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
31	0.001906	0.2067	b0198	metI	-9.82	0.132421	237 -- 257	48 -- 68	DL-methionine transporter subunit	_____________236____________________258\n_____________\|______________________\|\n5'-UCA...GUGGC__A__________C________ACCUU...CGG-3'\n______________GU_UGGGAAA_CG_UGGCAAUG\n______________\|\|_\|\|\|:\|\|\|_\|:_\|\|\|\|\|\|\|\|\n______________CA_ACCUUUU_GU_ACCGUUAC\n3'-UUU...AUAUA__________A__C________GUUAC...UUG-5'\n_____________\|______________________\|\n_____________69_____________________47\n	251 -- 257	48 -- 54	-20.2902 kcal/mol	6.26471 kcal/mol	4.20468 kcal/mol	236 258@LB@ \| \|@LB@5'-UCA...GUGGC A C ACCUU...CGG-3'@LB@ GU UGGGAAA CG UGGCAAUG@LB@ \|\| \|\|\|:\|\|\| \|: \|\|\|\|\|\|\|\|@LB@ CA ACCUUUU GU ACCGUUAC@LB@3'-UUU...AUAUA A C GUUAC...UUG-5'@LB@ \| \|@LB@ 69 47@LB@@LB@@LB@Energy -9.82 kcal/mol@LB@Hybridization Energy -20.2902 kcal/mol@LB@Unfolding Energy - mRNA 6.26471 kcal/mol@LB@Unfolding Energy - sRNA 4.20468 kcal/mol@LB@@LB@Position - mRNA 237 -- 257@LB@Position - sRNA 48 -- 68@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 48 -- 54@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@
183	0.02285	0.4143	b3262	yhdJ	-12.72	0.029953	3 -- 23	44 -- 69	DNA adenine methyltransferase SAM-dependent	_____________2__________________________24\n_____________\|__________________________\|\n_________5'-CC__________________________ACACC...GUG-3'\n______________UGUUGGA____CA_UGGUGAUGCAAU\n______________\|\|\|\|\|\|\|____\|\|_\|\|\|::\|\|\|\|\|\|\|\n______________ACAACCU____GU_ACCGUUACGUUA\n3'-UUU...AAUAU_______UUUA__C____________CCGGG...UUG-5'\n_____________\|__________________________\|\n_____________70_________________________43\n	17 -- 23	44 -- 50	-23.8856 kcal/mol	6.69358 kcal/mol	4.47358 kcal/mol	2 24@LB@ \| \|@LB@ 5'-CC ACACC...GUG-3'@LB@ UGUUGGA CA UGGUGAUGCAAU@LB@ \|\|\|\|\|\|\| \|\| \|\|\|::\|\|\|\|\|\|\|@LB@ ACAACCU GU ACCGUUACGUUA@LB@3'-UUU...AAUAU UUUA C CCGGG...UUG-5'@LB@ \| \|@LB@ 70 43@LB@@LB@@LB@Energy -12.72 kcal/mol@LB@Hybridization Energy -23.8856 kcal/mol@LB@Unfolding Energy - mRNA 6.69358 kcal/mol@LB@Unfolding Energy - sRNA 4.47358 kcal/mol@LB@@LB@Position - mRNA 3 -- 23@LB@Position - sRNA 44 -- 69@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 44 -- 50@LB@
93	0.008233	0.2977	b2669	stpA	-8.51	0.236304	244 -- 255	39 -- 50	DNA binding protein nucleoid-associated	_____________243__________256\n_____________\|____________\|\n5'-UUC...CCUCC____________GCGAA...UCA-3'\n______________GUGCGAUGGCUC\n______________:\|\|\|:\|\|\|\|\|:\|\n______________UACGUUACCGGG\n3'-UUU...ACCGU____________UUGUC...UUG-5'\n_____________\|____________\|\n_____________51___________38\n	249 -- 255	39 -- 45	-19.1222 kcal/mol	5.86982 kcal/mol	4.73799 kcal/mol	243 256@LB@ \| \|@LB@5'-UUC...CCUCC GCGAA...UCA-3'@LB@ GUGCGAUGGCUC@LB@ :\|\|\|:\|\|\|\|\|:\|@LB@ UACGUUACCGGG@LB@3'-UUU...ACCGU UUGUC...UUG-5'@LB@ \| \|@LB@ 51 38@LB@@LB@@LB@Energy -8.51 kcal/mol@LB@Hybridization Energy -19.1222 kcal/mol@LB@Unfolding Energy - mRNA 5.86982 kcal/mol@LB@Unfolding Energy - sRNA 4.73799 kcal/mol@LB@@LB@Position - mRNA 244 -- 255@LB@Position - sRNA 39 -- 50@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 39 -- 45@LB@
