Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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	0.01011	0.2071	b4086	alsC	-10.38	0.118114	189 -- 207	53 -- 70	D-allose ABC transporter permease	_____________188_________________208\n_____________\|___________________\|\n5'-CGC...GAAGA_______A____A__G___UUACC...CGA-3'\n______________GGAGAUU_UGGC_UG_GCU\n______________\|\|\|:\|\|:_\|\|\|\|_\|\|_\|\|:\n______________CCUUUAG_ACCG_AC_CGG\n3'-UUU...UGGUC_______A_______G___CAUUU...GUG-5'\n_____________\|___________________\|\n_____________71__________________52\n	189 -- 195	64 -- 70	-21.9341 kcal/mol	4.72392 kcal/mol	6.83419 kcal/mol	188 208@LB@ \| \|@LB@5'-CGC...GAAGA A A G UUACC...CGA-3'@LB@ GGAGAUU UGGC UG GCU@LB@ \|\|\|:\|\|: \|\|\|\| \|\| \|\|:@LB@ CCUUUAG ACCG AC CGG@LB@3'-UUU...UGGUC A G CAUUU...GUG-5'@LB@ \| \|@LB@ 71 52@LB@@LB@@LB@Energy -10.38 kcal/mol@LB@Hybridization Energy -21.9341 kcal/mol@LB@Unfolding Energy - mRNA 4.72392 kcal/mol@LB@Unfolding Energy - sRNA 6.83419 kcal/mol@LB@@LB@Position - mRNA 189 -- 207@LB@Position - sRNA 53 -- 70@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 64 -- 70@LB@
172	0.0102	0.2071	b1383	ydbL	-9.96	0.141752	21 -- 31	52 -- 62	DUF1318 family protein	_____________20__________32\n_____________\|___________\|\n5'-AAA...UUUAC___________ACGUC...UAG-3'\n______________UGGCUGCGUUG\n______________\|\|\|\|\|\|\|\|::\|\n______________ACCGACGCGGC\n3'-UUU...UUAGA___________AUUUA...GUG-5'\n_____________\|___________\|\n_____________63__________51\n	25 -- 31	52 -- 58	-19.6889 kcal/mol	4.85225 kcal/mol	4.8804 kcal/mol	20 32@LB@ \| \|@LB@5'-AAA...UUUAC ACGUC...UAG-3'@LB@ UGGCUGCGUUG@LB@ \|\|\|\|\|\|\|\|::\|@LB@ ACCGACGCGGC@LB@3'-UUU...UUAGA AUUUA...GUG-5'@LB@ \| \|@LB@ 63 51@LB@@LB@@LB@Energy -9.96 kcal/mol@LB@Hybridization Energy -19.6889 kcal/mol@LB@Unfolding Energy - mRNA 4.85225 kcal/mol@LB@Unfolding Energy - sRNA 4.8804 kcal/mol@LB@@LB@Position - mRNA 21 -- 31@LB@Position - sRNA 52 -- 62@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 52 -- 58@LB@
173	0.01023	0.2071	b3297	rpsK	-11.54	0.070538	32 -- 43	48 -- 59	30S ribosomal subunit protein S11	_____________31___________44\n_____________\|____________\|\n5'-CGA...GUGAU____________AUCAG...CUA-3'\n______________CUGCGCCGUGAA\n______________\|\|\|\|\|\|\|\|\|:\|\|\n______________GACGCGGCAUUU\n3'-UUU...GAACC____________AAUAA...GUG-5'\n_____________\|____________\|\n_____________60___________47\n	37 -- 43	48 -- 54	-20.6796 kcal/mol	2.9935 kcal/mol	6.14631 kcal/mol	31 44@LB@ \| \|@LB@5'-CGA...GUGAU AUCAG...CUA-3'@LB@ CUGCGCCGUGAA@LB@ \|\|\|\|\|\|\|\|\|:\|\|@LB@ GACGCGGCAUUU@LB@3'-UUU...GAACC AAUAA...GUG-5'@LB@ \| \|@LB@ 60 47@LB@@LB@@LB@Energy -11.54 kcal/mol@LB@Hybridization Energy -20.6796 kcal/mol@LB@Unfolding Energy - mRNA 2.9935 kcal/mol@LB@Unfolding Energy - sRNA 6.14631 kcal/mol@LB@@LB@Position - mRNA 32 -- 43@LB@Position - sRNA 48 -- 59@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 48 -- 54@LB@
