270	47 -- 59	malonyl-CoA-[acyl-carrier-protein] transacylase	_____________257___________271\n_____________\|_____________\|\n5'-AAC...UGCUG_____U_______CGAGC...UUG-3'\n______________GCUGA_AUGGCGG\n______________:\|:\|\|_\|\|\|\|\|\|\|\n______________UGGCU_UACCGCC\n3'-UUU...GAACU_____U_______CCAAC...CCG-5'\n_____________\|_____________\|\n_____________60____________46\n	264 -- 270	47 -- 53	-17.9053 kcal/mol	4.19285 kcal/mol	3.96442 kcal/mol	257 271@LB@ \| \|@LB@5'-AAC...UGCUG U CGAGC...UUG-3'@LB@ GCUGA AUGGCGG@LB@ :\|:\|\| \|\|\|\|\|\|\|@LB@ UGGCU UACCGCC@LB@3'-UUU...GAACU U CCAAC...CCG-5'@LB@ \| \|@LB@ 60 46@LB@@LB@@LB@Energy -9.75 kcal/mol@LB@Hybridization Energy -17.9053 kcal/mol@LB@Unfolding Energy - mRNA 4.19285 kcal/mol@LB@Unfolding Energy - sRNA 3.96442 kcal/mol@LB@@LB@Position - mRNA 258 -- 270@LB@Position - sRNA 47 -- 59@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 47 -- 53@LB@
130	0.009344	0.2491	b2840	ygeA	-9.74	0.301486	266 -- 295	2 -- 29	Asp/Glu_racemase family protein	_____________265____________________________296\n_____________\|______________________________\|\n5'-AAA...UUGAU_____AA_________C__C___UU_____GCUUC-3'\n______________AAAUG__GGCAUUAAA_AG_GGC__GGUGG\n______________\|\|\|\|\|__\|:\|\|\|:\|\|\|_\|:_:\|\|__:\|\|\|\|\n______________UUUAC__CUGUAGUUU_UU_UCG__UCACC\n3'-UUU...GGUGU_____CC_________C__U__________G-5'\n_____________\|______________________________\|\n_____________30_____________________________1\n	275 -- 281	14 -- 20	-20.8158 kcal/mol	8.56062 kcal/mol	2.51906 kcal/mol	265 296@LB@ \| \|@LB@5'-AAA...UUGAU AA C C UU GCUUC-3'@LB@ AAAUG GGCAUUAAA AG GGC GGUGG@LB@ \|\|\|\|\| \|:\|\|\|:\|\|\| \|: :\|\| :\|\|\|\|@LB@ UUUAC CUGUAGUUU UU UCG UCACC@LB@3'-UUU...GGUGU CC C U G-5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -20.8158 kcal/mol@LB@Unfolding Energy - mRNA 8.56062 kcal/mol@LB@Unfolding Energy - sRNA 2.51906 kcal/mol@LB@@LB@Position - mRNA 266 -- 295@LB@Position - sRNA 2 -- 29@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 14 -- 20@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)

Job resubmission

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service.

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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