98	0.009218	0.3118	b3391	hofQ	-10.83	0.081241	8 -- 57	7 -- 65	DNA catabolic putative fimbrial transporter	_____________7_____________________________________________________________58\n_____________\|_____________________________________________________________\|\n____5'-CUAUCAG____UGG_________G____GC__A___U___UGU_________________________AAAGA...UAG-3'\n______________GGGA___UAG_GGCGA_GCGA__GC_UCA_CGG___AAUAAAA_____GAC_____GGGCA\n______________\|\|:\|___:\|\|_\|\|\|:\|_\|\|:\|__\|\|_:\|\|_\|:\|___\|\|\|\|\|\|\|_____\|\|\|_____:\|\|\|\|\n______________CCUU___GUC_CCGUU_CGUU__CG_GGU_GUC___UUAUUUU_____CUG_____UCCGU\n3'-UUU...UACAA____UUA___A_____A____AC______U___UU________AGACA___UUAUU_____AUAUUG-5'\n_____________\|_____________________________________________________________\|\n_____________66____________________________________________________________6\n	43 -- 49	25 -- 31	-34.6984 kcal/mol	11.715 kcal/mol	12.1538 kcal/mol	7 58@LB@ \| \|@LB@ 5'-CUAUCAG UGG G GC A U UGU AAAGA...UAG-3'@LB@ GGGA UAG GGCGA GCGA GC UCA CGG AAUAAAA GAC GGGCA@LB@ \|\|:\| :\|\| \|\|\|:\| \|\|:\| \|\| :\|\| \|:\| \|\|\|\|\|\|\| \|\|\| :\|\|\|\|@LB@ CCUU GUC CCGUU CGUU CG GGU GUC UUAUUUU CUG UCCGU@LB@3'-UUU...UACAA UUA A A AC U UU AGACA UUAUU AUAUUG-5'@LB@ \| \|@LB@ 66 6@LB@@LB@@LB@Energy -10.83 kcal/mol@LB@Hybridization Energy -34.6984 kcal/mol@LB@Unfolding Energy - mRNA 11.715 kcal/mol@LB@Unfolding Energy - sRNA 12.1538 kcal/mol@LB@@LB@Position - mRNA 8 -- 57@LB@Position - sRNA 7 -- 65@LB@Position Seed - mRNA 43 -- 49@LB@Position Seed - sRNA 25 -- 31@LB@
46	0.003168	0.2306	b3066	dnaG	-7.10	0.407270	188 -- 205	41 -- 63	DNA primase	_____________187_____________________206\n_____________\|_______________________\|\n5'-ACC...UGCUA____________CU_________UGGAC...GCA-3'\n______________AAAAUCGG_GGC______AUGGC\n______________\|\|\|\|\|\|:\|_\|\|\|______\|\|\|\|\|\n______________UUUUAGUC_CCG______UACCG\n3'-UUU...CAACC________A___UUACGU_____GGUUG...UUG-5'\n_____________\|_______________________\|\n_____________64______________________40\n	189 -- 195	56 -- 62	-16.4791 kcal/mol	5.10709 kcal/mol	4.27657 kcal/mol	187 206@LB@ \| \|@LB@5'-ACC...UGCUA CU UGGAC...GCA-3'@LB@ AAAAUCGG GGC AUGGC@LB@ \|\|\|\|\|\|:\| \|\|\| \|\|\|\|\|@LB@ UUUUAGUC CCG UACCG@LB@3'-UUU...CAACC A UUACGU GGUUG...UUG-5'@LB@ \| \|@LB@ 64 40@LB@@LB@@LB@Energy -7.10 kcal/mol@LB@Hybridization Energy -16.4791 kcal/mol@LB@Unfolding Energy - mRNA 5.10709 kcal/mol@LB@Unfolding Energy - sRNA 4.27657 kcal/mol@LB@@LB@Position - mRNA 188 -- 205@LB@Position - sRNA 41 -- 63@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 56 -- 62@LB@
