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
161	0.01751	0.3504	b3394	hofN	-4.92	0.333288	275 -- 286	18 -- 29	DNA catabolic putative fimbrial assembly protein	_____________274__________287\n_____________\|____________\|\n5'-UGG...CUGAU____________UCUGC...CCG-3'\n______________GUUCGUUGCGCC\n______________:\|\|\|\|\|\|:\|:\|\|\n______________UAAGCAAUGUGG\n3'-UUU...UUUUU____________UCCUU...CAA-5'\n_____________\|____________\|\n_____________30___________17\n	275 -- 281	23 -- 29	-17.9024 kcal/mol	4.53191 kcal/mol	8.4513 kcal/mol	274 287@LB@ \| \|@LB@5'-UGG...CUGAU UCUGC...CCG-3'@LB@ GUUCGUUGCGCC@LB@ :\|\|\|\|\|\|:\|:\|\|@LB@ UAAGCAAUGUGG@LB@3'-UUU...UUUUU UCCUU...CAA-5'@LB@ \| \|@LB@ 30 17@LB@@LB@@LB@Energy -4.92 kcal/mol@LB@Hybridization Energy -17.9024 kcal/mol@LB@Unfolding Energy - mRNA 4.53191 kcal/mol@LB@Unfolding Energy - sRNA 8.4513 kcal/mol@LB@@LB@Position - mRNA 275 -- 286@LB@Position - sRNA 18 -- 29@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 23 -- 29@LB@
189	0.02233	0.3796	b3417	malP	-8.63	0.040366	227 -- 245	35 -- 53	maltodextrin phosphorylase	_____________226_________________246\n_____________\|___________________\|\n5'-ACA...GAUAA__AAUUU____________UCACG...GCC-3'\n______________GC_____CAGGAAGCGCUU\n______________\|\|_____\|\|:\|\|\|\|\|:\|\|\|\n______________CG_____GUUCUUCGUGAA\n3'-UUU...UUGAA__AAUUC____________UUUUU...CAA-5'\n_____________\|___________________\|\n_____________54__________________34\n	239 -- 245	35 -- 41	-18.4249 kcal/mol	3.68713 kcal/mol	6.10399 kcal/mol	226 246@LB@ \| \|@LB@5'-ACA...GAUAA AAUUU UCACG...GCC-3'@LB@ GC CAGGAAGCGCUU@LB@ \|\| \|\|:\|\|\|\|\|:\|\|\|@LB@ CG GUUCUUCGUGAA@LB@3'-UUU...UUGAA AAUUC UUUUU...CAA-5'@LB@ \| \|@LB@ 54 34@LB@@LB@@LB@Energy -8.63 kcal/mol@LB@Hybridization Energy -18.4249 kcal/mol@LB@Unfolding Energy - mRNA 3.68713 kcal/mol@LB@Unfolding Energy - sRNA 6.10399 kcal/mol@LB@@LB@Position - mRNA 227 -- 245@LB@Position - sRNA 35 -- 53@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 35 -- 41@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@
152	0.01589	0.3359	b3428	glgP	-3.42	0.610648	252 -- 258	36 -- 42	glycogen phosphorylase	_____________251_____259\n_____________\|_______\|\n5'-CCA...CUCUU_______CUAUC...CGG-3'\n______________AAGCACU\n______________\|\|\|\|\|\|\|\n______________UUCGUGA\n3'-UUU...CGUUC_______AUUUU...CAA-5'\n_____________\|_______\|\n_____________43______35\n	252 -- 258	36 -- 42	-8.34293 kcal/mol	3.32239 kcal/mol	1.60154 kcal/mol	251 259@LB@ \| \|@LB@5'-CCA...CUCUU CUAUC...CGG-3'@LB@ AAGCACU@LB@ \|\|\|\|\|\|\|@LB@ UUCGUGA@LB@3'-UUU...CGUUC AUUUU...CAA-5'@LB@ \| \|@LB@ 43 35@LB@@LB@@LB@Energy -3.42 kcal/mol@LB@Hybridization Energy -8.34293 kcal/mol@LB@Unfolding Energy - mRNA 3.32239 kcal/mol@LB@Unfolding Energy - sRNA 1.60154 kcal/mol@LB@@LB@Position - mRNA 252 -- 258@LB@Position - sRNA 36 -- 42@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 36 -- 42@LB@
