Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
101	0.009525	0.3118	b2101	yegW	-12.09	0.042153	47 -- 73	39 -- 66	putative DNA-binding transcriptional regulator	_____________46____________________________74\n_____________\|_____________________________\|\n5'-CGG...GACCG____CAGG___A_____U___________GGUGG...AAA-3'\n______________UGGA____UAG_UGGCA___CAAUGGUCC\n______________\|\|\|\|____:\|\|_\|\|\|\|\|___\|\|\|\|\|\|:\|\|\n______________ACCU____GUC_ACCGU___GUUACCGGG\n3'-UUU...AUACA____UUUA_________UAC_________UUGUC...UUG-5'\n_____________\|_____________________________\|\n_____________67____________________________38\n	67 -- 73	39 -- 45	-28.0375 kcal/mol	9.27172 kcal/mol	6.67256 kcal/mol	46 74@LB@ \| \|@LB@5'-CGG...GACCG CAGG A U GGUGG...AAA-3'@LB@ UGGA UAG UGGCA CAAUGGUCC@LB@ \|\|\|\| :\|\| \|\|\|\|\| \|\|\|\|\|\|:\|\|@LB@ ACCU GUC ACCGU GUUACCGGG@LB@3'-UUU...AUACA UUUA UAC UUGUC...UUG-5'@LB@ \| \|@LB@ 67 38@LB@@LB@@LB@Energy -12.09 kcal/mol@LB@Hybridization Energy -28.0375 kcal/mol@LB@Unfolding Energy - mRNA 9.27172 kcal/mol@LB@Unfolding Energy - sRNA 6.67256 kcal/mol@LB@@LB@Position - mRNA 47 -- 73@LB@Position - sRNA 39 -- 66@LB@Position Seed - mRNA 67 -- 73@LB@Position Seed - sRNA 39 -- 45@LB@
119	0.01177	0.3326	b4262	lptG	-9.06	0.186805	47 -- 70	7 -- 29	lipopolysaccharide export ABC permease	_____________46_______________________71\n_____________\|________________________\|\n5'-CCA...CUCCC_______GAAC_____________AGCUG...UCA-3'\n______________UGAAAUC____GGCGGUAAAGGUA\n______________\|:\|\|\|\|\|____\|:\|::\|\|\|\|\|\|:\|\n______________AUUUUAG____CUGUUAUUUCCGU\n3'-UUU...CUUUU_______ACA______________AUAUUG-5'\n_____________\|________________________\|\n_____________30_______________________6\n	64 -- 70	7 -- 13	-21.2282 kcal/mol	7.28231 kcal/mol	4.88318 kcal/mol	46 71@LB@ \| \|@LB@5'-CCA...CUCCC GAAC AGCUG...UCA-3'@LB@ UGAAAUC GGCGGUAAAGGUA@LB@ \|:\|\|\|\|\| \|:\|::\|\|\|\|\|\|:\|@LB@ AUUUUAG CUGUUAUUUCCGU@LB@3'-UUU...CUUUU ACA AUAUUG-5'@LB@ \| \|@LB@ 30 6@LB@@LB@@LB@Energy -9.06 kcal/mol@LB@Hybridization Energy -21.2282 kcal/mol@LB@Unfolding Energy - mRNA 7.28231 kcal/mol@LB@Unfolding Energy - sRNA 4.88318 kcal/mol@LB@@LB@Position - mRNA 47 -- 70@LB@Position - sRNA 7 -- 29@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 7 -- 13@LB@
103	0.009615	0.3118	b4045	yjbJ	-8.83	0.207064	48 -- 67	39 -- 60	stress-induced protein UPF0337 family	_____________47______________________68\n_____________\|_______________________\|\n5'-CGU...GCGGC____C_______________A__UGGUU...AAG-3'\n______________GUCA_UGGC___GCAAUGGU_CC\n______________:\|\|\|_\|\|\|\|___\|\|\|\|\|\|\|:_\|\|\n______________UAGU_ACCG___CGUUACCG_GG\n3'-UUU...CCUUU____C____UUA___________UUGUC...UUG-5'\n_____________\|_______________________\|\n_____________61______________________38\n	