146	0.01679	0.3828	b2699	recA	-5.90	0.590167	190 -- 206	40 -- 58	DNA recombination and repair protein; ssDNA-dependent ATPase; synaptase; ssDNA and dsDNA binding protein; ATP-dependent homologous DNA strand exchanger; recombinase A; LexA autocleavage cofactor	_____________189_________________207\n_____________\|___________________\|\n5'-UGC...CAUGA___GA____A_________AUCGA...ACC-3'\n______________CAG__GUAA___AAUGGCU\n______________\|\|\|__\|:\|\|___\|\|\|\|\|\|:\n______________GUC__CGUU___UUACCGG\n3'-UUU...UUUUA___AC____ACG_______GUUGU...UUG-5'\n_____________\|___________________\|\n_____________59__________________39\n	200 -- 206	40 -- 46	-15.424 kcal/mol	3.45581 kcal/mol	6.06808 kcal/mol	189 207@LB@ \| \|@LB@5'-UGC...CAUGA GA A AUCGA...ACC-3'@LB@ CAG GUAA AAUGGCU@LB@ \|\|\| \|:\|\| \|\|\|\|\|\|:@LB@ GUC CGUU UUACCGG@LB@3'-UUU...UUUUA AC ACG GUUGU...UUG-5'@LB@ \| \|@LB@ 59 39@LB@@LB@@LB@Energy -5.90 kcal/mol@LB@Hybridization Energy -15.424 kcal/mol@LB@Unfolding Energy - mRNA 3.45581 kcal/mol@LB@Unfolding Energy - sRNA 6.06808 kcal/mol@LB@@LB@Position - mRNA 190 -- 206@LB@Position - sRNA 40 -- 58@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 40 -- 46@LB@
12	0.0004505	0.1262	b3248	yhdE	-11.12	0.070056	184 -- 205	1 -- 21	dTTP/UTP pyrophosphatase; m(5)UTP/m(5)CTP/pseudo-UTP pyrophosphatase	_____________183_____________________206\n_____________\|_______________________\|\n5'-UUA...UUGCA______________UUC______UUCUC...AGC-3'\n______________GUG_CAAUAAAGGU___UAUGAC\n______________\|\|\|_\|\|\|\|\|\|\|\|\|:___\|\|\|:\|\|\n______________CAC_GUUAUUUCCG___AUAUUG\n3'-UUU...UUAGA___U__________U________-5'\n_____________\|______________________\|\n_____________22_____________________1\n	190 -- 196	8 -- 14	-19.9684 kcal/mol	4.43203 kcal/mol	4.41334 kcal/mol	183 206@LB@ \| \|@LB@5'-UUA...UUGCA UUC UUCUC...AGC-3'@LB@ GUG CAAUAAAGGU UAUGAC@LB@ \|\|\| \|\|\|\|\|\|\|\|\|: \|\|\|:\|\|@LB@ CAC GUUAUUUCCG AUAUUG@LB@3'-UUU...UUAGA U U -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -19.9684 kcal/mol@LB@Unfolding Energy - mRNA 4.43203 kcal/mol@LB@Unfolding Energy - sRNA 4.41334 kcal/mol@LB@@LB@Position - mRNA 184 -- 205@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 8 -- 14@LB@
4	6.145e-05	0.05167	b4217	ytfK	-14.33	0.011783	150 -- 205	11 -- 68	DUF1107 family protein	