25	0.0007384	0.09021	b3434	yhgN	-11.94	0.004015	159 -- 197	7 -- 41	UPF0056 family inner membrane protein	_____________158_____________________________________198\n_____________\|_______________________________________\|\n5'-UUU...UUGUU_____GC_______CCG__GCAAU_______________GUUAU...CGA-3'\n______________AGCAC__AGAAAGU___CG_____UAUCAGGGAAUUUGA\n______________\|\|\|\|\|__\|:\|\|\|:\|___\|\|_____:\|:\|\|\|\|:\|\|\|:\|\|\|\n______________UCGUG__UUUUUUA___GC_____GUGGUCCUUUAGACU\n3'-UUU...GUUCU_____AA_______A____AAU_________________ACACAA-5'\n_____________\|_______________________________________\|\n_____________42______________________________________6\n	188 -- 194	10 -- 16	-30.001 kcal/mol	8.83552 kcal/mol	9.22092 kcal/mol	158 198@LB@ \| \|@LB@5'-UUU...UUGUU GC CCG GCAAU GUUAU...CGA-3'@LB@ AGCAC AGAAAGU CG UAUCAGGGAAUUUGA@LB@ \|\|\|\|\| \|:\|\|\|:\| \|\| :\|:\|\|\|\|:\|\|\|:\|\|\|@LB@ UCGUG UUUUUUA GC GUGGUCCUUUAGACU@LB@3'-UUU...GUUCU AA A AAU ACACAA-5'@LB@ \| \|@LB@ 42 6@LB@@LB@@LB@Energy -11.94 kcal/mol@LB@Hybridization Energy -30.001 kcal/mol@LB@Unfolding Energy - mRNA 8.83552 kcal/mol@LB@Unfolding Energy - sRNA 9.22092 kcal/mol@LB@@LB@Position - mRNA 159 -- 197@LB@Position - sRNA 7 -- 41@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 10 -- 16@LB@
52	0.002466	0.1527	b3527	yhjJ	-8.40	0.046956	207 -- 220	25 -- 41	putative periplasmic M16 family chaperone	_____________206_______________221\n_____________\|_________________\|\n5'-CUC...UGCAG_________________ACUUU...GGC-3'\n______________GGCAC___AAAAAUUCG\n______________:\|\|\|\|___\|\|\|\|\|\|\|\|\|\n______________UCGUG___UUUUUAAGC\n3'-UUU...GUUCU_____AAU_________AAUGU...CAA-5'\n_____________\|_________________\|\n_____________42________________24\n	214 -- 220	25 -- 31	-13.4116 kcal/mol	3.36563 kcal/mol	1.64839 kcal/mol	206 221@LB@ \| \|@LB@5'-CUC...UGCAG ACUUU...GGC-3'@LB@ GGCAC AAAAAUUCG@LB@ :\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ UCGUG UUUUUAAGC@LB@3'-UUU...GUUCU AAU AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -13.4116 kcal/mol@LB@Unfolding Energy - mRNA 3.36563 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 207 -- 220@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 25 -- 31@LB@
13	0.0002543	0.06302	b3583	sgbE	-8.82	0.035786	171 -- 191	39 -- 61	L-ribulose-5-phosphate 4-epimerase	_____________170_____________________192\n_____________\|_______________________\|\n5'-CAA...UGGAU__________GUAU_________UGGAU...ACG-3'\n______________UGAAGC__GC____GCAGGAGGC\n______________\|\|\|\|:\|__\|\|____\|\|\|:\|\|:\|\|\n______________ACUUUG__CG____CGUUCUUCG\n3'-UUU...GCCCU______AA__AAUU_________UGAAU...CAA-5'\n_____________\|_______________________\|\n_____________62______________________38\n	185 -- 191	39 -- 45	-21.2799 kcal/mol	5.20492 kcal/mol	7.25518 kcal/mol	170 192@LB@ \| \|@LB@5'-CAA...UGGAU GUAU UGGAU...ACG-3'@LB@ UGAAGC GC GCAGGAGGC@LB@ \|\|\|\|:\| \|\| \|\|\|:\|\|:\|\|@LB@ ACUUUG CG CGUUCUUCG@LB@3'-UUU...GCCCU AA AAUU UGAAU...CAA-5'@LB@ \| \|@LB@ 62 38@LB@@LB@@LB@Energy -8.82 kcal/mol@LB@Hybridization Energy -21.2799 kcal/mol@LB@Unfolding Energy - mRNA 5.20492 kcal/mol@LB@Unfolding Energy - sRNA 7.25518 kcal/mol@LB@@LB@Position - mRNA 171 -- 191@LB@Position - sRNA 39 -- 61@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 39 -- 45@LB@