58 -- 64	41 -- 47	-22.6105 kcal/mol	7.1744 kcal/mol	6.61009 kcal/mol	47 68@LB@ \| \|@LB@5'-CGU...GCGGC C A UGGUU...AAG-3'@LB@ GUCA UGGC GCAAUGGU CC@LB@ :\|\|\| \|\|\|\| \|\|\|\|\|\|\|: \|\|@LB@ UAGU ACCG CGUUACCG GG@LB@3'-UUU...CCUUU C UUA UUGUC...UUG-5'@LB@ \| \|@LB@ 61 38@LB@@LB@@LB@Energy -8.83 kcal/mol@LB@Hybridization Energy -22.6105 kcal/mol@LB@Unfolding Energy - mRNA 7.1744 kcal/mol@LB@Unfolding Energy - sRNA 6.61009 kcal/mol@LB@@LB@Position - mRNA 48 -- 67@LB@Position - sRNA 39 -- 60@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 41 -- 47@LB@
193	0.02433	0.4239	b1125	potB	-7.71	0.326143	48 -- 60	50 -- 66	spermidine/putrescine ABC transporter permease	_____________47________________61\n_____________\|_________________\|\n5'-UCG...UGAAC_________________GAUGG...UUG-3'\n______________UGGAAAA____UGGCAA\n______________\|\|\|\|\|\|\|____\|\|\|\|\|\|\n______________ACCUUUU____ACCGUU\n3'-UUU...AUACA_______AGUC______ACGUU...UUG-5'\n_____________\|_________________\|\n_____________67________________49\n	48 -- 54	60 -- 66	-13.9172 kcal/mol	3.09187 kcal/mol	3.11877 kcal/mol	47 61@LB@ \| \|@LB@5'-UCG...UGAAC GAUGG...UUG-3'@LB@ UGGAAAA UGGCAA@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ ACCUUUU ACCGUU@LB@3'-UUU...AUACA AGUC ACGUU...UUG-5'@LB@ \| \|@LB@ 67 49@LB@@LB@@LB@Energy -7.71 kcal/mol@LB@Hybridization Energy -13.9172 kcal/mol@LB@Unfolding Energy - mRNA 3.09187 kcal/mol@LB@Unfolding Energy - sRNA 3.11877 kcal/mol@LB@@LB@Position - mRNA 48 -- 60@LB@Position - sRNA 50 -- 66@LB@Position Seed - mRNA 48 -- 54@LB@Position Seed - sRNA 60 -- 66@LB@
139	0.0159	0.3828	b2108	yehA	-9.84	0.131393	50 -- 60	55 -- 65	putative fimbrial-like adhesin protein	_____________49__________61\n_____________\|___________\|\n5'-GUU...GGCCA___________UAUUU...UUG-3'\n______________GGGAAGUCAGU\n______________\|\|:\|\|:\|\|\|\|\|\n______________CCUUUUAGUCA\n3'-UUU...UACAA___________CCGUU...UUG-5'\n_____________\|___________\|\n_____________66__________54\n	54 -- 60	55 -- 61	-13.8721 kcal/mol	3.08221 kcal/mol	0.952476 kcal/mol	49 61@LB@ \| \|@LB@5'-GUU...GGCCA UAUUU...UUG-3'@LB@ GGGAAGUCAGU@LB@ \|\|:\|\|:\|\|\|\|\|@LB@ CCUUUUAGUCA@LB@3'-UUU...UACAA CCGUU...UUG-5'@LB@ \| \|@LB@ 66 54@LB@@LB@@LB@Energy -9.84 kcal/mol@LB@Hybridization Energy -13.8721 kcal/mol@LB@Unfolding Energy - mRNA 3.08221 kcal/mol@LB@Unfolding Energy - sRNA 0.952476 kcal/mol@LB@@LB@Position - mRNA 50 -- 60@LB@Position - sRNA 55 -- 65@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 55 -- 61@LB@