_____________149________________________________________________________________206\n_____________\|__________________________________________________________________\|\n5'-GAA...UAAUA______CC___________CC___CA___GUAAUAC______________________________AAUUU...AAU-3'\n______________GUUGGG__GAUU_GUGGCA__GCA__GGC_______UCAGCAGGAGAUA_________ACAAUGAA\n______________\|\|\|\|\|:__:\|\|:_\|\|\|\|\|\|__\|\|\|__\|\|\|_______:\|\|:\|\|\|:\|:\|\|\|_________\|\|\|\|\|:\|\|\n______________CAACCU__UUAG_CACCGU__CGU__CCG_______GGUUGUCUUUUAU_________UGUUAUUU\n3'-UUU...AUAUA______U_____U______UA___UA_______________________UUUAGACAC________CCGUA...UUG-5'\n_____________\|__________________________________________________________________\|\n_____________69_________________________________________________________________10\n	199 -- 205	11 -- 17	-43.2853 kcal/mol	16.8726 kcal/mol	12.0809 kcal/mol	149 206@LB@ \| \|@LB@5'-GAA...UAAUA CC CC CA GUAAUAC AAUUU...AAU-3'@LB@ GUUGGG GAUU GUGGCA GCA GGC UCAGCAGGAGAUA ACAAUGAA@LB@ \|\|\|\|\|: :\|\|: \|\|\|\|\|\| \|\|\| \|\|\| :\|\|:\|\|\|:\|:\|\|\| \|\|\|\|\|:\|\|@LB@ CAACCU UUAG CACCGU CGU CCG GGUUGUCUUUUAU UGUUAUUU@LB@3'-UUU...AUAUA U U UA UA UUUAGACAC CCGUA...UUG-5'@LB@ \| \|@LB@ 69 10@LB@@LB@@LB@Energy -14.33 kcal/mol@LB@Hybridization Energy -43.2853 kcal/mol@LB@Unfolding Energy - mRNA 16.8726 kcal/mol@LB@Unfolding Energy - sRNA 12.0809 kcal/mol@LB@@LB@Position - mRNA 150 -- 205@LB@Position - sRNA 11 -- 68@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 11 -- 17@LB@
148	0.01733	0.3828	b1760	ynjH	-7.42	0.362448	2 -- 64	11 -- 71	DUF1496 family protein	_____________1________________________________________________________________65\n_____________\|________________________________________________________________\|\n__________5'-U_______UUUAU____U___CUUU______U_______UAUACCAUCAAGAA____________CAAGA...AAG-3'\n______________UAUGUUG_____GUCA_GUG____UGCAGU__UUCGAC______________UGUGACGGUAAG\n______________\|\|\|\|\|\|\|_____:\|\|\|_\|\|\|____\|\|\|\|:\|__::\|:\|\|______________\|\|\|\|\|\|::\|\|\|:\n______________AUACAAC_____UAGU_CAC____ACGUUA__GGGUUG______________ACACUGUUAUUU\n3'-UUU...AAAAU_______CUUU_________CGUU______CC______UCUUUUAUUUUAG_____________CCGUA...UUG-5'\n_____________\|________________________________________________________________\|\n_____________72_______________________________________________________________10\n	58 -- 64	11 -- 17	-35.6179 kcal/mol	16.0903 kcal/mol	12.1045 kcal/mol	1 65@LB@ \| \|@LB@ 5'-U UUUAU U CUUU U UAUACCAUCAAGAA CAAGA...AAG-3'@LB@ UAUGUUG GUCA GUG UGCAGU UUCGAC UGUGACGGUAAG@LB@ \|\|\|\|\|\|\| :\|\|\| \|\|\| \|\|\|\|:\| ::\|:\|\| \|\|\|\|\|\|::\|\|\|:@LB@ AUACAAC UAGU CAC ACGUUA GGGUUG ACACUGUUAUUU@LB@3'-UUU...AAAAU CUUU CGUU CC UCUUUUAUUUUAG CCGUA...UUG-5'@LB@ \| \|@LB@ 72 10@LB@@LB@@LB@Energy -7.42 kcal/mol@LB@Hybridization Energy -35.6179 kcal/mol@LB@Unfolding Energy - mRNA 16.0903 kcal/mol@LB@Unfolding Energy - sRNA 12.1045 kcal/mol@LB@@LB@Position - mRNA 2 -- 64@LB@Position - sRNA 11 -- 71@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 11 -- 17@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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