144	0.01453	0.3231	b3614	yibQ	-4.49	0.404320	261 -- 267	34 -- 40	putative polysaccharide deacetylase	_____________260_____268\n_____________\|_______\|\n5'-UGG...CCCCC_______CUGGC...UUG-3'\n______________GUACUUG\n______________\|:\|\|\|\|:\n______________CGUGAAU\n3'-UUU...UUCUU_______UUUUU...CAA-5'\n_____________\|_______\|\n_____________41______33\n	261 -- 267	34 -- 40	-7.10274 kcal/mol	0.998159 kcal/mol	1.61352 kcal/mol	260 268@LB@ \| \|@LB@5'-UGG...CCCCC CUGGC...UUG-3'@LB@ GUACUUG@LB@ \|:\|\|\|\|:@LB@ CGUGAAU@LB@3'-UUU...UUCUU UUUUU...CAA-5'@LB@ \| \|@LB@ 41 33@LB@@LB@@LB@Energy -4.49 kcal/mol@LB@Hybridization Energy -7.10274 kcal/mol@LB@Unfolding Energy - mRNA 0.998159 kcal/mol@LB@Unfolding Energy - sRNA 1.61352 kcal/mol@LB@@LB@Position - mRNA 261 -- 267@LB@Position - sRNA 34 -- 40@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 34 -- 40@LB@
127	0.01193	0.3024	b3625	waaY	-10.33	0.012897	24 -- 38	26 -- 41	lipopolysaccharide core biosynthesis protein	_____________23_______________39\n_____________\|________________\|\n5'-CCA...AAAAU________________CCCCU...UAA-3'\n______________AGC_UUUAGAAAAUUC\n______________\|\|\|_:\|\|\|:\|\|\|\|\|\|\|\n______________UCG_GAAUUUUUUAAG\n3'-UUU...GUUCU___U____________CAAUG...CAA-5'\n_____________\|________________\|\n_____________42_______________25\n	32 -- 38	26 -- 32	-12.5754 kcal/mol	0.594404 kcal/mol	1.64829 kcal/mol	23 39@LB@ \| \|@LB@5'-CCA...AAAAU CCCCU...UAA-3'@LB@ AGC UUUAGAAAAUUC@LB@ \|\|\| :\|\|\|:\|\|\|\|\|\|\|@LB@ UCG GAAUUUUUUAAG@LB@3'-UUU...GUUCU U CAAUG...CAA-5'@LB@ \| \|@LB@ 42 25@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -12.5754 kcal/mol@LB@Unfolding Energy - mRNA 0.594404 kcal/mol@LB@Unfolding Energy - sRNA 1.64829 kcal/mol@LB@@LB@Position - mRNA 24 -- 38@LB@Position - sRNA 26 -- 41@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 26 -- 32@LB@
68	0.003533	0.1645	b3650	spoT	-9.27	0.026581	116 -- 140	36 -- 60	bifunctional (p)ppGpp synthetase II/ guanosine-3' 5'-bis pyrophosphate 3'-pyrophosphohydrolase	_____________115________________________141\n_____________\|__________________________\|\n5'-UAG...CGCCA_____A___AA___________C___GAAUU...CUC-3'\n______________GGAAC__GC__GAGCAGGAAGC_GCU\n______________\|:\|\|\|__\|\|__:\|\|\|\|:\|\|\|\|\|_:\|\|\n______________CUUUG__CG__UUCGUUCUUCG_UGA\n3'-UUU...CCCUA_____AA__AA_______________AUUUU...CAA-5'\n_____________\|__________________________\|\n_____________61_________________________35\n	130 -- 136	39 -- 45	-24.6059 kcal/mol	9.08429 kcal/mol	6.24973 kcal/mol	115 141@LB@ \| \|@LB@5'-UAG...CGCCA A AA C GAAUU...CUC-3'@LB@ GGAAC GC GAGCAGGAAGC GCU@LB@ \|:\|\|\| \|\| :\|\|\|\|:\|\|\|\|\| :\|\|@LB@ CUUUG CG UUCGUUCUUCG UGA@LB@3'-UUU...CCCUA AA AA AUUUU...CAA-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -9.27 kcal/mol@LB@Hybridization Energy -24.6059 kcal/mol@LB@Unfolding Energy - mRNA 9.08429 kcal/mol@LB@Unfolding Energy - sRNA 6.24973 kcal/mol@LB@@LB@Position - mRNA 116 -- 140@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 39 -- 45@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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