174	0.01024	0.2071	b0889	lrp	-11.01	0.089440	79 -- 112	38 -- 78	leucine-responsive global transcriptional regulator	_____________78________________________________________113\n_____________\|_________________________________________\|\n5'-GUG...CCGUA_________C______________________CU_C_____UUCGG...AGC-3'\n______________GAC_CCAGG___AUU___GC_GCGCCGUGAAU__U_AUGAU\n______________:\|\|_\|\|\|\|\|___\|\|:___\|\|_\|\|\|\|\|\|\|:\|\|\|__\|_\|\|\|\|\|\n______________UUG_GGUCC___UAG___CG_CGCGGCAUUUA__A_UACUA\n3'-UUU...CGCGG___U_____CUU___AAC__A___________AU_A_____CUCAA...GUG-5'\n_____________\|_________________________________________\|\n_____________79________________________________________37\n	96 -- 102	48 -- 54	-32.0055 kcal/mol	11.6338 kcal/mol	9.36467 kcal/mol	78 113@LB@ \| \|@LB@5'-GUG...CCGUA C CU C UUCGG...AGC-3'@LB@ GAC CCAGG AUU GC GCGCCGUGAAU U AUGAU@LB@ :\|\| \|\|\|\|\| \|\|: \|\| \|\|\|\|\|\|\|:\|\|\| \| \|\|\|\|\|@LB@ UUG GGUCC UAG CG CGCGGCAUUUA A UACUA@LB@3'-UUU...CGCGG U CUU AAC A AU A CUCAA...GUG-5'@LB@ \| \|@LB@ 79 37@LB@@LB@@LB@Energy -11.01 kcal/mol@LB@Hybridization Energy -32.0055 kcal/mol@LB@Unfolding Energy - mRNA 11.6338 kcal/mol@LB@Unfolding Energy - sRNA 9.36467 kcal/mol@LB@@LB@Position - mRNA 79 -- 112@LB@Position - sRNA 38 -- 78@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 48 -- 54@LB@
175	0.01031	0.2074	b1834	yebT	-10.32	0.121003	270 -- 282	51 -- 62	MCE domain protein	_____________269___________283\n_____________\|_____________\|\n5'-UCU...CUUUC_______U_____UCAUC...UUG-3'\n______________UGGCUGC_GCCGU\n______________\|\|\|\|\|\|\|_\|\|\|\|\|\n______________ACCGACG_CGGCA\n3'-UUU...UUAGA_____________UUUAA...GUG-5'\n_____________\|_____________\|\n_____________63____________50\n	270 -- 276	56 -- 62	-21.4836 kcal/mol	6.28034 kcal/mol	4.8826 kcal/mol	269 283@LB@ \| \|@LB@5'-UCU...CUUUC U UCAUC...UUG-3'@LB@ UGGCUGC GCCGU@LB@ \|\|\|\|\|\|\| \|\|\|\|\|@LB@ ACCGACG CGGCA@LB@3'-UUU...UUAGA UUUAA...GUG-5'@LB@ \| \|@LB@ 63 50@LB@@LB@@LB@Energy -10.32 kcal/mol@LB@Hybridization Energy -21.4836 kcal/mol@LB@Unfolding Energy - mRNA 6.28034 kcal/mol@LB@Unfolding Energy - sRNA 4.8826 kcal/mol@LB@@LB@Position - mRNA 270 -- 282@LB@Position - sRNA 51 -- 62@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 56 -- 62@LB@