159	0.01815	0.3828	b2418	pdxK	-7.58	0.341503	51 -- 77	38 -- 65	pyridoxal-pyridoxamine kinase/hydroxymethylpyrimidine kinase	_____________50___________________________78\n_____________\|____________________________\|\n5'-CAU...AACGG____U____UUA___________A____GACAA...GCA-3'\n______________GGAG_GUCA___GUAGUGUAAUG__CCA\n______________\|\|\|:_:\|\|\|___\|:\|:\|\|:\|\|\|\|__\|\|\|\n______________CCUU_UAGU___CGUUACGUUAC__GGU\n3'-UUU...UACAA____U____CAC___________CG___UGUCU...UUG-5'\n_____________\|____________________________\|\n_____________66___________________________37\n	67 -- 73	43 -- 49	-23.6415 kcal/mol	9.38399 kcal/mol	6.67322 kcal/mol	50 78@LB@ \| \|@LB@5'-CAU...AACGG U UUA A GACAA...GCA-3'@LB@ GGAG GUCA GUAGUGUAAUG CCA@LB@ \|\|\|: :\|\|\| \|:\|:\|\|:\|\|\|\| \|\|\|@LB@ CCUU UAGU CGUUACGUUAC GGU@LB@3'-UUU...UACAA U CAC CG UGUCU...UUG-5'@LB@ \| \|@LB@ 66 37@LB@@LB@@LB@Energy -7.58 kcal/mol@LB@Hybridization Energy -23.6415 kcal/mol@LB@Unfolding Energy - mRNA 9.38399 kcal/mol@LB@Unfolding Energy - sRNA 6.67322 kcal/mol@LB@@LB@Position - mRNA 51 -- 77@LB@Position - sRNA 38 -- 65@LB@Position Seed - mRNA 67 -- 73@LB@Position Seed - sRNA 43 -- 49@LB@
161	0.01858	0.3864	b3237	argR	-5.47	0.658327	53 -- 70	1 -- 21	l-arginine-responsive arginine metabolism regulon transcriptional regulator	_____________52____________________71\n_____________\|_____________________\|\n5'-ACA...AUGCC______C___________UU_UCAAU...UGC-3'\n______________GUGACG____AGGCAUGU__C\n______________\|\|\|\|\|:____\|\|\|\|\|\|:\|__\|\n______________CACUGU____UCCGUAUA__G\n3'-UUU...UUAGA______UAUU________UU_-5'\n_____________\|____________________\|\n_____________22___________________1\n	61 -- 67	4 -- 10	-16.8661 kcal/mol	6.97949 kcal/mol	4.41334 kcal/mol	52 71@LB@ \| \|@LB@5'-ACA...AUGCC C UU UCAAU...UGC-3'@LB@ GUGACG AGGCAUGU C@LB@ \|\|\|\|\|: \|\|\|\|\|\|:\| \|@LB@ CACUGU UCCGUAUA G@LB@3'-UUU...UUAGA UAUU UU -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -5.47 kcal/mol@LB@Hybridization Energy -16.8661 kcal/mol@LB@Unfolding Energy - mRNA 6.97949 kcal/mol@LB@Unfolding Energy - sRNA 4.41334 kcal/mol@LB@@LB@Position - mRNA 53 -- 70@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 61 -- 67@LB@Position Seed - sRNA 4 -- 10@LB@
122	0.01263	0.3462	b0537	intD	-10.49	0.096065	54 -- 80	48 -- 76	DLP12 prophage; putative phage integrase	_____________53____________________________81\n_____________\|_____________________________\|\n5'-GAG...AUUGG____________________A________ACGCA...AAG-3'\n______________UUUUGUAU_UUGGGGAG_CA_UGGCGAUG\n______________\|\|\|\|:\|\|\|_\|\|\|\|::\|:_\|\|_\|\|\|\|:\|\|\|\n______________AAAAUAUA_AACCUUUU_GU_ACCGUUAC\n3'-UUU...ACAGA________C________A__C________GUUAC...UUG-5'\n_____________\|_____________________________\|\n_____________77____________________________47\n	74 -- 80	48 -- 54	-25.3626 kcal/mol	9.83015 