176	0.01044	0.208	b0933	ssuB	-9.69	0.158756	203 -- 226	69 -- 90	aliphatic sulfonate ABC transporter ATPase	_____________202______________________227\n_____________\|________________________\|\n5'-AUU...GGUAU_________UC___UGA_______CACGC...AUA-3'\n______________GAAUACUGC__GUC___ACCAGGG\n______________\|\|\|\|\|\|\|\|\|__\|:\|___\|\|\|\|\|\|\|\n______________CUUAUGACG__CGG___UGGUCCC\n3'-UUU...ACGCG______________UUG_______UUUAG...GUG-5'\n_____________\|________________________\|\n_____________91_______________________68\n	220 -- 226	69 -- 75	-28.101 kcal/mol	8.24441 kcal/mol	10.1628 kcal/mol	202 227@LB@ \| \|@LB@5'-AUU...GGUAU UC UGA CACGC...AUA-3'@LB@ GAAUACUGC GUC ACCAGGG@LB@ \|\|\|\|\|\|\|\|\| \|:\| \|\|\|\|\|\|\|@LB@ CUUAUGACG CGG UGGUCCC@LB@3'-UUU...ACGCG UUG UUUAG...GUG-5'@LB@ \| \|@LB@ 91 68@LB@@LB@@LB@Energy -9.69 kcal/mol@LB@Hybridization Energy -28.101 kcal/mol@LB@Unfolding Energy - mRNA 8.24441 kcal/mol@LB@Unfolding Energy - sRNA 10.1628 kcal/mol@LB@@LB@Position - mRNA 203 -- 226@LB@Position - sRNA 69 -- 90@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 69 -- 75@LB@
177	0.01048	0.208	b2416	ptsI	-10.21	0.127224	180 -- 212	6 -- 36	PEP-protein phosphotransferase of PTS system (enzyme I)	_____________179________________________________213\n_____________\|__________________________________\|\n5'-GUG...AAAUC___C_____UAA____G___UA__A_________AUUUU...CCG-3'\n______________AGU_ACAAG___GGUA_GGU__UG__UUUCAGGC\n______________\|\|\|_\|\|\|\|\|___\|\|:\|_:\|:__\|\|__\|\|\|\|\|\|\|\|\n______________UCA_UGUUC___CCGU_UCG__AC__AAAGUCCG\n3'-UUU...ACUAC___A____________G___UG__AA________GCGUG-5'\n_____________\|__________________________________\|\n_____________37_________________________________5\n	206 -- 212	6 -- 12	-27.3223 kcal/mol	5.11839 kcal/mol	11.9979 kcal/mol	179 213@LB@ \| \|@LB@5'-GUG...AAAUC C UAA G UA A AUUUU...CCG-3'@LB@ AGU ACAAG GGUA GGU UG UUUCAGGC@LB@ \|\|\| \|\|\|\|\| \|\|:\| :\|: \|\| \|\|\|\|\|\|\|\|@LB@ UCA UGUUC CCGU UCG AC AAAGUCCG@LB@3'-UUU...ACUAC A G UG AA GCGUG-5'@LB@ \| \|@LB@ 37 5@LB@@LB@@LB@Energy -10.21 kcal/mol@LB@Hybridization Energy -27.3223 kcal/mol@LB@Unfolding Energy - mRNA 5.11839 kcal/mol@LB@Unfolding Energy - sRNA 11.9979 kcal/mol@LB@@LB@Position - mRNA 180 -- 212@LB@Position - sRNA 6 -- 36@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 6 -- 12@LB@
178	0.01053	0.208	b3582	sgbU	-5.91	0.640260	169 -- 196	65 -- 84	putative L-xylulose 5-phosphate 3-epimerase	_____________168__________________________197\n_____________\|____________________________\|\n5'-UCU...UUCCA_____AAAU_______AUCU________GCGCG...UUG-3'\n______________UGCGC____CGACGCU____GGGGAGGU\n______________\|\|\|\|\|____\|:\|\|:\|:____:\|\|\|\|::\|\n______________ACGCG____GUUGUGG____UCCCUUUA\n3'-UUU...UUAUG____________________________GAACC...GUG-5'\n_____________\|____________________________\|\n_____________85___________________________64\n	190 -- 196	65 -- 71	-23.9168 kcal/mol	10.6467 kcal/mol	7.36194 kcal/mol	168 197@LB@ \| \|@LB@5'-UCU...UUCCA AAAU AUCU GCGCG...UUG-3'@LB@ UGCGC CGACGCU GGGGAGGU@LB@ \|\|\|\|\| \|:\|\|:\|: :\|\|\|\|::\|@LB@ ACGCG GUUGUGG UCCCUUUA@LB@3'-UUU...UUAUG GAACC...GUG-5'@LB@ \| \|@LB@ 85 64@LB@@LB@@LB@Energy -5.91 kcal/mol@LB@Hybridization Energy -23.9168 kcal/mol@LB@Unfolding Energy - mRNA 10.6467 kcal/mol@LB@Unfolding Energy - sRNA 7.36194 kcal/mol@LB@@LB@Position - mRNA 169 -- 196@LB@Position - sRNA 65 -- 84@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 65 -- 71@LB@