kcal/mol	5.0412 kcal/mol	53 81@LB@ \| \|@LB@5'-GAG...AUUGG A ACGCA...AAG-3'@LB@ UUUUGUAU UUGGGGAG CA UGGCGAUG@LB@ \|\|\|\|:\|\|\| \|\|\|\|::\|: \|\| \|\|\|\|:\|\|\|@LB@ AAAAUAUA AACCUUUU GU ACCGUUAC@LB@3'-UUU...ACAGA C A C GUUAC...UUG-5'@LB@ \| \|@LB@ 77 47@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -25.3626 kcal/mol@LB@Unfolding Energy - mRNA 9.83015 kcal/mol@LB@Unfolding Energy - sRNA 5.0412 kcal/mol@LB@@LB@Position - mRNA 54 -- 80@LB@Position - sRNA 48 -- 76@LB@Position Seed - mRNA 74 -- 80@LB@Position Seed - sRNA 48 -- 54@LB@
135	0.01531	0.3774	b3224	nanT	-10.34	0.103537	56 -- 77	28 -- 54	sialic acid transporter	_____________55__________________________78\n_____________\|___________________________\|\n5'-CGC...CUGAA_____________________UU____CAAGA...GUU-3'\n______________GGC___GC__UGGCCCAGCAG__GAUG\n______________\|\|\|___\|\|__\|\|\|\|\|\|\|:\|\|\|__:\|\|:\n______________CCG___CG__ACCGGGUUGUC__UUAU\n3'-UUU...AGUCA___UUA__UU___________UU____UUUAG...UUG-5'\n_____________\|___________________________\|\n_____________55__________________________27\n	63 -- 69	36 -- 42	-28.0045 kcal/mol	8.68418 kcal/mol	8.98285 kcal/mol	55 78@LB@ \| \|@LB@5'-CGC...CUGAA UU CAAGA...GUU-3'@LB@ GGC GC UGGCCCAGCAG GAUG@LB@ \|\|\| \|\| \|\|\|\|\|\|\|:\|\|\| :\|\|:@LB@ CCG CG ACCGGGUUGUC UUAU@LB@3'-UUU...AGUCA UUA UU UU UUUAG...UUG-5'@LB@ \| \|@LB@ 55 27@LB@@LB@@LB@Energy -10.34 kcal/mol@LB@Hybridization Energy -28.0045 kcal/mol@LB@Unfolding Energy - mRNA 8.68418 kcal/mol@LB@Unfolding Energy - sRNA 8.98285 kcal/mol@LB@@LB@Position - mRNA 56 -- 77@LB@Position - sRNA 28 -- 54@LB@Position Seed - mRNA 63 -- 69@LB@Position Seed - sRNA 36 -- 42@LB@
56	0.003989	0.237	b0453	ybaY	-12.27	0.038324	59 -- 73	39 -- 55	outer membrane lipoprotein	_____________58________________74\n_____________\|_________________\|\n5'-AAG...UCCGA_________________GAAUU...CAA-3'\n______________UGG__GUGCAAUGGUCU\n______________\|\|\|__:\|\|\|\|\|\|\|\|:\|:\n______________ACC__UACGUUACCGGG\n3'-UUU...UAGUC___GU____________UUGUC...UUG-5'\n_____________\|_________________\|\n_____________56________________38\n	67 -- 73	39 -- 45	-20.8095 kcal/mol	3.77686 kcal/mol	4.76312 kcal/mol	58 74@LB@ \| \|@LB@5'-AAG...UCCGA GAAUU...CAA-3'@LB@ UGG GUGCAAUGGUCU@LB@ \|\|\| :\|\|\|\|\|\|\|\|:\|:@LB@ ACC UACGUUACCGGG@LB@3'-UUU...UAGUC GU UUGUC...UUG-5'@LB@ \| \|@LB@ 56 38@LB@@LB@@LB@Energy -12.27 kcal/mol@LB@Hybridization Energy -20.8095 kcal/mol@LB@Unfolding Energy - mRNA 3.77686 kcal/mol@LB@Unfolding Energy - sRNA 4.76312 kcal/mol@LB@@LB@Position - mRNA 59 -- 73@LB@Position - sRNA 39 -- 55@LB@Position Seed - mRNA 67 -- 73@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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