179	0.01058	0.208	b1325	ycjG	-11.81	0.062523	258 -- 297	32 -- 77	L-Ala-D/L-Glu epimerase	_____________257_______________________________________________298\n_____________\|_________________________________________________\|\n5'-AAG...UGAUU______________GCA__GAA____G______________________AAC-3'\n______________GC_CCGGGGAAGUC___GU___GCGC_CGUG_______GUGGUG_GUUG\n______________:\|_\|\|:\|\|\|\|\|:\|\|___\|:___\|\|\|\|_\|\|\|:_______:\|\|:\|\|_\|\|\|:\n______________UG_GGUCCCUUUAG___CG___CGCG_GCAU_______UACUAC_CAAU\n3'-UUU...GCGGU__U___________AAC__A___________UUAAUAA______U____GUUCC...GUG-5'\n_____________\|_________________________________________________\|\n_____________78________________________________________________31\n	264 -- 270	64 -- 70	-38.4326 kcal/mol	17.2613 kcal/mol	9.36253 kcal/mol	257 298@LB@ \| \|@LB@5'-AAG...UGAUU GCA GAA G AAC-3'@LB@ GC CCGGGGAAGUC GU GCGC CGUG GUGGUG GUUG@LB@ :\| \|\|:\|\|\|\|\|:\|\| \|: \|\|\|\| \|\|\|: :\|\|:\|\| \|\|\|:@LB@ UG GGUCCCUUUAG CG CGCG GCAU UACUAC CAAU@LB@3'-UUU...GCGGU U AAC A UUAAUAA U GUUCC...GUG-5'@LB@ \| \|@LB@ 78 31@LB@@LB@@LB@Energy -11.81 kcal/mol@LB@Hybridization Energy -38.4326 kcal/mol@LB@Unfolding Energy - mRNA 17.2613 kcal/mol@LB@Unfolding Energy - sRNA 9.36253 kcal/mol@LB@@LB@Position - mRNA 258 -- 297@LB@Position - sRNA 32 -- 77@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 64 -- 70@LB@
180	0.01069	0.2089	b4529	ydbJ	-7.20	0.426635	222 -- 243	41 -- 61	DUF333 family putative lipoprotein	_____________221____________________244\n_____________\|______________________\|\n5'-GCA...GGGUA__G_______C_UU________CGGCG...GUU-3'\n______________GG_UGUGCCG_U__AUUGUUGU\n______________\|\|_\|\|:\|\|\|\|_\|__\|\|\|:\|\|:\|\n______________CC_ACGCGGC_A__UAAUAAUA\n3'-UUU...UAGAA__G_________UU________CUACU...GUG-5'\n_____________\|______________________\|\n_____________62_____________________40\n	225 -- 231	52 -- 58	-21.8046 kcal/mol	7.13894 kcal/mol	7.46625 kcal/mol	221 244@LB@ \| \|@LB@5'-GCA...GGGUA G C UU CGGCG...GUU-3'@LB@ GG UGUGCCG U AUUGUUGU@LB@ \|\| \|\|:\|\|\|\| \| \|\|\|:\|\|:\|@LB@ CC ACGCGGC A UAAUAAUA@LB@3'-UUU...UAGAA G UU CUACU...GUG-5'@LB@ \| \|@LB@ 62 40@LB@@LB@@LB@Energy -7.20 kcal/mol@LB@Hybridization Energy -21.8046 kcal/mol@LB@Unfolding Energy - mRNA 7.13894 kcal/mol@LB@Unfolding Energy - sRNA 7.46625 kcal/mol@LB@@LB@Position - mRNA 222 -- 243@LB@Position - sRNA 41 -- 61@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 52 -- 58@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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